1
|
Reason T, Rawlinson W, Langham J, Gimblett A, Malcolm B, Klijn S. Artificial Intelligence to Automate Health Economic Modelling: A Case Study to Evaluate the Potential Application of Large Language Models. Pharmacoecon Open 2024; 8:191-203. [PMID: 38340276 PMCID: PMC10884386 DOI: 10.1007/s41669-024-00477-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Current generation large language models (LLMs) such as Generative Pre-Trained Transformer 4 (GPT-4) have achieved human-level performance on many tasks including the generation of computer code based on textual input. This study aimed to assess whether GPT-4 could be used to automatically programme two published health economic analyses. METHODS The two analyses were partitioned survival models evaluating interventions in non-small cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We developed prompts which instructed GPT-4 to programme the NSCLC and RCC models in R, and which provided descriptions of each model's methods, assumptions and parameter values. The results of the generated scripts were compared to the published values from the original, human-programmed models. The models were replicated 15 times to capture variability in GPT-4's output. RESULTS GPT-4 fully replicated the NSCLC model with high accuracy: 100% (15/15) of the artificial intelligence (AI)-generated NSCLC models were error-free or contained a single minor error, and 93% (14/15) were completely error-free. GPT-4 closely replicated the RCC model, although human intervention was required to simplify an element of the model design (one of the model's fifteen input calculations) because it used too many sequential steps to be implemented in a single prompt. With this simplification, 87% (13/15) of the AI-generated RCC models were error-free or contained a single minor error, and 60% (9/15) were completely error-free. Error-free model scripts replicated the published incremental cost-effectiveness ratios to within 1%. CONCLUSION This study provides a promising indication that GPT-4 can have practical applications in the automation of health economic model construction. Potential benefits include accelerated model development timelines and reduced costs of development. Further research is necessary to explore the generalisability of LLM-based automation across a larger sample of models.
Collapse
Affiliation(s)
- Tim Reason
- Estima Scientific, Mediaworks, 191 Wood Ln, London, W12 7FP, UK.
| | | | - Julia Langham
- Estima Scientific, Mediaworks, 191 Wood Ln, London, W12 7FP, UK
| | - Andy Gimblett
- Estima Scientific, Mediaworks, 191 Wood Ln, London, W12 7FP, UK
| | | | - Sven Klijn
- Bristol Myers Squibb, Princeton, NJ, USA
| |
Collapse
|
2
|
Marinelli T, Masters J, Buckland ME, Lee M, Rawlinson W, Kim KW, Urriola N, van Hal S. Chronic and neurotropic: A paradigm-challenging case of dengue virus encephalitis in patient with advanced human immunodeficiency virus infection. Clin Infect Dis 2024:ciae061. [PMID: 38321565 DOI: 10.1093/cid/ciae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/06/2024] [Accepted: 02/02/2024] [Indexed: 02/08/2024] Open
Abstract
A 32-year-old female with advanced HIV infection presented to an Australian hospital with subacute but worsening symptoms of encephalitis. Metagenomic sequencing and Dengue NS3 antigen staining of brain tissue confirmed active Dengue virus (DENV) encephalitis. The most recent possible DENV exposure was months prior in West Africa, indicating chronicity.
Collapse
Affiliation(s)
- Tina Marinelli
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, New South Wales, Sydney, Australia
| | - Jeffrey Masters
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, New South Wales, Sydney, Australia
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael E Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Maggie Lee
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - William Rawlinson
- Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, New South Wales, Australia
| | - Ki Wook Kim
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, New South Wales, Australia
| | - Nicolas Urriola
- Department of Clinical Immunology and Allergy, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Sebastiaan van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, New South Wales, Sydney, Australia
| |
Collapse
|
3
|
Hurley S, Kim KW, Domazetovska A, Yau C, Yeang M, Donovan L, Kok J, Rawlinson W. Mpox detection in clinical specimens by three commercial real-time PCR assays demonstrates comparable results. Pathology 2024:S0031-3025(24)00051-5. [PMID: 38395680 DOI: 10.1016/j.pathol.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/26/2023] [Accepted: 11/12/2023] [Indexed: 02/25/2024]
Affiliation(s)
- Siobhan Hurley
- Department of Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Ki Wook Kim
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New Souh Wales, Sydney, NSW, Australia; Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Ana Domazetovska
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Cynthia Yau
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New Souh Wales, Sydney, NSW, Australia; Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Malinna Yeang
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Linda Donovan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - William Rawlinson
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia; Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, UNSW, Kensington, NSW, Australia.
| |
Collapse
|
4
|
Dyda A, Broome A, Rawlinson W, Mahimbo A, Saha A, Kefalas B, Seale H, Macintyre CR, Zwar N, Gidding HF, Heywood AE. Measles, mumps, rubella and varicella antibodies among international and domestic university students. J Travel Med 2024; 31:taae004. [PMID: 38195239 DOI: 10.1093/jtm/taae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/19/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024]
Abstract
BACKGROUND Vaccine-preventable infections are generally well controlled in Australia. However, gaps in immunity can lead to outbreaks and are important to identify. Young adults are a highly mobile population and a potential source of imported infections. We aimed to evaluate anti- measles, mumps, rubella and varicella (MMR&V) IgG seroprevalence and explore factors relating to antibody seropositivity. METHODS A cross-sectional online survey was conducted among students from a large Australian university to collect demographic, vaccination, infection and travel characteristics. Blood samples were collected to measure MMR&V seroprevalence. Logistic regression was used to identify factors associated with seropositivity. RESULTS Among 804 university students, seroprevalence (positive or equivocal) for measles was 82.3% (95% CI 79.6-84.8%), mumps 79.5% (95% CI 76.7-82.3%), rubella 91.5% (95% CI 89.6-93.5%) and varicella 86.2% (95% CI 84.1-88.8%), with 452 (56.2%, 95% CI 52.8-59.6) seropositive to all four viruses. Varicella seropositivity was highest in the older birth cohort (born 1988-1991). Measles seropositivity was higher for international students compared to domestic students. Among international students, mumps seroprevalence was significantly lower than measles and rubella seroprevalence. International travel in the previous 12 months was reported by 63.1% of students, but only 18.2% of travellers reported seeking pre-travel health advice prior to most recent international travel. CONCLUSIONS Overall, this study suggests immunity to MMR&V is sub-optimal. We found the university student population to be highly mobile and unlikely to seek pre-travel advice; thus, they are a potential source of infection importation. The implementation of university immunization policies could address the gaps identified and our findings can inform the development of targeted vaccination campaigns.
Collapse
Affiliation(s)
- Amalie Dyda
- School of Public Health, University of Queensland, Brisbane, QLD 4072, Australia
| | - Audrey Broome
- Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - William Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, NSW 2031, Australia
| | - Abela Mahimbo
- School of Public Health, Faculty of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Amit Saha
- The Kirby Institute, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bill Kefalas
- UNSW Health Service, University of New South Wales, Sydney, NSW 2052, Australia
| | - Holly Seale
- School of Population Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - C Raina Macintyre
- The Kirby Institute, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicholas Zwar
- School of Population Health, University of New South Wales, Sydney, NSW 2052, Australia
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, QLD 4226, Australia
| | - Heather F Gidding
- School of Population Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anita E Heywood
- School of Population Health, University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
5
|
Walker GJ, Foster CSP, Sevendal A, Domazetovska A, Kamalakkannan A, Williams PCM, Kim KW, Condylios A, Stelzer-Braid S, Bartlett AW, Rawlinson W. Clinical, Genomic, and Immunological Characterization of RSV Surge in Sydney, Australia, 2022. Pediatrics 2024; 153:e2023063667. [PMID: 38225912 DOI: 10.1542/peds.2023-063667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
OBJECTIVES The 2022 seasonal respiratory syncytial virus (RSV) epidemic in Sydney, Australia saw an unprecedented number of RSV detections. We aimed to characterize genomic and immunologic factors associated with the surge in RSV cases. METHODS Whole genome sequences of RSV were generated from 264 RSV-infected infants and linked to case-matched clinical data from the 2022 southern hemisphere RSV season. We then performed an immunologic analysis of baseline RSV-specific humoral immunity in women of childbearing age before and throughout the coronavirus disease 2019 pandemic. RESULTS Clinical analysis revealed a high burden of disease across patients of all health backgrounds. More than one-half of RSV-related health care visits by infants resulted in hospitalization, and one-quarter required high-flow respiratory support or a higher level of care. Viral phylogenetic analyses revealed that 2022 Sydney RSV sequences were closely related to viruses that had been circulating globally since 2017, including those detected in recent US outbreaks. Nonsynonymous mutations within the palivizumab and nirsevimab binding sites were detected at low frequencies. There was no difference in baseline RSV-neutralizing antibody titers between 2020 and 2022. CONCLUSIONS Collectively, these findings suggest that neither the emergence of a novel RSV genotype nor hypothesized immune debt was associated with the surge of RSV cases and hospitalizations in 2022. Continued genomic and immunologic surveillance is required to further understand the factors driving outbreaks of RSV globally, and to inform guidelines for the rollout and ongoing use of recently developed immunotherapeutics and vaccines.
Collapse
Affiliation(s)
- Gregory J Walker
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health
| | - Charles S P Foster
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health
| | - Andrea Sevendal
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Ana Domazetovska
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Abbish Kamalakkannan
- School of Public Health, Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Phoebe C M Williams
- National Centre for Immunisation Research and Surveillance, Westmead, New South Wales, Australia
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Ki Wook Kim
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
- Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
| | - Anna Condylios
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Adam W Bartlett
- Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
- Department of Immunology and Infectious Diseases, Sydney Children's Hospital Network, Sydney, New South Wales, Australia
- National Centre for Immunisation Research and Surveillance, Westmead, New South Wales, Australia
| | - William Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health
| |
Collapse
|
6
|
Halley C, Honeywill C, Kang J, Pierse N, Robertson O, Rawlinson W, Stelzer-Braid S, Willink R, Crane J. Preventing upper respiratory tract infections with prophylactic nasal carrageenan: a feasibility study. Future Microbiol 2023; 18:1319-1328. [PMID: 37830932 DOI: 10.2217/fmb-2021-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Aim: To observe upper respiratory tract infection (URTI) symptoms, rhinovirus levels and compliance with daily carrageenan nasal spray. Methods: 102 adults were randomized to carrageenan or saline placebo three times daily for 8 weeks and URTI symptoms were recorded. A control group (n = 42) only recorded URTI symptoms. Participants collected nasal swabs when symptomatic. Results: Regular daily carrageenan prophylaxis resulted in consistent but nonsignificant reductions in URTI symptoms versus the placebo group. Saline placebo decreased and increased some cold symptoms compared with no treatment. Conclusion: Daily prophylactic administration of antiviral carrageenan may not significantly reduce URTI symptoms. Due to low compliance, use in a population with specific reasons to avoid URTIs may be more appropriate. Disease-specific outcomes may be more useful than symptom reporting.
Collapse
Affiliation(s)
- Caroline Halley
- Department of Medicine, University of Otago, 23A Mein Street, Wellington, 6021, New Zealand
| | - Claire Honeywill
- Department of Medicine, University of Otago, 23A Mein Street, Wellington, 6021, New Zealand
| | - Janice Kang
- Department of Medicine, University of Otago, 23A Mein Street, Wellington, 6021, New Zealand
| | - Nevil Pierse
- Department of Public Health, University of Otago, 23A Mein Street, Wellington, 6021, New Zealand
| | - Oliver Robertson
- Department of Public Health, University of Otago, 23A Mein Street, Wellington, 6021, New Zealand
| | - William Rawlinson
- Virology Research Laboratory, Level 3 Campus Centre, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Level 3 Campus Centre, Prince of Wales Hospital, Randwick, NSW 2031, Australia
- University of New South Wales, Sydney, NSW 2052, Australia
| | - Robin Willink
- Biostatistical Group, University of Otago, 23A Mein Street, Wellington, 6021, New Zealand
| | - Julian Crane
- Department of Medicine, University of Otago, 23A Mein Street, Wellington, 6021, New Zealand
| |
Collapse
|
7
|
Hurley S, Eden JS, Bingham J, Rodriguez M, Neave MJ, Johnson A, Howard-Jones AR, Kok J, Anazodo A, McMullan B, Williams DT, Watson J, Solinas A, Kim KW, Rawlinson W. Fatal Human Neurologic Infection Caused by Pigeon Avian Paramyxovirus-1, Australia. Emerg Infect Dis 2023; 29:2482-2487. [PMID: 37987582 PMCID: PMC10683822 DOI: 10.3201/eid2912.230250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
Avian paramyxovirus type 1 (APMV-1) is a virus of birds that results in a range of outcomes, from asymptomatic infections to outbreaks of systemic respiratory and neurologic disease, depending on the virus strain and the avian species affected. Humans are rarely affected; those who are predominantly experience mild conjunctivitis. We report a fatal case of neurologic disease in a 2-year-old immunocompromised child in Australia. Metagenomic sequencing and histopathology identified the causative agent as the pigeon variant of APMV-1. This diagnosis should be considered in neurologic conditions of undefined etiologies. Agnostic metagenomic sequencing methods are useful in such settings to direct diagnostic and therapeutic efforts.
Collapse
Affiliation(s)
| | | | - John Bingham
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Michael Rodriguez
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Matthew J. Neave
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Alexandra Johnson
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Annaleise R. Howard-Jones
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Jen Kok
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Antoinette Anazodo
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Brendan McMullan
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - David T. Williams
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - James Watson
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Annalisa Solinas
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | | | | |
Collapse
|
8
|
Bowden-Reid E, Ledger S, Zhang Y, Di Giallonardo F, Aggarwal A, Stella AO, Akerman A, Milogiannakis V, Walker G, Rawlinson W, Turville S, Kelleher AD, Ahlenstiel C. Novel siRNA therapeutics demonstrate multi-variant efficacy against SARS-CoV-2. Antiviral Res 2023; 217:105677. [PMID: 37478918 DOI: 10.1016/j.antiviral.2023.105677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a respiratory virus that causes COVID-19 disease, with an estimated global mortality of approximately 2%. While global response strategies, which are predominantly reliant on regular vaccinations, have shifted from zero COVID to living with COVID, there is a distinct lack of broad-spectrum direct acting antiviral therapies that maintain efficacy across evolving SARS-CoV-2 variants of concern. This is of most concern for immunocompromised and immunosuppressed individuals who lack robust immune responses following vaccination, and others at risk for severe COVID and long-COVID. RNA interference (RNAi) therapeutics induced by short interfering RNAs (siRNAs) offer a promising antiviral treatment option, with broad-spectrum antiviral capabilities unparalleled by current antiviral therapeutics and a high genetic barrier to antiviral escape. Here we describe novel siRNAs, targeting highly conserved regions of the SARS-CoV-1 and 2 genome of both human and animal species, with multi-variant antiviral potency against eight SARS-CoV-2 lineages - Ancestral VIC01, Alpha, Beta, Gamma, Delta, Zeta, Kappa and Omicron. Treatment with our siRNA resulted in significant protection against virus-mediated cell death in vitro, with >97% cell survival (P < 0.0001), and corresponding reductions of viral nucleocapsid RNA of up to 99.9% (P < 0.0001). When compared to antivirals; Sotrovimab and Remdesivir, the siRNAs demonstrated a more potent antiviral effect and similarly, when multiplexing siRNAs to target different viral regions simultaneously, an increased antiviral effect was observed compared to individual siRNA treatments (P < 0.0001). These results demonstrate the potential for a highly effective broad-spectrum direct acting antiviral against multiple SARS-CoV-2 variants, including variants resistant to antivirals and vaccine generated neutralizing antibodies.
Collapse
Affiliation(s)
| | - Scott Ledger
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Yuan Zhang
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | | | | | | | | | | | - Gregory Walker
- New South Wales Health Pathology, Sydney, NSW, Australia
| | - William Rawlinson
- New South Wales Health Pathology, Sydney, NSW, Australia; Virology Research Laboratory, Serology and Virology Division (SAViD), Prince of Wales Hospital, Sydney, NSW, Australia
| | - Stuart Turville
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia; RNA Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Anthony D Kelleher
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia; RNA Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Chantelle Ahlenstiel
- Kirby Institute, UNSW Sydney, Sydney, NSW, Australia; RNA Institute, UNSW Sydney, Sydney, NSW, Australia.
| |
Collapse
|
9
|
Barrios MH, Nicholson S, Bull RA, Martinello M, Rawlinson W, Mina M, Post JJ, Hudson B, Gilroy N, Lloyd AR, Konecny P, Mordant F, Catton M, Subbarao K, Caly L, Druce J, Netter HJ. Comparative Longitudinal Serological Study of Anti-SARS-CoV-2 Antibody Profiles in People with COVID-19. Microorganisms 2023; 11:1985. [PMID: 37630545 PMCID: PMC10458948 DOI: 10.3390/microorganisms11081985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Serological diagnostic assays are essential tools for determining an individual's protection against viruses like SARS-CoV-2, tracking the spread of the virus in the community, and evaluating population immunity. To assess the diversity and quality of the anti-SARS-CoV-2 antibody response, we have compared the antibody profiles of people with mild, moderate, and severe COVID-19 using a dot blot assay. The test targeted the four major structural proteins of SARS-CoV-2, namely the nucleocapsid (N), spike (S) protein domains S1 and S2, and receptor-binding domain (RBD). Serum samples were collected from 63 participants at various time points for up to 300 days after disease onset. The dot blot assay revealed patient-specific differences in the anti-SARS-CoV-2 antibody profiles. Out of the 63 participants with confirmed SARS-CoV-2 infections and clinical COVID-19, 35/63 participants exhibited diverse and robust responses against the tested antigens, while 14/63 participants displayed either limited responses to a subset of antigens or no detectable antibody response to any of the antigens. Anti-N-specific antibody levels decreased within 300 days after disease onset, whereas anti-S-specific antibodies persisted. The dynamics of the antibody response did not change during the test period, indicating stable antibody profiles. Among the participants, 28/63 patients with restricted anti-S antibody profiles or undetectable anti-S antibody levels in the dot blot assay also exhibited weak neutralization activity, as measured by a surrogate virus neutralization test (sVNT) and a microneutralization test. These results indicate that in some cases, natural infections do not lead to the production of neutralizing antibodies. Furthermore, the study revealed significant serological variability among patients, regardless of the severity of their COVID-19 illness. These differences need to be carefully considered when evaluating the protective antibody status of individuals who have experienced primary SARS-CoV-2 infections.
Collapse
Affiliation(s)
- Marilou H. Barrios
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (M.H.B.); (S.N.); (M.C.); (L.C.); (J.D.)
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (M.H.B.); (S.N.); (M.C.); (L.C.); (J.D.)
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
| | - Rowena A. Bull
- The Kirby Institute, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (R.A.B.); (M.M.); (A.R.L.)
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, NSW 2052, Australia;
| | - Marianne Martinello
- The Kirby Institute, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (R.A.B.); (M.M.); (A.R.L.)
| | - William Rawlinson
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, NSW 2052, Australia;
- Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Randwick, Sydney, NSW 2031, Australia
- Prince of Wales Hospital, Sydney, NSW 2031, Australia;
| | - Michael Mina
- Northern Beaches Hospital, Frenchs Forest, NSW 2086, Australia;
| | - Jeffrey J. Post
- Prince of Wales Hospital, Sydney, NSW 2031, Australia;
- School of Clinical Medicine, University of New South Wales (UNSW), Sydney, NSW 2052, Australia;
| | - Bernard Hudson
- Royal North Shore Hospital, Sydney, NSW 2065, Australia;
| | | | - Andrew R. Lloyd
- The Kirby Institute, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (R.A.B.); (M.M.); (A.R.L.)
| | - Pamela Konecny
- School of Clinical Medicine, University of New South Wales (UNSW), Sydney, NSW 2052, Australia;
- St. George Hospital, Sydney, NSW 2217, Australia
| | - Francesca Mordant
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Mike Catton
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (M.H.B.); (S.N.); (M.C.); (L.C.); (J.D.)
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
| | - Kanta Subbarao
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC 3000, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza at the Peter Doherty Institute, Melbourne, VIC 3000, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (M.H.B.); (S.N.); (M.C.); (L.C.); (J.D.)
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (M.H.B.); (S.N.); (M.C.); (L.C.); (J.D.)
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
| | - Hans J. Netter
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Royal Melbourne Hospital, Melbourne, VIC 3000, Australia; (M.H.B.); (S.N.); (M.C.); (L.C.); (J.D.)
- Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia; (F.M.); (K.S.)
- School of Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, VIC 3001, Australia
| |
Collapse
|
10
|
Gupta M, Balachandran H, Louie RHY, Li H, Agapiou D, Keoshkerian E, Christ D, Rawlinson W, Mina MM, Post JJ, Hudson B, Gilroy N, Konecny P, Bartlett AW, Sasson SC, Ahlenstiel G, Dwyer D, Lloyd AR, Martinello M, Luciani F, Bull RA. High activation levels maintained in receptor-binding domain-specific memory B cells in people with severe coronavirus disease 2019. Immunol Cell Biol 2022; 101:142-155. [PMID: 36353774 PMCID: PMC9878167 DOI: 10.1111/imcb.12607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 09/02/2022] [Accepted: 11/09/2022] [Indexed: 11/11/2022]
Abstract
The long-term health consequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are still being understood. The molecular and phenotypic properties of SARS-CoV-2 antigen-specific T cells suggest a dysfunctional profile that persists in convalescence in those who were severely ill. By contrast, the antigen-specific memory B-cell (MBC) population has not yet been analyzed to the same degree, but phenotypic analysis suggests differences following recovery from mild or severe coronavirus disease 2019 (COVID-19). Here, we performed single-cell molecular analysis of the SARS-CoV-2 receptor-binding domain (RBD)-specific MBC population in three patients after severe COVID-19 and four patients after mild/moderate COVID-19. We analyzed the transcriptomic and B-cell receptor repertoire profiles at ~2 months and ~4 months after symptom onset. Transcriptomic analysis revealed a higher level of tumor necrosis factor-alpha (TNF-α) signaling via nuclear factor-kappa B in the severe group, involving CD80, FOS, CD83 and TNFAIP3 genes that was maintained over time. We demonstrated the presence of two distinct activated MBCs subsets based on expression of CD80hi TNFAIP3hi and CD11chi CD95hi at the transcriptome level. Both groups revealed an increase in somatic hypermutation over time, indicating progressive evolution of humoral memory. This study revealed distinct molecular signatures of long-term RBD-specific MBCs in convalescence, indicating that the longevity of these cells may differ depending on acute COVID-19 severity.
Collapse
Affiliation(s)
- Money Gupta
- Faculty of Medicine, School of Medical SciencesUniversity of New South Wales AustraliaSydneyNSWAustralia,The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | - Harikrishnan Balachandran
- Faculty of Medicine, School of Medical SciencesUniversity of New South Wales AustraliaSydneyNSWAustralia,The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | - Raymond H Y Louie
- Faculty of Medicine, School of Medical SciencesUniversity of New South Wales AustraliaSydneyNSWAustralia,The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | - Hui Li
- The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | - David Agapiou
- The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | | | - Daniel Christ
- Antibody Therapeutics LabGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | - William Rawlinson
- Faculty of Medicine, School of Medical SciencesUniversity of New South Wales AustraliaSydneyNSWAustralia,Serology and Virology Division, Department of MicrobiologyNSW Health Pathology, Prince of Wales HospitalSydneyNSWAustralia
| | | | - Jeffrey J Post
- Prince of Wales Clinical SchoolUniversity of New South Wales, AustraliaSydneyNSWAustralia
| | - Bernard Hudson
- Infectious diseasesRoyal North Shore HospitalSydneyNSWAustralia
| | - Nicky Gilroy
- Infectious DiseasesWestmead HospitalSydneyNSWAustralia
| | - Pamela Konecny
- St George and Sutherland Clinical SchoolUniversity of New South Wales, SydneySydneyNSWAustralia
| | - Adam W Bartlett
- Faculty of Medicine, School of Medical SciencesUniversity of New South Wales AustraliaSydneyNSWAustralia,The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia,Sydney Children's Hospital RandwickSydneyNSWAustralia
| | - Sarah C Sasson
- The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | | | - Dominic Dwyer
- Infectious DiseasesWestmead HospitalSydneyNSWAustralia
| | - Andrew R Lloyd
- The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | - Marianne Martinello
- The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia,Infectious DiseasesWestmead HospitalSydneyNSWAustralia,Blacktown Mount Druitt HospitalBlacktownNSWAustralia
| | - Fabio Luciani
- Faculty of Medicine, School of Medical SciencesUniversity of New South Wales AustraliaSydneyNSWAustralia,The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | - Rowena A Bull
- Faculty of Medicine, School of Medical SciencesUniversity of New South Wales AustraliaSydneyNSWAustralia,The Kirby Institute, University of New South Wales, AustraliaSydneyNSWAustralia
| | | |
Collapse
|
11
|
Teutsch SM, Nunez CA, Morris A, Eslick GD, Berkhout A, Novakovic D, Brotherton JM, McGregor S, Khawar L, Khandaker G, Booy R, Jones CA, Rawlinson W, Thorley BR, Elliott EJ. Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2021. Commun Dis Intell (2018) 2022; 46. [PMID: 36303401 DOI: 10.33321/cdi.2022.46.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Australian Paediatric Surveillance Unit (APSU) has been conducting surveillance of rare communicable and non-communicable conditions in children since its inception in 1993. In this report, the results are described of surveillance of ten communicable diseases (and complications) for 2021, including the numbers of cases and incidence estimates; demographics; clinical features; and management and short-term outcomes. The included diseases are: acute flaccid paralysis (AFP); congenital cytomegalovirus (CMV); neonatal herpes simplex virus (HSV) infection; paediatric human immunodeficiency virus (HIV) infection; perinatal exposure to HIV; severe complications from influenza; juvenile-onset respiratory papillomatosis (JoRRP); congenital rubella syndrome; congenital varicella syndrome; and neonatal varicella infection. In 2021, cases of JoRRP were reported to the APSU for the first time since 2017, indicating potential gaps in HPV vaccination. AFP surveillance by APSU again contributed to Australia achieving a minimum target incidence of one AFP case per 100,000 children aged < 15 years. There were no cases of children with severe complications of influenza. No cases of varicella or congenital rubella were reported; however, at-risk populations, especially young migrant and refugee women from countries without universal vaccination programs, need to be screened and prioritised for vaccination prior to pregnancy. Cases of perinatal exposure to HIV continue to increase; however, the rate of mother-to-child-transmission remains at low levels due to the use of effective intervention strategies. Case numbers of congenital CMV and neonatal HSV remain steady in the absence of vaccines, prompting the need for greater awareness and education, with recent calls for target screening of at-risk infants for congenital CMV.
Collapse
Affiliation(s)
- Suzy M Teutsch
- The Australian Paediatric Surveillance Unit
- The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health
- The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Carlos A Nunez
- The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health
- The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
- The Australian Paediatric Surveillance Unit
| | - Anne Morris
- The Australian Paediatric Surveillance Unit
- The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health
- The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Guy D Eslick
- The Australian Paediatric Surveillance Unit
- The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health
- The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Angela Berkhout
- Infection Management & Prevention Service, The Queensland Children's Hospital
- The University of Queensland, Faculty of Medicine, Brisbane, Queensland, AUSTRALIA
| | - Daniel Novakovic
- Dr Liang Voice Program, The University of Sydney, Faculty of Medicine and Health, Central Clinical School, Sydney, New South Wales, AUSTRALIA
| | - Julia Ml Brotherton
- Australian Centre for the Prevention of Cervical Cancer
- Melbourne School of Population and Global Health, University of Melbourne, Victoria, AUSTRALIA
| | - Skye McGregor
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, AUSTRALIA
| | - Laila Khawar
- The Kirby Institute, The University of New South Wales, Sydney, New South Wales, AUSTRALIA
| | - Gulam Khandaker
- Central Queensland Hospital and Health Service, Rockhampton, Queensland, AUSTRALIA
| | - Robert Booy
- The University of Sydney, Faculty of Medicine and Health
- The National Centre for Immunisation Research and Surveillance, Sydney, New South Wales, AUSTRALIA
| | - Cheryl A Jones
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, AUSTRALIA
| | - William Rawlinson
- Virology and OTDS Laboratories, NSW Health Pathology Randwick and UNSW Sydney, New South Wales, AUSTRALIA
| | - Bruce R Thorley
- National Enterovirus Reference Laboratory and WHO Polio Regional Reference Laboratory, Victorian Infectious Disease Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, AUSTRALIA
| | - Elizabeth J Elliott
- The Australian Paediatric Surveillance Unit
- The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health
- The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| |
Collapse
|
12
|
Adhikari A, Abayasingam A, Rodrigo C, Agapiou D, Pandzic E, Brasher NA, Fernando BSM, Keoshkerian E, Li H, Kim HN, Lord M, Popovic G, Rawlinson W, Mina M, Post JJ, Hudson B, Gilroy N, Dwyer D, Sasson SC, Grubor-Bauk B, Lloyd AR, Martinello M, Bull RA, Tedla N. Longitudinal Characterization of Phagocytic and Neutralization Functions of Anti-Spike Antibodies in Plasma of Patients after Severe Acute Respiratory Syndrome Coronavirus 2 Infection. J I 2022; 209:1499-1512. [DOI: 10.4049/jimmunol.2200272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/01/2022] [Indexed: 11/06/2022]
|
13
|
Swinburn MK, Sheedy HS, Waight ME, King MR, Hall MB, Hui L, Jones C, Daly MK, Rawlinson W, McIntyre S, Webb MA, Badawi N, Bowen A, Britton P, Palasanthiran P, Lainchbury MA, Shand A. eLearning significantly improves midwives’ knowledge of the congenital cytomegalovirus prevention guidelines. Women Birth 2022. [DOI: 10.1016/j.wombi.2022.07.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
14
|
Shrestha LB, Foster C, Rawlinson W, Tedla N, Bull RA. Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission. Rev Med Virol 2022; 32:e2381. [PMID: 35856385 PMCID: PMC9349777 DOI: 10.1002/rmv.2381] [Citation(s) in RCA: 210] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022]
Abstract
The first dominant SARS‐CoV‐2 Omicron variant BA.1 harbours 35 mutations in its Spike protein from the original SARS‐CoV‐2 variant that emerged late 2019. Soon after its discovery, BA.1 rapidly emerged to become the dominant variant worldwide and has since evolved into several variants. Omicron is of major public health concern owing to its high infectivity and antibody evasion. This review article examines the theories that have been proposed on the evolution of Omicron including zoonotic spillage, infection in immunocompromised individuals and cryptic spread in the community without being diagnosed. Added to the complexity of Omicron's evolution are the multiple reports of recombination events occurring between co‐circulating variants of Omicron with Delta and other variants such as XE. Current literature suggests that the combination of the novel mutations in Omicron has resulted in the variant having higher infectivity than the original Wuhan‐Hu‐1 and Delta variant. However, severity is believed to be less owing to the reduced syncytia formation and lower multiplication in the human lung tissue. Perhaps most challenging is that several studies indicate that the efficacy of the available vaccines have been reduced against Omicron variant (8–127 times reduction) as compared to the Wuhan‐Hu‐1 variant. The administration of booster vaccine, however, compensates with the reduction and improves the efficacy by 12–35 fold. Concerningly though, the broadly neutralising monoclonal antibodies, including those approved by FDA for therapeutic use against previous SARS‐CoV‐2 variants, are mostly ineffective against Omicron with the exception of Sotrovimab and recent reports suggest that the Omicron BA.2 is also resistant to Sotrovimab. Currently two new Omicron variants BA.4 and BA.5 are emerging and are reported to be more transmissible and resistant to immunity generated by previous variants including Omicron BA.1 and most monoclonal antibodies. As new variants of SARS‐CoV‐2 will likely continue to emerge it is important that the evolution, and biological consequences of new mutations, in existing variants be well understood.
Collapse
Affiliation(s)
- Lok Bahadur Shrestha
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Charles Foster
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - William Rawlinson
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Nicodemus Tedla
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| |
Collapse
|
15
|
Gulholm T, Yeang M, Nguyen I, Andrews PI, Balgahom R, Beresford R, Branley J, Briest R, Britton P, Burrell R, Gehrig N, Kesson A, Kok J, Maley M, Newcombe J, Samarasekara H, Van Hal S, Varadhan H, Thapa K, Jones S, Newton P, Naing Z, Stelzer-Braid S, Rawlinson W. Molecular typing of enteroviruses: comparing 5'UTR, VP1 and whole genome sequencing methods. Pathology 2022; 54:779-783. [PMID: 35738943 DOI: 10.1016/j.pathol.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
Enteroviruses (EV) commonly cause hand, foot and mouth disease (HFMD), and can also cause potentially fatal neurological and systemic complications. In our laboratory, sequencing 5' untranslated region (UTR) of the viral genome has been the routine method of genotyping EVs. During a recent localised outbreak of aseptic meningitis, sequencing the 5'UTR identified the causative virus as EV-A71, which did not fit with the clinical syndrome or illness severity. When genotyped using a different target gene, VP1, the result was different. This led us to evaluate the accuracy of the two different target genome regions and compare them against whole genome sequencing (WGS). We aimed to optimise the algorithm for detection and characterisation of EVs in the diagnostic laboratory. We hypothesised that VP1 and WGS genotyping would provide different results than 5'UTR in a subset of samples. Clinical samples from around New South Wales which were positive for EV by commercial polymerase chain reaction (PCR) assays were genotyped by targeting three different viral genome regions: the 5'UTR, VP1 and WGS. Sequencing was performed by Sanger and next generation sequencing. The subtyping results were compared. Of the 74/118 (63%) samples that were successfully typed using both the 5'UTR and the VP1 method, the EV typing result was identical for 46/74 (62%) samples compared to WGS as the gold standard. The same EV group but different EV types were found in 22/74 (30%) samples, and 6/74 (8%) samples belonged to different EV groups depending on typing method used. Genotyping with WGS and VP1 is more accurate than 5'UTR. Genotyping by the 5'UTR method is very sensitive, but less specific.
Collapse
Affiliation(s)
- T Gulholm
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; UNSW Clinical School, Faculty of Medicine UNSW, Kensington, NSW, Australia.
| | - M Yeang
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia
| | - I Nguyen
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - P I Andrews
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - R Balgahom
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - R Beresford
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Branley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - R Briest
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - P Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; University of Sydney Children's Hospital Westmead Clinical School, NSW, Australia
| | - R Burrell
- Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - N Gehrig
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - A Kesson
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health, The University of Sydney, Sydney, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - M Maley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Newcombe
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - H Samarasekara
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - S Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - H Varadhan
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - K Thapa
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Jones
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - P Newton
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - Z Naing
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - W Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
16
|
Smithers-Sheedy H, Swinburn K, Waight E, King R, Hui L, Jones CA, Daly K, Rawlinson W, Mcintyre S, Webb A, Badawi N, Bowen A, Britton PN, Palasanthiran P, Lainchbury A, Shand A. eLearning significantly improves maternity professionals' knowledge of the congenital cytomegalovirus prevention guidelines. Aust N Z J Obstet Gynaecol 2022; 62:445-452. [PMID: 35348198 PMCID: PMC9541485 DOI: 10.1111/ajo.13500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/17/2021] [Accepted: 01/29/2022] [Indexed: 11/29/2022]
Abstract
Aims Cytomegalovirus (CMV) is a preventable cause of neurodevelopmental disability. Australian guidelines recommend that pregnant women are informed about CMV to reduce their risk of infection; however, less than 10% of maternity health professionals routinely provide prevention advice. The aim was to develop and evaluate the effectiveness of an eLearning course for midwives to improve knowledge and confidence about CMV. Materials and Methods Participants undertaking the course between March and November 2020 were invited to complete an evaluation questionnaire: before the course (T1), immediately after (T2) and three months post completion (T3). A linear mixed model was used to evaluate change in participant scores; P < 0.05 was considered statistically significant. Results Midwives (316/363, 87%), midwifery students (29/363, 8%) and nurses (18/363, 5%) participated. At T1 80% indicated they had not received education about CMV. Total adjusted mean scores for questionnaires completed between T1 (n = 363) and T2 (n = 238) increased significantly (from 17.2 to 22.8, P < 0.001). Limited available T3 scores (n = 27) (−1.7, P < 0.001), while lower than T2, remained higher than at T1 (+3.6, P < 0.001). Participants’ awareness of CMV information resources improved from 10 to 97% from T1 to T2. Confidence in providing CMV advice increased from 6 to 95% between T1 and T2 (P < 0.001) and was maintained at T3. Almost all (99%) participants indicated they would recommend the course to colleagues. Conclusion Participants who completed the eLearning course had significantly improved knowledge and confidence in providing advice about CMV. Programs targeting other maternity health professionals should be considered, to further support the implementation of the congenital CMV prevention guidelines.
Collapse
Affiliation(s)
- Hayley Smithers-Sheedy
- Cerebral Palsy Alliance Research Institute, Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Katherine Swinburn
- Cerebral Palsy Alliance Research Institute, Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Emma Waight
- Cerebral Palsy Alliance Research Institute, Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Ruth King
- Nursing and Midwifery Office, ACT Health, Canberra, ustralian Capital Territory, Australia
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - Cheryl A Jones
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead and Sydney Medical School, The University of Sydney, Westmead, New South Wales, Australia
| | - Kate Daly
- CMV Australia, Normanhurst, New South Wales, Australia
| | - William Rawlinson
- NSW Health Pathology Randwick, Level 4 Campus Centre, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Sarah Mcintyre
- Cerebral Palsy Alliance Research Institute, Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Annabel Webb
- Cerebral Palsy Alliance Research Institute, Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Nadia Badawi
- Cerebral Palsy Alliance Research Institute, Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia.,The Grace Centre for Newborn Intensive Care, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Asha Bowen
- Department of Infectious Diseases, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead and Sydney Medical School, The University of Sydney, Westmead, New South Wales, Australia
| | - Pamela Palasanthiran
- Department of Immunology and Infectious Disease, Sydney Children's Hospitals Network, School of Women's and Child Health, University of New South Wales, Randwick, New South Wales, Australia
| | - Anne Lainchbury
- Royal Hospital for Women, Randwick, Western Australia, Australia
| | - Antonia Shand
- Royal Hospital for Women, Randwick, Western Australia, Australia.,Child Population and Translational Health Research, Children's Hospital at Westmead, Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
17
|
Saravanos GL, Hu N, Homaira N, Muscatello DJ, Jaffe A, Bartlett AW, Wood NJ, Rawlinson W, Kesson A, Lingam R, Britton PN. RSV Epidemiology in Australia Before and During COVID-19. Pediatrics 2022; 149:184564. [PMID: 35083489 DOI: 10.1542/peds.2021-053537] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Abstract
COVID-19 public health measures altered respiratory syncytial virus (RSV) epidemiology. We examined age-stratified trends in RSV-related disease in Australian children in 2020 compared with previous years.
Collapse
Affiliation(s)
- Gemma L Saravanos
- The University of Sydney, Camperdown, Australia.,National Centre for Immunisation Research and Surveillance, Westmead, Australia
| | - Nan Hu
- University of New South Wales Sydney, Randwick, Australia
| | - Nusrat Homaira
- University of New South Wales Sydney, Randwick, Australia.,Sydney Children's Hospital, Randwick, Australia
| | | | - Adam Jaffe
- University of New South Wales Sydney, Randwick, Australia.,Sydney Children's Hospital, Randwick, Australia
| | - Adam W Bartlett
- University of New South Wales Sydney, Randwick, Australia.,Sydney Children's Hospital, Randwick, Australia
| | - Nicholas J Wood
- The University of Sydney, Camperdown, Australia.,National Centre for Immunisation Research and Surveillance, Westmead, Australia.,The Children's Hospital at Westmead, Westmead, Australia
| | | | - Alison Kesson
- The University of Sydney, Camperdown, Australia.,The Children's Hospital at Westmead, Westmead, Australia
| | - Raghu Lingam
- University of New South Wales Sydney, Randwick, Australia
| | - Philip N Britton
- The University of Sydney, Camperdown, Australia.,The Children's Hospital at Westmead, Westmead, Australia
| |
Collapse
|
18
|
Balachandran H, Phetsouphanh C, Agapiou D, Adhikari A, Rodrigo C, Hammoud M, Shrestha LB, Keoshkerian E, Gupta M, Turville S, Christ D, King C, Sasson SC, Bartlett A, Grubor-Bauk B, Rawlinson W, Aggarwal A, Stella AO, Klemm V, Mina MM, Post JJ, Hudson B, Gilroy N, Konecny P, Ahlenstiel G, Dwyer DE, Sorrell TC, Kelleher A, Tedla N, Lloyd AR, Martinello M, Bull RA. Maintenance of broad neutralising antibodies and memory B cells 12 months post-infection is predicted by SARS-CoV-2 specific CD4+ T cell responses. Cell Rep 2022; 38:110345. [PMID: 35090598 PMCID: PMC8768427 DOI: 10.1016/j.celrep.2022.110345] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 12/02/2022] Open
Abstract
Understanding the long-term maintenance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity is critical for predicting protection against reinfection. In an age- and gender-matched cohort of 24 participants, the association of disease severity and early immune responses on the maintenance of humoral immunity 12 months post-infection is examined. All severely affected participants maintain a stable subset of SARS-CoV-2 receptor-binding domain (RBD)-specific memory B cells (MBCs) and good neutralizing antibody breadth against the majority of the variants of concern, including the Delta variant. Modeling these immune responses against vaccine efficacy data indicate a 45%–76% protection against symptomatic infection (variant dependent). Overall, these findings indicate durable humoral responses in most participants after infection, reasonable protection against reinfection, and implicate baseline antigen-specific CD4+ T cell responses as a predictor of maintenance of antibody neutralization breadth and RBD-specific MBC levels at 12 months post-infection.
Collapse
|
19
|
Teutsch SM, Nunez CA, Morris A, Eslick GD, Khandaker G, Berkhout A, Novakovic D, Brotherton JML, McGregor S, King J, Egilmezer E, Booy R, Jones CA, Rawlinson W, Thorley BR, Elliott EJ. Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2020. ACTA ACUST UNITED AC 2021; 45. [PMID: 34711146 DOI: 10.33321/cdi.2021.45.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract For 27 years, national prospective data on selected rare childhood diseases have been collected monthly by the Australian Paediatric Surveillance Unit (APSU) from paediatricians and other clinical specialists who report cases in children aged up to 16 years. We report here the annual results of APSU surveillance in 2020 for ten rare communicable diseases and complications of communicable diseases, namely: acute flaccid paralysis (AFP); congenital cytomegalovirus (CMV) infection; neonatal herpes simplex virus (HSV) infection; perinatal exposure to human immunodeficiency virus (HIV); paediatric HIV infection; severe complications of seasonal influenza; juvenile onset recurrent respiratory papillomatosis (JoRRP); congenital rubella syndrome; congenital varicella syndrome; and neonatal varicella infection. We describe the results for each disease in the context of the total period of study, including demographics, clinical characteristics, treatment and short-term outcomes. Despite challenges presented by the coronavirus disease 2019 (COVID-19) pandemic in 2020, more than 1,400 paediatricians reported regularly to the APSU and an overall monthly reporting rate of > 90% was achieved. The minimum AFP target of 1 case per 100,000 children aged less than 15 years was achieved and there were few cases of vaccine-preventable diseases (JoRRP, rubella, varicella). However, high cases of congenital CMV, neonatal HSV and perinatal exposure to HIV persist. There were no severe complications of seasonal influenza reported for the first time in 13 years. This is consistent with other surveillance data reporting a decline of influenza and other communicable diseases in 2020, and likely reflects the wider effects of public health measures to reduce transmission of SARS-CoV-2 in the Australian community.
Collapse
Affiliation(s)
- Suzy M Teutsch
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Carlos A Nunez
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Anne Morris
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Guy D Eslick
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Gulam Khandaker
- Director of Public Health/Public Health Physician and Director of Medical Research, Central Queensland Hospital and Health Service, Rockhampton, Queensland, AUSTRALIA
| | - Angela Berkhout
- Microbiology Registrar, Microbiology and laboratory services, The Royal Children's Hospital, Melbourne, Victoria, AUSTRALIA
| | - Daniel Novakovic
- ENT, Head and Neck Surgeon, Laryngologist, and Director, Dr Liang Voice Program, The University of Sydney, Faculty of Medicine and Health, Central Clinical School, Sydney, New South Wales, AUSTRALIA
| | - Julia M L Brotherton
- Medical Director, VCS Population Health, VCS Foundation, Melbourne, Victoria, AUSTRALIA.,Honorary Principal Fellow, Melbourne School of Population and Global Health, University of Melbourne, Victoria, AUSTRALIA
| | - Skye McGregor
- Epidemiologist, The Kirby Institute, UNSW Sydney, New South Wales, AUSTRALIA
| | - Jonathan King
- Epidemiologist, The Kirby Institute, UNSW Sydney, New South Wales, AUSTRALIA
| | - Ece Egilmezer
- Virology Research Laboratory, Prince of Wales Hospital, Randwick, Sydney, New South Wales, AUSTRALIA.,UNSW Sydney, New South Wales, AUSTRALIA
| | - Robert Booy
- Senior Professorial Fellow, National Centre for Immunisation Research and Surveillance, Sydney, New South Wales, AUSTRALIA
| | - Cheryl A Jones
- Dean and Head of Sydney Medical School, The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, AUSTRALIA
| | - William Rawlinson
- Senior Medical Virologist, Director of Serology, Virology and OTDS Laboratories, NSW Health Pathology Randwick, Sydney, New South Wales, AUSTRALIA.,UNSW Sydney, New South Wales, AUSTRALIA
| | - Bruce R Thorley
- Head, National Enterovirus Reference Laboratory and WHO Polio Regional Reference Laboratory, Victorian Infectious Disease Reference Laboratory, Melbourne, Victoria, AUSTRALIA.,The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, AUSTRALIA
| | - Elizabeth J Elliott
- The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| |
Collapse
|
20
|
Homaira N, Binks M, Walker G, Larter N, Clark K, Campbell M, McHugh L, Briggs N, Nyiro J, Stelzer-Braid S, Hu N, Macartney K, Snelling T, Omer SB, Rawlinson W, Andrews R, Jaffe A. Transplacental transfer of RSV antibody in Australian First Nations infants. J Med Virol 2021; 94:782-786. [PMID: 34633091 PMCID: PMC7613379 DOI: 10.1002/jmv.27383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/15/2021] [Accepted: 10/08/2021] [Indexed: 01/21/2023]
Abstract
Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory infection hospitalisations in Aboriginal infants specifically those aged <6 months. Maternally derived RSV antibody (Ab) can protect against severe RSV disease in infancy. However, the efficiency of transplacental transfer of maternal anti-RSV Ab remains unknown in Aboriginal infants. We characterised RSV Ab in Australian First Nations mother-infant pairs (n = 78). We investigated impact of covariates including low birthweight, gestational age (GA), sex of the baby, maternal age and multiparity of the mother on cord to maternal anti-RSV Ab titre ratio (CMTR) using multivariable logistic regression model. All (n = 78) but one infant was born full term (median GA: 39 weeks, interquartile range: 38-40 weeks) and 56% were males. The mean log2 RSV Ab titre was 10.7 (SD± 1.3) in maternal serum and 11.0 (SD ± 1.3) in cord serum at birth; a ratio of 1.02 (SD ± 0.06). One-third of the pairs had a CMTR of <1 indicating impaired transfer. Almost 9% (7/78) of the term infants had cord RSV Ab levels below <log2 9. Covariates showed no effect on CMTR. Further mechanistic research is needed to determine the significance of these findings on RSV disease in First Nations children.
Collapse
Affiliation(s)
- Nusrat Homaira
- Discipline of Paediatrics, School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, New South Wales, Australia.,Department of Respiratory, Sydney Children's Hospital, Randwick, UNSW, Sydney, New South Wales, Australia
| | - Michael Binks
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Gregory Walker
- Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Natasha Larter
- Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Katrina Clark
- National Centre for Immunisation Research and Surveillance (NCIRS), Sydney, New South Wales, Australia
| | - Megan Campbell
- Centre for Aboriginal Health, New South Wales Health, Sydney, New South Wales, Australia
| | - Lisa McHugh
- School of Public Health, University of Queensland, Brisbane, Queensland, Australia
| | - Nancy Briggs
- Stats Central, Mark Wainwright Analytical Centre, UNSW, Sydney, New South Wales, Australia
| | - Joyce Nyiro
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Nan Hu
- Discipline of Paediatrics, School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, New South Wales, Australia
| | - Kristine Macartney
- National Centre for Immunisation Research and Surveillance (NCIRS), Sydney, New South Wales, Australia
| | - Tom Snelling
- University of Sydney, Sydney, New South Wales, Australia
| | - Saad B Omer
- Yale Institute for Global Health, New Haven, Connecticut, USA
| | | | - Ross Andrews
- National Centre for Immunisation Research and Surveillance (NCIRS), Sydney, New South Wales, Australia.,Australian National University, Canberra, Australia
| | - Adam Jaffe
- Discipline of Paediatrics, School of Women's and Children's Health, Faculty of Medicine and Health, UNSW, Sydney, New South Wales, Australia.,Department of Respiratory, Sydney Children's Hospital, Randwick, UNSW, Sydney, New South Wales, Australia
| |
Collapse
|
21
|
Rezaei M, Razavi Bazaz S, Morshedi Rad D, Shimoni O, Jin D, Rawlinson W, Ebrahimi Warkiani M. A Portable RT-LAMP/CRISPR Machine for Rapid COVID-19 Screening. Biosensors (Basel) 2021; 11:bios11100369. [PMID: 34677325 PMCID: PMC8534004 DOI: 10.3390/bios11100369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/19/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic has changed people’s lives and has brought society to a sudden standstill, with lockdowns and social distancing as the preferred preventative measures. To lift these measurements and reduce society’s burden, developing an easy-to-use, rapid, and portable system to detect SARS-CoV-2 is mandatory. To this end, we developed a portable and semi-automated device for SARS-CoV-2 detection based on reverse transcription loop-mediated isothermal amplification followed by a CRISPR/Cas12a reaction. The device contains a heater element mounted on a printed circuit board, a cooler fan, a proportional integral derivative controller to control the temperature, and designated areas for 0.2 mL Eppendorf® PCR tubes. Our system has a limit of detection of 35 copies of the virus per microliter, which is significant and has the capability of being used in crisis centers, mobile laboratories, remote locations, or airports to diagnose individuals infected with SARS-CoV-2. We believe the current methodology that we have implemented in this article is beneficial for the early screening of infectious diseases, in which fast screening with high accuracy is necessary.
Collapse
Affiliation(s)
- Meysam Rezaei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
- Genea, Sydney, NSW 2000, Australia
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
| | - Dorsa Morshedi Rad
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
| | - Olga Shimoni
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
| | - Dayong Jin
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - William Rawlinson
- Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia;
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
- Genea, Sydney, NSW 2000, Australia
- Correspondence:
| |
Collapse
|
22
|
Heywood A, Dyda A, Hu W, Saha A, Mahimbo A, Gidding H, Kefalas B, Seale H, Macintyre CR, Zwar N, Rawlinson W. Seroprevalence of hepatitis B antibodies among international and domestic university students. J Viral Hepat 2021; 28:1400-1412. [PMID: 34309992 DOI: 10.1111/jvh.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 12/09/2022]
Abstract
Chronic hepatitis B prevalence is low in most Australian populations, with universal infant HBV vaccination introduced in 2000. Migrants from high prevalence countries are at risk of acquisition before arrival and non-immune adults are potentially at risk through skin penetrating procedures and sexual contact, particularly during international travel. The risk profile of young adult students, many from high prevalence countries, is inadequately understood. A cross-sectional online survey conducted among university students collected data on demographic, vaccination and travel characteristics and blood samples were tested for hepatitis B surface antibody (HBsAb) and hepatitis B core antibody (HBcAb). Analyses identified factors associated with HBsAb seroprevalence and self-reported vaccination. The serosurvey was completed by 804 students born between 1988 and 1993, with 613/804 (76.2%, 95% CI 73.2-79.1) self-reporting prior HBV vaccination. Overall, 526/804 (65.4%, 95% CI 62.0%-68.6%) students were seropositive to HBsAb, including 438/613 (71.5%, 95% CI 67.8-74.9) students self-reporting a prior HBV vaccine and 88/191 (46.1%, 95% CI 39.2-53.2) students self-reporting no prior HBV vaccine. Overall, 8/804 (1.0%, 95% CI 0.5%-2.0%) students were HBcAb positive, of whom 1/804 (0.1%, 95% CI 0.02%-0.7%) was currently infectious. The prevalence of chronic HBV infection was low. However, more than one in four students were susceptible to HBV and over-estimated their immunity. Future vaccination efforts should focus on domestic students born before the introduction of the infant program and all international students. Screening and vaccination of students, including through campus-based health services, are an opportunity to catch-up young adults prior to undertaking at-risk activities, including international travel.
Collapse
Affiliation(s)
- Anita Heywood
- School of Population Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Amalie Dyda
- University of Queensland, Brisbane, Queensland, Australia
| | - William Hu
- Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Amit Saha
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Abela Mahimbo
- University of Technology, Sydney, New South Wales, Australia
| | | | - Bill Kefalas
- UNSW Health Service, UNSW Sydney, Sydney, New South Wales, Australia
| | - Holly Seale
- School of Population Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - C Raina Macintyre
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicholas Zwar
- School of Population Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia.,Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Queensland, Australia
| | - William Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology SEALS-Randwick, Randwick, New South Wales, Australia.,Schools of Medical Sciences (SOMS), Biotechnology and Biomolecular Sciences (BABS), and Women's and Children's Health, UNSW Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
23
|
O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
Collapse
Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
24
|
Waight E, Swinburn K, Shand A, Hui L, Daly K, Rawlinson W, Jones C, Badawi N, Smithers-Sheedy H. 319Congenital cytomegalovirus education, translation and prevention. Int J Epidemiol 2021. [DOI: 10.1093/ije/dyab168.688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Focus of Presentation
Congenital cytomegalovirus (CMV) is a known cause of sensorineural hearing loss, cerebral palsy and other disabilities. International consensus guidelines (2017) and the Australasian Society of Infectious Diseases (2014) recommend all pregnant women be provided with information on CMV and strategies to reduce their risk of infection. Here we describe the multifaceted strategies implemented to date to promote uptake of these guidelines.
Findings
At policy level, we influenced national clinical practice standards through input into new CMV prevention recommendations by the Royal Australian and New Zealand College of Obstetricians and Gynaecologists and Department of Health, which sparked state public health campaigns. At the intervention level, we presented hospital in-services, podcasts and webinars and developed an e-learning course for midwives. In collaboration with the Department of Health >11,000 pamphlets were disseminated to NSW GPs. At the community level, we developed patient information and media resources. During a recent month-long campaign, our cCMV video had >62,000 views, CMV content on social media had >1.4M total impressions, >77,000 total engagements and >200,000 viewed CMV awareness pieces via television/radio/print.
Conclusions/Implications
Implementation of congenital CMV practice guidelines provide an important opportunity to prevent neurodevelopmental disability. Collaborations between families, clinicians, researchers, professional bodies and health departments are essential to drive translation.
Key messages
A multifaceted approach in implementing congenital CMV practice guidelines gives the opportunity to reach numerous stakeholders including policymakers, health professionals and expectant mothers.
Collapse
Affiliation(s)
- Emma Waight
- Cerebral Palsy Alliance, Camperdown, Australia
- Sydney Medical School, The University of Sydney, Camperdown, Australia
| | - Katherine Swinburn
- Cerebral Palsy Alliance, Camperdown, Australia
- Sydney Medical School, The University of Sydney, Camperdown, Australia
| | - Antonia Shand
- Royal Hospital for Women, Randwick, Australia
- Sydney Medical School, The University of Sydney, Camperdown, Australia
| | - Lisa Hui
- Royal Children's Hospital, Parkville, Australia
- University of Melbourne, Parkville, Australia
| | | | - William Rawlinson
- Prince of Wales Hospital, Randwick, Australia
- University of New South Wales, Randwick, Australia
| | - Cheryl Jones
- Sydney Medical School, The University of Sydney, Camperdown, Australia
| | - Nadia Badawi
- Cerebral Palsy Alliance, Camperdown, Australia
- Sydney Medical School, The University of Sydney, Camperdown, Australia
| | - Hayley Smithers-Sheedy
- Cerebral Palsy Alliance, Camperdown, Australia
- Sydney Medical School, The University of Sydney, Camperdown, Australia
| |
Collapse
|
25
|
Lane CR, Sherry NL, Porter AF, Duchene S, Horan K, Andersson P, Wilmot M, Turner A, Dougall S, Johnson SA, Sait M, Gonçalves da Silva A, Ballard SA, Hoang T, Stinear TP, Caly L, Sintchenko V, Graham R, McMahon J, Smith D, Leong LEX, Meumann EM, Cooley L, Schwessinger B, Rawlinson W, van Hal SJ, Stephens N, Catton M, Looker C, Crouch S, Sutton B, Alpren C, Williamson DA, Seemann T, Howden BP. Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study. Lancet Public Health 2021; 6:e547-e556. [PMID: 34252365 PMCID: PMC8270762 DOI: 10.1016/s2468-2667(21)00133-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia. METHODS In this observational, genomic epidemiological study, we did genomic sequencing of all laboratory-confirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK. FINDINGS Between Jan 25, 2020, and Jan 31, 2021, there were 20 451 laboratory-confirmed cases of COVID-19 in Victoria, Australia, of which 15 431 were submitted for sequencing, and 11 711 met all quality control metrics and were included in our analysis. We identified 595 genomic clusters, with a median of five cases per cluster (IQR 2-11). Overall, samples from 11 503 (98·2%) of 11 711 cases clustered with another sample in Victoria, either within a genomic cluster or transmission network. Genomic analysis revealed that 10 426 cases, including 10 416 (98·4%) of 10 584 locally acquired cases, diagnosed during the second wave (between June and October, 2020) were derived from a single incursion from hotel quarantine, with the outbreak lineage (transmission network G, lineage D.2) rapidly detected in other Australian states and territories. Phylodynamic analyses indicated that the epidemic growth rate of the outbreak lineage in Victoria during the initial growth phase (samples collected between June 4 and July 9, 2020; 47·4 putative transmission events, per branch, per year [1/years; 95% credible interval 26·0-85·0]), was similar to that of other reported variants, such as B.1.1.7 in the UK (mean approximately 71·5 1/years). Strict interventions were implemented, and the outbreak lineage has not been detected in Australia since Oct 29, 2020. Subsequent cases represented independent international or interstate introductions, with limited local spread. INTERPRETATION Our study highlights how rapid escalation of clonal outbreaks can occur from a single incursion. However, strict quarantine measures and decisive public health responses to emergent cases are effective, even with high epidemic growth rates. Real-time genomic surveillance can alter the way in which public health agencies view and respond to COVID-19 outbreaks. FUNDING The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.
Collapse
Affiliation(s)
- Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ashleigh F Porter
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mathilda Wilmot
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Sally Dougall
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Sandra A Johnson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Sydney, NSW, Australia,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Rikki Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Jamie McMahon
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - David Smith
- Department of Microbiology, PathWest Laboratory Medicine, QEII Medical Centre, Perth, WA, Australia,School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Lex EX Leong
- Public Health Laboratory, Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA, Australia
| | - Ella M Meumann
- Territory Pathology, Royal Darwin Hospital, Darwin, NT, Australia,Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Louise Cooley
- Royal Hobart Hospital, Hobart, TAS, Australia,School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | | | - William Rawlinson
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Infectious Disease and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Nicola Stephens
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Mike Catton
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Clare Looker
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Simon Crouch
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Brett Sutton
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Charles Alpren
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| |
Collapse
|
26
|
O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
Collapse
Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
27
|
Yong MK, Gottlieb D, Lindsay J, Kok J, Rawlinson W, Slavin M, Ritchie D, Bajel A, Grigg A. New advances in the management of cytomegalovirus in allogeneic haemopoietic stem cell transplantation. Intern Med J 2021; 50:277-284. [PMID: 31403736 DOI: 10.1111/imj.14462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
Cytomegalovirus (CMV) viraemia continues to be a frequent complication in the post-haemopoietic stem cell transplantation period despite a low incidence of CMV end-organ disease. Several significant advances in the understanding and management of CMV infection have occurred in the last few years including improved diagnostics, monitoring of CMV immunity, availability of novel anti-CMV drugs, and emerging use of immunotherapies including CMV-specific T-cell infusions. In addition to reviewing these advances we also explore some of the more practical prescribing issues of the older and newer CMV drugs including cost, toxicity and drug interactions to help clinicians navigate this new era of CMV management.
Collapse
Affiliation(s)
- Michelle K Yong
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Gottlieb
- Department of Haematology and Bone Marrow Transplantation, Westmead Hospital, Sydney, New South Wales, Australia.,Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia.,Sydney Cellular Therapies Laboratory, Westmead Hospital, Sydney, New South Wales, Australia
| | - Julian Lindsay
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Pharmacy Department, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - William Rawlinson
- NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Monica Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Ritchie
- Department of Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Ashish Bajel
- Department of Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Andrew Grigg
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Haematology and Olivia Newton John Cancer Research Institute, Austin Hospital, Melbourne, Victoria, Australia
| |
Collapse
|
28
|
Au Yeung V, Thapa K, Rawlinson W, Georgiou A, Post JJ, Overton K. Differences in antibiotic and antiviral use in people with confirmed influenza: a retrospective comparison of rapid influenza PCR and multiplex respiratory virus PCR tests. BMC Infect Dis 2021; 21:321. [PMID: 33827458 PMCID: PMC8024678 DOI: 10.1186/s12879-021-06030-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/30/2021] [Indexed: 11/12/2022] Open
Abstract
Background Influenza is a highly contagious respiratory virus with clinical impacts on patient morbidity, mortality and hospital bed management. The effect of rapid nucleic acid testing (RPCR) in comparison to standard multiplex PCR (MPCR) diagnosis in treatment decisions is unclear. This study aimed to determine whether RPCR influenza testing in comparison to standard MPCR testing was associated with differences in antibiotic and antiviral (oseltamivir) utilisation and hospital length of stay in emergency department and inpatient hospital settings. Methods A retrospective cohort study of positive influenza RPCR and MPCR patients was performed utilising data from the 2017 influenza season. Medical records of correlating patient presentations were reviewed for data collection. An analysis of RPCR versus MPCR patient outcomes was performed examining test turnaround time, antibiotic initiation, oseltamivir initiation and hospital length of stay for both emergency department and inpatient hospital stay. Subgroup analysis was performed to assess oseltamivir use in high risk populations for influenza complications. Statistical significance was assessed using Mann-Whitney test for numerical data and Chi-squared test for categorical data. Odds ratio with 95% confidence intervals were calculated where appropriate. Results Overall, 122 RPCR and 362 MPCR positive influenza patients were included in this study. Commencement of antibiotics was less frequent in the RPCR than MPCR cohorts (51% vs 67%; p < 0.01, OR 0.52; 95% CI 0.34–0.79). People at high risk of complications from influenza who were tested with the RPCR were more likely to be treated with oseltamivir compared to those tested with the MPCR (76% vs 63%; p = 0.03, OR 1.81; 95% CI 1.07–3.08). Hospital length of stay was not impacted when either test was used in the emergency department and inpatient settings. Conclusions These findings suggest utilisation of RPCR testing in influenza management can improve antibiotic stewardship through reduction in antibiotic use and improvement in oseltamivir initiation in those at higher risk of complications. Further research is required to determine other factors that may have influenced hospital length of stay and a cost-benefit analysis should be undertaken to determine the financial impact of the RPCR test.
Collapse
Affiliation(s)
- Victor Au Yeung
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, Sydney, NSW, Australia
| | - Kiran Thapa
- Serology and Virology Division (SAViD), Prince of Wales Hospital, Barker Street, Randwick, NSW, Australia
| | - William Rawlinson
- Serology and Virology Division (SAViD), Prince of Wales Hospital, Barker Street, Randwick, NSW, Australia.,School of Medical Sciences, School of Biotechnology and Biomolecular Sciences, School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Andrew Georgiou
- Australian Institute of Health Innovation, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Jeffrey J Post
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, Sydney, NSW, Australia.,Prince of Wales Clinical School, University of New South Wales, Randwick, NSW, Australia
| | - Kristen Overton
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, Sydney, NSW, Australia. .,Prince of Wales Clinical School, University of New South Wales, Randwick, NSW, Australia.
| |
Collapse
|
29
|
Polly DW, Larson AN, Samdani AF, Rawlinson W, Brechka H, Porteous A, Marsh W, Ditto R. Cost-Utility Analysis of Anterior Vertebral Body Tethering versus Spinal Fusion in Idiopathic Scoliosis from a US Integrated Healthcare Delivery System Perspective. Clinicoecon Outcomes Res 2021; 13:175-190. [PMID: 33758521 PMCID: PMC7979350 DOI: 10.2147/ceor.s289459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/23/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Anterior vertebral body tethering (VBT) is a non-fusion, minimally invasive, growth-modulating procedure with some early positive clinical outcomes reported in pediatric patients with idiopathic scoliosis (IS). VBT offers potential health-related quality of life (HRQoL) benefits over spinal fusion in allowing patients to retain a greater range of motion after surgery. We conducted an early cost-utility analysis (CUA) to compare VBT with fusion as a first-choice surgical treatment for skeletally immature patients (age >10 years) with moderate to severe IS, who have failed nonoperative management, from a US integrated healthcare delivery system perspective. Patients and Methods The CUA uses a Markov state transition model, capturing a 15-year period following index surgery. Transition probabilities, including revision risk and subsequent fusion, were based on published surgical outcomes and an ongoing VBT observational study (NCT02897453). Patients were assigned utilities derived from published patient-reported outcomes (PROs; SRS-22r mapped to EQ-5D) following fusion and the above VBT study. Index and revision procedure costs were included. Probabilistic (PSA) and deterministic sensitivity analyses (DSA) were performed. Results VBT was associated with higher costs but also higher quality-adjusted life years (QALYs) than fusion (incremental costs: $45,546; QALYs gained: 0.54). The subsequent incremental cost-effectiveness ratio for VBT vs fusion was $84,391/QALY gained. Mean PSA results were similar to the base case, indicating that results were generally robust to uncertainty. The DSA indicated that results were most sensitive to variations in utility values. Conclusion This is the first CUA comparing VBT with fusion in pediatric patients with IS and suggests that VBT may be a cost-effective alternative to fusion in the US, given recommended willingness-to-pay thresholds ($100,000–$150,000). The results rely on HRQoL benefits for VBT compared with fusion. For improved model accuracy, further analyses with longer-term PROs for VBT, and comparative effectiveness studies, would be needed.
Collapse
Affiliation(s)
- David W Polly
- Department of Orthopedic Surgery, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Abayasingam A, Balachandran H, Agapiou D, Hammoud M, Rodrigo C, Keoshkerian E, Li H, Brasher NA, Christ D, Rouet R, Burnet D, Grubor-Bauk B, Rawlinson W, Turville S, Aggarwal A, Stella AO, Fichter C, Brilot F, Mina M, Post JJ, Hudson B, Gilroy N, Dwyer D, Sasson SC, Tea F, Pilli D, Kelleher A, Tedla N, Lloyd AR, Martinello M, Bull RA. Long-term persistence of RBD + memory B cells encoding neutralizing antibodies in SARS-CoV-2 infection. Cell Rep Med 2021; 2:100228. [PMID: 33748788 PMCID: PMC7955929 DOI: 10.1016/j.xcrm.2021.100228] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022]
Abstract
Considerable concerns relating to the duration of protective immunity against severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) exist, with evidence of antibody titers declining rapidly after infection and reports of reinfection. Here, we monitor the antibody responses against SARS-CoV-2 receptor-binding domain (RBD) for up to 6 months after infection. While antibody titers are maintained, ∼13% of the cohort’s neutralizing responses return to background. However, encouragingly, in a selected subset of 13 participants, 12 have detectable RBD-specific memory B cells and these generally are increasing out to 6 months. Furthermore, we are able to generate monoclonal antibodies with SARS-CoV-2 neutralizing capacity from these memory B cells. Overall, our study suggests that the loss of neutralizing antibodies in plasma may be countered by the maintenance of neutralizing capacity in the memory B cell repertoire. Decay of antibody binding to RBD and spike antigen after 6 months 11 of 81 (13.6%) participants revert to background neutralizing levels Despite declining antibody titers, robust memory B cell populations are observed Memory B cells retain potent neutralizing capacity
Collapse
Affiliation(s)
- Arunasingam Abayasingam
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | - Harikrishnan Balachandran
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | - David Agapiou
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | | | - Chaturaka Rodrigo
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | | | - Hui Li
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | - Nicholas A. Brasher
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst 2010, NSW, Australia
| | - Romain Rouet
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst 2010, NSW, Australia
| | - Deborah Burnet
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst 2010, NSW, Australia
| | - Branka Grubor-Bauk
- Virology Laboratory, Discipline of Surgery, The University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide 5011, SA, Australia
| | - William Rawlinson
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia
- Serology and Virology Division, Department of Microbiology, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | | | | | | | | | - Fabienne Brilot
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Brain Autoimmunity Group, Kids Neurosciences Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Michael Mina
- Northern Beaches Hospital, Sydney, NSW, Australia
| | - Jeffrey J. Post
- Prince of Wales Clinical School, UNSW Australia, Sydney, NSW Australia
| | | | | | | | | | - Fiona Tea
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Brain Autoimmunity Group, Kids Neurosciences Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Deepti Pilli
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Brain Autoimmunity Group, Kids Neurosciences Centre, Kids Research at the Children’s Hospital at Westmead, Sydney, NSW, Australia
| | | | - Nicodemus Tedla
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia
| | | | - Marianne Martinello
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
- Westmead Hospital, Sydney, NSW, Australia
- Blacktown Mt Druitt Hospital, Blacktown, NSW, Australia
| | - Rowena A. Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW, Australia
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
- Corresponding author
| | | |
Collapse
|
31
|
Madala BS, Reis ALM, Deveson IW, Rawlinson W, Mercer TR. Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests. Sci Rep 2021; 11:2636. [PMID: 33514761 PMCID: PMC7846570 DOI: 10.1038/s41598-021-81760-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/11/2021] [Indexed: 11/25/2022] Open
Abstract
DNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target genetic material, and act only as positive controls to assess test sensitivity. However, negative controls are also required to evaluate test specificity. Using a pair of chimeric A/B RNA standards, this allowed incorporation of positive and negative controls into diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The chimeric standards constituted target regions for RT-PCR primer/probe sets that are joined in tandem across two separate synthetic molecules. Accordingly, a target region that is present in standard A provides a positive control, whilst being absent in standard B, thereby providing a negative control. This design enables cross-validation of positive and negative controls between the paired standards in the same reaction, with identical conditions. This enables control and test failures to be distinguished, increasing confidence in the accuracy of results. The chimeric A/B standards were assessed using the US Centres for Disease Control real-time RT-PCR protocol, and showed results congruent with other commercial controls in detecting SARS-CoV-2 in patient samples. This chimeric reference standard design approach offers extensive flexibility, allowing representation of diverse genetic features and distantly related sequences, even from different organisms.
Collapse
Affiliation(s)
- Bindu Swapna Madala
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Andre L M Reis
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - William Rawlinson
- School of Medical Sciences, Women's & Children's, and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia. .,Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
32
|
Rawlinson W. Contextualising SARS Coronavirus 2 and COVID-19. Microbiol Aust 2021. [DOI: 10.1071/ma21002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
It is timely to assess where we are in the current SARS Coronavirus-2 pandemic. This edition of Microbiology Australia has national, and international, authorities authoring a series of papers on SARS Coronavirus 2 and related subjects. We are extremely fortunate to have papers on the overarching issues of zoonotic spread (Gartner, Selleck) and how this relates to the practicalities of our responses via public health (Bennett), vaccination (Macintyre), antivirals (De Clercq), and immunotherapies (Kelleher). Diagnosis and transmission control have been at the centre of public health responses (Blackall, Speers), as has been research informing our understanding of the virus (Dhakal, Zaunders, Eden). A focus on basic research, translated into outcomes in real time, has been a very successful feature of the COVID-19 pandemic. We are privileged to be able to feature some of this research, in these papers, although this is only part of the extensive and excellent Australian work in reducing the impact of SARS CoV2 infection, and COVID-19 disease.
Collapse
|
33
|
Walker GJ, Clifford V, Bansal N, Stella AO, Turville S, Stelzer‐Braid S, Klein LD, Rawlinson W. SARS-CoV-2 in human milk is inactivated by Holder pasteurisation but not cold storage. J Paediatr Child Health 2020; 56:1872-1874. [PMID: 32767639 PMCID: PMC7436299 DOI: 10.1111/jpc.15065] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 12/23/2022]
Abstract
AIM As the COVID-19 pandemic evolves, human milk banks world-wide continue to provide donor human milk to vulnerable infants who lack access to mother's own milk. Under these circumstances, ensuring the safety of donor human milk is paramount, as the risk of vertical transmission of SARS-CoV-2 is not fully understood. Here, we investigate the inactivation of SARS-CoV-2 in human milk by pasteurisation and the stability of SARS-CoV-2 in human milk under cold storage. METHODS SARS-CoV-2 was experimentally inoculated into human milk samples from healthy donors or into a control medium. Triplicates of each sample were layered onto uninfected cells after Holder pasteurisation (63°C for 30 min), heating to 56°C for 30 min, or after 48 h of storage at 4°C or -30°C. Infectious titres of virus were determined at 72 h post-infection by endpoint titration. RESULTS Following heating to 63°C or 56°C for 30 min, replication competent (i.e. live) SARS-CoV-2 was undetected in both human milk and the control medium. Cold storage of SARS-CoV-2 in human milk (either at 4°C or -30°C) did not significantly impact infectious viral load over a 48 h period. CONCLUSION SARS-CoV-2 is effectively inactivated by Holder pasteurisation, suggesting that existing milk bank processes will effectively mitigate the risk of transmission of SARS-COV-2 to vulnerable infants through pasteurised donor human milk. The demonstrated stability of SARS-CoV-2 in refrigerated or frozen human milk may assist in the development of guidelines around safe expressing and storing of milk from COVID-19 infected mothers.
Collapse
Affiliation(s)
- Gregory J Walker
- Virology Research Laboratory, Serology and Virology Division (SAViD), Prince of Wales HospitalUniversity of New South WalesSydneyNew South WalesAustralia,Schools of Medical Sciences and of Women's and Childrens Health, Faculty of Medicine, School and Biotechnology and Biomolecular Sciences Faculty of ScienceUniversity of New South WalesSydneyNew South WalesAustralia
| | - Vanessa Clifford
- Clinical Services and ResearchAustralian Red Cross LifebloodMelbourneVictoriaAustralia,Department of Medicine, Dentistry and Health SciencesUniversity of MelbourneMelbourneVictoriaAustralia,Department of Microbiology, Laboratory ServicesRoyal Children's HospitalMelbourneVictoriaAustralia,Infection and Immunity, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Nidhi Bansal
- Department of Medicine, Dentistry and Health SciencesUniversity of MelbourneMelbourneVictoriaAustralia,School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneQueenslandAustralia,School of PharmacyUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Alberto O Stella
- Kirby InstituteUniversity of New South WalesSydneyNew South WalesAustralia
| | - Stuart Turville
- Kirby InstituteUniversity of New South WalesSydneyNew South WalesAustralia
| | - Sacha Stelzer‐Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), Prince of Wales HospitalUniversity of New South WalesSydneyNew South WalesAustralia,Schools of Medical Sciences and of Women's and Childrens Health, Faculty of Medicine, School and Biotechnology and Biomolecular Sciences Faculty of ScienceUniversity of New South WalesSydneyNew South WalesAustralia
| | - Laura D Klein
- Clinical Services and ResearchAustralian Red Cross LifebloodMelbourneVictoriaAustralia
| | - William Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), Prince of Wales HospitalUniversity of New South WalesSydneyNew South WalesAustralia,Schools of Medical Sciences and of Women's and Childrens Health, Faculty of Medicine, School and Biotechnology and Biomolecular Sciences Faculty of ScienceUniversity of New South WalesSydneyNew South WalesAustralia
| |
Collapse
|
34
|
van Bockel D, Munier CML, Turville S, Badman SG, Walker G, Stella AO, Aggarwal A, Yeang M, Condylios A, Kelleher AD, Applegate TL, Vallely A, Whiley D, Rawlinson W, Cunningham P, Kaldor J, Guy R. Evaluation of Commercially Available Viral Transport Medium (VTM) for SARS-CoV-2 Inactivation and Use in Point-of-Care (POC) Testing. Viruses 2020; 12:E1208. [PMID: 33114233 PMCID: PMC7690900 DOI: 10.3390/v12111208] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 01/14/2023] Open
Abstract
Critical to facilitating SARS-CoV-2 point-of-care (POC) testing is assurance that viruses present in specimens are inactivated onsite prior to processing. Here, we conducted experiments to determine the virucidal activity of commercially available Viral Transport Mediums (VTMs) to inactivate SARS-CoV-2. Independent testing methods for viral inactivation testing were applied, including a previously described World Health Organization (WHO) protocol, in addition to a buffer exchange method where the virus is physically separated from the VTM post exposure. The latter method enables sensitive detection of viral viability at higher viral titre when incubated with VTM. We demonstrate that VTM formulations, Primestore® Molecular Transport Medium (MTM) and COPAN eNAT™ completely inactivate high-titre SARS-CoV-2 virus (>1 × 107 copies/mL) and are compatible with POC processing. Furthermore, full viral inactivation was rapidly achieved in as little as 2 min of VTM exposure. We conclude that adding certain VTM formulations as a first step post specimen collection will render SARS-CoV-2 non-infectious for transport, or for further in-field POC molecular testing using rapid turnaround GeneXpert platforms or equivalent.
Collapse
Affiliation(s)
- David van Bockel
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - C. Mee Ling Munier
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Stuart Turville
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Steven G. Badman
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Gregory Walker
- NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW 2052, Australia; (G.W.); (M.Y.); (A.C.); (W.R.)
| | - Alberto Ospina Stella
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Anupriya Aggarwal
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Malinna Yeang
- NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW 2052, Australia; (G.W.); (M.Y.); (A.C.); (W.R.)
| | - Anna Condylios
- NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW 2052, Australia; (G.W.); (M.Y.); (A.C.); (W.R.)
| | - Anthony D. Kelleher
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Tanya L. Applegate
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Andrew Vallely
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - David Whiley
- NSW State Reference Laboratory for HIV-AIDS/St Vincent’s Hospital Sydney, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital Sydney Limited, Darlinghurst, NSW 2010, Australia;
- Australia Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, QLD 4006, Australia
| | - William Rawlinson
- NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW 2052, Australia; (G.W.); (M.Y.); (A.C.); (W.R.)
| | - Phillip Cunningham
- Centre for Clinical Research, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, QLD 4006, Australia;
| | - John Kaldor
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| | - Rebecca Guy
- Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; (C.M.L.M.); (S.T.); (S.G.B.); (A.O.S.); (A.A.); (A.D.K.); (T.L.A.); (A.V.); (J.K.); (R.G.)
| |
Collapse
|
35
|
Gulholm T, Basile K, Kok J, Chen SCA, Rawlinson W. Laboratory diagnosis of severe acute respiratory syndrome coronavirus 2. Pathology 2020; 52:745-753. [PMID: 33131799 PMCID: PMC7543760 DOI: 10.1016/j.pathol.2020.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/20/2022]
Abstract
The first laboratory confirmed case of Coronavirus disease 2019 (COVID-19) in Australia was in Victoria on 25 January 2020 in a man returning from Wuhan city, Hubei province, the People's Republic of China. This was followed by three cases in New South Wales the following day. The Australian Government activated the Australian Health Sector Emergency Response Plan for Novel Coronavirus on 27 February 2020 in anticipation of a pandemic. Subsequently, the World Health Organization declared COVID-19 to be a Public Health Emergency of International Concern followed by a pandemic on 30 January 2020 and 11 March 2020, respectively. Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is key in identifying infected persons to guide timely public health actions of contact tracing and patient isolation to limit transmission of infection. This article aims to provide a comprehensive overview of current laboratory diagnostic methods for SARS-CoV-2, including nucleic acid testing, serology, rapid antigen detection and antibody tests, virus isolation and whole genome sequencing. The relative advantages and disadvantages of the different diagnostic tests are presented, as well as their value in different clinical, infection control and public health contexts. We also describe the challenges in the provision of SARS-CoV-2 diagnostics in Australia, a country with a relatively low COVID-19 incidence in the first pandemic wave but in which prevalence could rapidly change.
Collapse
Affiliation(s)
- T Gulholm
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia.
| | - K Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - S C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead, NSW, Australia
| | - W Rawlinson
- NSW Health Pathology, Serology and Virology Division, Prince of Wales Hospital, Randwick, NSW, Australia; Virology Research Laboratory, Prince of Wales Hospital, University of New South Wales, Randwick, NSW, Australia; School of Medical Sciences and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Kensington, NSW, Australia
| |
Collapse
|
36
|
Wabe N, Lindeman R, Post JJ, Rawlinson W, Miao M, Westbrook JI, Georgiou A. Cepheid Xpert ® Flu/RSV and Seegene Allplex ™ RP1 show high diagnostic agreement for the detection of influenza A/B and respiratory syncytial viruses in clinical practice. Influenza Other Respir Viruses 2020; 15:245-253. [PMID: 32815622 PMCID: PMC7461471 DOI: 10.1111/irv.12799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Background Molecular assays based on reverse transcription‐polymerase chain reaction (RT‐PCR) provide reliable results for the detection of respiratory pathogens, although diagnostic agreement varies. This study determined the agreement between the RT‐PCR assays (Xpert® Flu/RSV vs Allplex™ RP1) in detecting influenza A, influenza B, and respiratory syncytial viruses (RSVs) in clinical practice. Methods We retrospectively identified 914 patient encounters where testing with both Xpert® Flu/RSV and Allplex™ RP1 was undertaken between October 2015 and September 2019 in seven hospitals across New South Wales, Australia. The diagnostic agreement of the two assays was evaluated using positive percent agreement, negative percent agreement, and prevalence and bias‐adjusted kappa. Results The positive percent agreement was 95.1% for influenza A, 87.5% for influenza B, and 77.8% for RSV. The negative percent agreement was 99.4% for influenza A, 99.9% for influenza B, and 100% for RSV. The prevalence and bias‐adjusted kappa was 0.98 for influenza A, 0.99 for influenza B, and 0.97 for RSV. In a sensitivity analysis, the positive percent agreement values were significantly higher during the non‐influenza season than the influenza season for influenza B and RSV. Conclusions The Xpert® Flu/RSV and Allplex™ RP1 demonstrated a high diagnostic agreement for all three viruses assessed. The seasonal variation in the positive percent agreement of the two assays for influenza B and RSV may have been due to lower numbers assessed, variability in the virology of infections outside the peak season, or changes in the physiology of the infected host in different seasons.
Collapse
Affiliation(s)
- Nasir Wabe
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
| | | | - Jeffrey J Post
- Department of Infectious Diseases, Prince of Wales Hospital and Community Health Services, Randwick, NSW, Australia.,Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - William Rawlinson
- NSW Health Pathology Randwick, Prince of Wales Hospital and Community Health Services, Randwick, NSW, Australia.,School of Medical Sciences, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Melissa Miao
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
| | - Johanna I Westbrook
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
| | - Andrew Georgiou
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
| |
Collapse
|
37
|
Teutsch SM, Nunez CA, Morris A, McGregor S, King J, Brotherton JM, Novakovic D, Booy R, Jones CA, Rawlinson W, Thorley BR, Elliott EJ. Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2019. ACTA ACUST UNITED AC 2020; 44. [PMID: 32829700 DOI: 10.33321/cdi.2020.44.60] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Australian Paediatric Surveillance Unit (APSU) has been prospectively collecting national data on rare childhood conditions since 1993, with monthly reporting of cases by paediatricians. In this report we describe annual results from studies for ten communicable diseases and complications of communicable diseases that were conducted using APSU surveillance in 2019 and place these in an historic context. Results are reported on acute flaccid paralysis, congenital cytomegalovirus infection, neonatal herpes simplex virus infection, perinatal exposure to HIV, paediatric HIV infection, severe complications of seasonal influenza, juvenile onset recurrent respiratory papillomatosis (JoRRP), congenital rubella syndrome, congenital varicella syndrome and neonatal varicella infection. APSU provides rich clinical data to complement data collected from other surveillance systems and to improve understanding and response to rare childhood infections.
Collapse
Affiliation(s)
- Suzy M Teutsch
- Research Fellow, The Australian Paediatric Surveillance Unit; The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health; and The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales
| | - Carlos A Nunez
- Research Associate, The Australian Paediatric Surveillance Unit and The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health and The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales
| | - Anne Morris
- Senior Research Fellow, The Australian Paediatric Surveillance Unit; and Paediatrician and Senior Lecturer, The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health and The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales
| | - Skye McGregor
- Epidemiologist, The Kirby Institute, UNSW Australia, Sydney, New South Wales
| | - Jonathan King
- Epidemiologist, The Kirby Institute, UNSW Australia, Sydney, New South Wales
| | - Julia Ml Brotherton
- Medical Director, VCS Population Health, VCS Foundation; and Honorary Principal Fellow, Melbourne School of Population and Global Health, University of Melbourne, Victoria
| | - Daniel Novakovic
- ENT, Head and Neck Surgeon, Laryngologist, and Director, Dr Liang Voice Program, The University of Sydney, Faculty of Medicine and Health, Central Clinical School, Sydney, New South Wales
| | - Robert Booy
- Senior Professorial Fellow, National Centre for Immunisation Research and Surveillance, Sydney, New South Wales
| | - Cheryl A Jones
- Dean and Head of Sydney Medical School, The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales
| | - William Rawlinson
- Senior Medical Virologist, Director of Serology, Virology and OTDS Laboratories, NSW Health Pathology Randwick, Sydney, New South Wales
| | - Bruce R Thorley
- Head, National Enterovirus Reference Laboratory and WHO Polio Regional Reference Laboratory, Victorian Infectious Disease Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Elizabeth J Elliott
- Professor of Paediatrics and Child Health and Director of The Australian Paediatric Surveillance Unit, The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health and The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales
| |
Collapse
|
38
|
Khatami A, Burrell R, McMullan BJ, Rawlinson W, Givney RC, Kok J, Alexandersen S, Jones CA, Macartney KK, Britton PN. Epidemic and Inter-epidemic Burden of Pediatric Human Parechovirus Infection in New South Wales, Australia, 2017-2018. Pediatr Infect Dis J 2020; 39:507-511. [PMID: 32118855 DOI: 10.1097/inf.0000000000002615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Human parechovirus (HPeV) typically infects young children, and although infection is often asymptomatic, some types (eg, HPeV3) are associated with severe clinical manifestations, including central nervous system infection or sepsis-like syndrome, particularly affecting young infants. The third documented national epidemic of HPeV occurred in Australia in 2017-2018. METHODS Four public laboratories that perform almost all of the HPeV PCR testing in New South Wales provided data regarding HPeV tests performed from July 1, 2017 to June 30, 2018. Limited demographic and clinical data were obtained from electronic medical records for laboratory test-positive cases that presented to each of the 3 pediatric hospitals in New South Wales. RESULTS Five hundred eighty-one HPeV-positive samples obtained from 395 cases were included in the analysis. The peak of the outbreak occurred in late November 2017 (approximately 35 new cases each week), with the main HPeV epidemic occurring between the spring and summer months of September 2017 to January 2018; although this seasonality was observed primarily in infants less than 12 months of age. Among the 388 pediatric cases, almost half were younger than 2 months (188; 47%) and only 10 were children older than 2 years. The annualized estimated incidence of laboratory confirmed HPeV infection in children was approximately 142.4 cases per 100,000 children younger than 5 years in New South Wales during the epidemic season. CONCLUSIONS The large burden of HPeV infection and disease identified in young infants in this and previous Australian studies highlight the need for more comprehensive national surveillance of HPeV infections and improved prevention strategies.
Collapse
Affiliation(s)
- Ameneh Khatami
- From the Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Rebecca Burrell
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Brendan J McMullan
- Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, The University of New South Wales, Sydney, NSW, Australia.,National Centre for Infections in Cancer and Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - William Rawlinson
- School of Women's and Children's Health, The University of New South Wales, Sydney, NSW, Australia.,Serology, Virology and Organ and Tissue Donation Service Laboratories, New South Wales Health Pathology, Randwick, NSW, Australia
| | - Rodney C Givney
- John Hunter Hospital Laboratory, New South Wales Health Pathology, Newcastle, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia.,National Centre for Immunisation Research and Surveillance, The Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Cheryl A Jones
- From the Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,National Centre for Infections in Cancer and Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia.,Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Kristine K Macartney
- From the Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Philip N Britton
- From the Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
39
|
Lindsay J, Yong MK, Greenwood M, Kong DCM, Chen SCA, Rawlinson W, Slavin M. Epstein-Barr virus related post-transplant lymphoproliferative disorder prevention strategies in allogeneic hematopoietic stem cell transplantation. Rev Med Virol 2020; 30:e2108. [PMID: 32301566 DOI: 10.1002/rmv.2108] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 12/12/2022]
Abstract
Epstein-Barr virus associated post-transplant lymphoproliferative disorders (EBV PTLD) are recognized as a significant cause of morbidity and mortality in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT). The number of patients at risk of developing EBV PTLD is increasing, partly as a result of highly immunosuppressive regimens, including the use of anti-thymocyte globulin (ATG). Importantly, there is heterogeneity in PTLD management strategies between alloHSCT centers worldwide. This review summarizes the different EBV PTLD prevention strategies being utilized including the alloHSCT and T-cell depletion regimes and the risk they confer; monitoring programs, including the timing and analytes used for EBV virus detection, as well as pre-emptive thresholds and therapy with rituximab. In the absence of an institution-specific policy, it is suggested that the optimal pre-emptive strategy in HSCT recipients with T-cell depleting treatments, acute graft vs host disease (GVHD) and a mismatched donor for PTLD prevention is (a) monitoring of EBV DNA post-transplant weekly using plasma or WB as analyte and (b) pre-emptively reducing immune suppression (if possible) at an EBV DNA threshold of >1000 copies/mL (plasma or WB), and treating with rituximab at a threshold of >1000 copies/mL (plasma) or >5000 copies/mL (WB). There is emerging evidence for prophylactic rituximab as a feasible and safe strategy for PTLD, particularly if pre-emptive monitoring is problematic. Future management strategies such as prophylactic EBV specific CTLs have shown promising results and as this procedure becomes less expensive and more accessible, it may become the strategy of choice for EBV PTLD prevention.
Collapse
Affiliation(s)
- Julian Lindsay
- Haematology Department, Royal North Shore Hospital, Sydney, New South Wales, Australia.,National Centre for Infection in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Michelle K Yong
- National Centre for Infection in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Matthew Greenwood
- Haematology Department, Royal North Shore Hospital, Sydney, New South Wales, Australia.,Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - David C M Kong
- National Centre for Infection in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,National Centre for Antimicrobial Stewardship at The Peter Doherty Institute for Infections and Immunity, Parkville, Victoria, Australia.,Centre for Medicine Use and Safety, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.,Pharmacy Department, Ballarat Health Services, Ballarat, Victoria, Australia
| | - Sharon C A Chen
- National Centre for Infection in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Centre for Infectious Diseases and Microbiology, New South Wales Health Pathology, Westmead Hospital, The University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
| | - William Rawlinson
- SAViD (Serology and Virology Division), NSW Health Pathology, Prince of Wales Hospital, and SOMS, BABS and School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Monica Slavin
- National Centre for Infection in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
40
|
Harjanto R, Smith DE, Barratt H, Kelly M, Chan D, Furner V, Smith M, Ronnachit A, Post J, Rawlinson W. Utility of rapid plasmin reagin titres in assessing treatment response and re-infection for infectious syphilis. Sex Health 2020; 17:330-336. [PMID: 32687780 DOI: 10.1071/sh20043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 11/23/2022]
Abstract
Background The rapid plasma reagin (RPR) assay is commonly used as a surrogate marker of infectious syphilis, but is non-specific, slow to change and variable in its rate of decline post treatment. METHODS Within an urban sexual health service testing predominantly men who have sex with men, a file review of RPR changes was undertaken in all subjects who had a dilution level of ≥1:4, between January 2015 to the end of December 2018. RESULTS Overall, 248 cases of infectious syphilis were identified in 215 subjects (165 HIV seropositive, 50 HIV seronegative). Among unique-subject cases with follow-up RPR recorded, seroreversion to a non-reactive titre was achieved in only 42.3% (71/168) cases at a median of 235 days (interquartile range: 138-348 days) and was significantly less likely if patients had HIV infection (P = 0.02), late latent syphilis (P = 0.003) or a subsequent syphilis infection (P < 0.0001). Having HIV infection (P = 0.03) or a subsequent episode of syphilis (P = 0.01) were associated with a lower likelihood of documented cure. CONCLUSIONS The slow decay in RPR titres post therapy and the inability of a significant number of subjects to achieve a non-reactive result over time makes RPR a poor test for assessing the adequacy of treatment or in diagnosing re-infection, especially in populations having repeated and frequent risk exposures. As the number of syphilis cases continue to climb, better tests that accurately assess pathogen presence are urgently needed.
Collapse
Affiliation(s)
- Ricky Harjanto
- The Albion Centre, 150 Albion Street, Surry Hills, NSW 2010, Australia
| | - Don E Smith
- The Albion Centre, 150 Albion Street, Surry Hills, NSW 2010, Australia; and School of Public Health & Community Medicine, University of New South Wales, High Street, Kensington, NSW 2033, Australia; and Corresponding author.
| | | | - Melissa Kelly
- The Albion Centre, 150 Albion Street, Surry Hills, NSW 2010, Australia; and Infectious Diseases Department, Prince of Wales Hospital, 320-346 Barker Street, Randwick, NSW 2031, Australia
| | - Derek Chan
- The Albion Centre, 150 Albion Street, Surry Hills, NSW 2010, Australia; and School of Public Health & Community Medicine, University of New South Wales, High Street, Kensington, NSW 2033, Australia
| | - Virginia Furner
- The Albion Centre, 150 Albion Street, Surry Hills, NSW 2010, Australia
| | - Maggie Smith
- The Albion Centre, 150 Albion Street, Surry Hills, NSW 2010, Australia
| | - Amrita Ronnachit
- Infectious Diseases Department, Prince of Wales Hospital, 320-346 Barker Street, Randwick, NSW 2031, Australia
| | - Jeffrey Post
- Infectious Diseases Department, Prince of Wales Hospital, 320-346 Barker Street, Randwick, NSW 2031, Australia
| | - William Rawlinson
- Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, 320-346 Barker Street, Randwick, NSW 2031, Australia
| |
Collapse
|
41
|
Gebbie S, Kaufer A, Rawlinson W. The risk from Security Sensitive Biological Agents (SSBAs) and the need for response. Microbiol Aust 2020. [DOI: 10.1071/ma20030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In 2011, the International Health Regulations Review Committee of the WHO suggested ‘The world is ill-prepared to respond to a severe influenza pandemic or to any similarly global, sustained and threatening public-health emergency’. This was presumably partly in response to known threats that had occurred over the previous decade – Severe Acute Respiratory Syndrome (SARS) in 2003,H1N1 pandemic influenza in 2009, avian influenza H5N1 in 2004, and predated outbreaks with Zikavirus (2015–2016), Ebolavirus (2014), and most recently SARS CoV2, the causative agent of COVID-19 (2020).
Collapse
|
42
|
Nunez CA, Morris A, Teutsch SM, McGregor S, Brotherton J, Novakovic D, Rawlinson W, Jones CA, Thorley BR, Elliott EJ. Australian Paediatric Surveillance Unit Annual Report 2018. ACTA ACUST UNITED AC 2019; 43. [PMID: 31738868 DOI: 10.33321/cdi.2019.43.53] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Carlos A Nunez
- Australian Paediatric Surveillance Unit. The Children's Hospital at Westmead, NSW 2145, Australia
| | - Anne Morris
- Australian Paediatric Surveillance Unit; Clinical School, Children's Hospital at Westmead, The University of Sydney
| | - Suzy M Teutsch
- Research Fellow, Australian Paediatric Surveillance Unit
| | | | | | - Daniel Novakovic
- The Canterbury Hospital; Faculty of Medicine and Health, Central Clinical School, The University of Sydney
| | | | - Cheryl A Jones
- Faculty of Medicine and Health, The University of Sydney
| | - Bruce R Thorley
- VIDRL, The Peter Doherty Institute for Infection and Immunity
| | - Elizabeth J Elliott
- University of Sydney; Sydney Children's Hospitals Network Westmead; Australian Paediatric Surveillance Unit
| |
Collapse
|
43
|
Karelehto E, Brouwer L, Benschop K, Kok J, Basile K, McMullan B, Rawlinson W, Druce J, Nicholson S, Selvarangan R, Harrison C, Lankachandra K, van Eijk H, Koen G, de Jong M, Pajkrt D, Wolthers KC. Seroepidemiology of Parechovirus A3 Neutralizing Antibodies, Australia, the Netherlands, and United States. Emerg Infect Dis 2019; 25:148-152. [PMID: 30561318 PMCID: PMC6302606 DOI: 10.3201/eid2501.180352] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recent parechovirus A3 (PeV-A3) outbreaks in Australia suggest lower population immunity compared with regions that have endemic PeV-A3 circulation. A serosurvey among populations in the Netherlands, the United States, and Australia before and after the 2013 Australia outbreak showed high PeV-A3 neutralizing antibody prevalence across all regions and time periods, indicating widespread circulation.
Collapse
|
44
|
Chughtai AA, Stelzer-Braid S, Rawlinson W, Pontivivo G, Wang Q, Pan Y, Zhang D, Zhang Y, Li L, MacIntyre CR. Contamination by respiratory viruses on outer surface of medical masks used by hospital healthcare workers. BMC Infect Dis 2019; 19:491. [PMID: 31159777 PMCID: PMC6547584 DOI: 10.1186/s12879-019-4109-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/20/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Medical masks are commonly used in health care settings to protect healthcare workers (HCWs) from respiratory and other infections. Airborne respiratory pathogens may settle on the surface of used masks layers, resulting in contamination. The main aim of this study was to study the presence of viruses on the surface of medical masks. METHODS Two pilot studies in laboratory and clinical settings were carried out to determine the areas of masks likely to contain maximum viral particles. A laboratory study using a mannequin and fluorescent spray showed maximum particles concentrated on upper right, middle and left sections of the medical masks. These findings were confirmed through a small clinical study. The main study was then conducted in high-risk wards of three selected hospitals in Beijing China. Participants (n = 148) were asked to wear medical masks for a shift (6-8 h) or as long as they could tolerate. Used samples of medical masks were tested for presence of respiratory viruses in upper sections of the medical masks, in line with the pilot studies. RESULTS Overall virus positivity rate was 10.1% (15/148). Commonly isolated viruses from masks samples were adenovirus (n = 7), bocavirus (n = 2), respiratory syncytial virus (n = 2) and influenza virus (n = 2). Virus positivity was significantly higher in masks samples worn for > 6 h (14.1%, 14/99 versus 1.2%, 1/49, OR 7.9, 95% CI 1.01-61.99) and in samples used by participants who examined > 25 patients per day (16.9%, 12/71 versus 3.9%, 3/77, OR 5.02, 95% CI 1.35-18.60). Most of the participants (83.8%, 124/148) reported at least one problem associated with mask use. Commonly reported problems were pressure on face (16.9%, 25/148), breathing difficulty (12.2%, 18/148), discomfort (9.5% 14/148), trouble communicating with the patient (7.4%, 11/148) and headache (6.1%, 9/148). CONCLUSION Respiratory pathogens on the outer surface of the used medical masks may result in self-contamination. The risk is higher with longer duration of mask use (> 6 h) and with higher rates of clinical contact. Protocols on duration of mask use should specify a maximum time of continuous use, and should consider guidance in high contact settings. Viruses were isolated from the upper sections of around 10% samples, but other sections of masks may also be contaminated. HCWs should be aware of these risks in order to protect themselves and people around them.
Collapse
Affiliation(s)
- Abrar Ahmad Chughtai
- School of Public Health and Community Medicine, UNSW Medicine, University of New South Wales, Level 2, Samuels Building, Sydney, 2052, Australia.
| | - Sacha Stelzer-Braid
- University of New South Wales, Virology Research Laboratory, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - William Rawlinson
- SAViD (Serology & Virology Division), Prince of Wales Hospital, Randwick, Australia
| | - Giulietta Pontivivo
- Infection Prevention Management and Staff Health Services- St Vincent's Hospital, Sydney, Australia
| | - Quanyi Wang
- Beijing Center for Diseases Prevention and Control, Beijing, China
| | - Yang Pan
- Beijing Center for Diseases Prevention and Control, Beijing, China
| | - Daitao Zhang
- Beijing Center for Diseases Prevention and Control, Beijing, China
| | - Yi Zhang
- Beijing Center for Diseases Prevention and Control, Beijing, China
| | - Lili Li
- Fangshan Center for Diseases Prevention and Control, Beijing, China
| | - C Raina MacIntyre
- Biosecurity Program, The Kirby Institute, University of New South Wales, Sydney, NSW, 2052, Australia.,College of Public Service & Community Solutions, and College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA
| |
Collapse
|
45
|
Lazzaro A, Vo ML, Zeltzer J, Rawlinson W, Nassar N, Daly K, Lainchbury A, Shand A. Knowledge of congenital cytomegalovirus (CMV) in pregnant women in Australia is low, and improved with education. Aust N Z J Obstet Gynaecol 2019; 59:843-849. [PMID: 31025720 DOI: 10.1111/ajo.12978] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/14/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND Cytomegalovirus (CMV) is the most common congenital infection and can cause hearing loss and neurodevelopmental disability in infected infants. International research shows women have limited knowledge about CMV. AIMS To assess pregnant women's knowledge and attitudes about CMV before and after provision of information. MATERIALS AND METHODS Cross-sectional survey of pregnant women between November 2017 and February 2018 at two Australian hospitals. Participating women completed an initial survey on maternal characteristics, knowledge of infections, and CMV risk behaviours. Participants were then given an information leaflet and completed a follow-up survey. RESULTS Four hundred and fifty-seven women completed the initial survey, of whom 73/457 (16%) had heard of CMV. Behaviours increasing risk of CMV transmission were common: 58% reported regularly kissing their child on the lips; 57% did not always wash their hands after changing a wet nappy. Knowledge about CMV significantly improved after reading the leaflet in the 145 women completing the follow-up survey. More women correctly identified that CMV could cause deafness in a baby (35% before, 85% after), was spread by saliva (38% vs 94%) or urine (27% vs 86%) and prevented by hand-washing (55% vs 99%; all P < 0.001). CONCLUSION Knowledge about CMV was low in pregnant women. An educational leaflet was effective in improving knowledge.
Collapse
Affiliation(s)
- Amanda Lazzaro
- Royal Hospital for Women, Sydney, New South Wales, Australia
| | - Mai Linh Vo
- The University of Sydney, Sydney, New South Wales, Australia
| | - Justin Zeltzer
- Child Translational Health Research, Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - William Rawlinson
- School of Medical Sciences, Biotechnology and Biomolecular Services, and Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.,Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Natasha Nassar
- Child Translational Health Research, Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Kate Daly
- Congenital CMV Association of Australia, Sydney, New South Wales, Australia
| | - Anne Lainchbury
- Royal Hospital for Women, Sydney, New South Wales, Australia
| | - Antonia Shand
- Child Translational Health Research, Children's Hospital at Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia.,Department of Maternal Fetal Medicine, Royal Hospital for Women, Sydney, New South Wales, Australia
| |
Collapse
|
46
|
Macdonald-Laurs E, Koirala A, Britton PN, Rawlinson W, Hiew CC, Mcrae J, Dale RC, Jones C, Macartney K, McMullan B, Pillai S. CSF neopterin, a useful biomarker in children presenting with influenza associated encephalopathy? Eur J Paediatr Neurol 2019; 23:204-213. [PMID: 30316638 PMCID: PMC7128712 DOI: 10.1016/j.ejpn.2018.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/07/2018] [Accepted: 09/23/2018] [Indexed: 12/18/2022]
Abstract
PURPOSE Neurological complications of influenza cause significant disease in children. Central nervous system inflammation, the presumed mechanism of influenza-associated encephalopathy, is difficult to detect. Characteristics of children presenting with severe neurological complications of influenza, and potential biomarkers of influenza-associated encephalopathy are described. METHODS A multi-center, retrospective case-series of children with influenza and neurological complications during 2017 was performed. Enrolled cases met criteria for influenza-associated encephalopathy or had status epilepticus. Functional outcome at discharge was compared between groups using the Modified Rankin Scale (mRS). RESULTS There were 22 children with influenza studied of whom 11/22 had encephalopathy and 11/22 had status epilepticus. Only one child had a documented influenza immunization. The biomarker CSF neopterin was tested in 10/11 children with encephalopathy and was elevated in 8/10. MRI was performed in all children with encephalopathy and was abnormal in 8 (73%). Treatment of children with encephalopathy was with corticosteroids or intravenous immunoglobulin in 9/11 (82%). In all cases oseltamivir use was low (59%) while admission to the intensive care unit was frequent (14/22, 66%). Clinical outcome at discharge was moderate to severe disability (mRS score > 2) in the majority of children with encephalopathy (7/11, 64%), including one child who died. Children with status epilepticus recovered to near-baseline function in all cases. CONCLUSION Raised CSF neopterin was present in most cases of encephalopathy, and along with diffusion restriction on MRI, is a useful diagnostic biomarker. Lack of seasonal influenza vaccination represents a missed opportunity to prevent illness in children, including severe neurological disease.
Collapse
Affiliation(s)
- Emma Macdonald-Laurs
- Sydney Children's Hospital Network (SCHN), Australia; The University of New South Wales, Australia.
| | - Archana Koirala
- Sydney Children's Hospital Network (SCHN), Australia; The University of New South Wales, Australia
| | - Philip N Britton
- Sydney Children's Hospital Network (SCHN), Australia; The University of Sydney, Discipline of Child and Adolescent Health, Australia
| | | | - Chee Chung Hiew
- Sydney Children's Hospital Network (SCHN), Australia; Prince of Wales Hospital, Sydney, Australia
| | | | - Russell C Dale
- Sydney Children's Hospital Network (SCHN), Australia; The University of Sydney, Discipline of Child and Adolescent Health, Australia
| | - Cheryl Jones
- Sydney Children's Hospital Network (SCHN), Australia; The University of Sydney, Discipline of Child and Adolescent Health, Australia; The Royal Children's Hospital, Melbourne, Australia; The University of Melbourne, Department of Paediatrics, Australia
| | - Kristine Macartney
- Sydney Children's Hospital Network (SCHN), Australia; The University of Sydney, Discipline of Child and Adolescent Health, Australia
| | - Brendan McMullan
- Sydney Children's Hospital Network (SCHN), Australia; The University of New South Wales, Australia
| | - Sekhar Pillai
- Sydney Children's Hospital Network (SCHN), Australia; The University of New South Wales, Australia
| |
Collapse
|
47
|
Affiliation(s)
- Sacha Stelzer-Braid
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Medical Sciences, and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - William Rawlinson
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Medical Sciences, and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
- Serology and Virology Division (SAViD), Microbiology NSW Health Pathology Randwick, NSW 2031, Australia
| |
Collapse
|
48
|
Chan DL, Young H, Palasanthiran P, Rawlinson W, Gray P, Andrews PI. Fulminant subacute sclerosing panencephalitis: Not only a disease of the past. J Paediatr Child Health 2018; 54:1264-1267. [PMID: 29923642 DOI: 10.1111/jpc.14090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Denise L Chan
- Department of Neurology, Sydney Children's Hospital, Sydney, New South Wales, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Helen Young
- Department of Paediatrics, Royal North Shore Hospital, Sydney, New South Wales, Australia.,Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Department of Neurogenetics, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Pamela Palasanthiran
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.,Department of Immunology and Infectious Disease, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - William Rawlinson
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia.,Serology and Virology Division, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Paul Gray
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.,Department of Immunology and Infectious Disease, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - P Ian Andrews
- Department of Neurology, Sydney Children's Hospital, Sydney, New South Wales, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
49
|
Garland SM, Dimech W, Collignon P, Cooley L, Nimmo GR, Smith DW, Baird R, Rawlinson W, Costa A, Higgins G. The new screening program to prevent cervical cancer using HPV DNA: getting the balance right in maintaining quality. J Pathol Clin Res 2018; 4:207-212. [PMID: 30058126 PMCID: PMC6175713 DOI: 10.1002/cjp2.110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/09/2018] [Accepted: 07/20/2018] [Indexed: 01/26/2023]
Abstract
Along with the reduction in human papillomavirus (HPV) infection and cervical abnormalities as a result of the successful HPV vaccination program, Australia is adopting a new screening strategy. This involves a new paradigm moving from cervical cytological screening to molecular nucleic acid technology (NAT), using HPV DNA assays as primary screening methodology for cervical cancer prevention. These assays must strike a balance between sufficient clinical sensitivity to detect or predict high-grade cervical intraepithelial lesions, the precursor to cervical cancer, without being too sensitive and detecting transient infection not destined for disease. Ensuring the highest quality HPV NAT is thus a priority in order to reduce the possibility of falsely negative screens and manage the risk associated with false positive HPV NAT test results. How to do this needs informed discussion and on-going refinement of the screening algorithm. This is of relevance as more countries move to more sensitive HPV NAT tests for secondary prevention of cervical cancer and as more HPV assays become available.
Collapse
Affiliation(s)
- Suzanne M Garland
- Department of Microbiology and Infectious DiseasesRoyal Women's HospitalParkvilleAustralia
- Infection and Immunity Murdoch Children's Research InstituteParkvilleAustralia
- Department of Obstetrics and GynaecologyUniversity of MelbourneParkvilleAustralia
| | - Wayne Dimech
- National Serology Reference Laboratory, Australia (NRL)FitzroyAustralia
| | - Peter Collignon
- Infectious Diseases and MicrobiologyCanberra HospitalGarranAustralia
- Medical SchoolAustralian National UniversityAustralia
| | - On behalf of the Australian Clinical Microbiologists Infectious Diseases Group
- Department of Microbiology and Infectious DiseasesRoyal Hobart HospitalHobartAustralia
- Department of Microbiology, Pathology Queensland Central LaboratoryHerstonAustralia
- Department of Microbiology, Griffith University School of MedicineSouthportAustralia
- Department of Microbiology, PathWest Laboratory Medicine WANedlandsAustralia
- Faculty of Health and Medical SciencesUniversity of Western AustraliaNedlandsAustralia
- Territory Pathology, Infectious Diseases, Royal Darwin HospitalDepartment of Health and FamiliesTiwiAustralia
- Virology, Serology and OTDS Laboratories, NSW Health PathologyRandwickAustralia
- Department of Microbiology, The Royal Children's HospitalParkvilleAustralia
- Microbiology and Infectious Disease, South Australia PathologyNorth TerraceAustralia
| | - Louise Cooley
- Department of Microbiology and Infectious DiseasesRoyal Hobart HospitalHobartAustralia
| | - Graeme R Nimmo
- Department of Microbiology, Pathology Queensland Central LaboratoryHerstonAustralia
- Department of Microbiology, Griffith University School of MedicineSouthportAustralia
| | - David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WANedlandsAustralia
- Faculty of Health and Medical SciencesUniversity of Western AustraliaNedlandsAustralia
| | - Rob Baird
- Territory Pathology, Infectious Diseases, Royal Darwin HospitalDepartment of Health and FamiliesTiwiAustralia
| | - William Rawlinson
- Virology, Serology and OTDS Laboratories, NSW Health PathologyRandwickAustralia
| | - Anna‐Maria Costa
- Department of Microbiology and Infectious DiseasesRoyal Women's HospitalParkvilleAustralia
- Department of Microbiology, The Royal Children's HospitalParkvilleAustralia
| | - Geoff Higgins
- Microbiology and Infectious Disease, South Australia PathologyNorth TerraceAustralia
| |
Collapse
|
50
|
Egilmezer E, Walker GJ, Bakthavathsalam P, Peterson JR, Gooding JJ, Rawlinson W, Stelzer-Braid S. Systematic review of the impact of point-of-care testing for influenza on the outcomes of patients with acute respiratory tract infection. Rev Med Virol 2018; 28:e1995. [PMID: 30101552 PMCID: PMC7169080 DOI: 10.1002/rmv.1995] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/11/2018] [Accepted: 06/14/2018] [Indexed: 12/23/2022]
Abstract
Acute respiratory tract infections are a major cause of morbidity and mortality and represent a significant burden on the health care system. Laboratory testing is required to definitively distinguish infecting influenza virus from other pathogens, resulting in prolonged emergency department (ED) visits and unnecessary antibiotic use. Recently available rapid point-of-care tests (POCT) may allow for appropriate use of antiviral and antibiotic treatments and decrease patient lengths of stay. We undertook a systematic review to assess the effect of POCT for influenza on three outcomes: (1) antiviral prescription, (2) antibiotic prescription, and (3) patient length of stay in the ED. The databases Medline and Embase were searched using MeSH terms and keywords for influenza, POCT, antivirals, antibiotics, and length of stay. Amongst 245 studies screened, 30 were included. The majority of papers reporting on antiviral prescription found that a positive POCT result significantly increased use of antivirals for influenza compared with negative POCT results and standard supportive care. A positive POCT result also led to decreased antibiotic use. The results of studies assessing the effect of POCT on ED length of stay were not definitive. The studies assessed in this systematic review support the use of POCT for diagnosis of influenza in patients suffering an acute respiratory infection. Diagnosis using POCT may lead to more appropriate prescription of treatments for infectious agents. Further studies are needed to assess the effect of POCT on the length of stay in ED.
Collapse
Affiliation(s)
- Ece Egilmezer
- Virology Research Laboratory, Prince of Wales Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Gregory J Walker
- Virology Research Laboratory, Prince of Wales Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Padmavathy Bakthavathsalam
- Australian Centre for NanoMedicine and School of Chemistry, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Joshua R Peterson
- Australian Centre for NanoMedicine and School of Chemistry, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - J Justin Gooding
- Australian Centre for NanoMedicine and School of Chemistry, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - William Rawlinson
- Virology Research Laboratory, Prince of Wales Hospital, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Prince of Wales Hospital, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|