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Cane J, Sanderson N, Barnett S, Vaughan A, Pott M, Kapel N, Morgan M, Jesuthasan G, Samuel R, Ehsaan M, Boothe H, Haduli E, Studley R, Rourke E, Diamond I, Fowler T, Watson C, Stoesser N, Walker AS, Street T, Eyre DW. Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23. J Infect 2024; 88:106164. [PMID: 38692359 PMCID: PMC11101610 DOI: 10.1016/j.jinf.2024.106164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/03/2024]
Abstract
OBJECTIVES We evaluated Nanopore sequencing for influenza surveillance. METHODS Influenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing following targeted rt-PCR amplification. RESULTS From 941 infections, successful sequencing was achieved in 292/388 (75 %) available Oxfordshire samples: 231 (79 %) A/H3N2, 53 (18 %) A/H1N1, and 8 (3 %) B/Victoria and in 53/113 (47 %) UK-wide samples. Sequencing was more successful at lower Ct values. Most same-sample replicate sequences had identical haemagglutinin segments (124/141, 88 %); 36/39 (92 %) Illumina vs. Nanopore comparisons were identical, and 3 (8 %) differed by 1 variant. Comparison of Oxfordshire and UK-wide sequences showed frequent inter-regional transmission. Infections were closely-related to 2022-23 vaccine strains. Only one sample had a neuraminidase inhibitor resistance mutation. 849/941 (90 %) Oxfordshire infections were community-acquired. 63/88 (72 %) potentially healthcare-associated cases shared a hospital ward with ≥ 1 known infectious case. 33 epidemiologically-plausible transmission links had sequencing data for both source and recipient: 8 were within ≤ 5 SNPs, of these, 5 (63 %) involved potential sources that were also hospital-acquired. CONCLUSIONS Nanopore influenza sequencing was reproducible and antiviral resistance rare. Inter-regional transmission was common; most infections were genomically similar. Hospital-acquired infections are likely an important source of nosocomial transmission and should be prioritised for infection prevention and control.
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Affiliation(s)
- Jennifer Cane
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicholas Sanderson
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Sophie Barnett
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Ali Vaughan
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Megan Pott
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Natalia Kapel
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Gerald Jesuthasan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Reggie Samuel
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Muhammad Ehsaan
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Hugh Boothe
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Eric Haduli
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Ruth Studley
- Office for National Statistics, Newport, United Kingdom
| | - Emma Rourke
- Office for National Statistics, Newport, United Kingdom
| | - Ian Diamond
- Office for National Statistics, Newport, United Kingdom
| | - Tom Fowler
- UK Health Security Agency, United Kingdom; William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | | | - Nicole Stoesser
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ann Sarah Walker
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Teresa Street
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - David W Eyre
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom; Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom.
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Lorenzo-Redondo R, de Sant’Anna Carvalho AM, Hultquist JF, Ozer EA. SARS-CoV-2 genomics and impact on clinical care for COVID-19. J Antimicrob Chemother 2023; 78:ii25-ii36. [PMID: 37995357 PMCID: PMC10667012 DOI: 10.1093/jac/dkad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Alexandre Machado de Sant’Anna Carvalho
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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Williams TGS, Snell LB, Alder C, Charalampous T, Alcolea-Medina A, Sehmi JK, Al-Yaakoubi N, Humayun G, Miah S, Lackenby A, Zambon M, Batra R, Douthwaite S, Edgeworth JD, Nebbia G. Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance. Microb Genom 2023; 9:mgen001083. [PMID: 37590039 PMCID: PMC10483427 DOI: 10.1099/mgen.0.001083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
Rapid respiratory viral whole genome sequencing (WGS) in a clinical setting can inform real-time outbreak and patient treatment decisions, but the feasibility and clinical utility of influenza A virus (IAV) WGS using Nanopore technology has not been demonstrated. A 24 h turnaround Nanopore IAV WGS protocol was performed on 128 reverse transcriptase PCR IAV-positive nasopharyngeal samples taken over seven weeks of the 2022-2023 winter influenza season, including 25 from patients with nosocomial IAV infections and 102 from patients attending the Emergency Department. WGS results were reviewed collectively alongside clinical details for interpretation and reported to clinical teams. All eight segments of the IAV genome were recovered for 97/128 samples (75.8 %) and the haemagglutinin gene for 117/128 samples (91.4 %). Infection prevention and control identified nosocomial IAV infections in 19 patients across five wards. IAV WGS revealed two separate clusters on one ward and excluded transmission across different wards with contemporaneous outbreaks. IAV WGS also identified neuraminidase inhibitor resistance in a persistently infected patient and excluded avian influenza in a sample taken from an immunosuppressed patient with a history of travel to Singapore which had failed PCR subtyping. Accurate IAV genomes can be generated in 24 h using a Nanopore protocol accessible to any laboratory with SARS-CoV-2 Nanopore sequencing capacity. In addition to replicating reference laboratory surveillance results, IAV WGS can identify antiviral resistance and exclude avian influenza. IAV WGS also informs management of nosocomial outbreaks, though molecular and clinical epidemiology were concordant in this study, limiting the impact on decision-making.
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Affiliation(s)
- Tom G. S. Williams
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Luke B. Snell
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Christopher Alder
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Themoula Charalampous
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Infection Sciences, Synnovis, London, UK
| | | | - Noor Al-Yaakoubi
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Gul Humayun
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Shahjahan Miah
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Angie Lackenby
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Maria Zambon
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Rahul Batra
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Jonathan D. Edgeworth
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
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Leece P, Whelan M, Costa AP, Daneman N, Johnstone J, McGeer A, Rochon P, Schwartz KL, Brown KA. Nursing home crowding and its association with outbreak-associated respiratory infection in Ontario, Canada before the COVID-19 pandemic (2014-19): a retrospective cohort study. THE LANCET. HEALTHY LONGEVITY 2023; 4:e107-e114. [PMID: 36870336 PMCID: PMC9989831 DOI: 10.1016/s2666-7568(23)00018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Studies conducted during the COVID-19 pandemic have shown that crowding in nursing homes is associated with high incidence of SARS-CoV-2 infections, but this effect has not been shown for other respiratory pathogens. We aimed to measure the association between crowding in nursing homes and outbreak-associated respiratory infection incidence and related mortality before the COVID-19 pandemic. METHODS We conducted a retrospective cohort study of nursing homes in Ontario, Canada. We identified, characterised, and selected nursing homes through the Ontario Ministry of Long-Term Care datasets. Nursing homes that were not funded by the Ontario Ministry of Long-Term Care and homes that closed before January, 2020 were excluded. Outcomes consisting of respiratory infection outbreaks were obtained from the Integrated Public Health Information System of Ontario. The crowding index equalled the mean number of residents per bedroom and bathroom. The primary outcomes were the incidence of outbreak-associated infections and mortality per 100 nursing home residents per year. We examined the incidence of infections and deaths as a function of the crowding index by use of negative binomial regression with adjustment for three home characteristics (ie, ownership, number of beds, and region) and nine mean resident characteristics (ie, age, female sex, dementia, diabetes, chronic heart failure, renal failure, cancer, chronic obstructive pulmonary disease, and activities of daily living score). FINDINGS Between Sept 1, 2014, and Aug 31, 2019, 5107 respiratory infection outbreaks in 588 nursing homes were recorded, of which 4921 (96·4%), involving 64 829 cases of respiratory infection and 1969 deaths, were included in this analysis. Nursing homes with a high crowding index had higher incidences of respiratory infection (26·4% vs 13·8%; adjusted rate ratio per one resident per room increase in crowding 1·89 [95% CI 1·64-2·17]) and mortality (0·8% vs 0·4%; 2·34 [1·88-2·92]) than did homes with a low crowding index. INTERPRETATION Respiratory infection and mortality rates were higher in nursing homes with high crowding index than in homes with low crowding index, and the association was consistent across various respiratory pathogens. Decreasing crowding is an important safety target beyond the COVID-19 pandemic to help to promote resident wellbeing and decrease the transmission of prevalent respiratory pathogens. FUNDING None.
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Affiliation(s)
| | | | | | - Nick Daneman
- Public Health Ontario, Toronto, ON, Canada; Division of Infectious Diseases, Sunnybrook Research Institute, Toronto, ON, Canada
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Wan T, Lauring AS, Valesano AL, Fitzsimmons WJ, Bendall EE, Kaye KS, Petrie JG. Investigating Epidemiologic and Molecular Links Between Patients With Community- and Hospital-Acquired Influenza A: 2017-2018 and 2019-2020, Michigan. Open Forum Infect Dis 2023; 10:ofad061. [PMID: 36861093 PMCID: PMC9969740 DOI: 10.1093/ofid/ofad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Background Hospital-acquired influenza virus infection (HAII) can cause severe morbidity and mortality. Identifying potential transmission routes can inform prevention strategies. Methods We identified all hospitalized patients testing positive for influenza A virus at a large, tertiary care hospital during the 2017-2018 and 2019-2020 influenza seasons. Hospital admission dates, locations of inpatient service, and clinical influenza testing information were retrieved from the electronic medical record. Time-location groups of epidemiologically linked influenza patients were defined and contained ≥1 presumed HAII case (first positive ≥48 hours after admission). Genetic relatedness within time-location groups was assessed by whole genome sequencing. Results During the 2017-2018 season, 230 patients tested positive for influenza A(H3N2) or unsubtyped influenza A including 26 HAIIs. There were 159 influenza A(H1N1)pdm09 or unsubtyped influenza A-positive patients identified during the 2019-2020 season including 33 HAIIs. Consensus sequences were obtained for 177 (77%) and 57 (36%) of influenza A cases in 2017-2018 and 2019-2020, respectively. Among all influenza A cases, there were 10 time-location groups identified in 2017-2018 and 13 in 2019-2020; 19 of 23 groups included ≤4 patients. In 2017-2018, 6 of 10 groups had ≥2 patients with sequence data, including ≥1 HAII case. Two of 13 groups met this criteria in 2019-2020. Two time-location groups from 2017-2018 each contained 3 genetically linked cases. Conclusions Our results suggest that HAIIs arise from outbreak transmission from nosocomial sources as well as single infections from unique community introductions.
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Affiliation(s)
- Tiffany Wan
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew L Valesano
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - William J Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily E Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Keith S Kaye
- Division of Allergy, Immunology and Infectious Diseases, Department of Medicine, Rutgers-Robert Wood Johnson School of Medicine, New Brunswick, New Jersey, USA
| | - Joshua G Petrie
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
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Zhu A, Bruketa E, Svoboda T, Patel J, Elmi N, El-Khechen Richandi G, Baral S, Orkin AM. Respiratory infectious disease outbreaks among people experiencing homelessness: a systematic review of prevention and mitigation strategies. Ann Epidemiol 2023; 77:127-135. [PMID: 35342013 DOI: 10.1016/j.annepidem.2022.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 02/16/2022] [Accepted: 03/05/2022] [Indexed: 01/04/2023]
Abstract
PURPOSE People experiencing homelessness (PEH) are at increased risk of respiratory infections and associated morbidity and mortality. To characterize optimal intervention strategies, we completed a systematic review of mitigation strategies for PEH to minimize the spread and impact of respiratory infectious disease outbreaks, including COVID-19. METHODS The study protocol was registered in PROSPERO (#2020 CRD42020208964) and was consistent with the preferred reporting in systematic reviews and meta-analyses guidelines. A search algorithm containing keywords that were synonymous to the terms "Homeless" and "Respiratory Illness" was applied to the six databases. The search concluded on September 22, 2020. Quality assessment was performed at the study level. Steps were conducted by two independent team members. RESULTS A total of 4468 unique titles were retrieved with 21 meeting criteria for inclusion. Interventions included testing, tracking, screening, infection prevention and control, isolation support, and education. Historically, there has been limited study of intervention strategies specifically for PEH across the world. CONCLUSIONS Staff and organizations providing services for people experiencing homelessness face specific challenges in adhering to public health guidelines such as physical distancing, isolation, and routine hygiene practices. There is a discrepancy between the burden of infectious diseases among PEH and specific research characterizing optimal intervention strategies to mitigate transmission in the context of shelters. Improving health for people experiencing homelessness necessitates investment in programs scaling existing interventions and research to study new approaches.
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Affiliation(s)
- Alice Zhu
- Population Health Service, Inner City Health Associates. Toronto, ON, Canada; Department of Family and Community Medicine, University of Toronto, ON, Canada; Department of General Surgery, University of Toronto, Toronto, ON, Canada
| | - Eva Bruketa
- Population Health Service, Inner City Health Associates. Toronto, ON, Canada; Queen's University, School of Medicine, Kingston, ON, Canada
| | - Tomislav Svoboda
- Population Health Service, Inner City Health Associates. Toronto, ON, Canada; Department of Family and Community Medicine, University of Toronto, ON, Canada
| | - Jamie Patel
- Population Health Service, Inner City Health Associates. Toronto, ON, Canada; Ryerson University, Daphne Cockwell School of Nursing, Toronto, ON, Canada
| | - Nika Elmi
- Population Health Service, Inner City Health Associates. Toronto, ON, Canada; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | | | - Stefan Baral
- Population Health Service, Inner City Health Associates. Toronto, ON, Canada; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Aaron M Orkin
- Population Health Service, Inner City Health Associates. Toronto, ON, Canada; Department of Family and Community Medicine, University of Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, ON, Canada.
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Ganly KH, Bowyer JC, Bird PW, Willford NJ, Shaw J, Odedra M, Osborn G, Everett T, Warner M, Horne S, Dinn M, McMurray CL, Holmes CW, Koo SSF, Tang JWT. Prospective Surveillance of Respiratory Infections in British Antarctic Survey Bases During the COVID-19 Pandemic. J Infect Dis 2022; 226:2105-2112. [PMID: 36214778 PMCID: PMC9619699 DOI: 10.1093/infdis/jiac412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The British Antarctic bases offer a semiclosed environment for assessing the transmission and persistence of seasonal respiratory viruses. METHODS Weekly swabbing was performed for respiratory pathogen surveillance (including SARS-CoV-2), at 2 British Antarctic Survey bases, during 2020: King Edward Point (KEP, 30 June to 29 September, 9 participants, 124 swabs) and Rothera (9 May to 6 June, 27 participants, 127 swabs). Symptom questionnaires were collected for any newly symptomatic cases that presented during this weekly swabbing period. RESULTS At KEP, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (2), adenovirus (1), parainfluenza 3 (1), and respiratory syncytial virus B (1). At Rothera, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (3), adenovirus (2), parainfluenza 4 (1), and human metapneumovirus (1). All bacterial agents identified were considered to be colonizers and not pathogenic. CONCLUSIONS At KEP, the timeline indicated that the parainfluenza 3 and adenovirus infections could have been linked to some of the symptomatic cases that presented. For the other viruses, the only other possible sources were the visiting ship crew members. At Rothera, the single symptomatic case presented too early for this to be linked to the subsequent viral detections, and the only other possible source could have been a single nonparticipating staff member.
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Affiliation(s)
- Katharine H Ganly
- Emergency Department, British Antarctic Survey Medical Unit, University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | - James C Bowyer
- Emergency Department, British Antarctic Survey Medical Unit, University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | - Paul W Bird
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Nicholas J Willford
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Jessica Shaw
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Mina Odedra
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Georgia Osborn
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Tom Everett
- Emergency Department, British Antarctic Survey Medical Unit, University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | - Matthew Warner
- Emergency Department, British Antarctic Survey Medical Unit, University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | - Simon Horne
- Emergency Department, British Antarctic Survey Medical Unit, University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | - Michael Dinn
- Emergency Department, British Antarctic Survey Medical Unit, University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | - Claire L McMurray
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Christopher W Holmes
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Sharon S F Koo
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Julian Wei-Tze Tang
- Correspondence: J. W.-T. Tang, MBChB, MA, PhD, MRCP, Clinical Microbiology, 5/F Sandringham Building, Leicester Royal Infirmary, Infirmary Square, Leicester LE1 5WW, UK (; )
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From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol. Vaccines (Basel) 2022; 10:vaccines10081359. [PMID: 36016246 PMCID: PMC9412868 DOI: 10.3390/vaccines10081359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
(1) Background: Over the last few years, there has been growing interest in the whole genome sequencing (WGS) of rapidly mutating pathogens, such as influenza viruses (IVs), which has led us to carry out in-depth studies on viral evolution in both research and diagnostic settings. We aimed at describing and determining the validity of a WGS protocol that can obtain the complete genome sequence of A(H3N2) IVs directly from clinical specimens. (2) Methods: RNA was extracted from 80 A(H3N2)-positive respiratory specimens. A one-step RT-PCR assay, based on the use of a single set of specific primers, was used to retro-transcribe and amplify the entire IV type A genome in a single reaction, thus avoiding additional enrichment approaches and host genome removal treatments. Purified DNA was quantified; genomic libraries were prepared and sequenced by using Illumina MiSeq platform. The obtained reads were evaluated for sequence quality and read-pair length. (3) Results: All of the study specimens were successfully amplified, and the purified DNA concentration proved to be suitable for NGS (at least 0.2 ng/µL). An acceptable coverage depth for all eight genes of influenza A(H3N2) virus was obtained for 90% (72/80) of the clinical samples with viral loads >105 genome copies/mL. The mean depth of sequencing ranged from 105 to 200 reads per position, with the majority of the mean depth values being above 103 reads per position. The total turnaround time per set of 20 samples was four working days, including sequence analysis. (4) Conclusions: This fast and reliable high-throughput sequencing protocol should be used for influenza surveillance and outbreak investigation.
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Walker A, Houwaart T, Finzer P, Ehlkes L, Tyshaieva A, Damagnez M, Strelow D, Duplessis A, Nicolai J, Wienemann T, Tamayo T, Kohns Vasconcelos M, Hülse L, Hoffmann K, Lübke N, Hauka S, Andree M, Däumer MP, Thielen A, Kolbe-Busch S, Göbels K, Zotz R, Pfeffer K, Timm J, Dilthey AT. Characterization of SARS-CoV-2 infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting. Clin Infect Dis 2021; 74:1039-1046. [PMID: 34181711 PMCID: PMC8406867 DOI: 10.1093/cid/ciab588] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 01/02/2023] Open
Abstract
Background Tracing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction of viral transmission networks by integration of molecular epidemiology into classical contact tracing. Methods In collaboration with local public health authorities, we set up an integrated system of genomic surveillance in an urban setting, combining a) viral surveillance sequencing, b) genetically based identification of infection clusters in the population, c) integration of public health authority contact tracing data, and d) a user-friendly dashboard application as a central data analysis platform. Results Application of the integrated system from August to December 2020 enabled a characterization of viral population structure, analysis of 4 outbreaks at a maximum care hospital, and genetically based identification of 5 putative population infection clusters, all of which were confirmed by contact tracing. The system contributed to the development of improved hospital infection control and prevention measures and enabled the identification of previously unrecognized transmission chains, involving a martial arts gym and establishing a link between the hospital to the local population. Conclusions Integrated systems of genomic surveillance could contribute to the monitoring and, potentially, improved management of SARS-CoV-2 transmission in the population.
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Affiliation(s)
- Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick Finzer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Zotz
- Klimas, Düsseldorf, Germany
| | - Lutz Ehlkes
- Düsseldorf Health Department (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | - Alona Tyshaieva
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maximilian Damagnez
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Strelow
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ashley Duplessis
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jessica Nicolai
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Wienemann
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Teresa Tamayo
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Malte Kohns Vasconcelos
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisanna Hülse
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Nadine Lübke
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Andree
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Susanne Kolbe-Busch
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Klaus Göbels
- Düsseldorf Health Department (Gesundheitsamt Düsseldorf), Düsseldorf, Germany
| | | | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander T Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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10
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Hamilton WL, Tonkin-Hill G, Smith ER, Aggarwal D, Houldcroft CJ, Warne B, Meredith LW, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL, Khokhar FA, Yakovleva A, Hall G, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Brown CS, Gonçalves S, Amato R, Harrison EM, Brown NM, Beale MA, Spencer Chapman M, Jackson DK, Johnston I, Alderton A, Sillitoe J, Langford C, Dougan G, Peacock SJ, Kwiatowski DP, Goodfellow IG, Torok ME. Genomic epidemiology of COVID-19 in care homes in the east of England. eLife 2021; 10:e64618. [PMID: 33650490 PMCID: PMC7997667 DOI: 10.7554/elife.64618] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/25/2021] [Indexed: 01/12/2023] Open
Abstract
COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.
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Affiliation(s)
- William L Hamilton
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | | | - Emily R Smith
- Cambridgeshire County CouncilCambridgeUnited Kingdom
| | - Dinesh Aggarwal
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
- Public Health EnglandColindaleUnited Kingdom
| | - Charlotte J Houldcroft
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Ben Warne
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Luke W Meredith
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Aminu S Jahun
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | - Laura G Caller
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
- The Francis Crick InstituteLondonUnited Kingdom
| | - Sarah L Caddy
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Fahad A Khokhar
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Anna Yakovleva
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Grant Hall
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Theresa Feltwell
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Malte L Pinckert
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Iliana Georgana
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | | | | | | | | | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health LaboratoryCambridgeUnited Kingdom
| | | | - Michael Spencer Chapman
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS TrustLondonUnited Kingdom
| | | | | | | | | | | | - Gordon Dougan
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | - Sharon J Peacock
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
| | | | - Ian G Goodfellow
- University of Cambridge, Department of Pathology, Division of VirologyCambridgeUnited Kingdom
| | - M Estee Torok
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and MicrobiologyCambridgeUnited Kingdom
- University of Cambridge, Department of MedicineCambridgeUnited Kingdom
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11
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Baral S, Bond A, Boozary A, Bruketa E, Elmi N, Freiheit D, Ghosh SM, Goyer ME, Orkin AM, Patel J, Richter T, Robertson A, Sutherland C, Svoboda T, Turnbull J, Wong A, Zhu A. Seeking shelter: homelessness and COVID-19. Facets (Ott) 2021. [DOI: 10.1139/facets-2021-0004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Those experiencing homelessness in Canada are impacted inequitably by COVID-19 due to their increased exposure, vulnerability of environment and medical comorbidities, and their lack of access to preventive care and treatment in the context of the pandemic. In shelter environments one is unable to effectively physically distance, maintain hygiene, obtain a test, or isolate. As a result, unique strategies are required for this population to protect them and those who serve them. Recommendations are provided to reduce or prevent further negative consequences from the COVID-19 pandemic for people experiencing homelessness. These recommendations were informed by a systematic review of the literature, as well as a jurisdictional scan. Where evidence did not exist, expert consensus from key providers and those experiencing homelessness throughout Canada was included. These recommendations recognize the need for short-term interventions to mitigate the immediate risk to this community, including coordination of response, appropriate precautions and protective equipment, reducing congestion, cohorting, testing, case and contact management strategies, dealing with outbreaks, isolation centres, and immunization. Longer-term recommendations are also provided with a view to ending homelessness by addressing the root causes of homelessness and by the provision of adequate subsidized and supportive housing through a Housing First strategy. It is imperative that meaningful changes take place now in how we serve those experiencing homelessness and how we mitigate specific vulnerabilities. These recommendations call for intersectoral, collaborative engagement to work for solutions targeted towards protecting the most vulnerable within our community through both immediate actions and long-term planning to eliminate homelessness.
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Affiliation(s)
- Stefan Baral
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Inner City Health Associates, Toronto, ON M5C 1K6, Canada
| | - Andrew Bond
- Inner City Health Associates, Toronto, ON M5C 1K6, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
| | - Andrew Boozary
- Population Health and Social Medicine, University Health Network, Toronto, ON M5G 2C4, Canada
- University of Toronto, Toronto, ON M5S 1A8, Canada
- Columbia University, New York, NY 10032, USA
| | - Eva Bruketa
- Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Nika Elmi
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - S. Monty Ghosh
- Department of General Internal Medicine & Neurology, University of Alberta, Edmonton, AB T6G 2G3, Canada
- Department of Medicine & Psychiatry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Marie Eve Goyer
- Family Medicine and Emergency Department, University of Montréal, Montréal, QC H3T 1J4, Canada
| | - Aaron M. Orkin
- Inner City Health Associates, Toronto, ON M5C 1K6, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
- Department of Emergency Medicine, St. Joseph’s Health Centre, Toronto, ON M6R 1B5, Canada
- Department of Emergency Medicine, Humber River Hospital, Toronto, ON M3M 0B2, Canada
| | - Jamie Patel
- Faculty of Community Services, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Tim Richter
- Canadian Alliance to End Homelessness, Calgary, AB T3H 0N8, Canada
| | - Angela Robertson
- Parkdale Queen West Community Health Centre, Toronto, ON M6K 1L2, Canada
| | - Christy Sutherland
- PHS Community Services Society, Vancouver, BC V6A 1M9, Canada
- Department of Family Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Tomislav Svoboda
- Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
| | - Jeffrey Turnbull
- University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Ottawa Inner City Health, Ottawa, ON K1N 5N7, Canada
| | - Alexander Wong
- Department of Medicine, University of Saskatchewan, Regina, SK S4T 0H8, Canada
| | - Alice Zhu
- University of Toronto, Toronto, ON M5S 1A8, Canada
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12
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Meredith LW, Hamilton WL, Warne B, Houldcroft CJ, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL, Khokhar FA, Yakovleva A, Hall G, Feltwell T, Forrest S, Sridhar S, Weekes MP, Baker S, Brown N, Moore E, Popay A, Roddick I, Reacher M, Gouliouris T, Peacock SJ, Dougan G, Török ME, Goodfellow I. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. THE LANCET. INFECTIOUS DISEASES 2020; 20:1263-1272. [PMID: 32679081 PMCID: PMC7806511 DOI: 10.1016/s1473-3099(20)30562-4] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND The burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures. METHODS In this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases. FINDINGS Between March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting. INTERPRETATION We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings. FUNDING COVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.
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Affiliation(s)
- Luke W Meredith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - William L Hamilton
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - Ben Warne
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | | | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Aminu S Jahun
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Laura G Caller
- Department of Pathology, University of Cambridge, Cambridge, UK; Francis Crick Institute, London, UK
| | - Sarah L Caddy
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Fahad A Khokhar
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Anna Yakovleva
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Grant Hall
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Sally Forrest
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Sushmita Sridhar
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK
| | - Michael P Weekes
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - Nicholas Brown
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Elinor Moore
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - Ashley Popay
- Field Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK
| | - Iain Roddick
- Field Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK
| | - Mark Reacher
- Field Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK
| | - Theodore Gouliouris
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK; National Infection Service, Public Health England, London, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK.
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK.
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13
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Wang L, Ma H, Yiu KCY, Calzavara A, Landsman D, Luong L, Chan AK, Kustra R, Kwong JC, Boily MC, Hwang S, Straus S, Baral SD, Mishra S. Heterogeneity in testing, diagnosis and outcome in SARS-CoV-2 infection across outbreak settings in the Greater Toronto Area, Canada: an observational study. CMAJ Open 2020; 8:E627-E636. [PMID: 33037070 PMCID: PMC7567509 DOI: 10.9778/cmajo.20200213] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Congregate settings have been disproportionately affected by coronavirus disease 2019 (COVID-19). Our objective was to compare testing for, diagnosis of and death after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection across 3 settings (residents of long-term care homes, people living in shelters and the rest of the population). METHODS We conducted a population-based prospective cohort study involving individuals tested for SARS-CoV-2 in the Greater Toronto Area between Jan. 23, 2020, and May 20, 2020. We sourced person-level data from COVID-19 surveillance and reporting systems in Ontario. We calculated cumulatively diagnosed cases per capita, proportion tested, proportion tested positive and case-fatality proportion for each setting. We estimated the age- and sex-adjusted rate ratios associated with setting for test positivity and case fatality using quasi-Poisson regression. RESULTS Over the study period, a total of 173 092 individuals were tested for and 16 490 individuals were diagnosed with SARS-CoV-2 infection. We observed a shift in the proportion of cumulative cases from all cases being related to travel to cases in residents of long-term care homes (20.4% [3368/16 490]), shelters (2.3% [372/16 490]), other congregate settings (20.9% [3446/16 490]) and community settings (35.4% [5834/16 490]), with cumulative travel-related cases at 4.1% (674/16490). Cumulatively, compared with the rest of the population, the diagnosed cases per capita was 64-fold and 19-fold higher among long-term care home and shelter residents, respectively. By May 20, 2020, 76.3% (21 617/28 316) of long-term care home residents and 2.2% (150 077/6 808 890) of the rest of the population had been tested. After adjusting for age and sex, residents of long-term care homes were 2.4 (95% confidence interval [CI] 2.2-2.7) times more likely to test positive, and those who received a diagnosis of COVID-19 were 1.4-fold (95% CI 1.1-1.8) more likely to die than the rest of the population. INTERPRETATION Long-term care homes and shelters had disproportionate diagnosed cases per capita, and residents of long-term care homes diagnosed with COVID-19 had higher case fatality than the rest of the population. Heterogeneity across micro-epidemics among specific populations and settings may reflect underlying heterogeneity in transmission risks, necessitating setting-specific COVID-19 prevention and mitigation strategies.
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Affiliation(s)
- Linwei Wang
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Huiting Ma
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Kristy C Y Yiu
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Andrew Calzavara
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - David Landsman
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Linh Luong
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Adrienne K Chan
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Rafal Kustra
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Jeffrey C Kwong
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Marie-Claude Boily
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Stephen Hwang
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Sharon Straus
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Stefan D Baral
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions (Wang, Ma, Yiu, Landsman, Luong, Hwang, Mishra), St. Michael's Hospital, University of Toronto; ICES (Calzavara, Kwong); Division of Infectious Diseases, Department of Medicine (Chan, Mishra), University of Toronto; Division of Infectious Diseases (Chan), Sunnybrook Health Sciences Centre, University of Toronto; Dalla Lana School of Public Health (Kustra), University of Toronto; Department of Family and Community Medicine (Kwong), Faculty of Medicine, University of Toronto, Toronto, Ont.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology (Boily), Faculty of Medicine, Imperial College, London, UK; Division of General Internal Medicine (Hwang), Department of Medicine, University of Toronto; Department of Medicine (Straus), St. Michael's Hospital, University of Toronto, Toronto, Ont.; Bloomberg School of Public Health (Baral), Johns Hopkins University, Baltimore, Md.
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14
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Blackburn RM, Frampton D, Smith CM, Fragaszy EB, Watson SJ, Ferns RB, Binter Š, Coen PG, Grant P, Shallcross LJ, Kozlakidis Z, Pillay D, Kellam P, Hué S, Nastouli E, Hayward AC. Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014). Influenza Other Respir Viruses 2019; 13:556-563. [PMID: 31536169 PMCID: PMC6800305 DOI: 10.1111/irv.12679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/21/2019] [Accepted: 08/25/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral strains. OBJECTIVES We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely-collected data. METHODS All influenza samples taken through routine care from patients at University College London Hospitals NHS Foundation Trust (September 2012 to March 2014) were included. We conducted Illumina sequencing and identified genetic clusters. We compared nosocomial transmission estimates defined using classical methods (based on time from admission to sample) and genetic clustering. We identified pairs of cases with space-time links and assessed genetic relatedness. RESULTS We sequenced influenza sampled from 214 patients. There were 180 unique genetic strains, 16 (8.8%) of which seeded a new transmission chain. Nosocomial transmission was indicated for 32 (15.0%) cases using the classical definition and 34 (15.8%) based on genetic clustering. Of the 50 patients in a genetic cluster, 11 (22.0%) had known space-time links with other cases in the same cluster. Genetic distances between pairs of cases with space-time links were lower than for pairs without spatial links (P < .001). CONCLUSIONS Genetic data confirmed that nosocomial transmission contributes significantly to the hospital burden of influenza and elucidated transmission chains. Prospective next generation sequencing could support outbreak investigations and monitor the impact of infection and control measures.
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Affiliation(s)
| | | | | | - Ellen B. Fragaszy
- Institute of Health InformaticsUCLLondonUK
- Department of Infectious Disease EpidemiologyFaculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Simon J. Watson
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - R. Bridget Ferns
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Špela Binter
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - Pietro G. Coen
- Infection Control DepartmentUniversity College London HospitalsNHS Foundation TrustLondonUK
| | - Paul Grant
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
| | | | - Zisis Kozlakidis
- Institute of Health InformaticsUCLLondonUK
- International Agency for Research on CancerWorld Health OrganizationLyonFrance
| | - Deenan Pillay
- Division of Infection and ImmunityUCLLondonUK
- Africa Health Research InstituteDurbanSouth Africa
| | - Paul Kellam
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - Stéphane Hué
- Department of Infectious Disease EpidemiologyFaculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Eleni Nastouli
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Population, Policy and PracticeUCL Institute of Child HealthLondonUK
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15
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Imai K, Tamura K, Tanigaki T, Takizawa M, Nakayama E, Taniguchi T, Okamoto M, Nishiyama Y, Tarumoto N, Mitsutake K, Murakami T, Maesaki S, Maeda T. Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study. Front Microbiol 2018; 9:2748. [PMID: 30483243 PMCID: PMC6243006 DOI: 10.3389/fmicb.2018.02748] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 02/01/2023] Open
Abstract
Introduction: Whole genome sequencing (WGS) of influenza viruses is important for preparing vaccines and coping with newly emerging viruses. However, WGS is difficult to perform using conventional next-generation sequencers in developing countries, where facilities are often inadequate. In this study, we developed a high-throughput WGS method for influenza viruses in clinical specimens with the MinION portable sequencer. Methods: Whole genomes of influenza A and B viruses were amplified by multiplex RT-PCR from 13 clinical specimens collected in Tokyo, Japan. Barcode tags for multiplex MinION sequencing were added with each multiplex RT-PCR amplicon by nested PCR with custom barcoded primers. All barcoded amplicons were mixed and multiplex sequencing using the MinION sequencer with 1D2 sequencing kit. In addition, multiplex RT-PCR amplicons generated from each clinical specimen were sequenced using the Illumina MiSeq platform to validate the performance of MinION sequencer. The accuracy, recall, and precision rates of MinION sequencing were calculated by comparing the results of variant calling in the Illumina MiSeq platform and MinION sequencer. Results: Whole genomes of influenza A and B viruses were successfully amplified by multiplex RT-PCR from 13 clinical samples. We identified 6 samples as influenza type A virus H3N2 subtype and 7 as influenza B virus Yamagata lineage using the Illumina MiSeq platform. The overall accuracy, recall, and precision rates of the MinION sequencer were, respectively 99.95%, 89.41%, and 97.88% from 1D reads and 99.97%, 93.28%, and 99.86% from 1D2 reads. Conclusion: We developed a novel WGS method for influenza A and B viruses. It is necessary to improve read accuracy and analytical tools in order to better utilize the MinION sequencer for real-time monitoring of genetic rearrangements and for evaluation of newly emerging viruses.
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Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Infectious Diseases, Self-Defense Forces Central Hospital, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Kaku Tamura
- Department of Infectious Diseases, Self-Defense Forces Central Hospital, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Tomomi Tanigaki
- NBC Counter Medical Unit, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Mari Takizawa
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Eiko Nakayama
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Takahiko Taniguchi
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Misako Okamoto
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Yasumasa Nishiyama
- NBC Counter Medical Unit, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Infectious Disease and Infection Control, Saitama Medical University International Medical Center, Saitama, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Microbiology, Saitama Medical University, Saitama, Japan
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16
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Houlihan CF, Frampton D, Ferns RB, Raffle J, Grant P, Reidy M, Hail L, Thomson K, Mattes F, Kozlakidis Z, Pillay D, Hayward A, Nastouli E. Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak. J Infect Dis 2018; 218:1485-1489. [PMID: 29873767 PMCID: PMC6151078 DOI: 10.1093/infdis/jiy335] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 11/14/2022] Open
Abstract
Traditional epidemiological investigation of nosocomial transmission of influenza involves the identification of patients who have the same influenza virus type and who have overlapped in time and place. This method may misidentify transmission where it has not occurred or miss transmission when it has. We used influenza virus whole-genome sequencing (WGS) to investigate an outbreak of influenza A virus infection in a hematology/oncology ward and identified 2 separate introductions, one of which resulted in 5 additional infections and 79 bed-days lost. Results from WGS are becoming rapidly available and may supplement traditional infection control procedures in the investigation and management of nosocomial outbreaks.
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Affiliation(s)
- Catherine F Houlihan
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Dan Frampton
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - R Bridget Ferns
- Division of Infection and Immunity, University College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre, London, United Kingdom
| | - Jade Raffle
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Paul Grant
- Department of Clinical Virology, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Myriam Reidy
- Infection Control Service, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Leila Hail
- Infection Control Service, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Kirsty Thomson
- Department of Blood Diseases, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Frank Mattes
- Department of Clinical Virology, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Zisis Kozlakidis
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Infectious Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Andrew Hayward
- Institute of Epidemiology and Health Care, University College London, London, United Kingdom
- Department of Infectious Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Eleni Nastouli
- Department of Population, Policy, and Practice, Great Ormond Street Institute of Child Health, University College London (UCL), London, United Kingdom
- Department of Clinical Virology, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
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