1
|
Euzen V, Xhaard A, Berreira-Ibraim S, Deville L, Quentin A, Prata PHDEL, Gournay V, Prot M, Rahou Y, Barbet M, Mercier-Delarue S, Tour RPDELA, Simon-Loriere E, Legoff J. Zanamivir and Baloxavir Combination to cure Persistent Influenza and Coronavirus Infections after Hematopoietic Stem Cell Transplant. Int J Antimicrob Agents 2024:107281. [PMID: 39047913 DOI: 10.1016/j.ijantimicag.2024.107281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/14/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
OBJECTIVES . Immunocompromised patients may experience prolonged shedding of influenza virus potentially leading to severe infections. Alternatives to monotherapy with neuraminidase inhibitors should be evaluated to entirely suppress viral replication and prevent drug-resistant mutations. METHODS . We investigated the clinical and virological evolution in a case of persistent influenza A and human coronavirus OC43 (HCoV-OC43) coinfection in a hematopoietic stem cell transplant recipient after different therapeutic strategies. RESULTS . Successive oseltamivir and zanamivir monotherapies failed to control both infections, with positive results persisting for over 110 days each. This led to the emergence of highly resistant oseltamivir strains due to neuraminidase mutations (E119V and R292K) followed by a deletion (del245-248), while maintaining sensitivity to zanamivir. The intra-host viral diversity data showed that the treatments impacted viral diversity of influenza virus, but not of HCoV-OC43. Considering the patient's underlying condition and the impact of prolonged viral shedding on pulmonary function, eradicating the influenza virus was necessary. A 10-day regimen combining zanamivir and baloxavir-marboxil effectively controlled influenza virus replication and was associated with the clearance of HCoV-OC43, finally resulting in comprehensive respiratory recovery. CONCLUSION These observations underscore the importance of further investigating combination treatments as the primary approach to achieve influenza eradication in immunocompromised patients.
Collapse
Affiliation(s)
- Victor Euzen
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | - Aliénor Xhaard
- Hematology Transplantation, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | - Samar Berreira-Ibraim
- Institut Pasteur, National Reference Center for Respiratory Viruses, F-75015 Paris, France
| | - Laure Deville
- Pharmacy, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
| | - Aude Quentin
- Hematology, Hôpital Jean Jaures, F-75010 Paris, France
| | | | - Viviane Gournay
- Hematology Transplantation, AP-HP, Hôpital Saint Louis, F-75010 Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, F-75015 Paris, France
| | - Yannis Rahou
- Institut Pasteur, National Reference Center for Respiratory Viruses, F-75015 Paris, France
| | - Marion Barbet
- Institut Pasteur, National Reference Center for Respiratory Viruses, F-75015 Paris, France
| | | | | | - Etienne Simon-Loriere
- Institut Pasteur, National Reference Center for Respiratory Viruses, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, F-75015 Paris, France
| | - Jérôme Legoff
- Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France; Université Paris Cité, Inserm U976, Insight team, F-75010 Paris, France.
| |
Collapse
|
2
|
Cronk BD, Caserta LC, Laverack M, Gerdes RS, Hynes K, Hopf CR, Fadden MA, Nakagun S, Schuler KL, Buckles EL, Lejeune M, Diel DG. Infection and tissue distribution of highly pathogenic avian influenza A type H5N1 (clade 2.3.4.4b) in red fox kits ( Vulpes vulpes). Emerg Microbes Infect 2023; 12:2249554. [PMID: 37589241 PMCID: PMC10512766 DOI: 10.1080/22221751.2023.2249554] [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: 12/18/2022] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Avian influenza H5N1 is a highly pathogenic virus that primarily affects birds. However, it can also infect other animal species, including mammals. We report the infection of nine juvenile red foxes (Vulpes vulpes) with Highly Pathogenic Avian Influenza A type H5N1 (Clade 2.3.4.4b) in the spring of 2022 in the central, western, and northern regions of New York, USA. The foxes displayed neurologic signs, and examination of brain and lung tissue revealed lesions, with brain lesions ranging from moderate to severe meningoencephalitis. Analysis of tissue tropism using RT-PCR methods showed a comparatively lower Ct value in the brain, which was confirmed by in situ hybridization targeting Influenza A RNA. The viral RNA labelling was highly clustered and overlapped the brain lesions, observed in neurons, and grey matter. Whole viral genome sequences obtained from the affected foxes were subjected to phylogenetic and mutation analysis to determine influenza A clade, host specificity, and potential occurrence of viral reassortment. Infections in red foxes likely occurred due to preying on infected wild birds and are unlikely due to transmission between foxes or other mammals.
Collapse
Affiliation(s)
- Brittany D. Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Rhea S. Gerdes
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kevin Hynes
- New York State Department of Environmental Conservation, Wildlife Health Program, Albany, NY, USA
| | - Cynthia R. Hopf
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa A. Fadden
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Shotaro Nakagun
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Krysten L. Schuler
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elizabeth L. Buckles
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Manigandan Lejeune
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| |
Collapse
|
3
|
Noh EB, Heo GB, Lee KN, Kang YM, An SH, Kim N, Lee YJ. Subtype specific virus enrichment with immunomagnetic separation method followed by NGS unravels the mixture of H5 and H9 avian influenza virus. J Virol Methods 2023; 320:114773. [PMID: 37467847 DOI: 10.1016/j.jviromet.2023.114773] [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: 04/26/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023]
Abstract
Wild bird avian influenza type A virus (AIV) surveillance is important for the early detection of highly pathogenic AIVs and for providing early warnings to the poultry industry and veterinary services to implement more effective control measures against these viruses. Some field samples are often found to contain more than two kinds of AIV. Correct determination of the HA/NA subtype and complete nucleotide sequences of the component viruses in those samples are often critical for timely and accurate understanding of the field situation, but it is not easy to define the genomic structure of the constituent viruses unambiguously because AIV has eight segmented genomes. In this study, with immunomagnetic beads incorporating polyclonal antibodies of chicken for subtype-specific viral enrichment, we could selectively decrease the density of one of the two constituent viruses in a sample of different subtypes, H5 and H9, artificially generated; this was represented in the changes of Ct values with subtype specific real-time RT-PCR. Following this, with NGS, we could recover nearly complete genomic sequences and arrange the consensus sequences of gene segments of the constituent viruses confidently with the quantitative variable like genome coverage, linked along the gene segments and associated with the number of viral copies in a sample.
Collapse
Affiliation(s)
- Eun Bi Noh
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Gyeong-Beom Heo
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Kwang-Nyeong Lee
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Yong-Myung Kang
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Se-Hee An
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Nayeong Kim
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Youn-Jeong Lee
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| |
Collapse
|
4
|
King KL, Ham R, Smothers A, Lee I, Bowie T, Teetsel E, Peng C, Dean D. Repurposing a SARS-CoV-2 surveillance program for infectious respiratory diseases in a university setting. Front Public Health 2023; 11:1168551. [PMID: 37727605 PMCID: PMC10505707 DOI: 10.3389/fpubh.2023.1168551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/16/2023] [Indexed: 09/21/2023] Open
Abstract
Standard multiplex RT-qPCR diagnostic tests use nasopharyngeal swabs to simultaneously detect a variety of infections, but commercially available kits can be expensive and have limited throughput. Previously, we clinically validated a saliva-based RT-qPCR diagnostic test for SARS-CoV-2 to provide low-cost testing with high throughput and low turnaround time on a university campus. Here, we developed a respiratory diagnostic panel to detect SARS-CoV-2, influenza A and B within a single saliva sample. When compared to clinical results, our assay demonstrated 93.5% accuracy for influenza A samples (43/46 concordant results) with no effect on SARS-CoV-2 accuracy or limit of detection. In addition, our assay can detect simulated coinfections at varying virus concentrations generated from synthetic RNA controls. We also confirmed the stability of influenza A in saliva at room temperature for up to 5 days. The cost of the assay is lower than standard nasopharyngeal swab respiratory panel tests as saliva collection does not require specialized swabs or trained clinical personnel. By repurposing the lab infrastructure developed for the COVID-19 pandemic, our multiplex assay can be used to provide expanded access to respiratory disease diagnostics, especially for community, school, or university testing applications where saliva testing was effectively utilized during the COVID-19 pandemic.
Collapse
Affiliation(s)
- Kylie L. King
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Rachel Ham
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Austin Smothers
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Isaac Lee
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Tyler Bowie
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Erika Teetsel
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Congyue Peng
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| |
Collapse
|
5
|
Nabakooza G, Owuor DC, de Laurent ZR, Galiwango R, Owor N, Kayiwa JT, Jjingo D, Agoti CN, Nokes DJ, Kateete DP, Kitayimbwa JM, Frost SDW, Lutwama JJ. Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains. Sci Rep 2023; 13:5516. [PMID: 37015946 PMCID: PMC10072032 DOI: 10.1038/s41598-023-30667-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/28/2023] [Indexed: 04/06/2023] Open
Abstract
Genetic characterisation of circulating influenza viruses directs annual vaccine strain selection and mitigation of infection spread. We used next-generation sequencing to locally generate whole genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) positive patient swabs collected across Uganda between 2010 and 2018. We recovered sequences from 92% (215/234) of the swabs, 90% (193/215) of which were whole genomes. The newly-generated sequences were genetically and phylogenetically compared to the WHO-recommended vaccines and other Africa strains sampled since 1994. Uganda strain hemagglutinin (n = 206), neuraminidase (n = 207), and matrix protein (MP, n = 213) sequences had 95.23-99.65%, 95.31-99.79%, and 95.46-100% amino acid similarity to the 2010-2020 season vaccines, respectively, with several mutated hemagglutinin antigenic, receptor binding, and N-linked glycosylation sites. Uganda influenza type-A virus strains sequenced before 2016 clustered uniquely while later strains mixed with other Africa and global strains. We are the first to report novel A(H1N1)pdm09 subclades 6B.1A.3, 6B.1A.5(a,b), and 6B.1A.6 (± T120A) that circulated in Eastern, Western, and Southern Africa in 2017-2019. Africa forms part of the global influenza ecology with high viral genetic diversity, progressive antigenic drift, and local transmissions. For a continent with inadequate health resources and where social distancing is unsustainable, vaccination is the best option. Hence, African stakeholders should prioritise routine genome sequencing and analysis to direct vaccine selection and virus control.
Collapse
Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda.
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda.
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda.
- Oak Ridge Institute for Science and Education, Bioinformatics Research Fellow to the Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States.
| | - D Collins Owuor
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ronald Galiwango
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE), Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Nicholas Owor
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - John T Kayiwa
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Daudi Jjingo
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE), Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Department of Computer Science, College of Computing, Makerere University, Kampala, Uganda
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, United Kingdom
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - John M Kitayimbwa
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda
| | - Simon D W Frost
- Microsoft Research, Redmond, Washington, 98052, United States
- London School of Hygiene and Tropical Medicine (LSHTM), Keppel St, Bloomsbury, London, United Kingdom
| | - Julius J Lutwama
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| |
Collapse
|
6
|
Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
Collapse
Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
7
|
Su R, Yan H, Li N, Ding T, Li B, Xie Y, Gao C, Li X, Wang C. Application value of blood metagenomic next-generation sequencing in patients with connective tissue diseases. Front Immunol 2022; 13:939057. [PMID: 35979346 PMCID: PMC9376218 DOI: 10.3389/fimmu.2022.939057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 12/05/2022] Open
Abstract
Objective This study aimed to analyze the application value of blood metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) to provide a reference for infection diagnosis and guidance for treatment. Methods A total of 126 CTD patients with suspected infections who were hospitalized in the Department of Rheumatology, the Second Hospital of Shanxi Medical University from January 2020 to December 2021 were enrolled in this study. We retrospectively reviewed the results of mNGS and conventional diagnostic tests (CDTs). Results Systemic lupus erythematosus (SLE) and polymyositis/dermatomyositis (DM/PM) had the highest incidence of infections. The positive pathogen detection rates of mNGS were higher than those of CDT. The virus infections are the most common type in CTD patients with single or mixed infection, especially Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), and Human alphaherpesvirus 1. The incidence of prokaryote and eukaryote infections is secondary to viruses. Bloodstream infections of rare pathogens such as Pneumocystis jirovecii should be of concern. Meanwhile, the most common mixed infection was bacterial–virus coinfection. Conclusion mNGS has incremental application value in patients with CTD suspected of co-infection. It has a high sensitivity, and a wide detection range for microorganisms in CTD patients. Furthermore, the high incidence of opportunistic virus infections in CTD patients should be of sufficient concern.
Collapse
Affiliation(s)
- Rui Su
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Huanhuan Yan
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Na Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Tingting Ding
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Baochen Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuhuan Xie
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chong Gao
- Pathology, Joint Program in Transfusion Medicine, Brigham and Women’s Hospital/Children’s Hospital Boston, Harvard Medical School, Boston, MA, United States
| | - Xiaofeng Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Caihong Wang
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Caihong Wang,
| |
Collapse
|
8
|
Nabakooza G, Pastusiak A, Kateete DP, Lutwama JJ, Kitayimbwa JM, Frost SDW. Whole-genome analysis to determine the rate and patterns of intra-subtype reassortment among influenza type-A viruses in Africa. Virus Evol 2022; 8:veac005. [PMID: 35317349 PMCID: PMC8933723 DOI: 10.1093/ve/veac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/13/2022] [Accepted: 01/28/2022] [Indexed: 12/05/2022] Open
Abstract
Influenza type-A viruses (IAVs) present a global burden of human respiratory infections and mortality. Genome reassortment is an important mechanism through which epidemiologically novel influenza viruses emerge and a core step in the safe reassortment-incompetent live-attenuated influenza vaccine development. Currently, there are no data on the rate, spatial and temporal distribution, and role of reassortment in the evolution and diversification of IAVs circulating in Africa. We aimed to detect intra-subtype reassortment among Africa pandemic H1N1pdm09 (2009-10), seasonal H1N1pdm09 (2011-20), and seasonal H3N2 viruses and characterize the genomic architecture and temporal and spatial distribution patterns of the resulting reassortants. Our study was nested within the Uganda National Influenza Surveillance Programme. Next-generation sequencing was used to generate whole genomes (WGs) from 234 H1N1pdm09 (n = 116) and H3N2 (n = 118) viruses sampled between 2010 and 2018 from seven districts in Uganda. We combined our newly generated WGs with 658 H1N1pdm09 and 1131 H3N2 WGs sampled between 1994 and 2020 across Africa and identified reassortants using an automated Graph Incompatibility Based Reassortment Finder software. Viral reassortment rates were estimated using a coalescent reassortant constant population model. Phylogenetic analysis was used to assess the effect of reassortment on viral genetic evolution. We observed a high frequency of intra-subtype reassortment events, 12 · 4 per cent (94/758) and 20 · 9 per cent (256/1,224), and reassortants, 13 · 3 per cent (101/758) and 38 · 6 per cent (472/1,224), among Africa H1N1pdm09 and H3N2 viruses, respectively. H1N1pdm09 reassorted at higher rates (0.1237-0.4255) than H3N2 viruses (0 · 00912-0.0355 events/lineage/year), a case unique to Uganda. Viral reassortants were sampled in 2009 through 2020, except in 2012. 78 · 2 per cent (79/101) of H1N1pdm09 reassortants acquired new non-structural, while 57 · 8 per cent (273/472) of the H3N2 reassortants had new hemagglutinin (H3) genes. Africa H3N2 viruses underwent more reassortment events involving larger reassortant sets than H1N1pdm09 viruses. Viruses with a specific reassortment architecture circulated for up to five consecutive years in specific countries and regions. The Eastern (Uganda and Kenya) and Western Africa harboured 84 · 2 per cent (85/101) and 55 · 9 per cent (264/472) of the continent's H1N1pdm09 and H3N2 reassortants, respectively. The frequent reassortment involving multi-genes observed among Africa IAVs showed the intracontinental viral evolution and diversification possibly sustained by viral importation from outside Africa and/or local viral genomic mixing and transmission. Novel reassortant viruses emerged every year, and some persisted in different countries and regions, thereby presenting a risk of influenza outbreaks in Africa. Our findings highlight Africa as part of the global influenza ecology and the advantage of implementing routine whole-over partial genome sequencing and analyses to monitor circulating and detect emerging viruses. Furthermore, this study provides evidence and heightens our knowledge on IAV evolution, which is integral in directing vaccine strain selection and the update of master donor viruses used in recombinant vaccine development.
Collapse
Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O Box 7072, Kampala, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Rd, P.O BOX 4, Mukono, Uganda
| | | | - David Patrick Kateete
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O Box 7072, Kampala, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
| | - Julius Julian Lutwama
- Department of Arbovirology Emerging & Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Plot No: 51-59, Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
| | - John Mulindwa Kitayimbwa
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Rd, P.O BOX 4, Mukono, Uganda
| | - Simon David William Frost
- Microsoft Research, 14820 NE 36th Street, Redmond, WA 98052, USA
- London School of Hygiene & Tropical Medicine (LSHTM), Keppel St, Bloomsbury, London WC1E 7HT, UK
| |
Collapse
|
9
|
Zhou T, Zhou S, Chen Y, Wang J, Zhang R, Xiang H, Xia Z, An M, Zhao X, Wu Y. Next-generation sequencing identification and multiplex RT-PCR detection for viruses infecting cigar and flue-cured tobacco. Mol Biol Rep 2022; 49:237-247. [PMID: 34705219 DOI: 10.1007/s11033-021-06864-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Early, precise and simultaneous identification of plant viruses is of great significance for preventing virus spread and reducing losses in agricultural yields. METHODS AND RESULTS In this study, the identification of plant viruses from symptomatic samples collected from a cigar tobacco planting area in Deyang and a flue-cured tobacco planting area in Luzhou city, Sichuan Province, China, was conducted by deep sequencing of small RNAs (sRNAs) through an Illumina sequencing platform, and plant virus-specific contigs were generated based on virus-derived siRNA sequences. Additionally, sequence alignment and phylogenetic analysis were performed to determine the species or strains of these viruses. A total of 27930450, 21537662 and 28194021 clean reads were generated from three pooled samples, with a total of 105 contigs mapped to the closest plant viruses with lengths ranging from 34 ~ 1720 nt. The results indicated that the major viruses were potato virus Y, Chilli veinal mottle virus, tobacco vein banding mosaic virus, tobacco mosaic virus and cucumber mosaic virus. Subsequently, a fast and sensitive multiplex reverse transcription polymerase chain reaction assay was developed for the simultaneous detection of the most frequent RNA viruses infecting cigar and flue-cured tobacco in Sichuan. CONCLUSIONS These results provide a theoretical basis and convenient methods for the rapid detection and control of viruses in cigar- and flue-cured tobacco.
Collapse
Affiliation(s)
- Tao Zhou
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Shidong Zhou
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Yong Chen
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Jun Wang
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Ruina Zhang
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Huan Xiang
- Deyang Company of Sichuan Provincial Tobacco Corporation, Deyang, 618400, Sichuan, People's Republic of China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China
| | - Xiuxiang Zhao
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China.
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, No.120 Dongling, Shenyang, 110866, Liaoning, People's Republic of China.
| |
Collapse
|
10
|
Lapa SA, Miftakhov RA, Klochikhina ES, Ammur YI, Blagodatskikh SA, Shershov VE, Zasedatelev AS, Chudinov AV. Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens. Mol Biol 2021; 55:828-838. [PMID: 34955557 PMCID: PMC8682033 DOI: 10.1134/s0026893321040063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022]
Abstract
A prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, which significantly reduces the background signal and increases the sensitivity of the analysis. The use of a specialized detector makes it possible to read the signals of elongated primers directly through the transparent cover film of the reaction chamber. This solution is designed to prevent cross-contamination and is suitable for simultaneous testing of a large number of test samples. The proposed platform is able to detect the presence of several pathogens of pneumonia in a sample and has an open architecture that allows expansion of the range of pathogenic bacteria and viruses that can be detected.
Collapse
Affiliation(s)
- S A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E S Klochikhina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Yu I Ammur
- Mechnikov Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - S A Blagodatskikh
- Scientific Center of Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - V E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
11
|
Peck H, Moselen J, Brown SK, Triantafilou M, Lau H, Grau M, Barr IG, Leung VK. Report on influenza viruses received and tested by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza in 2019. ACTA ACUST UNITED AC 2021; 45. [PMID: 34493178 DOI: 10.33321/cdi.2021.45.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract As part of its role in the World Health Organization's (WHO) Global Influenza Surveillance and Response System (GISRS), the WHO Collaborating Centre for Reference and Research on Influenza in Melbourne received a record total of 9,266 human influenza positive samples during 2019. Viruses were analysed for their antigenic, genetic and antiviral susceptibility properties. Selected viruses were propagated in qualified cells or embryonated hen's eggs for potential use in seasonal influenza virus vaccines. In 2019, influenza A(H3N2) viruses predominated over influenza A(H1N1)pdm09 and B viruses, accounting for a total of 51% of all viruses analysed. The majority of A(H1N1)pdm09, A(H3N2) and influenza B viruses analysed at the Centre were found to be antigenically similar to the respective WHO recommended vaccine strains for the Southern Hemisphere in 2019. However, phylogenetic analysis indicated that a significant proportion of circulating A(H3N2) viruses had undergone genetic drift relative to the WHO recommended vaccine strain for 2019. Of 5,301 samples tested for susceptibility to the neuraminidase inhibitors oseltamivir and zanamivir, four A(H1N1)pdm09 viruses showed highly reduced inhibition with oseltamivir, one A(H1N1)pdm09 virus showed highly reduced inhibition with zanamivir and three B/Victoria viruses showed highly reduced inhibition with zanamivir.
Collapse
Affiliation(s)
- Heidi Peck
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Jean Moselen
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Sook Kwan Brown
- WHO Collaborating Centre for Reference and Research on Influenza
| | | | - Hilda Lau
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Miguel Grau
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Vivian Ky Leung
- WHO Collaborating Centre for Reference and Research on Influenza
| |
Collapse
|
12
|
Faleye TOC, Adams D, Adhikari S, Sandrolini H, Halden RU, Varsani A, Scotch M. Use of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting. BMC Infect Dis 2021; 21:810. [PMID: 34388979 PMCID: PMC8360813 DOI: 10.1186/s12879-021-06526-5] [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: 03/01/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background Local transmission of seasonal influenza viruses (IVs) can be difficult to resolve. Here, we study if coupling high-throughput sequencing (HTS) of hemagglutinin (HA) and neuraminidase (NA) genes with variant analysis can resolve strains from local transmission that have identical consensus genome. We analyzed 24 samples collected over four days in January 2020 at a large university in the US. We amplified complete hemagglutinin (HA) and neuraminidase (NA) genomic segments followed by Illumina sequencing. We identified consensus complete HA and NA segments using BLASTn and performed variant analysis on strains whose HA and NA segments were 100% similar. Results Twelve of the 24 samples were PCR positive, and we detected complete HA and/or NA segments by de novo assembly in 83.33% (10/12) of them. Similarity and phylogenetic analysis showed that 70% (7/10) of the strains were distinct while the remaining 30% had identical consensus sequences. These three samples also had IAV and IBV co-infection. However, subsequent variant analysis showed that they had distinct variant profiles. While the IAV HA of one sample had no variant, another had a T663C mutation and another had both C1379T and C1589A. Conclusion In this study, we showed that HTS coupled with variant analysis of only HA and NA genes can help resolve variants that are closely related. We also provide evidence that during a short time period in the 2019–2020 season, co-infection of IAV and IBV occurred on the university campus and both 2020/2021 and 2021/2022 WHO recommended H1N1 vaccine strains were co-circulating. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06526-5.
Collapse
Affiliation(s)
- Temitope O C Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Deborah Adams
- Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
| | - Helen Sandrolini
- Arizona State University Health Services, Arizona State University, Tempe, AZ, 85287, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA.
| |
Collapse
|
13
|
Shi Y, Chen W, Zeng M, Shen G, Sun C, Liu G, Gong H, Wang C, Ge M, Xu J, Wang L, Lu A, Lu G, Zhai X. Clinical features and risk factors for severe influenza in children: A study from multiple hospitals in Shanghai. Pediatr Neonatol 2021; 62:428-436. [PMID: 34103261 DOI: 10.1016/j.pedneo.2021.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The incidence and mortality of influenza in children had risen, but data are limited on children with severe influenza virus infection in China. METHODS We conducted a retrospective case-control study and collected the patients' clinical data. Clinical data including demography, clinical presentation, laboratory findings, radiologic findings, treatment and outcomes were collected. Children were clinically confirmed to have virus infection in Shanghai in three hospitals from June 2014 to June 2019. RESULTS During the study, 36,047 children were enrolled. Among them, 118 met the criteria for severe flu. Clinical symptoms such as fever, cough, gastrointestinal symptoms, coma and epilepsy were higher in the severe group. Complications such as pneumorrhagia, heart failure, septic shock, acute renal failure and influenza-associated encephalitis were higher in the severe influenza group than the death group. The laboratory findings including decreased hemoglobin, high alanine aminotransferase, high urea nitrogen and high lactate levels were risk factors for death in children with influenza. CONCLUSION Influenza-associated encephalopathy (IAE), acute respiratory distress syndrome (ARDS) were the common clinical manifestations and complications for the severe influenza, and delayed use of oseltamivir was found to be associated with fatality.
Collapse
Affiliation(s)
- Yu Shi
- Division of Medical Administration, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Weiming Chen
- Department of Critical Care Medicine, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Mei Zeng
- Department of Infectious Disease, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Guomei Shen
- Outpatient and Emergency Management Office, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Chengjun Sun
- Department of Endocrinology, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Gongbao Liu
- Division of Medical Administration, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Hairong Gong
- Department of Critical Care Medicine, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Chuanqing Wang
- Department of Hospital Infection Control, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Mengmeng Ge
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Libo Wang
- Department of Respiration, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China; Department of Pediatrics, Jinshan Hospital of Fudan University, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Aizhen Lu
- Department of Respiration, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China; Department of Pediatrics, Central Hospital of Minhang District, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China
| | - Guoping Lu
- Department of Critical Care Medicine, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China.
| | - Xiaowen Zhai
- Department of Hematology/Oncology, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China; Hospital Administration, National Children's Medical Center, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai, China.
| |
Collapse
|
14
|
Xiao Y, Yang F, Liu F, Cheng L, Yao H, Wu N, Wu H. Development of an antigen-ELISA and a colloidal gold-based immunochromatographic strip based on monoclonal antibodies for detection of avian influenza A(H5) viruses. J Vet Diagn Invest 2021; 33:969-974. [PMID: 34166136 DOI: 10.1177/10406387211027538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Avian influenza A(H5) viruses (avian IAVs) pose a major threat to the economy and public health. We developed an antigen-ELISA (ag-ELISA) and a colloidal gold-based immunochromatographic strip for the rapid detection of avian A(H5) viruses. Both detection methods displayed no cross-reactivity with other viruses (e.g., other avian IAVs, infectious bursal disease virus, Newcastle disease virus, infectious bronchitis virus, avian paramyxovirus). The ag-ELISA was sensitive down to 0.5 hemagglutinin (HA) units/100 µL of avian A(H5) viruses and 7.5 ng/mL of purified H5 HA proteins. The immunochromatographic strip was sensitive down to 1 HA unit/100 µL of avian A(H5) viruses. Both detection methods exhibited good reproducibility with CVs < 10%. For 200 random poultry samples, the sensitivity and specificity of the ag-ELISA were 92.6% and 98.8%, respectively, and for test strips were 88.9% and 98.3%, respectively. Both detection methods displayed high specificity, sensitivity, and stability, making them suitable for rapid detection and field investigation of avian A(H5) viruses.
Collapse
Affiliation(s)
- Yixin Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fumin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Haibo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
15
|
Pathogenicity of H9N2 low pathogenic avian influenza viruses of different lineages isolated from live bird markets tested in three animal models: SPF chickens, Korean native chickens, and ducks. Poult Sci 2021; 100:101318. [PMID: 34284181 PMCID: PMC8313579 DOI: 10.1016/j.psj.2021.101318] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/22/2022] Open
Abstract
Since its first appearance in 1996, H9N2 avian influenza virus (AIV) of the Y439 lineage persisted in Korean live bird markets (LBMs) until the last documented occurrence in 2018. However, in June 2020, the avian influenza surveillance program detected a novel H9N2 AIV belonging to the Y280 lineage, which has zoonotic potential, in a Korean native chicken (KNC) from a LBM. In this study, we infected KNCs and ducks (the 2 major species held at LBMs), as well as SPF chickens, with Y280-lineage H9N2 AIV LBM261/20 and Y439-equivalent LBM294/18 to compare pathogenicity and transmissibility. In SPF chickens, LBM261/20 replicated mostly in the respiratory tract and spread rapidly among birds. By contrast, LBM294/18 replicated preferentially in the gastrointestinal tract and transmitted more slowly than LBM261/20. LBM261/20 replicated for a longer time in KNCs than in SPF chickens, and only in the respiratory tract; by contrast, LBM294/18 was detected in the oropharynx and cloaca. Ducks did not shed either virus or seroconvert. Taken together, the data suggest that the scheme used to monitor the newly introduced H9N2 AIV of the Y280 lineage needs to be modified to place emphasis on oropharyngeal sampling. Such changes will facilitate better disease control and protect public health.
Collapse
|
16
|
Nguyen THO, Koutsakos M, van de Sandt CE, Crawford JC, Loh L, Sant S, Grzelak L, Allen EK, Brahm T, Clemens EB, Auladell M, Hensen L, Wang Z, Nüssing S, Jia X, Günther P, Wheatley AK, Kent SJ, Aban M, Deng YM, Laurie KL, Hurt AC, Gras S, Rossjohn J, Crowe J, Xu J, Jackson D, Brown LE, La Gruta N, Chen W, Doherty PC, Turner SJ, Kotsimbos TC, Thomas PG, Cheng AC, Kedzierska K. Immune cellular networks underlying recovery from influenza virus infection in acute hospitalized patients. Nat Commun 2021; 12:2691. [PMID: 33976217 PMCID: PMC8113517 DOI: 10.1038/s41467-021-23018-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
How innate and adaptive immune responses work in concert to resolve influenza disease is yet to be fully investigated in one single study. Here, we utilize longitudinal samples from patients hospitalized with acute influenza to understand these immune responses. We report the dynamics of 18 important immune parameters, related to clinical, genetic and virological factors, in influenza patients across different severity levels. Influenza disease correlates with increases in IL-6/IL-8/MIP-1α/β cytokines and lower antibody responses. Robust activation of circulating T follicular helper cells correlates with peak antibody-secreting cells and influenza heamaglutinin-specific memory B-cell numbers, which phenotypically differs from vaccination-induced B-cell responses. Numbers of influenza-specific CD8+ or CD4+ T cells increase early in disease and retain an activated phenotype during patient recovery. We report the characterisation of immune cellular networks underlying recovery from influenza infection which are highly relevant to other infectious diseases.
Collapse
Affiliation(s)
- Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Ludivine Grzelak
- Biology Department, École Normale Supérieure Paris-Saclay, Université Paris-Saclay Cachan, Cachan, France
| | - Emma K Allen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Tim Brahm
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Maria Auladell
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Zhongfang Wang
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Simone Nüssing
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patrick Günther
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
- ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, VIC, Australia
| | - Malet Aban
- World Health Organisation (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Yi-Mo Deng
- World Health Organisation (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Karen L Laurie
- World Health Organisation (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Aeron C Hurt
- World Health Organisation (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stephanie Gras
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
- Department of Biochemistry and Genetics, La Trobe Institute For Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Jane Crowe
- Deepdene Surgery, Deepdene, VIC, Australia
| | - Jianqing Xu
- Shanghai Public Health Clinical Centre and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - David Jackson
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Lorena E Brown
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Nicole La Gruta
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute For Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Peter C Doherty
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Tom C Kotsimbos
- Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia
- Department of Medicine, Monash University, Central Clinical School, The Alfred Hospital, Melbourne, VIC, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia.
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, VIC, Australia.
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| |
Collapse
|
17
|
Molecular evolution and characterization of hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 viruses isolated in Beijing, China, during the 2017-2018 and 2018-2019 influenza seasons. Arch Virol 2020; 166:179-189. [PMID: 33145635 DOI: 10.1007/s00705-020-04869-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
We investigated and analysed the molecular evolution of hemagglutinin (HA) and neuraminidase (NA) of influenza A(H1N1)pdm09 virus during the 2017-2018 and 2018-2019 influenza seasons in Beijing, China. We collected and extracted RNA from influenza A(H1N1)pdm09 strains from Peking University People's Hospital and analyzed their HA and NA genes by RT-PCR and sequencing. Phylogenetic analysis of HA and NA sequences was used to compare the amino acid sequences of 51 strains with those of reference strains. All strains belonged to subclade 6B.1, with S162N and I216T substitutions (H1 numbering). Our strains differed from strain A/Michigan/45/2015, with the substitutions S91R, S181T and I312V in the HA antigenic epitope. An E189G mutation was detected in the 190 helix of the receptor binding region of HA. A new potential glycosylation site, 179 (NQT), which was not detected before the 2015 influenza season, was identified. Two strains were mutated at I223, the NA inhibitor resistance site. During 2012-2019, amino acids of HA and NA mutated over time. Co-occurrence mutations N146D, S200P, S202I and A273T in HA appeared along with Q51K, F74S and D416N in NA in six strains during two influenza seasons. Our work reveals the molecular changes and phylogenetic characteristics of influenza A(H1N1)pdm09 virus and suggests that a vaccine probably provides suboptimal protection. The biological characteristics of the new glycosylation and drug-resistance sites detected in this work need to be studied further. The co-occurrence of mutations in HA and NA might affect the characteristics of the virus and need to be given more attention.
Collapse
|
18
|
Leong NKC, Chu DKW, Chu JTS, Tam YH, Ip DKM, Cowling BJ, Poon LLM. A six-plex droplet digital RT-PCR assay for seasonal influenza virus typing, subtyping, and lineage determination. Influenza Other Respir Viruses 2020; 14:720-729. [PMID: 32519796 PMCID: PMC7578307 DOI: 10.1111/irv.12769] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND There are two influenza A subtypes (H1 and H3) and two influenza B lineages (Victoria and Yamagata) that currently co-circulate in humans. In this study, we report the development of a six-plex droplet digital RT-PCR (ddRT-PCR) assay that can detect HA and M segments of influenza A (H1, H3, and M) and influenza B (Yamagata HA, Victoria HA, and M) viruses in a single reaction mixture. It can simultaneously detect six different nucleic acid targets in a ddRT-PCR platform. METHODS The six-plex ddRT-PCR used in this study is an amplitude-based multiplex assay. The analytical performance of the assay was evaluated. Correlation with standard qRT-PCR methodology was assessed using 55 clinical samples. RESULTS The assay has a wide dynamic range, and it has good reproducibility within and between runs. The limit of quantification of each target in this assay ranged from 15 copies/reaction for influenza B Victoria M gene to 45 copies/reaction for influenza B Yamagata M gene. In addition, this assay can accurately quantify each of these targets in samples containing viral RNAs from two different viruses that were mixed in a highly skewed ratio. Typing, subtyping, and lineage differentiation data of 55 tested clinical respiratory specimens were found to be identical to those deduced from standard monoplex qRT-PCR assays. CONCLUSIONS The six-plex ddRT-PCR test was demonstrated to be highly suitable for detecting dual influenza infection cases. This assay is expected to be a useful diagnostic tool for clinical and research use.
Collapse
Affiliation(s)
- Nathaniel K. C. Leong
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Daniel K. W. Chu
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Julie T. S. Chu
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Yat H. Tam
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Dennis K. M. Ip
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Benjamin J. Cowling
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Leo L. M. Poon
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| |
Collapse
|
19
|
Monoclonal Antibody Therapy Protects Pharmacologically Immunosuppressed Mice from Lethal Infection with Influenza B Virus. Antimicrob Agents Chemother 2020; 64:AAC.00284-20. [PMID: 32631823 DOI: 10.1128/aac.00284-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/27/2020] [Indexed: 11/20/2022] Open
Abstract
Human influenza A and B viruses are highly contagious and cause similar illnesses and seasonal epidemics. Currently available antiviral drugs have limited efficacy in humans with compromised immune systems; therefore, alternative strategies for protection are needed. Here, we investigated whether monoclonal antibodies (MAbs) targeting hemagglutinin (HA) and/or neuraminidase (NA) proteins would protect immunosuppressed mice from severe infections with influenza B virus. Pharmacologically immunosuppressed BALB/c mice were inoculated with B/Brisbane/60/2008 (BR/08) influenza virus and were treated with a single dose of 1, 5, or 25 mg/kg of body weight per day of either an anti-HA MAb (1D2) or an anti-NA MAb (1F2) starting at 24 hours postinoculation (hpi). Monotherapy with 1D2 or 1F2 MAbs provided dose-dependent protection of mice, with decreased BR/08 virus replication and spread in the mouse lungs, compared with those of controls. Combination treatment with 1D2 and 1F2 provided greater protection than did monotherapy, even when started at 48 hpi. Virus spread was also efficiently restrained within the lungs, being limited to 6%, 10%, and 10% of that seen in active infection when treatment was initiated at 24, 48, and 72 hpi, respectively. In most cases, the expression of cytokines and chemokines was altered according to when treatment was initiated. Higher expression of proinflammatory IP-10 and MCP-1 in combination-treatment groups, but not in monotherapy groups, to some extent, promoted better control of virus spread within the lungs. This study demonstrates the potential value of MAb immunotherapy in treating influenza in immunocompromised hosts who are at increased risk of severe disease.
Collapse
|
20
|
Price OH, Spirason N, Rynehart C, Brown SK, Todd A, Peck H, Patel M, Soppe S, Barr IG, Chow MK. Report on influenza viruses received and tested by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza in 2018. ACTA ACUST UNITED AC 2020; 44. [PMID: 32178606 DOI: 10.33321/cdi.2020.44.16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As part of its role in the World Health Organization's (WHO) Global Influenza Surveillance and Response System (GISRS), the WHO Collaborating Centre for Reference and Research on Influenza in Melbourne received a total of 3993 human influenza-positive samples during 2018. Viruses were analysed for their antigenic, genetic and antiviral susceptibility properties. Selected viruses were propagated in qualified cells or hens' eggs for use as potential seasonal influenza vaccine virus candidates. In 2018, influenza A(H1)pdm09 viruses predominated over influenza A(H3) and B viruses, accounting for a total of 53% of all viruses analysed. The majority of A(H1)pdm09, A(H3) and influenza B viruses analysed at the Centre were found to be antigenically similar to the respective WHO-recommended vaccine strains for the Southern Hemisphere in 2018. However, phylogenetic analysis indicated that a significant proportion of circulating A(H3) viruses had undergone genetic drift relative to the WHO-recommended vaccine strain for 2018. Of 2864 samples tested for susceptibility to the neuraminidase inhibitors oseltamivir and zanamivir, three A(H1)pdm09 viruses showed highly reduced inhibition by oseltamivir, while one B/Victoria virus showed highly reduced inhibition by both oseltamivir and zanamivir.
Collapse
Affiliation(s)
- Olivia H Price
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Natalie Spirason
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Cleve Rynehart
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Sook Kwan Brown
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Angela Todd
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Heidi Peck
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Manisha Patel
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Sally Soppe
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| | - Michelle K Chow
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria
| |
Collapse
|
21
|
Horwood PF, Karlsson EA, Horm SV, Ly S, Heng S, Chin S, Darapheak C, Saunders D, Chanthap L, Rith S, Y P, Chea KL, Sar B, Parry A, Ieng V, Tsuyouka R, Deng YM, Hurt AC, Barr IG, Komadina N, Buchy P, Dussart P. Circulation and characterization of seasonal influenza viruses in Cambodia, 2012-2015. Influenza Other Respir Viruses 2019; 13:465-476. [PMID: 31251478 PMCID: PMC6692578 DOI: 10.1111/irv.12647] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 12/13/2018] [Accepted: 04/26/2019] [Indexed: 12/04/2022] Open
Abstract
Background Influenza virus circulation is monitored through the Cambodian influenza‐like illness (ILI) sentinel surveillance system and isolates are characterized by the National Influenza Centre (NIC). Seasonal influenza circulation has previously been characterized by year‐round activity and a peak during the rainy season (June‐November). Objectives We documented the circulation of seasonal influenza in Cambodia for 2012‐2015 and investigated genetic, antigenic, and antiviral resistance characteristics of influenza isolates. Patients/Methods Respiratory samples were collected from patients presenting with influenza‐like illness (ILI) at 11 hospitals throughout Cambodia. First‐line screening was conducted by the National Institute of Public Health and the Armed Forces Research Institute of Medical Sciences. Confirmation of testing and genetic, antigenic and antiviral resistance characterization was conducted by Institute Pasteur in Cambodia, the NIC. Additional virus characterization was conducted by the WHO Collaborating Centre for Reference and Research on Influenza (Melbourne, Australia). Results Between 2012 and 2015, 1,238 influenza‐positive samples were submitted to the NIC. Influenza A(H3N2) (55.3%) was the dominant subtype, followed by influenza B (30.9%; predominantly B/Yamagata‐lineage) and A(H1N1)pdm09 (13.9%). Circulation of influenza viruses began earlier in 2014 and 2015 than previously described, coincident with the emergence of A(H3N2) clades 3C.2a and 3C.3a, respectively. There was high diversity in the antigenicity of A(H3N2) viruses, and to a smaller extent influenza B viruses, during this period, with some mismatches with the northern and southern hemisphere vaccine formulations. All isolates tested were susceptible to the influenza antiviral drugs oseltamivir and zanamivir. Conclusions Seasonal and year‐round co‐circulation of multiple influenza types/subtypes were detected in Cambodia during 2012‐2015.
Collapse
Affiliation(s)
- Paul F Horwood
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia.,Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Erik A Karlsson
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia
| | - Srey Viseth Horm
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia
| | - Sovann Ly
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Seng Heng
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Savuth Chin
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Chau Darapheak
- National Institute of Public Health, Phnom Penh, Cambodia
| | - David Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Lon Chanthap
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sareth Rith
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia
| | - Phalla Y
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia
| | - Kim Lay Chea
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia
| | - Borann Sar
- Centers for Disease Control and Prevention, Phnom Penh, Cambodia
| | - Amy Parry
- World Health Organization, Phnom Penh, Cambodia
| | - Vanra Ieng
- World Health Organization, Phnom Penh, Cambodia
| | | | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Naomi Komadina
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, Peter Doherty Institute, Melbourne, Victoria, Australia.,Monash University, Melbourne, Victoria, Australia
| | - Philippe Buchy
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia.,GlaxoSmithKline Vaccines R&D Intercontinental, Singapore, Singapore
| | - Philippe Dussart
- Virology Unit, Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh, Cambodia
| |
Collapse
|
22
|
Roe M, Kaye M, Iannello P, Lau H, Buettner I, Tolosa MX, Zakis T, Leung VK, Chow MK. Report on influenza viruses received and tested by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza in 2017. Commun Dis Intell (2018) 2019. [DOI: 10.33321/cdi.2019.43.25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
As part of its role in the World Health Organization’s (WHO) Global Influenza Surveillance and Response System (GISRS), the WHO Collaborating Centre for Reference and Research on Influenza in Melbourne received a record total of 5866 human influenza positive samples during 2017. Viruses were analysed for their antigenic, genetic and antiviral susceptibility properties and were propagated in qualified cells and hens’ eggs for use as potential seasonal influenza vaccine virus candidates. In 2017, influenza A(H3) viruses predominated over influenza A(H1)pdm09 and B viruses, accounting for a total of 54% of all viruses analysed. The majority of A(H1)pdm09, A(H3) and influenza B viruses analysed at the Centre were found to be antigenically similar to the respective WHO recommended vaccine strains for the Southern Hemisphere in 2017. However, phylogenetic analysis indicated that the majority of circulating A(H3) viruses had undergone genetic drift relative to the WHO recommended vaccine strain for 2017. Of 3733 samples tested for susceptibility to the neuraminidase inhibitors oseltamivir and zanamivir, only two A(H1)pdm09 viruses and one A(H3) virus showed highly reduced inhibition by oseltamivir, while just one A(H1)pdm09 virus showed highly reduced inhibition by zanamivir.
Collapse
Affiliation(s)
- Merryn Roe
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Matthew Kaye
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Pina Iannello
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Hilda Lau
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Iwona Buettner
- WHO Collaborating Centre for Reference and Research on Influenza
| | - M Ximena Tolosa
- WHO Collaborating Centre for Reference and Research on Influenza; National Centre for Epidemiology and Population Health, Australian National University
| | - Tasoula Zakis
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Vivian K Leung
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Michelle K Chow
- WHO Collaborating Centre for Reference and Research on Influenza
| |
Collapse
|
23
|
Lakdawala SS, Lee N, Brooke CB. Teaching an Old Virus New Tricks: A Review on New Approaches to Study Age-Old Questions in Influenza Biology. J Mol Biol 2019; 431:4247-4258. [PMID: 31051174 DOI: 10.1016/j.jmb.2019.04.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 01/31/2023]
Abstract
Influenza viruses have been studied for over 80 years, yet much about the basic viral lifecycle remain unknown. However, new imaging, biochemical, and sequencing techniques have revealed significant insight into many age-old questions of influenza virus biology. In this review, we will cover the role of imaging techniques to describe unique aspects of influenza virus assembly, biochemical techniques to study viral genomic organization, and next-generation sequencing to explore influenza genomic evolution. Our goal is to provide a brief overview of how emerging techniques are being used to answer basic questions about influenza viruses. This is not a comprehensive list of emerging techniques, rather ones that we feel will continue to make significant contributions to field of influenza biology.
Collapse
Affiliation(s)
- Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine Pittsburgh, PA 15219, USA.
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine Pittsburgh, PA 15219, USA.
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
| |
Collapse
|
24
|
Regan AK, Fielding JE, Chilver MB, Carville KS, Minney-Smith CA, Grant KA, Thomson C, Hahesy T, Deng YM, Stocks N, Sullivan SG. Intraseason decline in influenza vaccine effectiveness during the 2016 southern hemisphere influenza season: A test-negative design study and phylogenetic assessment. Vaccine 2019; 37:2634-2641. [PMID: 30952499 DOI: 10.1016/j.vaccine.2019.02.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND We estimated the effectiveness of seasonal inactivated influenza vaccine and the potential influence of timing of immunization on vaccine effectiveness (VE) using data from the 2016 southern hemisphere influenza season. METHODS Data were pooled from three routine syndromic sentinel surveillance systems in general practices in Australia. Each system routinely collected specimens for influenza testing from patients presenting with influenza-like illness. Next generation sequencing was used to characterize viruses. Using a test-negative design, VE was estimated based on the odds of vaccination among influenza-positive cases as compared to influenza-negative controls. Subgroup analyses were used to estimate VE by type, subtype and lineage, as well as age group and time between vaccination and symptom onset. RESULTS A total of 1085 patients tested for influenza in 2016 were included in the analysis, of whom 447 (41%) tested positive for influenza. The majority of detections were influenza A/H3N2 (74%). One-third (31%) of patients received the 2016 southern hemisphere formulation influenza vaccine. Overall, VE was estimated at 40% (95% CI: 18-56%). VE estimates were highest for patients immunized within two months prior to symptom onset (VE: 60%; 95% CI: 26-78%) and lowest for patients immunized >4 months prior to symptom onset (VE: 19%; 95% CI: -73-62%). DISCUSSION Overall, the 2016 influenza vaccine showed good protection against laboratory-confirmed infection among general practice patients. Results by duration of vaccination suggest a significant decline in effectiveness during the 2016 influenza season, indicating immunization close to influenza season offered optimal protection.
Collapse
Affiliation(s)
- Annette K Regan
- School of Public Health, Texas A&M University, 212 Adriance Drive, College Station, TX 77843, United States; School of Public Health, Curtin University, GPO Box U1987, Perth, WA 6845, Australia; Communicable Disease Control Directorate, Department of Health Western Australia, 227 Stubbs Terrace, Shenton Park, WA 6008, Australia; Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute, 15 Hospital Avenue, Nedlands, WA 6008, Australia.
| | - James E Fielding
- Victorian Infectious Diseases Reference Laboratory, 792 Elizabeth Street, Melbourne, VIC 3000, Australia; Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, 207 Bouverie Street, Melbourne, VIC 3010, Australia
| | - Monique B Chilver
- Discipline of General Practice, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Kylie S Carville
- Victorian Infectious Diseases Reference Laboratory, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | - Cara A Minney-Smith
- PathWest Laboratory Medicine WA, Locked Bag 2009, Nedlands, WA 6909, Australia
| | - Kristina A Grant
- Victorian Infectious Diseases Reference Laboratory, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | - Chloe Thomson
- Communicable Disease Control Directorate, Department of Health Western Australia, 227 Stubbs Terrace, Shenton Park, WA 6008, Australia
| | - Trish Hahesy
- SA Pathology, Frome Road, Adelaide, SA 5000, Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | - Nigel Stocks
- Discipline of General Practice, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Sheena G Sullivan
- Victorian Infectious Diseases Reference Laboratory, 792 Elizabeth Street, Melbourne, VIC 3000, Australia; Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, 207 Bouverie Street, Melbourne, VIC 3010, Australia; WHO Collaborating Centre for Reference and Research on Influenza at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3000, Australia; Fielding School of Public Health, University of California Los Angeles, 650 Charles E Young Dr South, Los Angeles, CA 90095, United States
| |
Collapse
|
25
|
Hurt A, Komadina N, Deng YM, Kaye M, Sullivan S, Subbarao K, Barr I. Detection of adamantane-sensitive influenza A(H3N2) viruses in Australia, 2017: a cause for hope? ACTA ACUST UNITED AC 2018; 22. [PMID: 29183552 PMCID: PMC5710658 DOI: 10.2807/1560-7917.es.2017.22.47.17-00731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
For over a decade virtually all A(H3N2) influenza viruses have been resistant to the adamantane class of antivirals. However, during the 2017 influenza season in Australia, 15/461 (3.3%) adamantane-sensitive A(H3N2) viruses encoding serine at residue 31 of the M2 protein were detected, more than the total number identified globally during the last 6 years. A return to wide circulation of adamantane-sensitive A(H3N2) viruses would revive the option of using these drugs for treatment and prophylaxis.
Collapse
Affiliation(s)
- Aeron Hurt
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Naomi Komadina
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Matthew Kaye
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sheena Sullivan
- School of Global and Population Health, The University of Melbourne, Victoria, Australia.,WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ian Barr
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| |
Collapse
|