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Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection. mBio 2020; 11:mBio.02880-19. [PMID: 31937643 PMCID: PMC6960286 DOI: 10.1128/mbio.02880-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Defective influenza virus particles generated during viral replication carry incomplete viral genomes and can interfere with the replication of competent viruses. These defective genomes are thought to modulate the disease severity and pathogenicity of an influenza virus infection. Different defective viral genomes also introduce another source of variation across a heterogeneous cell population. Evaluating the impact of defective virus genomes on host cell responses cannot be fully resolved at the population level, requiring single-cell transcriptional profiling. Here, we characterized virus and host transcriptomes in individual influenza virus-infected cells, including those of defective viruses that arise during influenza A virus infection. We established an association between defective virus transcription and host responses and validated interfering and immunostimulatory functions of identified dominant defective viral genome species in vitro. This study demonstrates the intricate effects of defective viral genomes on host transcriptional responses and highlights the importance of capturing host-virus interactions at the single-cell level. Virus and host factors contribute to cell-to-cell variation in viral infections and determine the outcome of the overall infection. However, the extent of the variability at the single-cell level and how it impacts virus-host interactions at a system level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. We observed substantial variability in viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show (i) a correlation between DVGs and virus-induced variation of the host transcriptional program and (ii) an association between differential inductions of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single-cell level improve our understanding of the complex virus-host interplay during influenza virus infection.
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202
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Kim GS, Kim TS, Son JS, Lai VD, Park JE, Wang SJ, Jheong WH, Mo IP. The difference of detection rate of avian influenza virus in the wild bird surveillance using various methods. J Vet Sci 2020; 20:e56. [PMID: 31565899 PMCID: PMC6769331 DOI: 10.4142/jvs.2019.20.e56] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/17/2019] [Accepted: 08/28/2019] [Indexed: 11/20/2022] Open
Abstract
Korea is located within the East Asian-Australian flyway of wild migratory birds during the fall and winter seasons. Consequently, the likelihood of introduction of numerous subtypes and pathotypes of the Avian influenza (AI) virus to Korea has been thought to be very high. In the current study, we surveyed wild bird feces for the presence of AI virus that had been introduced to Korea between September 2017 and February 2018. To identify and characterize the AI virus, we employed commonly used methods, namely, virus isolation (VI) via egg inoculation, real-time reverse transcription-polymerase chain reaction (rRT-PCR), conventional RT-PCR (cRT-PCR) and a newly developed next generation sequencing (NGS) approach. In this study, 124 out of 11,145 fresh samples of wild migratory birds tested were rRT-PCR positive; only 52.0% of VI positive samples were determined as positive by rRT-PCR from fecal supernatant. Fifty AI virus specimens were isolated from fresh fecal samples and typed. The cRT-PCR subtyping results mostly coincided with the NGS results, although NGS detected the presence of 11 HA genes and four NA genes that were not detected by cRT-PCR. NGS analysis confirmed that 12% of the identified viruses were mixed-subtypes which were not detected by cRT-PCR. Prevention of the occurrence of AI virus requires a workflow for rapid and accurate virus detection and verification. However, conventional methods of detection have some limitations. Therefore, different methods should be combined for optimal surveillance, and further studies are needed in aspect of the introduction and application of new methods such as NGS.
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Affiliation(s)
- Gang San Kim
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Tae Sik Kim
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Joo Sung Son
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Van Dam Lai
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Jung Eun Park
- Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea
| | - Seung Jun Wang
- Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea
| | - Weon Hwa Jheong
- Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea
| | - In Pil Mo
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea.
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203
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Reply to 'Reconciling disparate estimates of viral genetic diversity during human influenza infections'. Nat Genet 2020; 51:1301-1303. [PMID: 31406345 DOI: 10.1038/s41588-019-0486-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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204
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Chan M, Leung A, Hisanaga T, Pickering B, Griffin BD, Vendramelli R, Tailor N, Wong G, Bi Y, Babiuk S, Berhane Y, Kobasa D. H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Viruses 2020; 12:v12010065. [PMID: 31948040 PMCID: PMC7020020 DOI: 10.3390/v12010065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/23/2019] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
Abstract
Low pathogenic avian influenza (LPAI) H7N9 viruses have recently evolved to gain a polybasic cleavage site in the hemagglutinin (HA) protein, resulting in variants with increased lethality in poultry that meet the criteria for highly pathogenic avian influenza (HPAI) viruses. Both LPAI and HPAI variants can cause severe disease in humans (case fatality rate of ~40%). Here, we investigated the virulence of HPAI H7N9 viruses containing a polybasic HA cleavage site (H7N9-PBC) in mice. Inoculation of mice with H7N9-PBC did not result in observable disease; however, mice inoculated with a mouse-adapted version of this virus, generated by a single passage in mice, caused uniformly lethal disease. In addition to the PBC site, we identified three other mutations that are important for host-adaptation and virulence in mice: HA (A452T), PA (D347G), and PB2 (M483K). Using reverse genetics, we confirmed that the HA mutation was the most critical for increased virulence in mice. Our study identifies additional disease determinants in a mammalian model for HPAI H7N9 virus. Furthermore, the ease displayed by the virus to adapt to a new host highlights the potential for H7N9-PBC viruses to rapidly acquire mutations that may enhance their risk to humans or other animal species.
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Affiliation(s)
- Mable Chan
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada; (M.C.); (A.L.); (B.D.G.); (R.V.); (N.T.)
| | - Anders Leung
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada; (M.C.); (A.L.); (B.D.G.); (R.V.); (N.T.)
| | - Tamiko Hisanaga
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada; (T.H.); (B.P.); (S.B.); (Y.B.)
| | - Brad Pickering
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada; (T.H.); (B.P.); (S.B.); (Y.B.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
| | - Bryan D. Griffin
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada; (M.C.); (A.L.); (B.D.G.); (R.V.); (N.T.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
| | - Robert Vendramelli
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada; (M.C.); (A.L.); (B.D.G.); (R.V.); (N.T.)
| | - Nikesh Tailor
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada; (M.C.); (A.L.); (B.D.G.); (R.V.); (N.T.)
| | - Gary Wong
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Life Science Research Building 320 Yueyang Road, Xuhui District, Shanghai 200031, China;
- Département de microbiologie-infectiologie et d’immunologie, Université Laval, 1050 avenue de la Médecine, QC G1V 0A6, Canada
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China;
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada; (T.H.); (B.P.); (S.B.); (Y.B.)
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada; (T.H.); (B.P.); (S.B.); (Y.B.)
| | - Darwyn Kobasa
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada; (M.C.); (A.L.); (B.D.G.); (R.V.); (N.T.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
- Correspondence:
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205
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Flannery B, Kondor RJG, Chung JR, Gaglani M, Reis M, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Martin ET, Belongia EA, McLean HQ, Kim SS, Blanton L, Kniss K, Budd AP, Brammer L, Stark TJ, Barnes JR, Wentworth DE, Fry AM, Patel M. Spread of Antigenically Drifted Influenza A(H3N2) Viruses and Vaccine Effectiveness in the United States During the 2018-2019 Season. J Infect Dis 2020; 221:8-15. [PMID: 31665373 PMCID: PMC7325528 DOI: 10.1093/infdis/jiz543] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/16/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Increased illness due to antigenically drifted A(H3N2) clade 3C.3a influenza viruses prompted concerns about vaccine effectiveness (VE) and vaccine strain selection. We used US virologic surveillance and US Influenza Vaccine Effectiveness (Flu VE) Network data to evaluate consequences of this clade. METHODS Distribution of influenza viruses was described using virologic surveillance data. The Flu VE Network enrolled ambulatory care patients aged ≥6 months with acute respiratory illness at 5 sites. Respiratory specimens were tested for influenza by means of reverse-transcriptase polymerase chain reaction and were sequenced. Using a test-negative design, we estimated VE, comparing the odds of influenza among vaccinated versus unvaccinated participants. RESULTS During the 2018-2019 influenza season, A(H3N2) clade 3C.3a viruses caused an increasing proportion of influenza cases. Among 2763 Flu VE Network case patients, 1325 (48%) were infected with A(H1N1)pdm09 and 1350 (49%) with A(H3N2); clade 3C.3a accounted for 977 (93%) of 1054 sequenced A(H3N2) viruses. VE was 44% (95% confidence interval, 37%-51%) against A(H1N1)pdm09 and 9% (-4% to 20%) against A(H3N2); VE was 5% (-10% to 19%) against A(H3N2) clade 3C.3a viruses. CONCLUSIONS The predominance of A(H3N2) clade 3C.3a viruses during the latter part of the 2018-2019 season was associated with decreased VE, supporting the A(H3N2) vaccine component update for 2019-2020 northern hemisphere influenza vaccines.
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Affiliation(s)
- Brendan Flannery
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Jessie R Chung
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Manjusha Gaglani
- Baylor Scott & White Health, Texas A&M University College of Medicine, Temple, Texas
| | - Michael Reis
- Baylor Scott & White Health, Texas A&M University College of Medicine, Temple, Texas
| | - Richard K Zimmerman
- University of Pittsburgh Schools of Health Sciences and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mary Patricia Nowalk
- University of Pittsburgh Schools of Health Sciences and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Lisa A Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Arnold S Monto
- University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, Michigan
| | | | - Huong Q McLean
- Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Sara S Kim
- Oak Ridge Institute for Science and Education Fellowship Program, Oak Ridge, Tennessee
| | - Lenee Blanton
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Krista Kniss
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alicia P Budd
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lynnette Brammer
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas J Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alicia M Fry
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Manish Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
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206
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Li YT, Chen CC, Chang AM, Chao DY, Smith GJD. Co-circulation of both low and highly pathogenic avian influenza H5 viruses in current poultry epidemics in Taiwan. Virus Evol 2020; 6:veaa037. [PMID: 32661493 PMCID: PMC7326300 DOI: 10.1093/ve/veaa037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) A(H5) viruses belonging to clade 2.3.4.4c of the A/goose/Guangdong/1/96-like (Gs/GD) lineage caused severe global outbreaks in domestic birds from 2014 to 2015, that also represented the first incursions of Gs/GD viruses into Taiwan and the USA. However, few studies have investigated the circulation of clade 2.3.4.4c viruses after 2015. Here, we describe Gs/GD clade 2.3.4.4c and Mexican-like H5N2 viruses that were isolated in Taiwan during active surveillance conducted in chicken farms from February to March 2019. Phylogenetic analysis demonstrated two distinct genome constellations of the clade 2.3.4.4c H5 viruses, with the internal genes of one of the new genotypes closely related to a virus isolated from a pintail (Anas acuta) in Taiwan, providing the first direct evidence that migratory birds play a role in importing viruses into Taiwan. Our study also confirmed the co-circulation of Gs/GD clade 2.3.4.4c and Mexican-like H5 lineage viruses in Taiwan, presenting a rare case where Gs/GD viruses developed sustained transmission alongside another enzootic H5 lineage, raising the possibility that homosubtypic immunity may mask virus transmission, potentially frustrating detection, and the implementation of appropriate control measures. To eradicate H5 viruses from poultry in Taiwan, further studies on the effect of co-circulation in poultry of low pathogenic avian influenza and HPAI viruses are needed. Furthermore, only with continued surveillance efforts globally can we fully discern dispersal patterns and risk factors of virus transmission both to and within Taiwan.
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Affiliation(s)
- Yao-Tsun Li
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Chen-Chih Chen
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Ai-Mei Chang
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Day-Yu Chao
- College of Veterinary Medicine, Graduate Institute of Microbiology and Public Health, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, 169857, Singapore
- Global Health Institute, Duke University, Durham, NC 27710, USA
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207
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Lee DH. Complete Genome Sequencing of Influenza A Viruses Using Next-Generation Sequencing. Methods Mol Biol 2020; 2123:69-79. [PMID: 32170681 DOI: 10.1007/978-1-0716-0346-8_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, chain termination sequencing methods have been replaced by more efficient next-generation sequencing (NGS) methods. For influenza A, NGS allows for deep sequencing to characterize virus populations, efficient complete genome sequencing, and a non-sequence-dependent method to identify viral variants. There are numerous approaches to preparing samples for NGS and subsequent data processing methods that can be applied to influenza A sequencing. This chapter provides a brief overview of the process of NGS for influenza A and some useful bioinformatics tools for developing an NGS workflow for influenza A viruses.
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Affiliation(s)
- Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, The University of Connecticut, Storrs, CT, USA.
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208
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Armstrong GL, MacCannell DR, Taylor J, Carleton HA, Neuhaus EB, Bradbury RS, Posey JE, Gwinn M. Pathogen Genomics in Public Health. N Engl J Med 2019; 381:2569-2580. [PMID: 31881145 PMCID: PMC7008580 DOI: 10.1056/nejmsr1813907] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" through more effective investigations of outbreaks of foodborne illnesses, better-targeted tuberculosis control, and more timely and granular influenza surveillance to inform the selection of vaccine strains. In this article, we describe how public health agencies have been adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given the ongoing development in sequencing and sequencing-related technologies.
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Affiliation(s)
- Gregory L Armstrong
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Duncan R MacCannell
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Jill Taylor
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Heather A Carleton
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Elizabeth B Neuhaus
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Richard S Bradbury
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - James E Posey
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Marta Gwinn
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
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Abolnik C. Outbreaks of Clade 2.3.4.4 H5N8 highly pathogenic avian influenza in 2018 in the northern regions of South Africa were unrelated to those of 2017. Transbound Emerg Dis 2019; 67:1371-1381. [PMID: 31833671 DOI: 10.1111/tbed.13448] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 11/28/2022]
Abstract
Asian-origin H5N8 highly pathogenic avian influenza (HPAI) viruses of the H5 Goose/Guangdong/96 lineage, clade 2.3.4.4 group B, reached South Africa by June 2017. By the end of that year, 5.4 million layers and broiler chickens died or were culled, with total losses in the poultry industry estimated at US$ 140 million, and thousands of exotic birds in zoological collections, endangered endemic species and backyard poultry and pet birds also perished. The 2017 H5N8 HPAI outbreaks were characterized by two distinct spatial clusters, each associated with specific reassortant viral genotypes. Genotypes 1, 2, 3 and 5 were restricted to the northern regions, spanning the provinces of Limpopo, Gauteng, North West, Mpumalanga, KwaZulu-Natal and Free State. The second, much larger cluster of outbreaks was in the south, in the Western and Eastern Cape provinces, wherein 2017 and 2018 outbreaks were caused solely by genotype 4. The last confirmed case of H5N8 HPAI in the northern region in 2017 was in early October, and the viruses seemed to disappear over the summer. However, starting in mid-February 2018, H5N8 HPAI outbreaks resurged in the north. Viruses from two of the eight outbreaks were sequenced, one from an outbreak in quails (Coturnix japonica) in the North West Province, and another from commercial pullets in the Gauteng province. Phylogenetic analysis identified the viruses as a distinct sixth genotype that was most likely a new introduction to South Africa in early 2018.
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Affiliation(s)
- Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
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210
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Nirmala J, Bender JB, Lynfield R, Yang M, Rene Culhane M, Nelson MI, Sreevatsan S, Torremorell M. Genetic diversity of influenza A viruses circulating in pigs between winter and summer in a Minnesota live animal market. Zoonoses Public Health 2019; 67:243-250. [PMID: 31868300 DOI: 10.1111/zph.12679] [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: 12/18/2018] [Revised: 10/07/2019] [Accepted: 11/19/2019] [Indexed: 11/26/2022]
Abstract
There has been little surveillance of influenza A viruses (IAVs) circulating in swine at live animal markets, particularly in the United States. To address this gap, we conducted active surveillance of IAVs in pigs, the air, and the environment during a summer and winter season in a live animal market in St. Paul, Minnesota, that had been epidemiologically associated with swine-origin influenza cases in humans previously. High rates of IAV were detected by PCR in swine lungs and oral fluids during both summer and winter seasons. Rates of IAV detection by PCR in the air were similar during summer and winter, although rates of successful virus isolation in the air were lower during summer than in winter (26% and 67%, respectively). H3N2 was the most prevalent subtype in both seasons, followed by H1N2. Genetically diverse viruses with multiple gene constellations were isolated from both winter and summer, with a total of 19 distinct genotypes identified. Comparative phylogenetic analysis of all eight segments of 40 virus isolates from summer and 122 isolates from winter revealed that the summer and winter isolates were genetically distinct, indicating IAVs are not maintained in the market, but rather are re-introduced, likely from commercial swine. These findings highlight the extent of IAV genetic diversity circulating in swine in live animal markets, even during summer months, and the ongoing risk to humans.
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Affiliation(s)
- Jayaveeramuthu Nirmala
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Jeff B Bender
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.,School of Public Health, Environmental Health Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ruth Lynfield
- Minnesota State Health Department, St. Paul, MN, USA
| | - My Yang
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Marie Rene Culhane
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Martha Irene Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Montserrat Torremorell
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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211
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Baranovskaya I, Sergeeva M, Fadeev A, Kadirova R, Ivanova A, Ramsay E, Vasin A. Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection. Virol J 2019; 16:162. [PMID: 31864377 PMCID: PMC6925897 DOI: 10.1186/s12985-019-1271-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/13/2019] [Indexed: 11/10/2022] Open
Abstract
RNA secondary structures play a key role in splicing, gene expression, microRNA biogenesis, RNA editing, and other biological processes. The importance of RNA structures has been demonstrated in the life cycle of RNA-containing viruses, including the influenza virus. At least two regions of conserved secondary structure in NS segment (+) RNA are predicted to vary among influenza virus strains with respect to thermodynamic stability; both fall in the NS1 open reading frame. The NS1 protein is involved in multiple virus-host interaction processes, and its main function is to inhibit the cellular immune response to viral infection. Using a reverse genetics approach, four influenza virus strains were constructed featuring mutations that have different effects on RNA secondary structure. Growth curve experiments and ELISA data show that, at least in the first viral replication cycle, mutations G123A and A132G affecting RNA structure in the (82-148) NS RNA region influence NS1 protein expression.
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Affiliation(s)
- Irina Baranovskaya
- Smorodintsev Research Institute of Influenza, 15/17 Prof. Popova Str, Saint Petersburg, 197376, Russia. .,Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str, Saint Petersburg, 195251, Russia.
| | - Mariia Sergeeva
- Smorodintsev Research Institute of Influenza, 15/17 Prof. Popova Str, Saint Petersburg, 197376, Russia.,Global Viral Network, 725 West Lombard St Room S413, Baltimore, MD, 21201, USA
| | - Artem Fadeev
- Smorodintsev Research Institute of Influenza, 15/17 Prof. Popova Str, Saint Petersburg, 197376, Russia
| | - Renata Kadirova
- Smorodintsev Research Institute of Influenza, 15/17 Prof. Popova Str, Saint Petersburg, 197376, Russia
| | - Anna Ivanova
- Smorodintsev Research Institute of Influenza, 15/17 Prof. Popova Str, Saint Petersburg, 197376, Russia
| | - Edward Ramsay
- Smorodintsev Research Institute of Influenza, 15/17 Prof. Popova Str, Saint Petersburg, 197376, Russia
| | - Andrey Vasin
- Smorodintsev Research Institute of Influenza, 15/17 Prof. Popova Str, Saint Petersburg, 197376, Russia.,Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str, Saint Petersburg, 195251, Russia.,Global Viral Network, 725 West Lombard St Room S413, Baltimore, MD, 21201, USA
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212
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Lestari, Wibawa H, Lubis EP, Dharmawan R, Rahayu RA, Mulyawan H, Charoenkul K, Nasamran C, Poermadjaja B, Amonsin A. Co-circulation and characterization of HPAI-H5N1 and LPAI-H9N2 recovered from a duck farm, Yogyakarta, Indonesia. Transbound Emerg Dis 2019; 67:994-1007. [PMID: 31770478 DOI: 10.1111/tbed.13434] [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: 06/12/2019] [Revised: 10/30/2019] [Accepted: 11/18/2019] [Indexed: 01/27/2023]
Abstract
In July 2016, an avian influenza outbreak in duck farms in Yogyakarta province was reported to Disease Investigation Center (DIC), Wates, Indonesia, with approximately 1,000 ducks died or culled. In this study, two avian influenza (AI) virus subtypes, A/duck/Bantul/04161291-OR/2016 (H5N1) and A/duck/Bantul/04161291-OP/2016 (H9N2) isolated from ducks in the same farm during an AI outbreak in Bantul district, Yogyakarta province, were sequenced and characterized. Our results showed that H5N1 virus was closely related to the highly pathogenic AI (HPAI) H5N1 of clade 2.3.2.1c, while the H9N2 virus was clustered with LPAI viruses from China, Vietnam and Indonesia H9N2 (CVI lineage). Genetic analysis revealed virulence characteristics for both in avian and in mammalian species. In summary, co-circulation of HPAI-H5N1 of clade 2.3.2.1c and LPAI-H9N2 was identified in a duck farm during an AI outbreak in Yogyakarta province, Indonesia. Our findings raise a concern of the potential risk of the viruses, which could increase viral transmission and/or threat to human health. Routine surveillance of avian influenza viruses should be continuously conducted to understand the dynamic and diversity of the viruses for influenza prevention and control in Indonesia and SEA region.
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Affiliation(s)
- Lestari
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Elly Puspasari Lubis
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Rama Dharmawan
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Rina Astuti Rahayu
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Herdiyanto Mulyawan
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Kamonpan Charoenkul
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Chanakarn Nasamran
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Bagoes Poermadjaja
- Disease Investigation Center Wates Yogyakarta, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture Indonesia, Yogyakarta, Indonesia
| | - Alongkorn Amonsin
- Department of Veterinary Public Health, Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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213
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Diversity of A(H5N1) clade 2.3.2.1c avian influenza viruses with evidence of reassortment in Cambodia, 2014-2016. PLoS One 2019; 14:e0226108. [PMID: 31815962 PMCID: PMC6901219 DOI: 10.1371/journal.pone.0226108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022] Open
Abstract
In Cambodia, highly pathogenic avian influenza A(H5N1) subtype viruses circulate endemically causing poultry outbreaks and zoonotic human cases. To investigate the genomic diversity and development of endemicity of the predominantly circulating clade 2.3.2.1c A(H5N1) viruses, we characterised 68 AIVs detected in poultry, the environment and from a single human A(H5N1) case from January 2014 to December 2016. Full genomes were generated for 42 A(H5N1) viruses. Phylogenetic analysis shows that five clade 2.3.2.1c genotypes, designated KH1 to KH5, were circulating in Cambodia during this period. The genotypes arose through multiple reassortment events with the neuraminidase (NA) and internal genes belonging to H5N1 clade 2.3.2.1a, clade 2.3.2.1b or A(H9N2) lineages. Phylogenies suggest that the Cambodian AIVs were derived from viruses circulating between Cambodian and Vietnamese poultry. Molecular analyses show that these viruses contained the hemagglutinin (HA) gene substitutions D94N, S133A, S155N, T156A, T188I and K189R known to increase binding to the human-type α2,6-linked sialic acid receptors. Two A(H5N1) viruses displayed the M2 gene S31N or A30T substitutions indicative of adamantane resistance, however, susceptibility testing towards neuraminidase inhibitors (oseltamivir, zanamivir, lananmivir and peramivir) of a subset of thirty clade 2.3.2.1c viruses showed susceptibility to all four drugs. This study shows that A(H5N1) viruses continue to reassort with other A(H5N1) and A(H9N2) viruses that are endemic in the region, highlighting the risk of introduction and emergence of novel A(H5N1) genotypes in Cambodia.
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214
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Hemida MG, Chu D, Abdelaziz A, Alnaeem A, Chan SMS, Peiris M. Molecular characterisation of an avian influenza (H5N8) outbreak in backyard flocks in Al Ahsa, Eastern Saudi Arabia, 2017-2018. Vet Rec Open 2019; 6:e000362. [PMID: 31897300 PMCID: PMC6924712 DOI: 10.1136/vetreco-2019-000362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/28/2022] Open
Abstract
Background Avian influenza viruses are still causing major concern not only to the poultry industry but also to human health across the globe. The live poultry markets and the small-scale local breeding of various species of birds in backyards are still playing important roles in the sustainability of most virulent influenza viruses, especially H5N8. Methods The authors investigated an outbreak of highly pathogenic avian influenza H5N8 in backyard flocks in Al Ahsa, Eastern Saudi Arabia that occurred in 2017–2018. Results A range of poultry including chickens, ostriches, ducks, pigeons and turkeys were clinically affected. Phylogenetic analysis suggested that this was a common source outbreak caused by a virus closely related to H5N8 viruses causing outbreaks elsewhere in Saudi Arabia in early 2018. Conclusions Small backyard flocks are still contributing to the epidemiology and transmission of H5N8.
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Affiliation(s)
- Maged G Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia.,Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr el-Sheikh, Egypt
| | - Daniel Chu
- School of Public Health, The University of Hong Kong, Hong Kong
| | - Adel Abdelaziz
- Veterinary Education Hospital, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Abdelmohsen Alnaeem
- College of Veterinary Medicine, King Faisal University, Al-Hasa, Saudi Arabia
| | | | - M Peiris
- School of Public Health, The University of Hong Kong, Hong Kong
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215
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Wasik BR, Voorhees IEH, Barnard KN, Alford-Lawrence BK, Weichert WS, Hood G, Nogales A, Martínez-Sobrido L, Holmes EC, Parrish CR. Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. J Virol 2019; 93:e01039-19. [PMID: 31511393 PMCID: PMC6854484 DOI: 10.1128/jvi.01039-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/09/2019] [Indexed: 12/19/2022] Open
Abstract
Influenza A viruses have regularly jumped to new host species to cause epidemics or pandemics, an evolutionary process that involves variation in the viral traits necessary to overcome host barriers and facilitate transmission. Mice are not a natural host for influenza virus but are frequently used as models in studies of pathogenesis, often after multiple passages to achieve higher viral titers that result in clinical disease such as weight loss or death. Here, we examine the processes of influenza A virus infection and evolution in mice by comparing single nucleotide variations of a human H1N1 pandemic virus, a seasonal H3N2 virus, and an H3N2 canine influenza virus during experimental passage. We also compared replication and sequence variation in wild-type mice expressing N-glycolylneuraminic acid (Neu5Gc) with those seen in mice expressing only N-acetylneuraminic acid (Neu5Ac). Viruses derived from plasmids were propagated in MDCK cells and then passaged in mice up to four times. Full-genome deep sequencing of the plasmids, cultured viruses, and viruses from mice at various passages revealed only small numbers of mutational changes. The H3N2 canine influenza virus showed increases in frequency of sporadic mutations in the PB2, PA, and NA segments. The H1N1 pandemic virus grew well in mice, and while it exhibited the maintenance of some minority mutations, there was no clear evidence for adaptive evolution. The H3N2 seasonal virus did not establish in the mice. Finally, there were no clear sequence differences associated with the presence or absence of Neu5Gc.IMPORTANCE Mice are commonly used as a model to study the growth and virulence of influenza A viruses in mammals but are not a natural host and have distinct sialic acid receptor profiles compared to humans. Using experimental infections with different subtypes of influenza A virus derived from different hosts, we found that evolution of influenza A virus in mice did not necessarily proceed through the linear accumulation of host-adaptive mutations, that there was variation in the patterns of mutations detected in each repetition, and that the mutation dynamics depended on the virus examined. In addition, variation in the viral receptor, sialic acid, did not affect influenza virus evolution in this model. Overall, our results show that while mice provide a useful animal model for influenza virus pathology, host passage evolution will vary depending on the specific virus tested.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Karen N Barnard
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brynn K Alford-Lawrence
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Wendy S Weichert
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Grace Hood
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- College of Veterinary Medicine, University of Queensland, Gatton, Queensland, Australia
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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216
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Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza. Nat Commun 2019; 10:5310. [PMID: 31757953 PMCID: PMC6874648 DOI: 10.1038/s41467-019-13287-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022] Open
Abstract
The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.
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217
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Nearly Complete Genome Sequence of Human Influenza Virus Strain A/Almaty/6327/2014 (H1N1) from Central Asia. Microbiol Resour Announc 2019; 8:8/47/e00527-19. [PMID: 31753934 PMCID: PMC6872876 DOI: 10.1128/mra.00527-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An influenza virus strain, A/Almaty/6327/2014 (H1N1), was isolated in Almaty (in southeastern Kazakhstan) during a human population surveillance study in 2014. Here, we present the nearly complete genome sequence of this epidemic strain that was compared to the postpandemic variants of A(H1N1)pdm09. An influenza virus strain, A/Almaty/6327/2014 (H1N1), was isolated in Almaty (in southeastern Kazakhstan) during a human population surveillance study in 2014. Here, we present the nearly complete genome sequence of this epidemic strain that was compared to the postpandemic variants of A(H1N1)pdm09.
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218
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Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Abdo Z. Predicting whole genome sequencing success for archived avian influenza virus (Orthomyxoviridae) samples using real-time and droplet PCRs. J Virol Methods 2019; 276:113777. [PMID: 31730870 DOI: 10.1016/j.jviromet.2019.113777] [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: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
Long-term viral archives are valuable sources of research data. Each archive can store hundreds of thousands of diverse sample types. In the current era of whole genome sequencing, archived samples become a rich source of evolutionary and epidemiological data that can span years, and even decades. However, the ability to obtain high quality viral whole genome sequences from samples of various types, age, and quality is inconsistent. A minimum quality threshold that helps predict the best success of obtaining high quality genomic sequences for both recent and archived samples is highly valuable. Real-time reverse transcription PCR (rrt-PCR) and droplet digital PCR (ddPCR) are useful tools to evaluate nucleic acid integrity. We hypothesized that diagnostic rrt-PCR and ddPCR data for avian influenza virus (AIV) can predict viral whole genome sequencing success. To test this hypothesis we used RNA extracted from cloacal and oropharyngeal swabs stored in the USDA-APHIS National Wildlife Disease Program Wildlife Tissue Archive. We determined that a specific rrt-PCR Cq value or ddPCR copies/μL resulted in recovery of complete sequences of all eight AIV gene segments. We used logistic regression to estimate probabilities of whole genome recovery at 0.95 (Cq = 15, copies/μL = 49,350), 0.75 (Cq = 24, copies/μL = 16,800), 0.50 (Cq = 29, copies/μL = <1), and 0.25 (Cq = 235, copies/μL = <1). We also identified values at which we predictably recovered HA and NA segments for diagnosing subtypes (Cq = 27.29; copies/μL = 757.50). This approach will allow researchers to assess the potential success of AIV whole genome recovery from diagnostic samples collected in routine AIV surveillance.
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Affiliation(s)
- Matthew W Hopken
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Theodore Anderson
- Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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219
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Cobey S, Gouma S, Parkhouse K, Chambers BS, Ertl HC, Schmader KE, Halpin RA, Lin X, Stockwell TB, Das SR, Landon E, Tesic V, Youngster I, Pinsky BA, Wentworth DE, Hensley SE, Grad YH. Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013. Clin Infect Dis 2019; 67:327-333. [PMID: 29471464 PMCID: PMC6051447 DOI: 10.1093/cid/ciy097] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 02/03/2018] [Indexed: 12/28/2022] Open
Abstract
Background Influenza vaccination aims to prevent infection by influenza virus and reduce associated morbidity and mortality; however, vaccine effectiveness (VE) can be modest, especially for subtype A(H3N2). Low VE has been attributed to mismatches between the vaccine and circulating influenza strains and to the vaccine’s elicitation of protective immunity in only a subset of the population. The low H3N2 VE in the 2012–2013 season was attributed to egg-adaptive mutations that created antigenic mismatch between the actual vaccine strain (IVR-165) and both the intended vaccine strain (A/Victoria/361/2011) and the predominant circulating strains (clades 3C.2 and 3C.3). Methods We investigated the basis of low VE in 2012–2013 by determining whether vaccinated and unvaccinated individuals were infected by different viral strains and by assessing the serologic responses to IVR-165, A/Victoria/361/2011, and 3C.2 and 3C.3 strains in an adult cohort before and after vaccination. Results We found no significant genetic differences between the strains that infected vaccinated and unvaccinated individuals. Vaccination increased titers to A/Victoria/361/2011 and 3C.2 and 3C.3 representative strains as much as to IVR-165. These results are consistent with the hypothesis that vaccination boosted cross-reactive immune responses instead of specific responses against unique vaccine epitopes. Only approximately one-third of the cohort achieved a ≥4-fold increase in titer. Conclusions In contrast to analyses based on ferret studies, low H3N2 VE in 2012–2013 in adults does not appear to be due to egg adaptation of the vaccine strain. Instead, low VE might have been caused by low vaccine immunogenicity in a subset of the population.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology & Evolution, University of Chicago, Illinois
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Kaela Parkhouse
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Benjamin S Chambers
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Hildegund C Ertl
- Division of Geriatrics, Duke University Medical Center, North Carolina.,Geriatric Research, Education, and Clinical Center, Durham VA Medical Center, North Carolina
| | - Kenneth E Schmader
- Division of Geriatrics, Duke University Medical Center, North Carolina.,Geriatric Research, Education, and Clinical Center, Durham VA Medical Center, North Carolina
| | - Rebecca A Halpin
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Xudong Lin
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Timothy B Stockwell
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Suman R Das
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Emily Landon
- Department of Medicine, University of Chicago, Illinois
| | - Vera Tesic
- Department of Pathology, University of Chicago, Illinois
| | - Ilan Youngster
- Division of Pediatrics and the Center for Microbiome Research, Assaf Harofeh Medical Center, Tel Aviv University, Israel.,Division of Infectious Diseases, Boston Children's Hospital, Massachusetts
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, California.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, California
| | - David E Wentworth
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, Maryland
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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220
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Alghamdi A, Hassan AM, Tolah AM, Alamari SS, Alzahrani AA, Alsaaidi GA, Abujamel TS, Azhar EI, Hashem AM. Molecular Evidence of Influenza A Virus Circulation in African Dromedary Camels Imported to Saudi Arabia, 2017-2018. Open Forum Infect Dis 2019; 6:ofz370. [PMID: 31660338 PMCID: PMC6767964 DOI: 10.1093/ofid/ofz370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/13/2019] [Indexed: 01/11/2023] Open
Abstract
Little is known about influenza A viruses in dromedaries. Here, we detected influenza A viral RNA in 11 specimens (1.7 %) out of 665 nasal swabs collected from dromedaries between 2017 and 2018 in Saudi Arabia. Positive samples were detected only in imported camels from Sudan and Djibouti but not local ones. Partial genome sequencing indicates a close relationship to 2009–2019 human/swine influenza A H1N1 isolates from different countries, suggesting possible interspecies transmission. Taken together, dromedaries could represent a potentially unrecognized permissive host for these viruses, highlighting the need for enhanced surveillance in animals to aid implementation of one-health strategies.
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Affiliation(s)
- Abdulaziz Alghamdi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sawsan S Alamari
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulrahman A Alzahrani
- Directorate of Agriculture, Ministry of Environment, Water, and Agriculture, Makkah Region, Saudi Arabia
| | - Ghaleb A Alsaaidi
- Directorate of Agriculture, Ministry of Environment, Water, and Agriculture, Makkah Region, Saudi Arabia
| | - Turki S Abujamel
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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221
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Favié LM, Murk JL, Meijer A, Nijstad AL, van Maarseveen EM, Sikma MA. Pharmacokinetics of favipiravir during continuous venovenous haemofiltration in a critically ill patient with influenza. Antivir Ther 2019; 23:457-461. [PMID: 29185991 DOI: 10.3851/imp3210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
Favipiravir is a novel antiviral drug approved for influenza treatment in Japan. Little is known about favipiravir pharmacokinetics in critically ill patients. Here, we report a patient with influenza treated with favipiravir and undergoing continuous venovenous haemofiltration (CVVH) on the Intensive Care Unit of a tertiary hospital in the Netherlands. Pharmacokinetic analyses showed increased clearance and decreased plasma levels compared to healthy volunteers. CVVH has no clinically relevant contribution to total clearance. Despite susceptibility to favipiravir, the influenza virus was not cleared. A multi-disciplinary approach is needed to ensure optimal favipiravir treatment in critically ill patients.
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Affiliation(s)
- Laurent Ma Favié
- Department of Clinical Pharmacy, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jean-Luc Murk
- Laboratory of Medical Microbiology and Immunology, St Elisabeth Hospital Tilburg, Tilburg, the Netherlands
| | - Adam Meijer
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - A Laura Nijstad
- Department of Clinical Pharmacy, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Erik M van Maarseveen
- Department of Clinical Pharmacy, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Maaike A Sikma
- Intensive Care, University Medical Center Utrecht, Utrecht, the Netherlands.,Dutch Poisons Information Center, University Medical Center Utrecht, Utrecht, the Netherlands
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Zhu W, Dong J, Zhang Y, Yang L, Li X, Chen T, Zhao X, Wei H, Bo H, Zeng X, Huang W, Li Z, Tang J, Zhou J, Gao R, Xin L, Yang J, Zou S, Chen W, Liu J, Shu Y, Wang D. A Gene Constellation in Avian Influenza A (H7N9) Viruses May Have Facilitated the Fifth Wave Outbreak in China. Cell Rep 2019; 23:909-917. [PMID: 29669294 DOI: 10.1016/j.celrep.2018.03.081] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/26/2018] [Accepted: 03/17/2018] [Indexed: 01/11/2023] Open
Abstract
The 2016-2017 epidemic of influenza A (H7N9) virus in China prompted concern that a genetic change may underlie increased virulence. Based on an evolutionary analysis of H7N9 viruses from all five outbreak waves, we find that additional subclades of the H7 and N9 genes have emerged. Our analysis indicates that H7N9 viruses inherited NP genes from co-circulating H7N9 instead of H9N2 viruses. Genotypic diversity among H7N9 viruses increased following wave I, peaked during wave III, and rapidly deceased thereafter with minimal diversity in wave V, suggesting that the viruses entered a relatively stable evolutionary stage. The ZJ11 genotype caused the majority of human infections in wave V. We suggest that the largest outbreak of wave V may be due to a constellation of genes rather than a single mutation. Therefore, continuous surveillance is necessary to minimize the threat of H7N9 viruses.
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Affiliation(s)
- Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Jie Dong
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Ye Zhang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Tao Chen
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Xiang Zhao
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Hejiang Wei
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Xiaoxu Zeng
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Weijuan Huang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Zi Li
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Jing Tang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Jianfang Zhou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Rongbao Gao
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Li Xin
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Jing Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Shumei Zou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Wenbing Chen
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong 510275, P.R. China.
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, P.R. China.
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Zou X, Guo Q, Zhang W, Chen H, Bai W, Lu B, Zhang W, Fan Y, Liu C, Wang Y, Zhou F, Cao B. Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. J Infect Dis 2019; 218:586-594. [PMID: 29688498 PMCID: PMC6047446 DOI: 10.1093/infdis/jiy217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/22/2018] [Indexed: 11/25/2022] Open
Abstract
Background Signature amino acids of H7N9 influenza A virus play critical roles in human adaption and pathogenesis, but their dynamic variation is unknown during disease development. Methods We sequentially collected respiratory samples from H7N9 patients at different timepoints and applied next-generation sequencing (NGS) to the whole genome of the H7N9 virus to investigate the variation at signature sites. Results A total of 11 patients were involved, from whom 29 samples were successfully sequenced, including samples from multiple timepoints in 9 patients. Neuraminidase (NA) R292K, basic polymerase 2 (PB2) E627K, and D701N were the 3 most dynamic mutations. The oseltamivir resistance-related NA R292K mutation was present in 9 samples from 5 patients, including 1 sample obtained before antiviral therapy. In all patients with the NA 292K mutation, the oseltamivir-sensitive 292R genotype persisted and was not eliminated by antiviral treatment. The PB2 E627K substitution was present in 18 samples from 8 patients, among which 12 samples demonstrated a mixture of E/K and the 627K frequency exhibited dynamic variation. Dual D701N and E627K mutations emerged but failed to achieve predominance in any of the samples. Conclusions Signature amino acids in PB2 and NA demonstrated high polymorphism and dynamic variation within individual patients during H7N9 virus infection.
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Affiliation(s)
- Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
| | - Qiang Guo
- Department of Respiratory, Emergency and Critical Care Medicine, First Affiliated Hospital of Soochow University, Jiangsu
| | - Wei Zhang
- First Affiliated Hospital of Nanchang University, Jiangxi, People's Republic of China
| | - Hui Chen
- Department of Respiratory, Emergency and Critical Care Medicine, First Affiliated Hospital of Soochow University, Jiangsu
| | - Wei Bai
- First Affiliated Hospital of Nanchang University, Jiangxi, People's Republic of China
| | - Binghuai Lu
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
| | - Wang Zhang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
| | - Yanyan Fan
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
| | - Chao Liu
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
| | - Fei Zhou
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing
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Barman S, Turner JCM, Hasan MK, Akhtar S, El-Shesheny R, Franks J, Walker D, Seiler P, Friedman K, Kercher L, Jeevan T, McKenzie P, Webby RJ, Webster RG, Feeroz MM. Continuing evolution of highly pathogenic H5N1 viruses in Bangladeshi live poultry markets. Emerg Microbes Infect 2019; 8:650-661. [PMID: 31014196 PMCID: PMC6493222 DOI: 10.1080/22221751.2019.1605845] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Since November 2008, we have conducted active avian influenza surveillance in Bangladesh. Clades 2.2.2, 2.3.4.2, and 2.3.2.1a of highly pathogenic avian influenza H5N1 viruses have all been identified in Bangladeshi live poultry markets (LPMs), although, since the end of 2014, H5N1 viruses have been exclusively from clade 2.3.2.1a. In June 2015, a new reassortant H5N1 virus (H5N1-R1) from clade 2.3.2.1a was identified, containing haemagglutinin, neuraminidase, and matrix genes of H5N1 viruses circulating in Bangladesh since 2011, plus five other genes of Eurasian-lineage low pathogenic avian influenza A (LPAI) viruses. Here we report the status of circulating avian influenza A viruses in Bangladeshi LPMs from March 2016 to January 2018. Until April 2017, H5N1 viruses exclusively belonged to H5N1-R1 clade 2.3.2.1a. However, in May 2017, we identified another reassortant H5N1 (H5N1-R2), also of clade 2.3.2.1a, wherein the PA gene segment of H5N1-R1 was replaced by that of another Eurasian-lineage LPAI virus related to A/duck/Bangladesh/30828/2016 (H3N8), detected in Bangladeshi LPM in September 2016. Currently, both reassortant H5N1-R1 and H5N1-R2 co-circulate in Bangladeshi LPMs. Furthermore, some LPAI viruses isolated from LPMs during 2016–2017 were closely related to those from ducks in free-range farms and wild birds in Tanguar haor, a wetland region of Bangladesh where ducks have frequent contact with migratory birds. These data support a hypothesis where Tanguar haor-like ecosystems provide a mechanism for movement of LPAI viruses to LPMs where reassortment with poultry viruses occurs adding to the diversity of viruses at this human-animal interface.
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Affiliation(s)
- Subrata Barman
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Jasmine C M Turner
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - M Kamrul Hasan
- b Department of Zoology , Jahangirnagar University , Dhaka , Bangladesh
| | - Sharmin Akhtar
- b Department of Zoology , Jahangirnagar University , Dhaka , Bangladesh
| | - Rabeh El-Shesheny
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA.,c Center of Scientific Excellence for Influenza Viruses , National Research Centre , Giza , Egypt
| | - John Franks
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - David Walker
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Patrick Seiler
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Kimberly Friedman
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Lisa Kercher
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Trushar Jeevan
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Pamela McKenzie
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Richard J Webby
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Robert G Webster
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Mohammed M Feeroz
- b Department of Zoology , Jahangirnagar University , Dhaka , Bangladesh
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225
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Sealy JE, Fournie G, Trang PH, Dang NH, Sadeyen JR, Thanh TL, van Doorn HR, Bryant JE, Iqbal M. Poultry trading behaviours in Vietnamese live bird markets as risk factors for avian influenza infection in chickens. Transbound Emerg Dis 2019; 66:2507-2516. [PMID: 31357255 PMCID: PMC6899644 DOI: 10.1111/tbed.13308] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 01/16/2023]
Abstract
Vietnamese poultry are host to co‐circulating subtypes of avian influenza viruses, including H5N1 and H9N2, which pose a great risk to poultry productivity and to human health. AIVs circulate throughout the poultry trade network in Vietnam, with live bird markets being an integral component to this network. Traders at LBMs exhibit a variety of trading practices, which may influence the transmission of AIVs. We identified trading practices that impacted on AIV prevalence in chickens marketed in northern Vietnamese LBMs. We generated sequencing data for 31 H9N2 and two H5N6 viruses. Viruses isolated in the same LBM or from chickens sourced from the same province were genetically closer than viruses isolated in different LBMs or from chickens sourced in different provinces. The position of a vendor in the trading network impacted on their odds of having AIV‐infected chickens. Being a retailer and purchasing chickens from middlemen was associated with increased odds of infection, whereas odds decreased if vendors purchased chickens directly from large farms. Odds of infection were also higher for vendors having a greater volume of ducks unsold per day. These results indicate how the spread of AIVs is influenced by the structure of the live poultry trading network.
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Affiliation(s)
- Joshua E Sealy
- The Pirbright Institute, Pirbright, Woking, UK.,The Royal Veterinary College, London, UK
| | | | - Pham Hong Trang
- The National Centre for Veterinary Diagnostics, Hanoi, Vietnam
| | | | | | - To Long Thanh
- The National Centre for Veterinary Diagnostics, Hanoi, Vietnam.,The Department of Animal Health, Hanoi, Vietnam
| | | | - Juliet E Bryant
- Laboratory of Emerging Pathogens, Fondation Mérieux, Lyon, France
| | - Munir Iqbal
- The Pirbright Institute, Pirbright, Woking, UK
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226
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Comparison of nucleic acid extraction methods for next-generation sequencing of avian influenza A virus from ferret respiratory samples. J Virol Methods 2019; 270:95-105. [DOI: 10.1016/j.jviromet.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/13/2019] [Accepted: 04/15/2019] [Indexed: 11/13/2022]
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227
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Świętoń E, Olszewska-Tomczyk M, Giza A, Śmietanka K. Evolution of H9N2 low pathogenic avian influenza virus during passages in chickens. INFECTION GENETICS AND EVOLUTION 2019; 75:103979. [PMID: 31351233 DOI: 10.1016/j.meegid.2019.103979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022]
Abstract
The process of avian influenza virus (AIV) evolution in a new host was investigated in the experiment in which ten serial passages of a turkey-derived H9N2 AIV were carried out in specific pathogen free chickens (3 birds/group) inoculated by oculonasal route. Oropharyngeal swabs collected 3 days post infection were used for inoculation of birds in the next passage and subjected to analysis using deep sequencing. In total, eight mutations in the consensus sequence were found in the viral pool derived from the 10th passage: four mutations (2 in PB1 and 2 in HA) were present in the inoculum as minority variants while the other four (2 in NP, 1 in PA and 1 in HA) emerged during the passages in chickens. The detected fluctuations in the genetic heterogeneity of viral pools from consecutive passages were most likely attributed to the selective bottleneck. The genes known for bearing molecular determinants of the AIV host specificity (HA, PB2, PB1, PA) contributed most to the overall virus diversity. In some cases, a fast selection of the novel variant was noticed. For example, the amino-acid substitution N337K in the haemagglutinin (HA) cleavage site region detected in the 6th passage as low frequency variant had undergone rapid selection and became predominant in the 7th passage. Interestingly, detection of identical mutation in the field H9N2 isolates 1-year apart suggests that this substitution might provide the virus with a selective advantage. However, the role of specific mutations and their influence on the virus adaptation or fitness are mostly unknown and require further investigations.
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Affiliation(s)
- Edyta Świętoń
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland.
| | - Monika Olszewska-Tomczyk
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Aleksandra Giza
- Department of Omics Analyses, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Krzysztof Śmietanka
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
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228
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Genome Sequences of an H9N2 Avian Influenza Virus Strain Found in Pakistan in 2017. Microbiol Resour Announc 2019; 8:8/28/e00433-19. [PMID: 31296678 PMCID: PMC6624761 DOI: 10.1128/mra.00433-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In 2017, we isolated an H9N2 avian influenza virus in Pakistan. Genetic analysis showed that the A/chicken/Kasoor/SI36/2017(H9N2) isolate belongs to the G1 lineage. In addition, this isolate possesses mammalian host-specific mutations which could possibly favor interspecies transmission, suggesting that Pakistani H9N2 viruses are still potentially infectious for mammals. In 2017, we isolated an H9N2 avian influenza virus in Pakistan. Genetic analysis showed that the A/chicken/Kasoor/SI36/2017(H9N2) isolate belongs to the G1 lineage. In addition, this isolate possesses mammalian host-specific mutations which could possibly favor interspecies transmission, suggesting that Pakistani H9N2 viruses are still potentially infectious for mammals.
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229
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Prokopyeva EA, Zinserling VA, Bae YC, Kwon Y, Kurskaya OG, Sobolev IA, Kozhin PM, Komissarov A, Fadeev A, Petrov V, Shestopalov AM, Sharshov KA. Pathology of A(H5N8) (Clade 2.3.4.4) Virus in Experimentally Infected Chickens and Mice. Interdiscip Perspect Infect Dis 2019; 2019:4124865. [PMID: 31354812 PMCID: PMC6637675 DOI: 10.1155/2019/4124865] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/18/2019] [Indexed: 11/18/2022] Open
Abstract
The emergence of novel highly pathogenic avian influenza viruses (HPAIVs) in migratory birds raises serious concerns as these viruses have the potential to spread during fall migration. We report the identification of novel HPAIV A(H5N8) clade 2.3.4.4 virus that was isolated from sick domestic duck at commercial farm during the second wave of spread that began in October and affected poultry (ducks; chiсkens) in several European regions of Russia and Western Siberia in 2016. The strain was highly lethal in experimental infection of chickens and mice with IVPI = 2.34 and MLD50 = 1.3log10 EID50, accordingly. Inoculation of chickens with the HPAIV A/H5N8 demonstrated neuroinvasiveness, multiorgan failure, and death of chickens on the 3rd day post inoculation. Virus replicated in all collected organ samples in high viral titers with the highest titer in the brain (6.75±0.1 log10TCID50/ml). Effective virus replication was found in the following cells: neurons and glial cells of a brain; alveolar cells and macrophages of lungs; epithelial cells of a small intestine; hepatocytes and Kupffer cells of a liver; macrophages and endothelial cells of a spleen; and the tubular epithelial cells of kidneys. These findings advance our understanding of histopathological effect of A(H5N8) HPAIV infection.
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Affiliation(s)
- Elena A. Prokopyeva
- Department of Experimental Research, Federal Research Center for Basic and Translational Medicine, Novosibirsk 630117, Russia
- Medical Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vsevolod A. Zinserling
- Institute of Experimental Medicine, Almazov National Federal Research Centre, Saint Petersburg 197341, Russia
| | - You-Chan Bae
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Yongkuk Kwon
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Olga G. Kurskaya
- Department of Experimental Research, Federal Research Center for Basic and Translational Medicine, Novosibirsk 630117, Russia
| | - Ivan A. Sobolev
- Department of Experimental Research, Federal Research Center for Basic and Translational Medicine, Novosibirsk 630117, Russia
| | - Peter M. Kozhin
- Department of Experimental Research, Federal Research Center for Basic and Translational Medicine, Novosibirsk 630117, Russia
| | - Andrey Komissarov
- Department of etiology and epidemiology, Smorodintsev Research Institute of Influenza, Saint Petersburg 197376, Russia
| | - Artem Fadeev
- Department of etiology and epidemiology, Smorodintsev Research Institute of Influenza, Saint Petersburg 197376, Russia
| | - Vladimir Petrov
- Department of Experimental Research, Federal Research Center for Basic and Translational Medicine, Novosibirsk 630117, Russia
| | - Alexander M. Shestopalov
- Department of Experimental Research, Federal Research Center for Basic and Translational Medicine, Novosibirsk 630117, Russia
| | - Kirill A. Sharshov
- Department of Experimental Research, Federal Research Center for Basic and Translational Medicine, Novosibirsk 630117, Russia
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230
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Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status. mBio 2019; 10:mBio.01296-19. [PMID: 31266874 PMCID: PMC6606809 DOI: 10.1128/mbio.01296-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Our results suggest that there is a significant association between the composition of the microbiota in the nasopharynx and the influenza virus type causing the infection. We observe that vaccination status, especially in more senior individuals, also has an association with the microbial community profile. This indicates that vaccination against influenza, even when ineffective to prevent disease, could play a role in controlling secondary bacterial complications. Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with influenza A/H3N2 or influenza B virus and profiled the microbiota by target sequencing of the 16S rRNA gene. We identified signature taxonomic groups by performing linear discriminant analysis and effective size comparisons (LEfSe) and defined bacterial community types using Dirichlet multinomial mixture (DMM) models. Influenza infection was shown to be significantly associated with microbial composition of the nasopharynx according to the virus type and the vaccination status of the patient. We identified four microbial community types across the combined cohort of influenza patients and healthy individuals with one community type most representative of the influenza virus-infected group. We also identified microbial taxa for which relative abundance was significantly higher in the unvaccinated elderly group; these taxa include species known to be associated with pneumonia.
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Guan M, Hall JS, Zhang X, Dusek RJ, Olivier AK, Liu L, Li L, Krauss S, Danner A, Li T, Rutvisuttinunt W, Lin X, Hallgrimsson GT, Ragnarsdottir SB, Vignisson SR, TeSlaa J, Nashold SW, Jarman R, Wan XF. Aerosol Transmission of Gull-Origin Iceland Subtype H10N7 Influenza A Virus in Ferrets. J Virol 2019; 93:e00282-19. [PMID: 30996092 PMCID: PMC6580963 DOI: 10.1128/jvi.00282-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/09/2019] [Indexed: 01/02/2023] Open
Abstract
Subtype H10 influenza A viruses (IAVs) have been recovered from domestic poultry and various aquatic bird species, and sporadic transmission of these IAVs from avian species to mammals (i.e., human, seal, and mink) are well documented. In 2015, we isolated four H10N7 viruses from gulls in Iceland. Genomic analyses showed four gene segments in the viruses were genetically associated with H10 IAVs that caused influenza outbreaks and deaths among European seals in 2014. Antigenic characterization suggested minimal antigenic variation among these H10N7 isolates and other archived H10 viruses recovered from human, seal, mink, and various avian species in Asia, Europe, and North America. Glycan binding preference analyses suggested that, similar to other avian-origin H10 IAVs, these gull-origin H10N7 IAVs bound to both avian-like alpha 2,3-linked sialic acids and human-like alpha 2,6-linked sialic acids. However, when the gull-origin viruses were compared with another Eurasian avian-origin H10N8 IAV, which caused human infections, the gull-origin virus showed significantly higher binding affinity to human-like glycan receptors. Results from a ferret experiment demonstrated that a gull-origin H10N7 IAV replicated well in turbinate, trachea, and lung, but replication was most efficient in turbinate and trachea. This gull-origin H10N7 virus can be transmitted between ferrets through the direct contact and aerosol routes, without prior adaptation. Gulls share their habitat with other birds and mammals and have frequent contact with humans; therefore, gull-origin H10N7 IAVs could pose a risk to public health. Surveillance and monitoring of these IAVs at the wild bird-human interface should be continued.IMPORTANCE Subtype H10 avian influenza A viruses (IAVs) have caused sporadic human infections and enzootic outbreaks among seals. In the fall of 2015, H10N7 viruses were recovered from gulls in Iceland, and genomic analyses showed that the viruses were genetically related with IAVs that caused outbreaks among seals in Europe a year earlier. These gull-origin viruses showed high binding affinity to human-like glycan receptors. Transmission studies in ferrets demonstrated that the gull-origin IAV could infect ferrets, and that the virus could be transmitted between ferrets through direct contact and aerosol droplets. This study demonstrated that avian H10 IAV can infect mammals and be transmitted among them without adaptation. Thus, avian H10 IAV is a candidate for influenza pandemic preparedness and should be monitored in wildlife and at the animal-human interface.
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Affiliation(s)
- Minhui Guan
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jeffrey S Hall
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Xiaojian Zhang
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Robert J Dusek
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Alicia K Olivier
- Department of Population and Pathobiology Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Liyuan Liu
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Lei Li
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Angela Danner
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Xiaoxu Lin
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | - Josh TeSlaa
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Sean W Nashold
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Xiu-Feng Wan
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
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232
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Awuni JA, Bianco A, Dogbey OJ, Fusaro A, Yingar DT, Salviato A, Ababio PT, Milani A, Bonfante F, Monne I. Avian influenza H9N2 subtype in Ghana: virus characterization and evidence of co-infection. Avian Pathol 2019; 48:470-476. [PMID: 31142135 DOI: 10.1080/03079457.2019.1624687] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Between November 2017 and February 2018, Ghanaian poultry producers reported to animal health authorities a dramatic increase in mortality rate and a relevant drop in egg production in several layer hen farms. Laboratory investigations revealed that the farms had been infected by the H9N2 influenza subtype. Virological and molecular characterization of the viruses identified in Ghana is described here for the first time. Whole genome analysis showed that the viruses belong to the G1-lineage and cluster with viruses identified in North and West Africa. The low pathogenicity of the virus was confirmed by the intravenous pathogenicity index assay. Further investigations revealed co-infection with infectious bronchitis virus of the GI-19 lineage, which very likely explained the severity of the disease observed during the outbreaks. The H9N2 outbreaks in Ghana highlight the importance of performing a differential diagnosis and an in-depth characterization of emerging viruses. In addition, the detection of a potentially zoonotic subtype, such as the H9N2, in a region where highly pathogenic avian influenza H5Nx is currently circulating highlights the urgency of implementing enhanced monitoring strategies and supporting improved investments in regional diagnostic technologies. RESEARCH HIGHLIGHTS Influenza A H9N2 subtype was detected in layer hens in Ghana in 2017-2018 Whole genome characterization of seven H9N2 viruses was performed Phylogenetic trees revealed that the H9N2 viruses belong to the G1 lineage The HA protein possesses the amino acid mutations 226L and 155T Co-infection with infectious bronchitis virus of the GI-19 lineage was identified.
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Affiliation(s)
| | - Alice Bianco
- Istituto Zooprofilattico Sperimentale delle Venezie , Legnaro , Italy
| | | | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie , Legnaro , Italy
| | | | - Annalisa Salviato
- Istituto Zooprofilattico Sperimentale delle Venezie , Legnaro , Italy
| | | | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie , Legnaro , Italy
| | | | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie , Legnaro , Italy
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233
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Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. mBio 2019; 10:mBio.01162-19. [PMID: 31213560 PMCID: PMC6581862 DOI: 10.1128/mbio.01162-19] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The emergence of the PB2 E627K substitution is critical in the mammalian adaptation and pathogenesis of AIV. H7N9 AIVs that emerged in 2013 possess a prominent ability in gaining the PB2 E627K mutation in humans. Here, we demonstrate that the acquisition of the H7N9 PB2 E627K mutation is driven by the low polymerase activity conferred by the viral PA protein in human cells, and four PA residues are collectively involved in this process. Notably, the H7N9 PA protein leads to significant dependence of viral polymerase function on human ANP32A protein, and Anp32a knockout abolishes PB2 E627K acquisition in mice. These findings reveal that viral PA and host ANP32A are crucial for the emergence of PB2 E627K during adaptation of H7N9 AIVs to humans. Avian influenza viruses (AIVs) must acquire mammalian-adaptive mutations before they can efficiently replicate in and transmit among humans. The PB2 E627K mutation is known to play a prominent role in the mammalian adaptation of AIVs. The H7N9 AIVs that emerged in 2013 in China easily acquired the PB2 E627K mutation upon replication in humans. Here, we generate a series of reassortant or mutant H7N9 AIVs and test them in mice. We show that the low polymerase activity attributed to the viral PA protein is the intrinsic driving force behind the emergence of PB2 E627K during H7N9 AIV replication in mice. Four residues in the N-terminal region of PA are critical in mediating the PB2 E627K acquisition. Notably, due to the identity of viral PA protein, the polymerase activity and growth of H7N9 AIV are highly sensitive to changes in expression levels of human ANP32A protein. Furthermore, the impaired viral polymerase activity of H7N9 AIV caused by the depletion of ANP32A led to reduced virus replication in Anp32a−/− mice, abolishing the acquisition of the PB2 E627K mutation and instead driving the virus to acquire the alternative PB2 D701N mutation. Taken together, our findings show that the emergence of the PB2 E627K mutation of H7N9 AIV is driven by the intrinsic low polymerase activity conferred by the viral PA protein, which also involves the engagement of mammalian ANP32A.
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234
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Hussain S, Turnbull ML, Pinto RM, McCauley JW, Engelhardt OG, Digard P. Segment 2 from influenza A(H1N1) 2009 pandemic viruses confers temperature-sensitive haemagglutinin yield on candidate vaccine virus growth in eggs that can be epistatically complemented by PB2 701D. J Gen Virol 2019; 100:1079-1092. [PMID: 31169484 DOI: 10.1099/jgv.0.001279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Candidate vaccine viruses (CVVs) for seasonal influenza A virus are made by reassortment of the antigenic virus with an egg-adapted strain, typically A/Puerto Rico/8/34 (PR8). Many 2009 A(H1N1) pandemic (pdm09) high-growth reassortants (HGRs) selected this way contain pdm09 segment 2 in addition to the antigenic genes. To investigate this, we made CVV mimics by reverse genetics (RG) that were either 6 : 2 or 5 : 3 reassortants between PR8 and two pdm09 strains, A/California/7/2009 (Cal7) and A/England/195/2009, differing in the source of segment 2. The 5 : 3 viruses replicated better in MDCK-SIAT1 cells than the 6 : 2 viruses, but the 6 : 2 CVVs gave higher haemagglutinin (HA) antigen yields from eggs. This unexpected phenomenon reflected temperature sensitivity conferred by pdm09 segment 2, as the egg HA yields of the 5 : 3 viruses improved substantially when viruses were grown at 35 °C compared with 37.5 °C, whereas the 6 : 2 virus yields did not. However, the authentic 5 : 3 pdm09 HGRs, X-179A and X-181, were not markedly temperature sensitive despite their PB1 sequences being identical to that of Cal7, suggesting compensatory mutations elsewhere in the genome. Sequence comparisons of the PR8-derived backbone genes identified polymorphisms in PB2, NP, NS1 and NS2. Of these, PB2 N701D affected the temperature dependence of viral transcription and, furthermore, improved and drastically reduced the temperature sensitivity of the HA yield from the 5 : 3 CVV mimic. We conclude that the HA yield of pdm09 CVVs can be affected by an epistatic interaction between PR8 PB2 and pdm09 PB1, but that this can be minimized by ensuring that the backbones used for vaccine manufacture in eggs contain PB2 701D.
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Affiliation(s)
- Saira Hussain
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.,2 The Francis Crick Institute, London, NW1 1AT, UK
| | - Matthew L Turnbull
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Rute M Pinto
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | | | - Othmar G Engelhardt
- 3 National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Paul Digard
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
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235
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Choi WS, Jeong JH, Lloren KKS, Ahn SJ, Antigua KJC, Kim YI, Si YJ, Baek YH, Choi YK, Song MS. Development of a rapid, simple and efficient one-pot cloning method for a reverse genetics system of broad subtypes of influenza A virus. Sci Rep 2019; 9:8318. [PMID: 31165766 PMCID: PMC6549168 DOI: 10.1038/s41598-019-44813-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/21/2019] [Indexed: 11/09/2022] Open
Abstract
The reverse genetics (RG) system of influenza A viruses is well established. However, the conventional sequence-dependent method for cloning influenza genome segments is time-consuming and requires multiple processes (eg. enzyme digestion and ligation) and exhibits low cloning efficiency compared to the sequence-independent cloning method. In this study, we improved influenza genome cloning into the pHW2000 vector for an RG system by incorporating a sequence-independent circular polymerase extension cloning (CPEC) approach which requires only 2 steps (reverse transcription and one-pot CPEC-PCR) and takes about 4 hours before the transformation. The specifically designed viral gene and vector primers used for CPEC-PCR have improved cloning efficiency ranging from 63.6 to 100% based on the results of gene-specific colony PCR which was additionally confirmed by enzyme digestion. We successfully cloned all genes from broad subtypes of influenza A viruses (H1-H12, N1-N9) and rescued by the RG system. Our results demonstrate that this method-one-Pot cloning for influenza A virus-was efficient in terms of required time and cloning rate. In conclusion, the novel cloning method for influenza A virus will contribute to a significant reduction in the time required for genetic studies of emerging influenza viruses.
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Affiliation(s)
- Won-Suk Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Khristine Kaith S Lloren
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Su Jeong Ahn
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Khristine Joy C Antigua
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Young-Il Kim
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Young-Jae Si
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea.
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Republic of Korea.
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236
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Alnaji FG, Holmes JR, Rendon G, Vera JC, Fields CJ, Martin BE, Brooke CB. Sequencing Framework for the Sensitive Detection and Precise Mapping of Defective Interfering Particle-Associated Deletions across Influenza A and B Viruses. J Virol 2019; 93:e00354-19. [PMID: 30867305 PMCID: PMC6532088 DOI: 10.1128/jvi.00354-19] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 11/20/2022] Open
Abstract
The mechanisms and consequences of defective interfering particle (DIP) formation during influenza virus infection remain poorly understood. The development of next-generation sequencing (NGS) technologies has made it possible to identify large numbers of DIP-associated sequences, providing a powerful tool to better understand their biological relevance. However, NGS approaches pose numerous technical challenges, including the precise identification and mapping of deletion junctions in the presence of frequent mutation and base-calling errors, and the potential for numerous experimental and computational artifacts. Here, we detail an Illumina-based sequencing framework and bioinformatics pipeline capable of generating highly accurate and reproducible profiles of DIP-associated junction sequences. We use a combination of simulated and experimental control data sets to optimize pipeline performance and demonstrate the absence of significant artifacts. Finally, we use this optimized pipeline to reveal how the patterns of DIP-associated junction formation differ between different strains and subtypes of influenza A and B viruses and to demonstrate how these data can provide insight into mechanisms of DIP formation. Overall, this work provides a detailed roadmap for high-resolution profiling and analysis of DIP-associated sequences within influenza virus populations.IMPORTANCE Influenza virus defective interfering particles (DIPs) that harbor internal deletions within their genomes occur naturally during infection in humans and during cell culture. They have been hypothesized to influence the pathogenicity of the virus; however, their specific function remains elusive. The accurate detection of DIP-associated deletion junctions is crucial for understanding DIP biology but is complicated by an array of technical issues that can bias or confound results. Here, we demonstrate a combined experimental and computational framework for detecting DIP-associated deletion junctions using next-generation sequencing (NGS). We detail how to validate pipeline performance and provide the bioinformatics pipeline for groups interested in using it. Using this optimized pipeline, we detect hundreds of distinct deletion junctions generated during infection with a diverse panel of influenza viruses and use these data to test a long-standing hypothesis concerning the molecular details of DIP formation.
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Affiliation(s)
- Fadi G Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jessica R Holmes
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - J Cristobal Vera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brigitte E Martin
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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237
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Lack of selective resistance of influenza A virus in presence of host-targeted antiviral, UV-4B. Sci Rep 2019; 9:7484. [PMID: 31097731 PMCID: PMC6522537 DOI: 10.1038/s41598-019-43030-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023] Open
Abstract
Development of antiviral drug resistance is a continuous concern for viruses with high mutation rates such as influenza. The use of antiviral drugs targeting host proteins required for viral replication is less likely to result in the selection of resistant viruses than treating with direct-acting antivirals. The iminosugar UV-4B is a host-targeted glucomimetic that inhibits endoplasmic reticulum α-glucosidase I and II enzymes resulting in improper glycosylation and misfolding of viral glycoproteins. UV-4B has broad-spectrum antiviral activity against diverse viruses including dengue and influenza. To examine the ability of influenza virus to develop resistance against UV-4B, mouse-adapted influenza virus was passaged in mice in the presence or absence of UV-4B and virus isolated from lungs was used to infect the next cohort of mice, for five successive passages. Deep sequencing was performed to identify changes in the viral genome during passaging in the presence or absence of UV-4B. Relatively few minor variants were identified within each virus and the ratio of nonsynonymous to synonymous (dN/dS) substitutions of minor variants confirmed no apparent positive selection following sustained exposure to UV-4B. Three substitutions (one synonymous in PB2, one nonsynonymous in M and PA each) were specifically enriched (>3%) in UV-4B-treated groups at passage five. Recombinant viruses containing each individual or combinations of these nonsynonymous mutations remained sensitive to UV-4B treatment in mice. Overall, these data provide evidence that there is a high genetic barrier to the generation and selection of escape mutants following exposure to host-targeted iminosugar antivirals.
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238
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Ferreri LM, Ortiz L, Geiger G, Barriga GP, Poulson R, Gonzalez-Reiche AS, Crum JA, Stallknecht D, Moran D, Cordon-Rosales C, Rajao D, Perez DR. Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material. Ecol Evol 2019; 9:6534-6546. [PMID: 31236242 PMCID: PMC6580304 DOI: 10.1002/ece3.5232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real-time RT-PCR (rRT-PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next-generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT-PCR-positive swabs collected during the 2013-14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT-PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.
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Affiliation(s)
- Lucas M Ferreri
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Lucia Ortiz
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia.,Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Ginger Geiger
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Gonzalo P Barriga
- Laboratory of Emerging Viruses, Virology Program Institute of Biomedical Sciences, Faculty of Medicine Universidad de Chile Santiago Chile
| | - Rebecca Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | | | - Jo Anne Crum
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Moran
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Celia Cordon-Rosales
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Daniela Rajao
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Daniel R Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
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239
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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.
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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.
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240
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Liu G, Lu Y, Liu Q, Zhou Y. Inhibition of Ongoing Influenza A Virus Replication Reveals Different Mechanisms of RIG-I Activation. J Virol 2019; 93:e02066-18. [PMID: 30602605 PMCID: PMC6401434 DOI: 10.1128/jvi.02066-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022] Open
Abstract
Pattern recognition receptors provide essential nonself immune surveillance within distinct cellular compartments. Retinoic acid-inducible gene I (RIG-I) is one of the primary cytosolic RNA sensors, with an emerging role in the nucleus. It is involved in the spatiotemporal sensing of influenza A virus (IAV) replication, leading to the induction of type I interferons (IFNs). Nonetheless, the physiological viral ligands activating RIG-I during IAV infection remain underexplored. Other than full-length viral genomes, cellular constraints that impede ongoing viral replication likely potentiate an erroneous viral polymerase generating aberrant viral RNA species with RIG-I-activating potential. Here, we investigate the origins of RIG-I-activating viral RNA under two such constraints. Using chemical inhibitors that inhibit continuous viral protein synthesis, we identify the incoming, but not de novo-synthesized, viral defective interfering (DI) genomes contributing to RIG-I activation. In comparison, deprivation of viral nucleoprotein (NP), the key RNA chain elongation factor for the viral polymerase, leads to the production of aberrant viral RNA species activating RIG-I; however, their nature is likely to be distinct from that of DI RNA. Moreover, RIG-I activation in response to NP deprivation is not adversely affected by expression of the nuclear export protein (NEP), which diminishes the generation of a major subset of aberrant viral RNA but facilitates the accumulation of small viral RNA (svRNA). Overall, our results indicate the existence of fundamentally different mechanisms of RIG-I activation under cellular constraints that impede ongoing IAV replication.IMPORTANCE The induction of an IFN response by IAV is mainly mediated by the RNA sensor RIG-I. The physiological RIG-I ligands produced during IAV infection are not fully elucidated. Cellular constraints leading to the inhibition of ongoing viral replication likely potentiate an erroneous viral polymerase producing aberrant viral RNA species activating RIG-I. Here, we demonstrate that RIG-I activation during chemical inhibition of continuous viral protein synthesis is attributable to the incoming DI genomes. Erroneous viral replication driven by NP deprivation promotes the generation of RIG-I-activating aberrant viral RNA, but their nature is likely to be distinct from that of DI RNA. Our results thus reveal distinct mechanisms of RIG-I activation by IAV under cellular constraints impeding ongoing viral replication. A better understanding of RIG-I sensing of IAV infection provides insight into the development of novel interventions to combat influenza virus infection.
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Affiliation(s)
- GuanQun Liu
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yao Lu
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Qiang Liu
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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241
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Matsumoto S, Chong Y, Kang D, Ikematsu H. High genetic stability in MDCK-SIAT1 passaged human influenza viruses. J Infect Chemother 2019; 25:222-224. [DOI: 10.1016/j.jiac.2018.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/12/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
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242
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Genomics Analyses of GIV and GVI Noroviruses Reveal the Distinct Clustering of Human and Animal Viruses. Viruses 2019; 11:v11030204. [PMID: 30823663 PMCID: PMC6466045 DOI: 10.3390/v11030204] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 01/23/2023] Open
Abstract
Noroviruses are highly diverse viruses that are the major viral cause of acute gastroenteritis in humans. Although these viruses can infect multiple mammalian species, their potential for zoonosis is not well understood, especially within Genogroup IV (GIV), which contains viruses that infect humans, canines, and felines. The study of GIV viruses has been, in part, hindered by the limited number of complete genomes. Here, we developed a full-genome amplicon-based platform that facilitated the sequencing of canine noroviruses circulating in the United States. Eight novel nearly full-length canine norovirus genomes and two nearly complete VP1 sequences, including four GIV.2, three GVI.1, and three GVI.2 viruses, were successfully obtained. Only animal strains exhibited GVI/GIV chimeric viruses, demonstrating restrictions in norovirus recombination. Using genomic, phylogenetic, and structural analyses, we show that differences within the major capsid protein and the non-structural proteins of GIV and GVI noroviruses could potentially limit cross-species transmission between humans, canines, and felines.
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243
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Jadhav V, Hoogerheide DP, Korlach J, Wanunu M. Porous Zero-Mode Waveguides for Picogram-Level DNA Capture. NANO LETTERS 2019; 19:921-929. [PMID: 30484321 PMCID: PMC9701543 DOI: 10.1021/acs.nanolett.8b04170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have recently shown that nanopore zero-mode waveguides are effective tools for capturing picogram levels of long DNA fragments for single-molecule DNA sequencing. Despite these key advantages, the manufacturing of large arrays is not practical due to the need for serial nanopore fabrication. To overcome this challenge, we have developed an approach for the wafer-scale fabrication of waveguide arrays on low-cost porous membranes, which are deposited using molecular-layer deposition. The membrane at each waveguide base contains a network of serpentine pores that allows for efficient electrophoretic DNA capture at picogram levels while eliminating the need for prohibitive serial pore milling. Here, we show that the loading efficiency of these porous waveguides is up to 2 orders of magnitude greater than their nanopore predecessors. This new device facilitates the scaling-up of the process, greatly reducing the cost and effort of manufacturing. Furthermore, the porous zero-mode waveguides can be used for applications that benefit from low-input single-molecule real-time sequencing.
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Affiliation(s)
- Vivek Jadhav
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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244
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Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016⁻2017 Season. Viruses 2019; 11:v11020108. [PMID: 30695992 PMCID: PMC6410005 DOI: 10.3390/v11020108] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/17/2022] Open
Abstract
Influenza viruses cause a remarkable disease burden and significant morbidity and mortality worldwide, and these impacts vary between seasons. To understand the mechanisms associated with these differences, a comprehensive approach is needed to characterize the impact of influenza genomic traits on the burden of disease. During 2016–2017, a year with severe A(H3N2), we sequenced 176 A(H3N2) influenza genomes using next generation sequencing (NGS) for routine surveillance of circulating influenza viruses collected via the French national influenza community-based surveillance network or from patients hospitalized in the intensive care units of the University Hospitals of Lyon, France. Taking into account confounding factors, sequencing and clinical data were used to identify genomic variants and quasispecies associated with influenza severity or vaccine failure. Several amino acid substitutions significantly associated with clinical traits were found, including NA V263I and NS1 K196E which were associated with severity and co-occurred only in viruses from the 3c.2a1 clade. Additionally, we observed that intra-host diversity as a whole and on a specific set of gene segments increased with severity. These results support the use of whole genome sequencing as a tool for the identification of genetic traits associated with severe influenza in the context of influenza surveillance.
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245
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MacFadden DR, McGeer A, Athey T, Perusini S, Olsha R, Li A, Eshaghi A, Gubbay JB, Hanage WP. Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15. Emerg Infect Dis 2019; 24:492-497. [PMID: 29460729 PMCID: PMC5823344 DOI: 10.3201/eid2403.171499] [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] [Indexed: 01/10/2023] Open
Abstract
Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis of institutional influenza outbreaks that occurred during the 2014-15 influenza season in Toronto, Canada. We sequenced the 2 earliest submitted samples positive for influenza A(H3N2) from each of 38 reported institutional outbreaks in long-term care facilities. Genome sequencing showed most outbreak pairs identified by using the current clinical definition were highly related. Inclusion of surveillance samples demonstrated that outbreak sources were likely introductions from broader circulating lineages. Pairwise distance analysis using majority genome and hemagglutinin-specific genes enabled identification of thresholds for discrimination of within and between outbreak pairs; the area under the curve ranged 0.93-0.95. Routine genome sequencing for defining influenza outbreaks in long-term care facilities is unlikely to add significantly to the current clinical definition. Sequencing may prove most useful for investigating sources of outbreak introductions.
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246
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Determining the Mutation Bias of Favipiravir in Influenza Virus Using Next-Generation Sequencing. J Virol 2019; 93:JVI.01217-18. [PMID: 30381482 PMCID: PMC6321902 DOI: 10.1128/jvi.01217-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/21/2018] [Indexed: 12/15/2022] Open
Abstract
New antiviral drugs are needed as a first line of defense in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic. Favipiravir is a broad-spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen, but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole-genome sequencing of virus. IMPORTANCE New antiviral drugs are needed as a first line of defense in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.
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247
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Identification of a Divergent Avian Influenza H3N2 Virus from Domestic Ducks in France. Microbiol Resour Announc 2018; 7:MRA00943-18. [PMID: 30574576 PMCID: PMC6298543 DOI: 10.1128/mra.00943-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022] Open
Abstract
An avian influenza H3N2 virus was isolated from domestic ducks in France in 2016. Although this French H3N2 virus possesses traits of an avian virus, the genetic distances observed for hemagglutinin (HA) and neuraminidase (NA) show that these two genes most likely evolved independently from other avian influenza sequences. An avian influenza H3N2 virus was isolated from domestic ducks in France in 2016. Although this French H3N2 virus possesses traits of an avian virus, the genetic distances observed for hemagglutinin (HA) and neuraminidase (NA) show that these two genes most likely evolved independently from other avian influenza sequences.
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248
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Mulatti P, Fusaro A, Scolamacchia F, Zecchin B, Azzolini A, Zamperin G, Terregino C, Cunial G, Monne I, Marangon S. Integration of genetic and epidemiological data to infer H5N8 HPAI virus transmission dynamics during the 2016-2017 epidemic in Italy. Sci Rep 2018; 8:18037. [PMID: 30575785 PMCID: PMC6303474 DOI: 10.1038/s41598-018-36892-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/24/2018] [Indexed: 12/30/2022] Open
Abstract
Between October 2016 and December 2017, several European Countries had been involved in a massive Highly Pathogenic Avian Influenza (HPAI) epidemic sustained by H5N8 subtype virus. Starting on December 2016, also Italy was affected by H5N8 HPAI virus, with cases occurring in two epidemic waves: the first between December 2016 and May 2017, and the second in July-December 2017. Eighty-three outbreaks were recorded in poultry, 67 of which (80.72%) occurring in the second wave. A total of 14 cases were reported in wild birds. Epidemiological information and genetic analyses were conjointly used to get insight on the spread dynamics. Analyses indicated multiple introductions from wild birds to the poultry sector in the first epidemic wave, and noteworthy lateral spread from October 2017 in a limited geographical area with high poultry densities. Turkeys, layers and backyards were the mainly affected types of poultry production. Two genetic sub-groups were detected in the second wave in non-overlapping geographical areas, leading to speculate on the involvement of different wild bird populations. The integration of epidemiological data and genetic analyses allowed to unravel the transmission dynamics of H5N8 virus in Italy, and could be exploited to timely support in implementing tailored control measures.
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Affiliation(s)
- P Mulatti
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy.
| | - A Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - F Scolamacchia
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - B Zecchin
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - A Azzolini
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - G Zamperin
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - C Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - G Cunial
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - I Monne
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
| | - S Marangon
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, (Padua), Italy
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249
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Chong Y, Matsumoto S, Kang D, Ikematsu H. Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. Influenza Other Respir Viruses 2018; 13:115-122. [PMID: 30548432 PMCID: PMC6379637 DOI: 10.1111/irv.12624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 01/07/2023] Open
Abstract
Background The large consumption of neuraminidase inhibitors (NAIs) for the treatment of influenza virus infections places Japan at risk of becoming the epicenter of the global spread of NAI‐resistant viruses. Objective To clarify NA amino acid mutations of epidemic influenza viruses in Japan and their related NAI resistance. Methods A total of 1791 samples, including 396 A/H1N1pdm09, 1117 A/H3N2, and 278 B isolates, were collected to determine of their 50% inhibitory concentration (IC50) values by NAIs (oseltamivir, zanamivir, peramivir, and laninamivir) during the Japanese seasons from 2011‐2012 to 2016‐2017. Then, 380 samples including 49 A/H1N1pdm09, 251 A/H3N2, and 80 B isolates were sequenced for the entire NA genes. Results Neuraminidase inhibitor‐resistant A/H1N1pdm09 viruses were detected at a frequency of 1.3% (5/396 isolates) in the epidemic seasons. None of the A/H3N2 and B viruses developed resistance to any of the four NAIs during the six seasons. Only five and 13 AA mutations were detected in the NA catalytic sites of A/H1N1pdm09 and A/H3N2 viruses, respectively. No mutations were observed in the catalytic sites of B viruses. Four of the five mutations in the catalytic sites of A/H1N1pdm09 consisted of H275Y, which was related to high resistance to oseltamivir and peramivir. Most (10/13) of the catalytic site mutations in A/H3N2 were associated with MDCK‐passaged induction (D151G/N). Finally, no mutations related to substantial NAI resistance were detected in the A/H3N2 and B viruses examined. Conclusion These findings suggest that the NA catalytic sites of influenza viruses are well preserved. Even in Japan, no spread of NAI‐resistant viruses has been observed, and A/H1N1pdm09 viruses carrying H275Y remain limited.
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Affiliation(s)
- Yong Chong
- Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinya Matsumoto
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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250
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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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