102
|
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.
Collapse
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:
| |
Collapse
|
103
|
Lewandowski K, Xu Y, Pullan ST, Lumley SF, Foster D, Sanderson N, Vaughan A, Morgan M, Bright N, Kavanagh J, Vipond R, Carroll M, Marriott AC, Gooch KE, Andersson M, Jeffery K, Peto TEA, Crook DW, Walker AS, Matthews PC. Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples. J Clin Microbiol 2019; 58:e00963-19. [PMID: 31666364 PMCID: PMC6935926 DOI: 10.1128/jcm.00963-19] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023] Open
Abstract
Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 102 to 103 genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10-5). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [CT ] values, <30) and 6/13 samples with low viral titers (CT values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.
Collapse
Affiliation(s)
- Kuiama Lewandowski
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Yifei Xu
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Steven T Pullan
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Sheila F Lumley
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicholas Sanderson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicole Bright
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Richard Vipond
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Miles Carroll
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Anthony C Marriott
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Karen E Gooch
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Philippa C Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| |
Collapse
|
104
|
Wang S, Huang B, Ma X, Liu P, Wang Y, Zhang X, Zhu L, Fan Q, Sun Y, Wang K. Reverse-transcription recombinase-aided amplification assay for H7 subtype avian influenza virus. Transbound Emerg Dis 2019; 67:877-883. [PMID: 31714018 DOI: 10.1111/tbed.13411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/15/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
H7 subtype avian influenza virus infection is an emerging zoonosis in some Asian countries and an important avian disease worldwide. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. In this study, we developed a reverse-transcription recombinase-aided amplification assay for the detection of H7 subtype avian influenza virus. Assays were performed at a single temperature (39°C), and the results were obtained within 20 min. The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus, which are the other main respiratory viruses affecting birds. The analytical sensitivity was 102 RNA copies per reaction at a 95% probability level according to probit regression analysis, with 100% specificity. Compared with published reverse-transcription quantitative real-time polymerase chain reaction assays, the κ value of the reverse-transcription recombinase-aided amplification assay in 342 avian clinical samples was 0.988 (p < .001). The sensitivity for avian clinical sample detection was 100% (95%CI, 90.40%-100%), and the specificity was 99.96% (95%CI, 97.83%-99.98%). These results indicated that our reverse-transcription recombinase-aided amplification assay may be a valuable tool for detecting avian influenza H7 subtype virus.
Collapse
Affiliation(s)
- Suchun Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Baoxu Huang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xuejun Ma
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Ping Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yang Wang
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiaoguang Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Lin Zhu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Qingying Fan
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Yawei Sun
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Kaicheng Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| |
Collapse
|