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Zhang X, Zhang Y, Wei F. Research progress on the nonstructural protein 1 (NS1) of influenza a virus. Virulence 2024; 15:2359470. [PMID: 38918890 PMCID: PMC11210920 DOI: 10.1080/21505594.2024.2359470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/19/2024] [Indexed: 06/27/2024] Open
Abstract
Influenza A virus (IAV) is the leading cause of highly contagious respiratory infections, which poses a serious threat to public health. The non-structural protein 1 (NS1) is encoded by segment 8 of IAV genome and is expressed in high levels in host cells upon IAV infection. It is the determinant of virulence and has multiple functions by targeting type Ι interferon (IFN-I) and type III interferon (IFN-III) production, disrupting cell apoptosis and autophagy in IAV-infected cells, and regulating the host fitness of influenza viruses. This review will summarize the current research on the NS1 including the structure and related biological functions of the NS1 as well as the interaction between the NS1 and host cells. It is hoped that this will provide some scientific basis for the prevention and control of the influenza virus.
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Affiliation(s)
- Xiaoyan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yuying Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Fanhua Wei
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
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Zhirnov OP, Lvov DK. Avian flu: «for whom the bell tolls»? Vopr Virusol 2024; 69:101-118. [PMID: 38843017 DOI: 10.36233/10.36233/0507-4088-213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Indexed: 06/14/2024]
Abstract
The family Orthomyxoviridae consists of 9 genera, including Alphainfluenzavirus, which contains avian influenza viruses. In two subtypes H5 and H7 besides common low-virulent strains, a specific type of highly virulent avian virus have been described to cause more than 60% mortality among domestic birds. These variants of influenza virus are usually referred to as «avian influenza virus». The difference between high (HPAI) and low (LPAI) virulent influenza viruses is due to the structure of the arginine-containing proteolytic activation site in the hemagglutinin (HA) protein. The highly virulent avian influenza virus H5 was identified more than 100 years ago and during this time they cause outbreaks among wild and domestic birds on all continents and only a few local episodes of the disease in humans have been identified in XXI century. Currently, a sharp increase in the incidence of highly virulent virus of the H5N1 subtype (clade h2.3.4.4b) has been registered in birds on all continents, accompanied by the transmission of the virus to various species of mammals. The recorded global mortality rate among wild, domestic and agricultural birds from H5 subtype is approaching to the level of 1 billion cases. A dangerous epidemic factor is becoming more frequent outbreaks of avian influenza with high mortality among mammals, in particular seals and marine lions in North and South America, minks and fur-bearing animals in Spain and Finland, domestic and street cats in Poland. H5N1 avian influenza clade h2.3.4.4b strains isolated from mammals have genetic signatures of partial adaptation to the human body in the PB2, NP, HA, NA genes, which play a major role in regulating the aerosol transmission and the host range of the virus. The current situation poses a real threat of pre-adaptation of the virus in mammals as intermediate hosts, followed by the transition of the pre-adapted virus into the human population with catastrophic consequences.
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Affiliation(s)
- O P Zhirnov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
- The Russian-German Academy of Medical-Social and Biotechnological Sciences, Skolkovo Innovation Center
| | - D K Lvov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
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Kleij L, Bruder E, Raoux-Barbot D, Lejal N, Nevers Q, Deloizy C, Da Costa B, Legrand L, Barrey E, Chenal A, Pronost S, Delmas B, Dhorne-Pollet S. Genomic characterization of equine influenza A subtype H3N8 viruses by long read sequencing and functional analyses of the PB1-F2 virulence factor of A/equine/Paris/1/2018. Vet Res 2024; 55:36. [PMID: 38520035 PMCID: PMC10960481 DOI: 10.1186/s13567-024-01289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/16/2024] [Indexed: 03/25/2024] Open
Abstract
Equine influenza virus (EIV) remains a threat to horses, despite the availability of vaccines. Strategies to monitor the virus and prevent potential vaccine failure revolve around serological assays, RT-qPCR amplification, and sequencing the viral hemagglutinin (HA) and neuraminidase (NA) genes. These approaches overlook the contribution of other viral proteins in driving virulence. This study assesses the potential of long-read nanopore sequencing for fast and precise sequencing of circulating equine influenza viruses. Therefore, two French Florida Clade 1 strains, including the one circulating in winter 2018-2019 exhibiting more pronounced pathogenicity than usual, as well as the two currently OIE-recommended vaccine strains, were sequenced. Our results demonstrated the reliability of this sequencing method in generating accurate sequences. Sequence analysis of HA revealed a subtle antigenic drift in the French EIV strains, with specific substitutions, such as T163I in A/equine/Paris/1/2018 and the N188T mutation in post-2015 strains; both substitutions were in antigenic site B. Antigenic site E exhibited modifications in post-2018 strains, with the N63D substitution. Segment 2 sequencing also revealed that the A/equine/Paris/1/2018 strain encodes a longer variant of the PB1-F2 protein when compared to other Florida clade 1 strains (90 amino acids long versus 81 amino acids long). Further biological and biochemistry assays demonstrated that this PB1-F2 variant has enhanced abilities to abolish the mitochondrial membrane potential ΔΨm and permeabilize synthetic membranes. Altogether, our results highlight the interest in rapidly characterizing the complete genome of circulating strains with next-generation sequencing technologies to adapt vaccines and identify specific virulence markers of EIV.
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Affiliation(s)
- Lena Kleij
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Elise Bruder
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dorothée Raoux-Barbot
- CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Nathalie Lejal
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Quentin Nevers
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Charlotte Deloizy
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Bruno Da Costa
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Loïc Legrand
- LABÉO Frank Duncombe, 14280, Saint-Contest, France
- BIOTARGEN, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Eric Barrey
- AgroParisTech, Unité de Génétique Animale et Biologie Intégrative, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Alexandre Chenal
- CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Stéphane Pronost
- LABÉO Frank Duncombe, 14280, Saint-Contest, France
- BIOTARGEN, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Bernard Delmas
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Sophie Dhorne-Pollet
- AgroParisTech, Unité de Génétique Animale et Biologie Intégrative, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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Gu C, Fan S, Dahn R, Babujee L, Chiba S, Guan L, Maemura T, Pattinson D, Neumann G, Kawaoka Y. Characterization of a human H3N8 influenza virus. EBioMedicine 2024; 101:105034. [PMID: 38408394 PMCID: PMC10904230 DOI: 10.1016/j.ebiom.2024.105034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND In 2022 and 2023, novel reassortant H3N8 influenza viruses infected three people, marking the first human infections with viruses of this subtype. METHODS Here, we generated one of these viruses (A/Henan/4-10CNIC/2022; hereafter called A/Henan/2022 virus) by using reverse genetics and characterized it. FINDINGS In intranasally infected mice, reverse genetics-generated A/Henan/2022 virus caused weight loss in all five animals (one of which had to be euthanized) and replicated efficiently in the respiratory tract. Intranasal infection of ferrets resulted in minor weight loss and moderate fever but no mortality. Reverse genetics-generated A/Henan/2022 virus replicated efficiently in the upper respiratory tract of ferrets but was not detected in the lungs. Virus transmission via respiratory droplets occurred in one of four pairs of ferrets. Deep-sequencing of nasal swab samples from inoculated and exposed ferrets revealed sequence polymorphisms in the haemagglutinin protein that may affect receptor-binding specificity. We also tested 90 human sera for neutralizing antibodies against reverse genetics-generated A/Henan/2022 virus and found that some of them possessed neutralizing antibody titres, especially sera from older donors with likely exposure to earlier human H3N2 viruses. INTERPRETATION Our data demonstrate that reverse genetics-generated A/Henan/2022 virus is a low pathogenic influenza virus (of avian influenza virus descent) with some antigenic resemblance to older human H3N2 viruses and limited respiratory droplet transmissibility in ferrets. FUNDING This work was supported by the Japan Program for Infectious Diseases Research and Infrastructure (JP23wm0125002), and the Japan Initiative for World-leading Vaccine Research and Development Centers (JP233fa627001) from the Japan Agency for Medical Research and Development (AMED).
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Affiliation(s)
- Chunyang Gu
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Shufang Fan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Randall Dahn
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Lavanya Babujee
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Lizheng Guan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Tadashi Maemura
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - David Pattinson
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA.
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; Division of Virology, Department of Microbiology and Immunology and International Research Center for Infectious Diseases, The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan; Pandemic Preparedness, Infection and Advanced Research Center, University of Tokyo, Tokyo 162-8655, Japan.
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Guan L, Babujee L, Presler R, Pattinson D, Nguyen HLK, Hoang VMP, Le MQ, van Bakel H, Kawaoka Y, Neumann G. Avian H6 Influenza Viruses in Vietnamese Live Bird Markets during 2018-2021. Viruses 2024; 16:367. [PMID: 38543733 PMCID: PMC10975462 DOI: 10.3390/v16030367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 04/01/2024] Open
Abstract
Avian influenza viruses of the H6 subtype are prevalent in wild ducks and likely play an important role in the ecology of influenza viruses through reassortment with other avian influenza viruses. Yet, only 152 Vietnamese H6 virus sequences were available in GISAID (Global Initiative on Sharing All Influenza Data) prior to this study with the most recent sequences being from 2018. Through surveillance in Vietnamese live bird markets from 2018 to 2021, we identified 287 samples containing one or several H6 viruses and other influenza A virus subtypes, demonstrating a high rate of co-infections among birds in Vietnamese live bird markets. For the 132 H6 samples with unique influenza virus sequences, we conducted phylogenetic and genetic analyses. Most of the H6 viruses were similar to each other and closely related to other H6 viruses; however, signs of reassortment with other avian influenza viruses were evident. At the genetic level, the Vietnamese H6 viruses characterized in our study encode a single basic amino acid at the HA cleavage site, consistent with low pathogenicity in poultry. The Vietnamese H6 viruses analyzed here possess an amino acid motif in HA that confers binding to both avian- and human-type receptors on host cells, consistent with their ability to infect mammals. The frequent detection of H6 viruses in Vietnamese live bird markets, the high rate of co-infections of birds with different influenza viruses, and the dual receptor-binding specificity of these viruses warrant their close monitoring for potential infection and spread among mammals.
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Affiliation(s)
- Lizheng Guan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin—Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (D.P.)
| | - Lavanya Babujee
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin—Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (D.P.)
| | - Robert Presler
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin—Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (D.P.)
| | - David Pattinson
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin—Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (D.P.)
| | - Hang Le Khanh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Vu Mai Phuong Hoang
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Mai Quynh Le
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Harm van Bakel
- Department of Genetics and Genomic Services, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin—Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (D.P.)
- Division of Virology, Department of Microbiology and Immunology, and International Research Center for Infectious Diseases, The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Research Center for Global Viral Diseases, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
- Infection and Advanced Research (UTOPIA) Center, The University of Tokyo Pandemic Preparedness, Tokyo 108-8639, Japan
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin—Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (D.P.)
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Lin S, Zhang Y, Yang J, Yang L, Li X, Bo H, Liu J, Tan M, Zhu W, Wang D, Shu Y. Cross-Species Transmission Potential of H4 Avian Influenza Viruses in China: Epidemiological and Evolutionary Study. Viruses 2024; 16:353. [PMID: 38543719 PMCID: PMC10974465 DOI: 10.3390/v16030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 05/23/2024] Open
Abstract
H4 avian influenza viruses (AIVs) have been widely detected in live poultry markets in China. However, the potential public health impact of H4 AIVs remains largely uncertain. Here, we fully analyzed the distribution and phylogenetic relationship of H4 AIVs in China. We obtained 31 isolates of H4 viruses in China during 2009-2022 through surveillance in poultry-associated environments, such as live poultry markets and poultry farms. Genomic sequence analysis together with publicly available data revealed that frequent reassortment and introduction of H4 AIV from wild birds to poultry may have occurred. We identified 62 genotypes among 127 whole genome sequences of H4 viruses in China, indicating that H4 AIVs had great genetic diversity in China. We also investigated molecular markers and found that drug resistance mutations frequently occurred in the M2 protein and a few mutations related to receptor binding and the host signature in H4 AIVs. Our study demonstrates the cross-species transmission potential of H4 AIVs in China and provides some reference significance for its risk assessment.
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Affiliation(s)
- Shuxia Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Ye Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Jiaying Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Min Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- Key Laboratory of Pathogen Infection Prevention and Control (MOE), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
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Tan M, Zeng X, Xie Y, Li X, Liu J, Yang J, Yang L, Wang D. Reported human infections of H9N2 avian influenza virus in China in 2021. Front Public Health 2023; 11:1255969. [PMID: 38155898 PMCID: PMC10753182 DOI: 10.3389/fpubh.2023.1255969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Introduction The continued emergence of human infections of H9N2 avian influenza virus (AIV) poses a serious threat to public health. The prevalent Y280/G9 lineage of H9N2 AIV in Chinese poultry can directly bind to human receptors, increasing the risk of spillover infections to humans. Since 2013, the number of human cases of H9N2 avian influenza has been increasing continuously, and in 2021, China reported the highest number of human cases, at 25. Methods In this study, we analyzed the age, geographic, temporal, and sex distributions of humans with H9N2 avian influenza in 2021 using data from the National Influenza Center (Beijing, China). We also conducted evolutionary, gene homology, and molecular characterization analyses of the H9N2 AIVs infecting humans. Results Our findings show that children under the age of 12 accounted for 80% of human cases in 2021, and females were more frequently affected than males. More cases occurred in winter than in summer, and most cases were concentrated in southern China. Human-infecting H9N2 viruses showed a high level of genetic homology and belonged to the prevalent G57 genotype. Several additional α2,6-SA-binding sites and sites of mammalian adaptation were also identified in the genomes of human-infecting H9N2 viruses. Discussion Therefore, continuous monitoring of H9N2 AIV and the implementation of further measures to control the H9N2 virus in poultry are essential to reduce the interspecies transmission of the virus.
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Affiliation(s)
- Min Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing, China
| | - Xiaoxu Zeng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing, China
| | - Yiran Xie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing, China
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing, China
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing, China
| | - Jiaying Yang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, Beijing, China
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Cronk BD, Caserta LC, Laverack M, Gerdes RS, Hynes K, Hopf CR, Fadden MA, Nakagun S, Schuler KL, Buckles EL, Lejeune M, Diel DG. Infection and tissue distribution of highly pathogenic avian influenza A type H5N1 (clade 2.3.4.4b) in red fox kits ( Vulpes vulpes). Emerg Microbes Infect 2023; 12:2249554. [PMID: 37589241 PMCID: PMC10512766 DOI: 10.1080/22221751.2023.2249554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Avian influenza H5N1 is a highly pathogenic virus that primarily affects birds. However, it can also infect other animal species, including mammals. We report the infection of nine juvenile red foxes (Vulpes vulpes) with Highly Pathogenic Avian Influenza A type H5N1 (Clade 2.3.4.4b) in the spring of 2022 in the central, western, and northern regions of New York, USA. The foxes displayed neurologic signs, and examination of brain and lung tissue revealed lesions, with brain lesions ranging from moderate to severe meningoencephalitis. Analysis of tissue tropism using RT-PCR methods showed a comparatively lower Ct value in the brain, which was confirmed by in situ hybridization targeting Influenza A RNA. The viral RNA labelling was highly clustered and overlapped the brain lesions, observed in neurons, and grey matter. Whole viral genome sequences obtained from the affected foxes were subjected to phylogenetic and mutation analysis to determine influenza A clade, host specificity, and potential occurrence of viral reassortment. Infections in red foxes likely occurred due to preying on infected wild birds and are unlikely due to transmission between foxes or other mammals.
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Affiliation(s)
- Brittany D. Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Rhea S. Gerdes
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kevin Hynes
- New York State Department of Environmental Conservation, Wildlife Health Program, Albany, NY, USA
| | - Cynthia R. Hopf
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa A. Fadden
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Shotaro Nakagun
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Krysten L. Schuler
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elizabeth L. Buckles
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Manigandan Lejeune
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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Alasiri A, Soltane R, Hegazy A, Khalil AM, Mahmoud SH, Khalil AA, Martinez-Sobrido L, Mostafa A. Vaccination and Antiviral Treatment against Avian Influenza H5Nx Viruses: A Harbinger of Virus Control or Evolution. Vaccines (Basel) 2023; 11:1628. [PMID: 38005960 PMCID: PMC10675773 DOI: 10.3390/vaccines11111628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the panzootic nature of emergent highly pathogenic avian influenza H5Nx viruses in wild migratory birds and domestic poultry, only a limited number of human infections with H5Nx viruses have been identified since its emergence in 1996. Few countries with endemic avian influenza viruses (AIVs) have implemented vaccination as a control strategy, while most of the countries have adopted a culling strategy for the infected flocks. To date, China and Egypt are the two major sites where vaccination has been adopted to control avian influenza H5Nx infections, especially with the widespread circulation of clade 2.3.4.4b H5N1 viruses. This virus is currently circulating among birds and poultry, with occasional spillovers to mammals, including humans. Herein, we will discuss the history of AIVs in Egypt as one of the hotspots for infections and the improper implementation of prophylactic and therapeutic control strategies, leading to continuous flock outbreaks with remarkable virus evolution scenarios. Along with current pre-pandemic preparedness efforts, comprehensive surveillance of H5Nx viruses in wild birds, domestic poultry, and mammals, including humans, in endemic areas is critical to explore the public health risk of the newly emerging immune-evasive or drug-resistant H5Nx variants.
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Affiliation(s)
- Ahlam Alasiri
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (A.A.); (R.S.)
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (A.A.); (R.S.)
| | - Akram Hegazy
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, Giza 12613, Egypt;
| | - Ahmed Magdy Khalil
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Center, Giza 12622, Egypt;
| | - Ahmed A. Khalil
- Veterinary Sera and Vaccines Research Institute (VSVRI), Agriculture Research Center (ARC), Cairo 11435, Egypt;
| | | | - Ahmed Mostafa
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
- Center of Scientific Excellence for Influenza Viruses, National Research Center, Giza 12622, Egypt;
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10
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Griffin EF, Tompkins SM. Fitness Determinants of Influenza A Viruses. Viruses 2023; 15:1959. [PMID: 37766365 PMCID: PMC10535923 DOI: 10.3390/v15091959] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A (IAV) is a major human respiratory pathogen that causes illness, hospitalizations, and mortality annually worldwide. IAV is also a zoonotic pathogen with a multitude of hosts, allowing for interspecies transmission, reassortment events, and the emergence of novel pandemics, as was seen in 2009 with the emergence of a swine-origin H1N1 (pdmH1N1) virus into humans, causing the first influenza pandemic of the 21st century. While the 2009 pandemic was considered to have high morbidity and low mortality, studies have linked the pdmH1N1 virus and its gene segments to increased disease in humans and animal models. Genetic components of the pdmH1N1 virus currently circulate in the swine population, reassorting with endemic swine viruses that co-circulate and occasionally spillover into humans. This is evidenced by the regular detection of variant swine IAVs in humans associated with state fairs and other intersections of humans and swine. Defining genetic changes that support species adaptation, virulence, and cross-species transmission, as well as mutations that enhance or attenuate these features, will improve our understanding of influenza biology. It aids in surveillance and virus risk assessment and guides the establishment of counter measures for emerging viruses. Here, we review the current understanding of the determinants of specific IAV phenotypes, focusing on the fitness, transmission, and virulence determinants that have been identified in swine IAVs and/or in relation to the 2009 pdmH1N1 virus.
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Affiliation(s)
- Emily Fate Griffin
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Stephen Mark Tompkins
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Center for Influenza Disease and Emergence Response (CIDER), Athens, GA 30602, USA
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11
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Hatibi N, Dumont-Lagacé M, Alouani Z, El Fatimy R, Abik M, Daouda T. Misclassified: identification of zoonotic transition biomarker candidates for influenza A viruses using deep neural network. Front Genet 2023; 14:1145166. [PMID: 37576548 PMCID: PMC10415530 DOI: 10.3389/fgene.2023.1145166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/25/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: Zoonotic transition of Influenza A viruses is the cause of epidemics with high rates of morbidity and mortality. Predicting which viral strains are likely to transition from their genetic sequence could help in the prevention and response against these zoonotic strains. We hypothesized that features predictive of viral hosts could be leveraged to identify biomarkers of zoonotic viral transition. Methods: We trained deep learning models to predict viral hosts based on the virus mRNA or protein sequences. Our multi-host dataset contained 848,630 unique nucleotide sequences obtained from the NCBI Influenza Virus and Influenza Research Databases. Each sequence, representing one gene from one viral strain, was classified into one of the three host categories: Avian, Human, and Swine. Trained models were analyzed using various neural network interpretation methods to identify interesting candidates for zoonotic transition biomarkers. Results: Using mRNA sequences as input led to higher prediction accuracies than amino acids, suggesting that the codon sequence contains information relevant to viral hosts that is lost during protein translation. UMAP visualization of the latent space of our classifiers showed that viral sequences clustered according to their host of origin. Interestingly, sequences from pandemic zoonotic viral strains localized at the margins between hosts, while zoonotic sequences incapable of Human-to-Human transmission localized with non-zoonotic viruses from the same host. In addition, host prediction for pandemic zoonotic sequences had low prediction accuracy, which was not the case for the other zoonotic strains. This supports our hypothesis that ambiguously predicted viral sequences bear features associated with cross-species infectivity. Finally, we compared misclassified sequences to well-classified ones to extract interesting candidates for zoonotic transition biomarkers. While features varied significantly between pairs of species and viral genes, several codons were conserved in Swine-to-Human and Avian-to-Human misclassified sequences, and in particular in the NA, HA, and NP genes, suggesting their importance for zoonosis in Humans. Discussion: Analysis of viral sequences using neural network interpretation approaches revealed important genetic differences between zoonotic viruses with pandemic potential, compared to non-zoonotic viral strains or zoonotic viruses incapable of Human-to-Human transmission.
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Affiliation(s)
- Nissrine Hatibi
- Ecole Nationale Supérieure d'Informatique et d'Analyse des Systèmes, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Biological Sciences (ISSB), UM6P Faculty of Medical Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | | | - Zakaria Alouani
- Institute of Biological Sciences (ISSB), UM6P Faculty of Medical Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid El Fatimy
- Institute of Biological Sciences (ISSB), UM6P Faculty of Medical Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mounia Abik
- Ecole Nationale Supérieure d'Informatique et d'Analyse des Systèmes, Mohammed V University in Rabat, Rabat, Morocco
| | - Tariq Daouda
- Institute of Biological Sciences (ISSB), UM6P Faculty of Medical Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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12
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Guan L, Babujee L, Browning VL, Presler R, Pattinson D, Nguyen HLK, Hoang VMP, Le MQ, van Bakel H, Neumann G, Kawaoka Y. Continued Circulation of Highly Pathogenic H5 Influenza Viruses in Vietnamese Live Bird Markets in 2018-2021. Viruses 2023; 15:1596. [PMID: 37515281 PMCID: PMC10384249 DOI: 10.3390/v15071596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
We isolated 77 highly pathogenic avian influenza viruses during routine surveillance in live poultry markets in northern provinces of Vietnam from 2018 to 2021. These viruses are of the H5N6 subtype and belong to HA clades 2.3.4.4g and 2.3.4.4h. Interestingly, we did not detect viruses of clade 2.3.4.4b, which in recent years have dominated in different parts of the world. The viruses isolated in this current study do not encode major determinants of mammalian adaptation (e.g., PB2-E627K or PB1-D701N) but possess amino acid substitutions that may affect viral receptor-binding, replication, or the responses to human antiviral factors. Several of the highly pathogenic H5N6 virus samples contained other influenza viruses, providing an opportunity for reassortment. Collectively, our study demonstrates that the highly pathogenic H5 viruses circulating in Vietnam in 2018-2021 were different from those in other parts of the world, and that the Vietnamese H5 viruses continue to evolve through mutations and reassortment.
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Affiliation(s)
- Lizheng Guan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Lavanya Babujee
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Victoria L. Browning
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Robert Presler
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - David Pattinson
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Hang Le Khanh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Vu Mai Phuong Hoang
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Mai Quynh Le
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (H.L.K.N.); (V.M.P.H.); (M.Q.L.)
| | - Harm van Bakel
- Department of Genetics and Genomic Services, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA; (L.G.); (L.B.); (V.L.B.); (R.P.); (D.P.)
- Division of Virology, Department of Microbiology and Immunology, International Research Center for Infectious Diseases, The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Research Center for Global Viral Diseases, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
- The University of Tokyo Pandemic Preparedness, Infection and Advanced Research (UTOPIA) Center, Tokyo 108-8639, Japan
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13
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Meseko C, Milani A, Inuwa B, Chinyere C, Shittu I, Ahmed J, Giussani E, Palumbo E, Zecchin B, Bonfante F, Maniero S, Angot A, Niang M, Fusaro A, Gobbo F, Terregino C, Olasoju T, Monne I, Muhammad M. The Evolution of Highly Pathogenic Avian Influenza A (H5) in Poultry in Nigeria, 2021-2022. Viruses 2023; 15:1387. [PMID: 37376688 DOI: 10.3390/v15061387] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
In 2021, amidst the COVID-19 pandemic and global food insecurity, the Nigerian poultry sector was exposed to the highly pathogenic avian influenza (HPAI) virus and its economic challenges. Between 2021 and 2022, HPAI caused 467 outbreaks reported in 31 of the 37 administrative regions in Nigeria. In this study, we characterized the genomes of 97 influenza A viruses of the subtypes H5N1, H5N2, and H5N8, which were identified in different agro-ecological zones and farms during the 2021-2022 epidemic. The phylogenetic analysis of the HA genes showed a widespread distribution of the H5Nx clade 2.3.4.4b and similarity with the HPAI H5Nx viruses that have been detected in Europe since late 2020. The topology of the phylogenetic trees indicated the occurrence of several independent introductions of the virus into the country, followed by a regional evolution of the virus that was most probably linked to its persistent circulation in West African territories. Additional evidence of the evolutionary potential of the HPAI viruses circulating in this region is the identification in this study of a putative H5N1/H9N2 reassortant virus in a mixed-species commercial poultry farm. Our data confirm Nigeria as a crucial hotspot for HPAI virus introduction from the Eurasian territories and reveal a dynamic pattern of avian influenza virus evolution within the Nigerian poultry population.
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Affiliation(s)
- Clement Meseko
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Bitrus Inuwa
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Chinonyerem Chinyere
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Ismaila Shittu
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - James Ahmed
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
| | - Edoardo Giussani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Elisa Palumbo
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Bianca Zecchin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Francesco Bonfante
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Silvia Maniero
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Angélique Angot
- Animal Health Service (NSAH), Food and Agriculture Organization of the United Nations (FAO-UN), 00198 Rome, Italy
| | - Mamadou Niang
- Regional Office for Africa (RAF), Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO-UN), Accra 00233, Ghana
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Federica Gobbo
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Taiwo Olasoju
- Federal Department of Veterinary and Pest Control Services (FDV&PCS), Federal Ministry of Agriculture and Rural Development (FMARD), Abuja 900108, Nigeria
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Division of Comparative Biomedical Sciences (BSBIO), 35128 Padova, Italy
| | - Maryam Muhammad
- Regional Laboratory for Animal Influenza & Transboundary Diseases, National Veterinary Research Institute (NVRI), Vom 930101, Nigeria
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14
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An SH, Hong SM, Song JH, Son SE, Lee CY, Choi KS, Kwon HJ. Engineering an Optimal Y280-Lineage H9N2 Vaccine Strain by Tuning PB2 Activity. Int J Mol Sci 2023; 24:ijms24108840. [PMID: 37240186 DOI: 10.3390/ijms24108840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/13/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
H9N2 avian influenza A viruses (AIVs) cause economic losses in the poultry industry and provide internal genomic segments for the evolution of H5N1 and H7N9 AIVs into more detrimental strains for poultry and humans. In addition to the endemic Y439/Korea-lineage H9N2 viruses, the Y280-lineage spread to Korea since 2020. Conventional recombinant H9N2 vaccine strains, which bear mammalian pathogenic internal genomes of the PR8 strain, are pathogenic in BALB/c mice. To reduce the mammalian pathogenicity of the vaccine strains, the PR8 PB2 was replaced with the non-pathogenic and highly productive PB2 of the H9N2 vaccine strain 01310CE20. However, the 01310CE20 PB2 did not coordinate well with the hemagglutinin (HA) and neuraminidase (NA) of the Korean Y280-lineage strain, resulting in a 10-fold lower virus titer compared to the PR8 PB2. To increase the virus titer, the 01310CE20 PB2 was mutated (I66M-I109V-I133V) to enhance the polymerase trimer integrity with PB1 and PA, which restored the decreased virus titer without causing mouse pathogenicity. The reverse mutation (L226Q) of HA, which was believed to decrease mammalian pathogenicity by reducing mammalian receptor affinity, was verified to increase mouse pathogenicity and change antigenicity. The monovalent Y280-lineage oil emulsion vaccine produced high antibody titers for homologous antigens but undetectable titers for heterologous (Y439/Korea-lineage) antigens. However, this defect was corrected by the bivalent vaccine. Therefore, the balance of polymerase and HA/NA activities can be achieved by fine-tuning PB2 activity, and a bivalent vaccine may be more effective in controlling concurrent H9N2 viruses with different antigenicities.
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Affiliation(s)
- Se-Hee An
- Laboratory of Avian Diseases, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Min Hong
- Laboratory of Avian Diseases, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Ha Song
- Laboratory of Avian Diseases, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Eun Son
- Laboratory of Avian Diseases, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyuk-Joon Kwon
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 88026, Republic of Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Pyeongchang 25354, Republic of Korea
- GeNiner Ltd., Seoul 08826, Republic of Korea
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15
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Emergence of a Reassortant 2.3.4.4b Highly Pathogenic H5N1 Avian Influenza Virus Containing H9N2 PA Gene in Burkina Faso, West Africa, in 2021. Viruses 2022; 14:v14091901. [PMID: 36146708 PMCID: PMC9504354 DOI: 10.3390/v14091901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 12/30/2022] Open
Abstract
Since 2006, the poultry population in Burkina Faso has been seriously hit by different waves of Highly Pathogenic Avian Influenza (HPAI) H5N1 epizootics. In December 2021, three distinct regions of Burkina Faso, namely, Gomboussougou, Bonyollo, and Koubri, detected HPAI H5N1 viruses in poultry. Whole genome characterization and statistical phylogenetic approaches were applied to shed light on the potential origin of these viruses and estimate the time of virus emergence. Our results revealed that the HPAI H5N1 viruses reported in the three affected regions of Burkina Faso cluster together within clade 2.3.4.4b, and are closely related to HPAI H5N1 viruses identified in Nigeria and Niger in the period 2021–2022, except for the PA gene, which clusters with H9N2 viruses of the zoonotic G1 lineage collected in West Africa between 2017 and 2020. These reassortant viruses possess several mutations that may be associated with an increased zoonotic potential. Although it is difficult to ascertain where and when the reassortment event occurred, the emergence of a H5N1/H9N2 reassortant virus in a vulnerable region, such as West Africa, raises concerns about its possible impact on animal and human health. These findings also highlight the risk that West Africa may become a new hotspot for the emergence of new genotypes of HPAI viruses.
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16
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A dominant internal gene cassette of high pathogenicity avian influenza H7N9 virus raised since 2018. Virus Genes 2022; 58:584-588. [PMID: 35974285 PMCID: PMC9380661 DOI: 10.1007/s11262-022-01928-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022]
Abstract
The zoonotic H7N9 avian influenza virus emerged with the H9N2-origin internal gene cassette. Previous studies have reported that genetic reassortments with H9N2 were common in the first five human H7N9 epidemic waves. However, our latest work found that the circulating high pathogenicity H7N9 virus has established a dominant internal gene cassette and has decreased the frequency of reassortment with H9N2 since 2018. This dominant cassette of H7N9 was distinct from the cocirculating H9N2, although they shared a common ancestor. As a result, we suppose that this dominant cassette may benefit the viral population fitness and promote its continuous circulation in chickens.
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17
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Zhang Y, Eskridge KM, Zhang S, Lu G. Identifying host-specific amino acid signatures for influenza A viruses using an adjusted entropy measure. BMC Bioinformatics 2022; 23:333. [PMID: 35962315 PMCID: PMC9372975 DOI: 10.1186/s12859-022-04885-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/02/2022] [Indexed: 11/29/2022] Open
Abstract
Background Influenza A viruses (IAV) exhibit vast genetic mutability and have great zoonotic potential to infect avian and mammalian hosts and are known to be responsible for a number of pandemics. A key computational issue in influenza prevention and control is the identification of molecular signatures with cross-species transmission potential. We propose an adjusted entropy-based host-specific signature identification method that uses a similarity coefficient to incorporate the amino acid substitution information and improve the identification performance. Mutations in the polymerase genes (e.g., PB2) are known to play a major role in avian influenza virus adaptation to mammalian hosts. We thus focus on the analysis of PB2 protein sequences and identify host specific PB2 amino acid signatures. Results Validation with a set of H5N1 PB2 sequences from 1996 to 2006 results in adjusted entropy having a 40% false negative discovery rate compared to a 60% false negative rate using unadjusted entropy. Simulations across different levels of sequence divergence show a false negative rate of no higher than 10% while unadjusted entropy ranged from 9 to 100%. In addition, under all levels of divergence adjusted entropy never had a false positive rate higher than 9%. Adjusted entropy also identifies important mutations in H1N1pdm PB2 previously identified in the literature that explain changes in divergence between 2008 and 2009 which unadjusted entropy could not identify. Conclusions Based on these results, adjusted entropy provides a reliable and widely applicable host signature identification approach useful for IAV monitoring and vaccine development.
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Affiliation(s)
- Yixiang Zhang
- Department of Statistics, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Kent M Eskridge
- Department of Statistics, University of Nebraska - Lincoln, Lincoln, NE, USA.
| | - Shunpu Zhang
- Department of Statistics, University of Central Florida, Orlando, USA
| | - Guoqing Lu
- Department of Biology, University of Nebraska - Omaha, Omaha, NE, USA
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18
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Durairaj K, Trinh TTT, Yun SY, Yeo SJ, Sung HW, Park H. Molecular Characterization and Pathogenesis of H6N6 Low Pathogenic Avian Influenza Viruses Isolated from Mallard Ducks (Anas platyrhynchos) in South Korea. Viruses 2022; 14:v14051001. [PMID: 35632743 PMCID: PMC9143286 DOI: 10.3390/v14051001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
The subtype H6N6 has been identified worldwide following the increasing frequency of avian influenza viruses (AIVs). These AIVs also have the ability to bind to human-like receptors, thereby increasing the risk of animal-human transmission. In September 2019, an H6N6 avian influenza virus—KNU2019-48 (A/Mallard (Anas platyrhynchos)/South Korea/KNU 2019-48/2019(H6N6))—was isolated from Anas platyrhynchos in South Korea. Phylogenetic analysis results revealed that the hemagglutinin (HA) gene of this strain belongs to the Korean lineage, whereas the neuraminidase (NA) and polymerase basic protein 1 (PB1) genes belong to the Chinese lineage. Outstanding internal proteins such as PB2, polymerase acidic protein, nucleoprotein, matrix protein, and non-structural protein belong to the Vietnamese lineage. Additionally, a monobasic amino acid (PRIETR↓GLF) at the HA cleavage site; non-deletion of the stalk region (residue 59–69) in the NA gene; and E627 in the PB2 gene indicate that the KNU2019-48 isolate is a typical low-pathogenic avian influenza (LPAI) virus. The nucleotide sequence similarity analysis of HA revealed that the highest homology (97.18%) of this isolate is to that of A/duck/Jiangxi/01.14 NCJD125-P/2015(H6N6), and the amino acid sequence of NA (97.38%) is closely related to that of A/duck/Fujian/10.11_FZHX1045-C/2016 (H6N6). An in vitro analysis of the KNU2019-48 virus shows a virus titer of not more than 2.8 Log10 TCID 50/mL until 72 h post-infection, whereas in the lungs, the virus is detected at 3 dpi (days post-infection). The isolated KNU2019-48 (H6N6) strain is the first reported AIV in Korea, and the H6 subtype virus has co-circulated in China, Vietnam, and Korea for half a decade. Overall, our study demonstrates that Korean H6N6 strain PB1-S375N, PA-A404S, and S409N mutations are infectious in humans and might contribute to the enhanced pathogenicity of this strain. Therefore, we emphasize the importance of continuous and intensive surveillance of the H6N6 virus not only in Korea but also worldwide.
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Affiliation(s)
- Kaliannan Durairaj
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (K.D.); (S.-Y.Y.)
| | - Thuy-Tien Thi Trinh
- Institute of Endemic Diseases, Medical Research Center, Department of Tropical Medicine and Parasitology, Seoul National University, Seoul 03080, Korea;
| | - Su-Yeon Yun
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (K.D.); (S.-Y.Y.)
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (S.-J.Y.); (H.-W.S.); (H.P.)
| | - Haan-Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (S.-J.Y.); (H.-W.S.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (K.D.); (S.-Y.Y.)
- Correspondence: (S.-J.Y.); (H.-W.S.); (H.P.)
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19
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Kandeil A, Moatasim Y, El Taweel A, El Sayes M, Rubrum A, Jeevan T, McKenzie PP, Webby RJ, Ali MA, Kayali G, El-Shesheny R. Genetic and Antigenic Characteristics of Highly Pathogenic Avian Influenza A(H5N8) Viruses Circulating in Domestic Poultry in Egypt, 2017–2021. Microorganisms 2022; 10:microorganisms10030595. [PMID: 35336170 PMCID: PMC8948635 DOI: 10.3390/microorganisms10030595] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023] Open
Abstract
In Egypt, the endemicity of avian influenza viruses is a serious concern. Since 2016, several outbreaks of H5N8 have been recorded among domestic poultry in various areas of the country. Active surveillance of domestic poultry across several governorates in Egypt from 2017 to 2021 detected at least six genotypes of Highly Pathogenic Avian Influenza (HPAI) H5N8 viruses with evidence of partial or complete annual replacement of dominant strains. Although all Egyptian H5N8 viruses had clade 2.3.4.4b hemagglutinin (HA) genes, the remaining viral gene segments were from multiple geographic origins, indicating that the H5N8 isolates resulted from multiple introductions. Mutations in the viral proteins associated with pathogenicity and antiviral drug resistance were detected. Some mutations in the HA resulted in antigenic drift. Heterogeneity in circulating H5N8 HPAI threatens poultry production and public health.
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Affiliation(s)
- Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (Y.M.); (A.E.T.); (M.E.S.); (M.A.A.)
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (T.J.); (P.P.M.)
| | - Yassmin Moatasim
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (Y.M.); (A.E.T.); (M.E.S.); (M.A.A.)
| | - Ahmed El Taweel
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (Y.M.); (A.E.T.); (M.E.S.); (M.A.A.)
| | - Mohamed El Sayes
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (Y.M.); (A.E.T.); (M.E.S.); (M.A.A.)
| | - Adam Rubrum
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (T.J.); (P.P.M.)
| | - Trushar Jeevan
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (T.J.); (P.P.M.)
| | - Pamela P. McKenzie
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (T.J.); (P.P.M.)
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.R.); (T.J.); (P.P.M.)
- Correspondence: (R.J.W.); (G.K.); (R.E.-S.)
| | - Mohamed A. Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (Y.M.); (A.E.T.); (M.E.S.); (M.A.A.)
| | - Ghazi Kayali
- Human Link, Dubai 971, United Arab Emirates
- Correspondence: (R.J.W.); (G.K.); (R.E.-S.)
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (Y.M.); (A.E.T.); (M.E.S.); (M.A.A.)
- Correspondence: (R.J.W.); (G.K.); (R.E.-S.)
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20
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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21
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Nguyen ATV, Hoang VT, Sung HW, Yeo SJ, Park H. Genetic Characterization and Pathogenesis of Three Novel Reassortant H5N2 Viruses in South Korea, 2018. Viruses 2021; 13:v13112192. [PMID: 34834997 PMCID: PMC8619638 DOI: 10.3390/v13112192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/03/2022] Open
Abstract
The outbreaks of H5N2 avian influenza viruses have occasionally caused the death of thousands of birds in poultry farms. Surveillance during the 2018 winter season in South Korea revealed three H5N2 isolates in feces samples collected from wild birds (KNU18-28: A/Wild duck/South Korea/KNU18-28/2018, KNU18-86: A/Bean Goose/South Korea/KNU18-86/2018, and KNU18-93: A/Wild duck/South Korea/KNU18-93/2018). Phylogenetic tree analysis revealed that these viruses arose from reassortment events among various virus subtypes circulating in South Korea and other countries in the East Asia–Australasian Flyway. The NS gene of the KNU18-28 and KNU18-86 isolates was closely related to that of China’s H10N3 strain, whereas the KNU18-93 strain originated from the H12N2 strain in Japan, showing two different reassortment events and different from a low pathogenic H5N3 (KNU18-91) virus which was isolated at the same day and same place with KNU18-86 and KNU18-93. These H5N2 isolates were characterized as low pathogenic avian influenza viruses. However, many amino acid changes in eight gene segments were identified to enhance polymerase activity and increase adaptation and virulence in mice and mammals. Experiments reveal that viral replication in MDCK cells was quite high after 12 hpi, showing the ability to replicate in mouse lungs. The hematoxylin and eosin-stained (H&E) lung sections indicated different degrees of pathogenicity of the three H5N2 isolates in mice compared with that of the control H1N1 strain. The continuing circulation of these H5N2 viruses may represent a potential threat to mammals and humans. Our findings highlight the need for intensive surveillance of avian influenza virus circulation in South Korea to prevent the risks posed by these reassortment viruses to animal and public health.
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Affiliation(s)
- Anh Thi Viet Nguyen
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
| | - Vui Thi Hoang
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (S.-J.Y.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
- Correspondence: (S.-J.Y.); (H.P.)
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22
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Hossain MG, Akter S, Dhole P, Saha S, Kazi T, Majbauddin A, Islam MS. Analysis of the Genetic Diversity Associated With the Drug Resistance and Pathogenicity of Influenza A Virus Isolated in Bangladesh From 2002 to 2019. Front Microbiol 2021; 12:735305. [PMID: 34603265 PMCID: PMC8484749 DOI: 10.3389/fmicb.2021.735305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
The subtype prevalence, drug resistance- and pathogenicity-associated mutations, and the distribution of the influenza A virus (IAV) isolates identified in Bangladesh from 2002 to 2019 were analyzed using bioinformatic tools. A total of 30 IAV subtypes have been identified in humans (4), avian species (29), and environment (5) in Bangladesh. The predominant subtypes in human and avian species are H1N1/H3N2 and H5N1/H9N2, respectively. However, the subtypes H5N1/H9N2 infecting humans and H3N2/H1N1 infecting avian species have also been identified. Among the avian species, the maximum number of subtypes (27) have been identified in ducks. A 3.56% of the isolates showed neuraminidase inhibitor (NAI) resistance with a prevalence of 8.50, 1.33, and 2.67% in avian species, humans, and the environment, respectively, the following mutations were detected: V116A, I117V, D198N, I223R, S247N, H275Y, and N295S. Prevalence of adamantane-resistant IAVs was 100, 50, and 30.54% in humans, the environment, and avian species, respectively, the subtypes H3N2, H1N1, H9N2, and H5N2 were highly prevalent, with the subtype H5N1 showing a comparatively lower prevalence. Important PB2 mutations such D9N, K526R, A588V, A588I, G590S, Q591R, E627K, K702R, and S714R were identified. A wide range of IAV subtypes have been identified in Bangladesh with a diversified genetic variation in the NA, M2, and PB2 proteins providing drug resistance and enhanced pathogenicity. This study provides a detailed analysis of the subtypes, and the host range of the IAV isolates and the genetic variations related to their proteins, which may aid in the prevention, treatment, and control of IAV infections in Bangladesh, and would serve as a basis for future investigations.
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Affiliation(s)
- Md Golzar Hossain
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sharmin Akter
- Department of Physiology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Priya Dhole
- Department of Biology, The Pennsylvania State University, Pennsylvania, PA, United States
| | - Sukumar Saha
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Taheruzzaman Kazi
- Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Abir Majbauddin
- Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Md Sayeedul Islam
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
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23
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Evseev D, Magor KE. Molecular Evolution of the Influenza A Virus Non-structural Protein 1 in Interspecies Transmission and Adaptation. Front Microbiol 2021; 12:693204. [PMID: 34671321 PMCID: PMC8521145 DOI: 10.3389/fmicb.2021.693204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/06/2021] [Indexed: 12/03/2022] Open
Abstract
The non-structural protein 1 (NS1) of influenza A viruses plays important roles in viral fitness and in the process of interspecies adaptation. It is one of the most polymorphic and mutation-tolerant proteins of the influenza A genome, but its evolutionary patterns in different host species and the selective pressures that underlie them are hard to define. In this review, we highlight some of the species-specific molecular signatures apparent in different NS1 proteins and discuss two functions of NS1 in the process of viral adaptation to new host species. First, we consider the ability of NS1 proteins to broadly suppress host protein expression through interaction with CPSF4. This NS1 function can be spontaneously lost and regained through mutation and must be balanced against the need for host co-factors to aid efficient viral replication. Evidence suggests that this function of NS1 may be selectively lost in the initial stages of viral adaptation to some new host species. Second, we explore the ability of NS1 proteins to inhibit antiviral interferon signaling, an essential function for viral replication without which the virus is severely attenuated in any host. Innate immune suppression by NS1 not only enables viral replication in tissues, but also dampens the adaptive immune response and immunological memory. NS1 proteins suppress interferon signaling and effector functions through a variety of protein-protein interactions that may differ from host to host but must achieve similar goals. The multifunctional influenza A virus NS1 protein is highly plastic, highly versatile, and demonstrates a diversity of context-dependent solutions to the problem of interspecies adaptation.
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Affiliation(s)
| | - Katharine E. Magor
- Department of Biological Sciences, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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24
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Yeo SJ, Hoang VT, Duong TB, Nguyen NM, Tuong HT, Azam M, Sung HW, Park H. Emergence of a Novel Reassortant H5N3 Avian Influenza Virus in Korean Mallard Ducks in 2018. Intervirology 2021; 65:1-16. [PMID: 34438407 DOI: 10.1159/000517057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/29/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The avian influenza (AI) virus causes a highly contagious disease which is common in wild and domestic birds and sporadic in humans. Mutations and genetic reassortments among the 8 negative-sense RNA segments of the viral genome alter its pathogenic potential, demanding well-targeted, active surveillance for infection control. METHODS Wild duck fecal samples were collected during the 2018 bird health annual surveillance in South Korea for tracking variations of the AI virus. One low-pathogenic avian influenza H5N3 reassortment virus (A/mallard duck/South Korea/KNU18-91/2018 [H5N3]) was isolated and genomically characterized by phylogenetic and molecular analyses in this study. RESULTS It was devoid of polybasic amino acids at the hemagglutinin (HA) cleavage site and exhibited a stalk region without deletion in the neuraminidase (NA) gene and NA inhibitor resistance-linked E/D627K/N and D701N marker mutations in the PB2 gene, suggesting its low-pathogenic AI. It showed a potential of a reassortment where only HA originated from the H5N3 poultry virus of China and other genes were derived from Mongolia. In phylogenetic analysis, HA was different from that of the isolate of H5N3 in Korea, 2015. In addition, this novel virus showed adaptation in Madin-Darby canine kidney cells, with 8.05 ± 0.14 log10 50% tissue culture infectious dose (TCID50) /mL at 36 h postinfection. However, it could not replicate in mice well, showing positive growth at 3 days postinfection (dpi) (2.1 ± 0.13 log10 TCID50/mL) but not at 6 dpi. CONCLUSIONS The HA antigenic relationship of A/mallard duck/South Korea/KNU18-91/2018 (H5N3) showed differences toward one of the old low-pathogenic H5N3 viruses in Korea. These results indicated that a novel reassortment low-pathogenic avian influenza H5N3 subtype virus emerged in South Korea in 2018 via novel multiple reassortments with Eurasian viruses, rather than one of old Korean H5N3 strains.
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Affiliation(s)
- Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, Republic of Korea,
| | - Vui Thi Hoang
- Department of Infection Biology, Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Tuan Bao Duong
- Department of Infection Biology, Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Ngoc Minh Nguyen
- Department of Infection Biology, Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Hien Thi Tuong
- Department of Infection Biology, Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Mudsser Azam
- Department of Infection Biology, Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyun Park
- Department of Infection Biology, Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea
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25
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Guo F, Roy A, Wang R, Yang J, Zhang Z, Luo W, Shen X, Chen RA, Irwin DM, Shen Y. Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Front Microbiol 2021; 12:655228. [PMID: 34194404 PMCID: PMC8236823 DOI: 10.3389/fmicb.2021.655228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Since its first isolation in around 2007, the avian-origin H3N2 canine influenza virus (CIV) has become established and continues to circulate in dog populations. This virus serves as a useful model for deciphering the complex evolutionary process of interspecies transmission of influenza A virus (IAV) from one species to its subsequent circulation in another mammalian host. The present investigation is a comprehensive effort to identify and characterize genetic changes that accumulated in the avian-origin H3N2 CIV during its circulation in the dog. We revealed that H3N2 CIV experiences greater selection pressure with extremely high global non-synonymous to synonymous substitution ratios per codon (dN/dS ratio) for each gene compared to the avian reservoir viruses. A total of 54 amino acid substitutions were observed to have accumulated and become fixed in the H3N2 CIV population based on our comprehensive codon-based frequency diagram analysis. Of these substitutions, 11 sites also display high prevalence in H3N8 CIV, indicating that convergent evolution has occurred on different lineages of CIV. Notably, six substitutions, including HA-G146S, M1-V15I, NS1-E227K, PA-C241Y, PB2-K251R, and PB2-G590S, have been reported to play imperative roles in facilitating the transmission and spillover of IAVs across species barriers. Most of these substitutions were found to have become fixed in around 2015, which might have been a favorable factor that facilitating the spread of these CIV lineages from South Asia to North America and subsequent further circulation in these areas. We also detected 12 sites in six viral genes with evidence for positive selection by comparing the rates of non-synonymous and synonymous substitutions at each site. Besides, our study reports trends of enhanced ongoing adaptation of H3N2 CIV to their respective host cellular systems, based on the codon adaptation index analysis, which points toward increasing fitness for efficient viral replication. In addition, a reduction in the abundance of the CpG motif, as evident from an analysis of relative dinucleotide abundance, may contribute to the successful evasion of host immune recognition. The present study provides key insights into the adaptive changes that have accumulated in the avian-origin H3N2 viral genomes during its establishment and circulation into dog populations.
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Affiliation(s)
- Fucheng Guo
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara, India
| | - Ruichen Wang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinjin Yang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhipeng Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wen Luo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Rui-Ai Chen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada
| | - Yongyi Shen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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26
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Liang Y, Nissen JN, Krog JS, Breum SØ, Trebbien R, Larsen LE, Hjulsager CK. Novel Clade 2.3.4.4b Highly Pathogenic Avian Influenza A H5N8 and H5N5 Viruses in Denmark, 2020. Viruses 2021; 13:886. [PMID: 34065033 PMCID: PMC8151437 DOI: 10.3390/v13050886] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
Since late 2020, outbreaks of H5 highly pathogenic avian influenza (HPAI) viruses belonging to clade 2.3.4.4b have emerged in Europe. To investigate the evolutionary history of these viruses, we performed genetic characterization on the first HPAI viruses found in Denmark during the autumn of 2020. H5N8 viruses from 14 wild birds and poultry, as well as one H5N5 virus from a wild bird, were characterized by whole genome sequencing and phylogenetic analysis. The Danish H5N8 viruses were found to be genetically similar to each other and to contemporary European clade 2.3.4.4b H5N8 viruses, while the Danish H5N5 virus was shown to be a unique genotype from the H5N5 viruses that circulated at the same time in Russia, Germany, and Belgium. Genetic analyses of one of the H5N8 viruses revealed the presence of a substitution (PB2-M64T) that is highly conserved in human seasonal influenza A viruses. Our analyses showed that the late 2020 clade 2.3.4.4b HPAI H5N8 viruses were most likely new incursions introduced by migrating birds to overwintering sites in Europe, rather than the result of continued circulation of H5N8 viruses from previous introductions to Europe in 2016/2017 and early 2020.
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Affiliation(s)
- Yuan Liang
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (Y.L.); (L.E.L.)
| | - Jakob N. Nissen
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.N.N.); (J.S.K.); (S.Ø.B.); (R.T.)
| | - Jesper S. Krog
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.N.N.); (J.S.K.); (S.Ø.B.); (R.T.)
| | - Solvej Ø. Breum
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.N.N.); (J.S.K.); (S.Ø.B.); (R.T.)
| | - Ramona Trebbien
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.N.N.); (J.S.K.); (S.Ø.B.); (R.T.)
| | - Lars E. Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (Y.L.); (L.E.L.)
| | - Charlotte K. Hjulsager
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.N.N.); (J.S.K.); (S.Ø.B.); (R.T.)
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Yang W, Schountz T, Ma W. Bat Influenza Viruses: Current Status and Perspective. Viruses 2021; 13:v13040547. [PMID: 33805956 PMCID: PMC8064322 DOI: 10.3390/v13040547] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
Bats are natural reservoirs for many viruses, including several that are zoonotic. Two unusual H17N10 and H18N11 influenza viruses have been found in New World bats. Although neither of these viruses have been isolated, infectious clone technology has permitted significant progress to understand their biology, which include unique features compared to all other known influenza A viruses. In addition, an H9N2-like influenza A virus was isolated from Old World bats and it shows similar characteristics of normal influenza A viruses. In this review, current status and perspective on influenza A viruses identified in bats is reviewed and discussed.
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Affiliation(s)
- Wenyu Yang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA;
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Tony Schountz
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA;
| | - Wenjun Ma
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA;
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
- Correspondence:
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L'vov DK, Burtseva EI, Kolobukhina LV, Fedyakina IT, Bovin NV, Ignatjeva AV, Krasnoslobodtsev KG, Feodoritova EL, Trushakova SV, Breslav NV, Merkulova LN, Mukasheva EA, Khlopova IN, Voronina OL, Aksyonova EI, Kunda MS, Ryzhova NN, Vartanjan RV, Kistenyova LB, Kirillov IM, Proshina ES, Rosatkevich AG, Kruzhkova IS, Zaplatnikov AL, Bazarova MV, Smetanina SV, Kharlamov MV, Karpov NL, Shikhin AV. [Peculiarities of the influenza and ARVI viruses circulation during epidemic season 2019-2020 in some regions of Russia]. Vopr Virusol 2021; 65:335-349. [PMID: 33533230 DOI: 10.36233/0507-4088-2020-65-6-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The surveillance of influenza viruses in ARVI structure and study of their properties in epidemic season 2019-2020 in Russian Federation are actual for investigations due to tasks of Global Influenza Strategy initiated by WHO in 2019. MATERIAL AND METHODS The data of epidemiological surveillance on influenza- and ARVI-associated morbidity and hospitalization in different age groups of population were analyzed; virological, genetic and statistical methods were used. RESULTS Preschool children were involved in epidemic the most. Meanwhile, the highest rate of hospitalization was observed in patients of 18-40 years old. Influenza A(H1N1)pdm09 virus dominated in etiology of ARVI in hospitalized patients and pneumonia. The role of respiratory viruses in severe cases of pneumonia and bronchoalveolar syndrome in children was shown. The differences in spectrum of circulating viruses caused ARVI in different regions of Russia were found. Influenza A(H1N1)pdm09 and B/Victoria-like viruses were the main etiological agents that caused of epidemic; its activity among all ARVI was 7.3 and 8.0%, respectively. The differences in antigenic properties of influenza A(H3N2) and B epidemic strains compared to vaccine viruses were found. The populations of epidemic strains were presented by following dominant genetic groups: 6B1.A5/183P for A(H1N1)pdm09, 3С.2а1b+137F for A(H3N2) and V1A.3 line B/Victoria-like for B viruses. The good profile of epidemic strains susceptibility to anti-neuraminidase inhibitors has been saved. The most of the studied influenza strains had the receptor specificity characteristic of human influenza viruses. CONCLUSIONS Obtained results identified the peculiarities of viruses caused the influenza and ARVI in epidemic season 2019-2020 in different regions of Russia. These results suggested the important role of influenza A(H1N1) pdm09 in severe cases and pneumonia in adults 18-40 years old. The continuing drift in influenza viruses was found, which, apparently, could not but affect the efficacy of vaccine prophylaxis and was also considered in the recommendations of WHO experts on the composition of influenza vaccines for the countries of the Northern Hemisphere in the 2020-2021 season.
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Affiliation(s)
- D K L'vov
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - E I Burtseva
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - L V Kolobukhina
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - I T Fedyakina
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - N V Bovin
- Institute of Bioorganic Chemistry named after academicians M.M. Shemyakin and Yu.A. Ovchinnikov of the Russian Academy of Sciences
| | - A V Ignatjeva
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - K G Krasnoslobodtsev
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - E L Feodoritova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - S V Trushakova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - N V Breslav
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - L N Merkulova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - E A Mukasheva
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - I N Khlopova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - O L Voronina
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - E I Aksyonova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - M S Kunda
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - N N Ryzhova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - R V Vartanjan
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - L B Kistenyova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - I M Kirillov
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - E S Proshina
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - A G Rosatkevich
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - I S Kruzhkova
- FSBI «National Research Centre of Epidemiology and Microbiology named after honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - A L Zaplatnikov
- FSBO DPE Russian Academy of Continuous Professional Education of the Ministry of Health of Russia
| | - M V Bazarova
- Clinical Hospital for Infectious Diseases №1 of the Department of Health of Moscow
| | - S V Smetanina
- Clinical Hospital for Infectious Diseases №1 of the Department of Health of Moscow
| | - M V Kharlamov
- FBIH «Center of hygiene and epidemiology in Novgorod region»
| | - N L Karpov
- FBIH «Center of hygiene and epidemiology in Yaroslavl' region»
| | - A V Shikhin
- FBIH «Center of hygiene and epidemiology in Tomsk region»
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Trinh TTT, Duong BT, Nguyen ATV, Tuong HT, Hoang VT, Than DD, Nam S, Sung HW, Yun KJ, Yeo SJ, Park H. Emergence of Novel Reassortant H1N1 Avian Influenza Viruses in Korean Wild Ducks in 2018 and 2019. Viruses 2020; 13:v13010030. [PMID: 33375376 PMCID: PMC7823676 DOI: 10.3390/v13010030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/19/2020] [Accepted: 12/24/2020] [Indexed: 02/08/2023] Open
Abstract
Influenza A virus subtype H1N1 has caused global pandemics like the “Spanish flu” in 1918 and the 2009 H1N1 pandemic several times. H1N1 remains in circulation and survives in multiple animal sources, including wild birds. Surveillance during the winter of 2018–2019 in Korea revealed two H1N1 isolates in samples collected from wild bird feces: KNU18-64 (A/Greater white-fronted goose/South Korea/KNU18-64/2018(H1N1)) and WKU19-4 (A/wild bird/South Korea/WKU19-4/2019(H1N1)). Phylogenetic analysis indicated that M gene of KNU18-64(H1N1) isolate resembles that of the Alaskan avian influenza virus, whereas WKU19-4(H1N1) appears to be closer to the Mongolian virus. Molecular characterization revealed that they harbor the amino acid sequence PSIQRS↓GLF and are low-pathogenicity influenza viruses. In particular, the two isolates harbored three different mutation sites, indicating that they have different virulence characteristics. The mutations in the PB1-F2 and PA protein of WKU19-4(H1N1) indicate increasing polymerase activity. These results corroborate the kinetic growth data for WKU19-4 in MDCK cells: a dramatic increase in the viral titer after 12 h post-inoculation compared with that in the control group H1N1 (CA/04/09(pdm09)). The KNU18-64(H1N1) isolate carries mutations indicating an increase in mammal adaptation; this characterization was confirmed by the animal study in mice. The KNU18-64(H1N1) group showed the presence of viruses in the lungs at days 3 and 6 post-infection, with titers of 2.71 ± 0.16 and 3.71 ± 0.25 log10(TCID50/mL), respectively, whereas the virus was only detected in the WKU19-4(H1N1) group at day 6 post-infection, with a lower titer of 2.75 ± 0.51 log10(TCID50/mL). The present study supports the theory that there is a relationship between Korea and America with regard to reassortment to produce novel viral strains. Therefore, there is a need for increased surveillance of influenza virus circulation in free-flying and wild land-based birds in Korea, particularly with regard to Alaskan and Asian strains.
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Affiliation(s)
- Thuy-Tien Thi Trinh
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Bao Tuan Duong
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Anh Thi Viet Nguyen
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Hien Thi Tuong
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Vui Thi Hoang
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Duong Duc Than
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - SunJeong Nam
- Division of EcoScience, Ewha University, Seoul 03760, Korea;
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 200-701, Korea;
| | - Ki-Jung Yun
- Department of Pathology, School of Medicine, Wonkwang University, Iksan 570-749, Korea;
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (S.-J.Y.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
- Correspondence: (S.-J.Y.); (H.P.)
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Roles of the Non-Structural Proteins of Influenza A Virus. Pathogens 2020; 9:pathogens9100812. [PMID: 33023047 PMCID: PMC7600879 DOI: 10.3390/pathogens9100812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Influenza A virus (IAV) is a segmented, negative single-stranded RNA virus that causes seasonal epidemics and has a potential for pandemics. Several viral proteins are not packed in the IAV viral particle and only expressed in the infected host cells. These proteins are named non-structural proteins (NSPs), including NS1, PB1-F2 and PA-X. They play a versatile role in the viral life cycle by modulating viral replication and transcription. More importantly, they also play a critical role in the evasion of the surveillance of host defense and viral pathogenicity by inducing apoptosis, perturbing innate immunity, and exacerbating inflammation. Here, we review the recent advances of these NSPs and how the new findings deepen our understanding of IAV–host interactions and viral pathogenesis.
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Barberis A, Boudaoud A, Gorrill A, Loupias J, Ghram A, Lachheb J, Alloui N, Ducatez MF. Full-length genome sequences of the first H9N2 avian influenza viruses isolated in the Northeast of Algeria. Virol J 2020; 17:108. [PMID: 32680533 PMCID: PMC7366561 DOI: 10.1186/s12985-020-01377-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/30/2020] [Indexed: 11/30/2022] Open
Abstract
Background H9N2 avian influenza viruses (AIV) has a worldwide geographic distribution and affects poultry of different types of production. H9N2 AIV was first reported in the Northeast of Algeria in April 2017, following an outbreak associated with high mortality, in broiler flocks. In the present study, we report full-length genome sequences of AIV H9N2, and the detailed phylogeny and molecular genetic analyses. Methods Ten AIV H9N2 strains, collected in broiler flocks, were amplified in 9-day-old embryonated specific pathogen free (SPF) chicken eggs. Their full-length genomes were successfully sequenced and phylogenetic and molecular characterizations were conducted. Results Phylogenetic analysis showed that the isolates were monophyletic, grouped within the G-1 lineage and were very close to Moroccan and Algerian strains identified in 2016 and 2017, respectively. The low pathogenicity of the strains was confirmed by the sequence motif (335RSSR/GLF341) at the hemagglutinin (HA) cleavage site. An exclusive substitution (T197A) that had not been previously reported for H9N2 viruses; but, conserved in some pandemic H1N1 viruses, was observed. When compared to the G1-like H9N2 prototype, the studied strains showed one less glycosylation site in HA, but 2–3 additional ones in the stalk of the neuraminidase (NA). The HA protein harbored the substitution 234 L, suggesting binding preference to human-like receptors. The NA protein harbored S372A and R403W substitutions, previously detected in H9N2 from Asia and the Middle East, and especially in H2N2 and H3N2 strains that caused human pandemics. Different molecular markers associated with virulence and mammalian infections have been detected in the viral internal proteins. The matrix M2 protein possessed the S31N substitution associated with drug resistance. The non-structural 1 (NS1) protein showed the “GSEV” PDZ ligand (PL) C-terminal motif and no 80–84 deletion. Conclusion Characterized Algerian AIV isolates showed mutations that suggest increased zoonotic potential. Additional studies in animal models are required to investigate the pathogenicity of these H9N2 AIV strains. Monitoring their evolution in both migratory and domestic birds is crucial to prevent transmission to humans. Implementation of adequate biosecurity measures that limit the introduction and the propagation of AIV H9N2 in Algerian poultry farm is crucial.
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Affiliation(s)
- Abdelheq Barberis
- Centre de Recherche en Biotechnologie, Nouvelle Ville Ali Mendjeli, El Khroub, Algeria. .,LESPA, Département vétérinaire, ISVSA, Université de Batna, Batna, Algeria.
| | - Amine Boudaoud
- LESPA, Département vétérinaire, ISVSA, Université de Batna, Batna, Algeria
| | - Angelina Gorrill
- IHAP, Université de Toulouse, INRAE, ENVT, 23 Chemin des Capelles, 31076, Toulouse cedex, France
| | - Josianne Loupias
- IHAP, Université de Toulouse, INRAE, ENVT, 23 Chemin des Capelles, 31076, Toulouse cedex, France
| | - Abdeljelil Ghram
- Laboratoire d'Epidémiologie et de Microbiologie Vétérinaire, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Jihene Lachheb
- Laboratoire d'Epidémiologie et de Microbiologie Vétérinaire, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Nadir Alloui
- LESPA, Département vétérinaire, ISVSA, Université de Batna, Batna, Algeria
| | - Mariette F Ducatez
- IHAP, Université de Toulouse, INRAE, ENVT, 23 Chemin des Capelles, 31076, Toulouse cedex, France.
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Everest H, Hill SC, Daines R, Sealy JE, James J, Hansen R, Iqbal M. The Evolution, Spread and Global Threat of H6Nx Avian Influenza Viruses. Viruses 2020; 12:v12060673. [PMID: 32580412 PMCID: PMC7354632 DOI: 10.3390/v12060673] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022] Open
Abstract
Avian influenza viruses of the subtype H6Nx are being detected globally with increasing frequency. Some H6Nx lineages are becoming enzootic in Asian poultry and sporadic incursions into European poultry are occurring more frequently. H6Nx viruses that contain mammalian adaptation motifs pose a zoonotic threat and have caused human cases. Although currently understudied globally, H6Nx avian influenza viruses pose a substantial threat to both poultry and human health. In this review we examine the current state of knowledge of H6Nx viruses including their global distribution, tropism, transmission routes and human health risk.
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Affiliation(s)
- Holly Everest
- The Pirbright Institute, Woking GU24 0NF, UK
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford OX1 3SZ UK
- Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Rebecca Daines
- The Pirbright Institute, Woking GU24 0NF, UK
- Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | | | - Joe James
- Department of Virology, Animal and Plant Health Agency, Addlestone KT15 3NB, UK
| | - Rowena Hansen
- Department of Virology, Animal and Plant Health Agency, Addlestone KT15 3NB, UK
| | - Munir Iqbal
- The Pirbright Institute, Woking GU24 0NF, UK
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Adaptation of H9N2 Influenza Viruses to Mammalian Hosts: A Review of Molecular Markers. Viruses 2020; 12:v12050541. [PMID: 32423002 PMCID: PMC7290818 DOI: 10.3390/v12050541] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 11/18/2022] Open
Abstract
As the number of human infections with avian and swine influenza viruses continues to rise, the pandemic risk posed by zoonotic influenza viruses cannot be underestimated. Implementation of global pandemic preparedness efforts has largely focused on H5 and H7 avian influenza viruses; however, the pandemic threat posed by other subtypes of avian influenza viruses, especially the H9 subtype, should not be overlooked. In this review, we summarize the literature pertaining to the emergence, prevalence and risk assessment of H9N2 viruses, and add new molecular analyses of key mammalian adaptation markers in the hemagglutinin and polymerase proteins. Available evidence has demonstrated that H9N2 viruses within the Eurasian lineage continue to evolve, leading to the emergence of viruses with an enhanced receptor binding preference for human-like receptors and heightened polymerase activity in mammalian cells. Furthermore, the increased prevalence of certain mammalian adaptation markers and the enhanced transmissibility of selected viruses in mammalian animal models add to the pandemic risk posed by this virus subtype. Continued surveillance of zoonotic H9N2 influenza viruses, inclusive of close genetic monitoring and phenotypic characterization in animal models, should be included in our pandemic preparedness efforts.
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34
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Lutz MM, Dunagan MM, Kurebayashi Y, Takimoto T. Key Role of the Influenza A Virus PA Gene Segment in the Emergence of Pandemic Viruses. Viruses 2020; 12:v12040365. [PMID: 32224899 PMCID: PMC7232137 DOI: 10.3390/v12040365] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/24/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza A viruses (IAVs) are a significant human pathogen that cause seasonal epidemics and occasional pandemics. Avian waterfowl are the natural reservoir of IAVs, but a wide range of species can serve as hosts. Most IAV strains are adapted to one host species and avian strains of IAV replicate poorly in most mammalian hosts. Importantly, IAV polymerases from avian strains function poorly in mammalian cells but host adaptive mutations can restore activity. The 2009 pandemic H1N1 (H1N1pdm09) virus acquired multiple mutations in the PA gene that activated polymerase activity in mammalian cells, even in the absence of previously identified host adaptive mutations in other polymerase genes. These mutations in PA localize within different regions of the protein suggesting multiple mechanisms exist to activate polymerase activity. Additionally, an immunomodulatory protein, PA-X, is expressed from the PA gene segment. PA-X expression is conserved amongst many IAV strains but activity varies between viruses specific for different hosts, suggesting that PA-X also plays a role in host adaptation. Here, we review the role of PA in the emergence of currently circulating H1N1pdm09 viruses and the most recent studies of host adaptive mutations in the PA gene that modulate polymerase activity and PA-X function.
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Affiliation(s)
- Michael M. Lutz
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA (M.M.D.); (Y.K.)
| | - Megan M. Dunagan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA (M.M.D.); (Y.K.)
| | - Yuki Kurebayashi
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA (M.M.D.); (Y.K.)
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi 422-8526, Japan
| | - Toru Takimoto
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA (M.M.D.); (Y.K.)
- Correspondence: ; Tel.: +1-585-273-2856
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Lee CY, An SH, Choi JG, Lee YJ, Kim JH, Kwon HJ. Rank orders of mammalian pathogenicity-related PB2 mutations of avian influenza A viruses. Sci Rep 2020; 10:5359. [PMID: 32210274 PMCID: PMC7093554 DOI: 10.1038/s41598-020-62036-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/05/2020] [Indexed: 11/09/2022] Open
Abstract
The PB2 gene is one of the key determinants for the mammalian adaptation of avian influenza A viruses (IAVs). Although mammalian pathogenicity-related mutations (MPMs) in PB2 genes were identified in different genetic backgrounds of avian IAVs, the relative effects of single or multiple mutations on viral fitness could not be directly compared. Furthermore, their mutational steps during mammalian adaptation had been unclear. In this study, we collectively compared the effects of individual and combined MPMs on viral fitness and determined their rank orders using a prototypic PB2 gene. Early acquired mutations may determine the function and potency of subsequent mutations and be important for recruiting multiple, competent combinations of MPMs. Higher mammalian pathogenicity was acquired with the greater accumulation of MPMs. Thus, the rank orders and the prototypic PB2 gene may be useful for predicting the present and future risks of PB2 genes of avian and mammalian IAVs.
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Affiliation(s)
- Chung-Young Lee
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea
| | - Se-Hee An
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea
| | - Jun-Gu Choi
- Avian Disease Division, Animal and Plant Quarantine Agency, 177, Hyeoksin 8-ro, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Youn-Jeong Lee
- Avian Disease Division, Animal and Plant Quarantine Agency, 177, Hyeoksin 8-ro, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Jae-Hong Kim
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea.,Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea
| | - Hyuk-Joon Kwon
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea. .,Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 08826, Seoul, Republic of Korea. .,Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Kangwon-do, Republic of Korea.
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Genetic Characterization of Avian Influenza A (H11N9) Virus Isolated from Mandarin Ducks in South Korea in 2018. Viruses 2020; 12:v12020203. [PMID: 32059510 PMCID: PMC7077279 DOI: 10.3390/v12020203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 01/17/2023] Open
Abstract
In July 2018, a novel avian influenza virus (A/Mandarin duck/South Korea/KNU18-12/2018(H11N9)) was isolated from Mandarin ducks in South Korea. Phylogenetic and molecular analyses were conducted to characterize the genetic origins of the H11N9 strain. Phylogenetic analysis indicated that eight gene segments of strain H11N9 belonged to the Eurasian lineages. Analysis of nucleotide sequence similarity of both the hemagglutinin (HA) and neuraminidase (NA) genes revealed the highest homology with A/duck/Kagoshima/KU57/2014 (H11N9), showing 97.70% and 98.00% nucleotide identities, respectively. Additionally, internal genes showed homology higher than 98% compared to those of other isolates derived from duck and wild birds. Both the polymerase acidic (PA) and polymerase basic 1 (PB1) genes were close to the H5N3 strain isolated in China; whereas, other internal genes were closely related to that of avian influenza virus in Japan. A single basic amino acid at the HA cleavage site (PAIASR↓GLF), the lack of a five-amino acid deletion (residue 69–73) in the stalk region of the NA gene, and E627 in the polymerase basic 2 (PB2) gene indicated that the A/Mandarin duck/South Korea/KNU18-12/2018(H11N9) isolate was a typical low-pathogenicity avian influenza. In vitro viral replication of H11N9 showed a lower titer than H1N1 and higher than H9N2. In mice, H11N9 showed lower adaptation than H1N1. The novel A/Mandarin duck/South Korea/KNU18-12/2018(H11N9) isolate may have resulted from an unknown reassortment through the import of multiple wild birds in Japan and Korea in approximately 2016–2017, evolving to produce a different H11N9 compared to the previous H11N9 in Korea (2016). Further reassortment events of this virus occurred in PB1 and PA in China-derived strains. These results indicate that Japanese- and Chinese-derived avian influenza contributes to the genetic diversity of A/Mandarin duck/South Korea/KNU18-12/2018(H11N9) in Korea.
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Kumar S, Yeo D, Harur Muralidharan N, Lai SK, Tong C, Tan BH, Sugrue RJ. Impaired Nuclear Export of the Ribonucleoprotein Complex and Virus-Induced Cytotoxicity Combine to Restrict Propagation of the A/Duck/Malaysia/02/2001 (H9N2) Virus in Human Airway Cells. Cells 2020; 9:cells9020355. [PMID: 32028682 PMCID: PMC7072679 DOI: 10.3390/cells9020355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 01/02/2023] Open
Abstract
In humans, (A549) cells impaired H9N2 virus nuclear export of the ribonucleoprotein (RNP) complex contrasted with the early and efficient nuclear export of the H1N1/WSN and pH1N1 virus RNP complexes. Although nuclear export of the RNP complex occurred via the nuclear pore complex, H9N2 virus infection also induced modifications in the nuclear envelope and induced cell cytotoxicity. Reduced PA protein levels in H9N2 virus-infected A549 cells occurred, and this phenomenon was independent of virus infection. Silencing the H1N1/WSN PA protein expression leads to impaired nuclear export of RNP complexes, suggesting that the impaired nuclear export of the H9N2 virus RNP complex may be one of the consequences of reduced PA protein levels. Early and efficient export of the RNP complex occurred in H9N2 virus-infected avian (CEF) cells, although structural changes in the nuclear envelope also occurred. Collectively our data suggest that a combination of delayed nuclear export and virus-induced cell cytotoxicity restricts H9N2 virus transmission in A549 cells. However, the early and efficient export of the RNP complex mitigated the effects of virus-induced cytotoxicity on H9N2 virus transmission in CEF cells. Our findings highlight the multi-factorial nature of host-adaptation of the polymerase proteins of avian influenza viruses in non-avian cell environments.
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Affiliation(s)
- Sriram Kumar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Dawn Yeo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
- Detection and Diagnostics Laboratory, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore;
| | - Nisha Harur Muralidharan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Cathlyn Tong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
| | - Boon Huan Tan
- Detection and Diagnostics Laboratory, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore;
| | - Richard J. Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; (S.K.); (D.Y.); (N.H.M.); (S.K.L.); (C.T.)
- Correspondence:
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Abolnik C, Strydom C, Rauff DL, Wandrag DBR, Petty D. Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. BMC Vet Res 2019; 15:455. [PMID: 31852473 PMCID: PMC6921544 DOI: 10.1186/s12917-019-2210-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/09/2019] [Indexed: 01/29/2023] Open
Abstract
Background The threat of poultry-origin H6 avian influenza viruses to human health emphasizes the importance of monitoring their evolution. South Africa’s H6N2 epidemic in chickens began in 2001 and two co-circulating antigenic sub-lineages of H6N2 could be distinguished from the outset. The true incidence and prevalence of H6N2 in the country has been difficult to determine, partly due to the continued use of an inactivated whole virus H6N2 vaccine and the inability to distinguish vaccinated from non-vaccinated birds on serology tests. In the present study, the complete genomes of 12 H6N2 viruses isolated from various farming systems between September 2015 and February 2019 in three major chicken-producing regions were analysed and a serological experiment was used to demonstrate the effects of antigenic mismatch in diagnostic tests. Results Genetic drift in H6N2 continued and antigenic diversity in sub-lineage I is increasing; no sub-lineage II viruses were detected. Reassortment patterns indicated epidemiological connections between provinces as well as different farming systems, but there was no reassortment with wild bird or ostrich influenza viruses. The sequence mismatch between the official antigens used for routine hemagglutination inhibition (HI) testing and circulating field strains has increased steadily, and we demonstrated that H6N2 field infections are likely to be missed. More concerning, sub-lineage I H6N2 viruses acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. Most sub-lineage I viruses isolated since 2015 acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the avian lysine marker. All strains had an unusual HA0 motif of PQVETRGIF or PQVGTRGIF. Conclusions The H6N2 viruses in South African chickens are mutating and reassorting amongst themselves but have remained a genetically pure lineage since they emerged more than 18 years ago. Greater efforts must be made by government and industry in the continuous isolation and characterization of field strains for use as HI antigens, new vaccine seed strains and to monitor the zoonotic threat of H6N2 viruses.
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Affiliation(s)
- Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, 0110, South Africa.
| | - Christine Strydom
- Deltamune (Pty) Ltd, 248 Jean Avenue, Lyttleton, Centurion, 0140, South Africa
| | - Dionne Linda Rauff
- Deltamune (Pty) Ltd, 248 Jean Avenue, Lyttleton, Centurion, 0140, South Africa
| | - Daniel Barend Rudolph Wandrag
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, 0110, South Africa
| | - Deryn Petty
- The Poultry Practice, PO Box 5615, Walmer, Port Elizabeth, 6065, South Africa
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Zhu W, Feng Z, Chen Y, Yang L, Liu J, Li X, Liu S, Zhou L, Wei H, Gao R, Wang D, Shu Y. Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Emerg Microbes Infect 2019; 8:989-999. [PMID: 31267843 PMCID: PMC6609330 DOI: 10.1080/22221751.2019.1635873] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
It has recently been proposed that the Eurasian avian-like H1N1 (EA H1N1) swine influenza virus (SIV) is one of the most likely zoonotic viruses to cause the next influenza pandemic. Two main genotypes EA H1N1 viruses have been recognized to be infected humans in China. Our study finds that one of the genotypes JS1-like viruses are avirulent in mice. However, the other are HuN-like viruses and are virulent in mice. The molecular mechanism underlying this difference shows that the NP gene determines the virulence of the EA H1N1 viruses in mice. In addition, a single substitution, Q357K, in the NP protein of the EA H1N1 viruses alters the virulence phenotype. This substitution is a typical human signature marker, which is prevalent in human viruses but rarely detected in avian influenza viruses. The NP-Q357K substitution is readily to be occurred when avian influenza viruses circulate in pigs, and may facilitate their infection of humans and allow viruses also carrying NP-357K to circulate in humans. Our study demonstrates that the substitution Q357K in the NP protein plays a key role in the virulence phenotype of EA H1N1 SIVs, and provides important information for evaluating the pandemic risk of field influenza strains.
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Affiliation(s)
- Wenfei Zhu
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Zhaomin Feng
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Yongkun Chen
- c School of Public Health (Shenzhen) , Sun Yat-sen University , Guangdong , People's Republic of China
| | - Lei Yang
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Jia Liu
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Xiyan Li
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Suli Liu
- c School of Public Health (Shenzhen) , Sun Yat-sen University , Guangdong , People's Republic of China
| | - Lijuan Zhou
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Hejiang Wei
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Rongbao Gao
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Dayan Wang
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Yuelong Shu
- a 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 , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China.,c School of Public Health (Shenzhen) , Sun Yat-sen University , Guangdong , People's Republic of China
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40
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Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 2019; 55:739-768. [PMID: 31428925 PMCID: PMC6831541 DOI: 10.1007/s11262-019-01700-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Avian influenza viruses (AIVs) circulate globally, spilling over into domestic poultry and causing zoonotic infections in humans. Fortunately, AIVs are not yet capable of causing sustained human-to-human infection; however, AIVs are still a high risk as future pandemic strains, especially if they acquire further mutations that facilitate human infection and/or increase pathogenesis. Molecular characterization of sequencing data for known genetic markers associated with AIV adaptation, transmission, and antiviral resistance allows for fast, efficient assessment of AIV risk. Here we summarize and update the current knowledge on experimentally verified molecular markers involved in AIV pathogenicity, receptor binding, replicative capacity, and transmission in both poultry and mammals with a broad focus to include data available on other AIV subtypes outside of A/H5N1 and A/H7N9.
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41
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Zhong G, Fan S, Lopes TJS, Le MQ, van Bakel H, Dutta J, Smith GJD, Jayakumar J, Nguyen HLK, Hoang PVM, Halfmann P, Hatta M, Su YCF, Neumann G, Kawaoka Y. Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009-2013 in Vietnam. Front Microbiol 2019; 10:1411. [PMID: 31293548 PMCID: PMC6603144 DOI: 10.3389/fmicb.2019.01411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/05/2019] [Indexed: 11/13/2022] Open
Abstract
Routine surveillance and surveillance in response to influenza outbreaks in avian species in Vietnam in 2009-2013 resulted in the isolation of numerous H5N1 influenza viruses of clades 1.1.2, 2.3.2.1a, 2.3.2.1b, 2.3.2.1c, and 2.3.4.1. Consistent with other studies, we found that viruses of clade 2.3.2.1c were dominant in Vietnam in 2013 and circulated in the northern, central, and southern parts of the country. Phylogenetic analysis revealed reassortment among viruses of clades 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c; in contrast, no reassortment was detected between clade 2.3.2.1 viruses and viruses of clades 1.1.2 or 2.3.4.1, respectively. Deep-sequencing of 42 of the 53 isolated H5N1 viruses revealed viral subpopulations encoding variants that may affect virulence, host range, or sensitivity to antiviral compounds; virus isolates containing these subpopulations may have a higher potential to transmit and adapt to mammals. Among the viruses sequenced, a relatively high number of non-synonymous nucleotide polymorphisms was detected in a virus isolated from a barn swallow, possibly suggesting influenza virus adaption to this host.
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Affiliation(s)
- Gongxun Zhong
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Shufang Fan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Tiago J S Lopes
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mai Quynh Le
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jayeeta Dutta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gavin J D Smith
- Duke-NUS Medical School, Singapore, Singapore.,Duke Global Health Institute, Duke University, Durham, NC, United States
| | | | | | | | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Masato Hatta
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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Soh YS, Moncla LH, Eguia R, Bedford T, Bloom JD. Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans. eLife 2019; 8:45079. [PMID: 31038123 PMCID: PMC6491042 DOI: 10.7554/elife.45079] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/31/2019] [Indexed: 12/11/2022] Open
Abstract
Viruses like influenza are infamous for their ability to adapt to new hosts. Retrospective studies of natural zoonoses and passaging in the lab have identified a modest number of host-adaptive mutations. However, it is unclear if these mutations represent all ways that influenza can adapt to a new host. Here we take a prospective approach to this question by completely mapping amino-acid mutations to the avian influenza virus polymerase protein PB2 that enhance growth in human cells. We identify numerous previously uncharacterized human-adaptive mutations. These mutations cluster on PB2’s surface, highlighting potential interfaces with host factors. Some previously uncharacterized adaptive mutations occur in avian-to-human transmission of H7N9 influenza, showing their importance for natural virus evolution. But other adaptive mutations do not occur in nature because they are inaccessible via single-nucleotide mutations. Overall, our work shows how selection at key molecular surfaces combines with evolutionary accessibility to shape viral host adaptation. Viruses copy themselves by hijacking the cells of an infected host, but this comes with some limitations. Cells from different species have different molecular machinery and so viruses often have to specialize to a narrow group of species. This specialization consists largely of fine-tuning the way that viral proteins interact with host proteins. For instance, in bird flu viruses, a protein known as PB2 does not interact well with the machinery in human cells. Because PB2 proteins form part of the viral polymerase (the structure that copies the viral genome), this prevents bird flu viruses from replicating efficiently in humans. Sometimes however, changes in the PB2 protein allow bird flu viruses to better replicate in humans, potentially leading to deadly flu pandemics. To understand exactly how this happens, researchers have previously used two approaches: examining the changes that have happened in past flu viruses, and monitoring the evolution of bird flu viruses grown in human cells in the lab. However, these approaches can only look at a small number of the many possible genetic changes to the virus. This makes it hard to anticipate the new ways that flu might adapt to human cells in the future. To overcome this problem, Soh et al. systematically created all of the single changes to the bird flu PB2, altering every element of the protein sequence one-by-one. They then tested which of the changes to PB2 helped the virus grow better in human cells. The modifications that made the viruses thrive were on the surface of the protein, suggesting that they might improve interaction with the cell machinery of the host. Some changes have been found in bird flu viruses that have recently jumped into humans in nature, although fortunately none of these viruses have yet spread widely to cause a pandemic. Many factors affect the evolution of viruses, and their ability to infect new species. Understanding which changes in proteins help these microbes adapt to new hosts is an important element that scientists could consider to assess future risks of pandemics.
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Affiliation(s)
- Yq Shirleen Soh
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Louise H Moncla
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Rachel Eguia
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Trevor Bedford
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, United States.,Howard Hughes Medical Institute, Seattle, United States
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Shen Q, Shi J, Zeng D, Zhao B, Li P, Hwang W, Cho JH. Molecular Mechanisms of Tight Binding through Fuzzy Interactions. Biophys J 2019; 114:1313-1320. [PMID: 29590589 DOI: 10.1016/j.bpj.2018.01.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) form fuzzy complexes upon binding to their targets. Although many IDPs are weakly bound in fuzzy complexes, some IDPs form high-affinity complexes. One example is the nonstructural protein 1 (NS1) of the 1918 Spanish influenza A virus, which hijacks cellular CRKII through the strong binding affinity (Kd ∼10 nM) of its proline-rich motif (PRMNS1) to the N-terminal Src-homology 3 domain of CRKII. However, its molecular mechanism remains elusive. Here, we examine the interplay between structural disorder of a bound PRMNS1 and its long-range electrostatic interactions. Using x-ray crystallography and NMR spectroscopy, we found that PRMNS1 retains substantial conformational flexibility in the bound state. Moreover, molecular dynamics simulations showed that structural disorder of the bound PRMNS1 increases the number of electrostatic interactions and decreases the mean distances between the positively charged residues in PRMNS1 and the acidic residues in the N-terminal Src-homology 3 domain. These results are analyzed using a polyelectrostatic model. Our results provide an insight into the molecular recognition mechanism for a high-affinity fuzzy complex.
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Affiliation(s)
- Qingliang Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Jie Shi
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
| | - Danyun Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Baoyu Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science and Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea.
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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Wade A, Jumbo SD, Zecchin B, Fusaro A, Taiga T, Bianco A, Rodrigue PN, Salomoni A, Kameni JMF, Zamperin G, Nenkam R, Foupouapouognigni Y, Abdoulkadiri S, Aboubakar Y, Wiersma L, Cattoli G, Monne I. Highly Pathogenic Avian Influenza A(H5N8) Virus, Cameroon, 2017. Emerg Infect Dis 2019; 24:1367-1370. [PMID: 29912710 PMCID: PMC6038759 DOI: 10.3201/eid2407.172120] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Highly pathogenic avian influenza A(H5N8) viruses of clade 2.3.4.4 spread into West Africa in late 2016 during the autumn bird migration. Genetic characterization of the complete genome of these viruses detected in wild and domestic birds in Cameroon in January 2017 demonstrated the occurrence of multiple virus introductions.
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45
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Kazmi SO, Rodrigue N. Detecting amino acid preference shifts with codon-level mutation-selection mixture models. BMC Evol Biol 2019; 19:62. [PMID: 30808289 PMCID: PMC6390532 DOI: 10.1186/s12862-019-1358-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/11/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND In recent years, increasing attention has been placed on the development of phylogeny-based statistical methodologies for uncovering site-specific changes in amino acid fitness profiles over time. The few available random-effects approaches, modelling across-site variation in amino acid profiles as random variables drawn from a statistical law, either lack a mechanistic codon-level formulation, or pose significant computational challenges. RESULTS Here, we bring together a few existing ideas to explore a simple and fast method based on a predefined finite mixture of amino acid profiles within a codon-level substitution model following the mutation-selection formulation. Our study is focused on the detection of site-specific shifts in amino acid profiles over a known sub-clade of a tree, using simulations with and without shifts over the sub-clade to study the properties of the method. Through modifications of the values of the amino acid profiles, our simulations show different levels of reliability under different forms of finite mixture models. Sites identified by our method in a real data set show obvious overlap with those identified using previous methods, with some notable differences. CONCLUSION Overall, our results show that when a site-specific shift in amino acid profile is strongly pronounced, involving two clearly different sets of profiles, the method performs very well; but shifts between profiles that share many features are difficult to correctly identify, highlighting the challenging nature of the problem.
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Affiliation(s)
- S Omar Kazmi
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada
| | - Nicolas Rodrigue
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada. .,Institute of Biochemistry and School of Mathematics and Statistics, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada.
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Guo F, Li Y, Yu S, Liu L, Luo T, Pu Z, Xiang D, Shen X, Irwin DM, Liao M, Shen Y. Adaptive Evolution of Human-Isolated H5Nx Avian Influenza A Viruses. Front Microbiol 2019; 10:1328. [PMID: 31249566 PMCID: PMC6582624 DOI: 10.3389/fmicb.2019.01328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/28/2019] [Indexed: 02/05/2023] Open
Abstract
Avian influenza A viruses (AIVs) H5N1, first identified in 1996, are highly pathogenic in domestic poultry and continue to occasionally infect humans. In this study, we sought to identify genetic changes that occurred during their multiple invasions to humans. We evaluated all available H5Nx AIV genomes. Significant signals of positive selection were detected in 29 host-shift branches. 126 parallel evolution sites were detected on these branches, including 17 well-known sites (such as T271A, A274T, T339M, Q591K, E627K, and D701N in PB2; A134V, D154N, S223N, and R497K in HA) that play roles in allowing AIVs to cross species barriers. Our study suggests that during human infections, H5Nx viruses have experienced adaptive evolution (positive selection and convergent evolution) that allowed them to adapt to their new host environments. Analyses of adaptive evolution should be useful in identifying candidate sites that play roles in human infections, which can be tested by functional experiments.
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Affiliation(s)
- Fucheng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yiliang Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shu Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lu Liu
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Tingting Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhiqing Pu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dan Xiang
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- *Correspondence: Yongyi Shen,
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Isolation and characterization of H5Nx highly pathogenic avian influenza viruses of clade 2.3.4.4 in Russia. Virology 2018; 525:216-223. [PMID: 30296682 DOI: 10.1016/j.virol.2018.09.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 11/23/2022]
Abstract
In 2016-2017, several subtypes of the highly pathogenic avian influenza (HPAI) virus were isolated on the territory of Russia. In the autumn of 2016, during the avian influenza virus surveillance in the territory of the Kamchatka region of Russia the HPAI A(H5N5) influenza virus was isolated. Then, during 2016-2017, multiple outbreaks among wild birds and poultry caused by HPAI A(H5N8) avian influenza virus were recorded in European part of Russia. At the end of 2017, an outbreak among poultry caused by HPAI A(H5N2) influenza virus was recorded in the European part of Russia. Phylogenetic analysis of HA of the A(H5N5), A(H5N8), A(H5N2) showed the strains belong to the clade 2.3.4.4 b. All isolated strains were antigenically closely related to candidate vaccine viruses of clade 2.3.4.4 and showed high virulence in mice. Genetic analysis revealed presence of genetic markers potentially related to high virulence in mice in all studied viruses.
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Wen L, Chu H, Wong BHY, Wang D, Li C, Zhao X, Chiu MC, Yuan S, Fan Y, Chen H, Zhou J, Yuen KY. Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses. Emerg Microbes Infect 2018; 7:47. [PMID: 29593225 PMCID: PMC5874250 DOI: 10.1038/s41426-018-0050-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/09/2018] [Accepted: 02/18/2018] [Indexed: 12/12/2022]
Abstract
To elucidate the adaptive strategies of influenza A viruses (IAVs) to human, we proposed a computational approach to identify human-adaptive mutations in seasonal IAVs, which have not been analyzed comprehensively. We compared representative PB2 sequences of 1425 avian IAVs and 2176 human IAVs and identified a total of 42 human-adaptive markers, including 28 and 31 markers in PB2 proteins of seasonal viruses H1N1 and H3N2, respectively. Notably, this comprehensive list encompasses almost all the markers identified in prior computational studies and 21 novel markers including an experimentally verified mutation K526R, suggesting the predictive power of our method. The strength of our analysis derives from the enormous amount of recently available sequences as well as the recognition that human-adaptive mutations are not necessarily conserved across subtypes. We also utilized mutual information to profile the inter-residue coevolution in PB2 protein. A total of 35 and 46 coevolving site pairs are identified in H1N1 and H3N2, respectively. Interestingly, 13 out of the 28 (46.4%) identified markers in H1N1 and 16 out of the 31 (51.6%) in H3N2 are embraced in the coevolving pairs. Many of them are paired with well-characterized human-adaptive mutations, indicating potential epistatic effect of these coevolving residues in human adaptation. Additionally, we reconstructed the PB2 evolutionary history of seasonal IAVs and demonstrated the distinct adaptive pathway of PB2 segment after reassortment from H1 to H3 lineage. Our study may provide clues for further experimental validation of human-adaptive mutations and shed light on the human adaptation process of seasonal IAVs.
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Affiliation(s)
- Lei Wen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hin Chu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
| | - Bosco Ho-Yin Wong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Dong Wang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Cun Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Xiaoyu Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Man-Chun Chiu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Yanhui Fan
- Department of Biochemistry, The University of Hong Kong, Hong Kong, China
| | - Honglin Chen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Jie Zhou
- Department of Microbiology, The University of Hong Kong, Hong Kong, China. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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Bakacs T, Safadi R, Kovesdi I. Post-infection viral superinfection technology could treat HBV and HCV patients with unmet needs. HEPATOLOGY, MEDICINE AND POLICY 2018; 3:2. [PMID: 30288325 PMCID: PMC5918728 DOI: 10.1186/s41124-017-0028-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
Background Viral hepatitis deaths from acute infection, cirrhosis, and liver cancer have risen from the tenth to the seventh leading cause of death worldwide between 1990 and 2013. Even in the oral direct acting antiviral (DAA) agent era there are still large numbers of patients with unmet needs. Medications approved for treatment of chronic hepatitis B virus (HBV) infection do not eradicate HBV often requiring treatment for life associated with risks of adverse reactions, drug resistance, nonadherence, and increased cost. Although DAAs increased virologic cure rates well over 90% in all hepatitis C virus (HCV) genotypes, HCV infection still cannot be cured in a small but significant minority of patients. While most of the medical issues of HCV treatment have been solved, the current costs of DAAs are prohibitive. Results The post-infection viral superinfection treatment (SIT) platform technology has been clinically proven to be safe and effective to resolve acute and persistent viral infections in 42 HBV and HCV patients (20 HBV, 22 HCV), and in 4 decompensated patients (2 HBV, 2 HCV). SIT employs a non-pathogenic avian double stranded RNA (dsRNA) virus, a potent activator of antiviral gene responses. Unexpectedly, SIT is active against unrelated DNA (HBV) and RNA (HCV) viruses. SIT does not require lifelong therapy, which is a major advantage considering present HBV treatments. The new viral drug candidate (R903/78) is homogeneously produced by reverse genetics in Vero cells. R903/78 has exceptional pH and temperature stability and also excellent long-term stability; therefore, it can be orally administered, stored and shipped without freezing. Since R903/78 is easy to stockpile, the post-infection SIT could also alleviate the logistic hurdles of surge capacity in vaccine production during viral pandemics. Conclusion To help large number of HBV and HCV patients with unmet needs, broad-spectrum antiviral drugs effective against whole classes of viruses are urgently needed. The innovative SIT technological platform will be a great additional armament to conquer viral hepatitis, which is still a major cause of death and disability worldwide.
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Affiliation(s)
| | - Rifaat Safadi
- 2Hadassah Hebrew University Medical Center, Jerusalem, Israel
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Hydrogen Bond Variations of Influenza A Viruses During Adaptation in Human. Sci Rep 2017; 7:14295. [PMID: 29085020 PMCID: PMC5662722 DOI: 10.1038/s41598-017-14533-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/11/2017] [Indexed: 01/12/2023] Open
Abstract
Many host specific mutations have been detected in influenza A viruses (IAVs). However, their effects on hydrogen bond (H-bond) variations have rarely been investigated. In this study, 60 host specific sites were identified in the internal proteins of avian and human IAVs, 27 of which contained mutations with effects on H-bonds. Besides, 30 group specific sites were detected in HA and NA. Twenty-six of 36 mutations existing at these group specific sites caused H-bond loss or formation in at least one subtype. The number of mutations in isolations of 2009 pandemic H1N1, human-infecting H5N1 and H7N9 varied. The combinations of mutations and H-bond changes in these three subtypes of IAVs were also different. In addition, the mutations in isolations of H5N1 distributed more scattered than those in 2009 pandemic H1N1 and H7N9. Eight wave specific mutations in isolations of the fifth H7N9 wave were also identified. Three of them, R140K in HA, Y170H in NA, and R340K in PB2, were capable of resulting in H-bond loss. As mentioned above, these host or group or wave specific H-bond variations provide us with a new field of vision for understanding the changes of structural features in the human adaptation of IAVs.
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