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Noisumdaeng P, Phadungsombat J, Weerated S, Wiriyarat W, Puthavathana P. Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand. PeerJ 2022; 10:e14419. [PMID: 36518286 PMCID: PMC9744161 DOI: 10.7717/peerj.14419] [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: 06/27/2022] [Accepted: 10/28/2022] [Indexed: 12/05/2022] Open
Abstract
Background Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses. Methods Full-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4. Results ML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4. Conclusion H5N1 viruses existed, and were presumably introduced and circulated in avian species in Thailand, before they were officially reported in 2004. HA and NA genes continuously evolved during circulation between 2004 and 2010. This study provides a better understanding of genetic evolution with respect to molecular epidemiology. Monitoring and surveillance of emerging variants/reassortants should be continued.
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Affiliation(s)
- Pirom Noisumdaeng
- Faculty of Public Health, Thammasat University, Khlong Luang, Pathum Thani, Thailand,Thammasat University Research Unit in Modern Microbiology and Public Health Genomics, Thammasat University, Khlong Luang, Pathum Thani, Thailand
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand,Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Sasrinakarn Weerated
- Faculty of Public Health, Thammasat University, Khlong Luang, Pathum Thani, Thailand
| | | | - Pilaipan Puthavathana
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
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2
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Ge Z, Xu L, Hu X, Zhu S, Zhao Y, Li Y, Liu K, Gao R, Wang X, Hu J, Liu X, Hu S, Peng D, Gu M, Liu X. Phylogenetic and phenotypic characterization of two novel clade 2.3.2.1 H5N2 subtype avian influenza viruses from chickens in China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105205. [PMID: 34999002 DOI: 10.1016/j.meegid.2022.105205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 11/16/2022]
Abstract
The extended co-circulation of H5 subtype highly pathogenic avian influenza (HPAI) viruses and H9N2 low pathogenic avian influenza (LPAI) viruses has inevitably facilitated gene reassortment between the two subtypes in fields. And, novel reassortant H5NX viruses harboring partial or even whole sets of H9N2 internal genes have continuously been detected, such as clade 2.3.4.4 H5N2 or H5N6 reassortants. Here, we report two novel H5N2 subtype HPAI isolates of HF9 and QY5 from chickens in live poultry markets during routine surveillance in 2018. Phylogenetic analysis showed that those two H5N2 strains both possessed the HA genes from clade 2.3.2.1e of H5N1 viruses but all the other seven gene segments consistently from the endemic S genotype of H9N2 subtype viruses. Further analysis revealed that HF9 and QY5 differed only in six sites including K353R, A588T and T661I in PB2, I682V and L704S in PB1 plus G631S in PA at the amino acid level. A chicken regression experiment confirmed that both HF9 and QY5 were lethal infection to all tested chickens via contact transmission. Moreover, those two isolates could immediately replicate in mice lungs without adaptation. However, mortality rate of those two variants were distinct in mice model, HF9 with 100% but QY5 with just 20% at the infection dosage of 106.0EID50 per mouse. We suppose that the phenotypic difference may probably be attributed to the amino acid substitutions in the polymerase genes between the two isolates that constitute of a subject of further ongoing research.
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Affiliation(s)
- Zhichuang Ge
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lijun Xu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Yangzhou Customs, Yangzhou, Jiangsu 225009, China
| | - Xiaomiao Hu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Shanshan Zhu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ying Zhao
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yang Li
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Kaituo Liu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ruyi Gao
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaoquan Wang
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jiao Hu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaowen Liu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shunlin Hu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Daxin Peng
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Min Gu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Xiufan Liu
- Animal Infectious Diseases Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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3
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Normal modes analysis and surface electrostatics of haemagglutinin proteins as fingerprints for high pathogenic type A influenza viruses. BMC Bioinformatics 2020; 21:354. [PMID: 32838732 PMCID: PMC7445075 DOI: 10.1186/s12859-020-03563-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background Type A influenza viruses circulate and spread among wild birds and mostly consist of low pathogenic strains. However, fast genome variation timely results in the insurgence of high pathogenic strains, which when infecting poultry birds may cause a million deaths and strong commercial damage. More importantly, the host shift may concern these viruses and sustained human-to-human transmission may result in a dangerous pandemic outbreak. Therefore, fingerprints specific to either low or high pathogenic strains may represent a very important tool for global surveillance. Results We combined Normal Modes Analysis and surface electrostatic analysis of a mixed strain dataset of influenza A virus haemagglutinins from high and low pathogenic strains in order to infer specific fingerprints. Normal Modes Analysis sorted the strains in two different, homogeneous clusters; sorting was independent of clades and specific instead to high vs low pathogenicity. A deeper analysis of fluctuations and flexibility regions unveiled a special role for the 110-helix region. Specific sorting was confirmed by surface electrostatics analysis, which further allowed to focus on regions and mechanisms possibly crucial to the low-to-high transition. Conclusions Evidence from previous work demonstrated that changes in surface electrostatics are associated with the evolution and spreading of avian influenza A virus clades, and seemingly involved also in the avian to mammalian host shift. This work shows that a combination of electrostatics and Normal Modes Analysis can also identify fingerprints specific to high and low pathogenicity. The possibility to predict which specific mutations may result in a shift to high pathogenicity may help in surveillance and vaccine development.
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4
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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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5
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Suttie A, Karlsson EA, Deng YM, Hurt AC, Greenhill AR, Barr IG, Dussart P, Horwood PF. Avian influenza in the Greater Mekong Subregion, 2003-2018. INFECTION GENETICS AND EVOLUTION 2019; 74:103920. [PMID: 31201870 DOI: 10.1016/j.meegid.2019.103920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
The persistent circulation of avian influenza viruses (AIVs) is an ongoing problem for many countries in South East Asia, causing large economic losses to both the agricultural and health sectors. This review analyses AIV diversity, evolution and the risk of AIV emergence in humans in countries of the Greater Mekong Subregion (GMS): Cambodia, Laos, Myanmar, Thailand and Vietnam (excluding China). The analysis was based on AIV sequencing data, serological studies, published journal articles and AIV outbreak reports available from January 2003 to December 2018. All countries of the GMS have suffered losses due repeated outbreaks of highly pathogenic (HP) H5N1 that has also caused human cases in all GMS countries. In Laos, Myanmar and Vietnam AIV outbreaks in domestic poultry have also been caused by clade 2.3.4.4 H5N6. A diverse range of low pathogenic AIVs (H1-H12) have been detected in poultry and wild bird species, though surveillance for and characterization of these subtypes is limited. Subtype H3, H4, H6 and H11 viruses have been detected over prolonged periods; whilst H1, H2, H7, H8, H10 and H12 viruses have only been detected transiently. H9 AIVs circulate endemically in Cambodia and Vietnam with seroprevalence data indicating human exposure to H9 AIVs in Cambodia, Thailand and Vietnam. As surveillance studies focus heavily on the detection of H5 AIVs in domestic poultry further research is needed to understand the true level of AIV diversity and the risk AIVs pose to humans in the GMS.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia; School of Applied and Biomedical Sciences, Federation University, Churchill, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Erik A Karlsson
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andrew R Greenhill
- School of Applied and Biomedical Sciences, Federation University, Churchill, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Philippe Dussart
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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6
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Carrique-Mas J, Van NTB, Cuong NV, Truong BD, Kiet BT, Thanh PTH, Lon NN, Giao VTQ, Hien VB, Padungtod P, Choisy M, Setyawan E, Rushton J, Thwaites G. Mortality, disease and associated antimicrobial use in commercial small-scale chicken flocks in the Mekong Delta of Vietnam. Prev Vet Med 2019; 165:15-22. [PMID: 30851923 PMCID: PMC6418316 DOI: 10.1016/j.prevetmed.2019.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 11/26/2022]
Abstract
High mortality (2.6 chickens/100 chickens/week) in small-scale Mekong Delta flocks. Disease most common in the brooding period; mortality peaks in the 5–10 week period. Antimicrobials use (AMU) most common in the early (‘brooding’) period. Farmers tend to repeat AMU behavior over consecutive flock cycles. AMU was associated with the density of veterinary drug shops.
Raising chickens in small-scale flocks following all-in-all-out management is common in the Mekong Delta of Vietnam. These flocks represent an intermediate category between backyard and intensive (industrial) farming systems. However, little is known about the occurrence and burden of disease and/or mortality in such flocks, and their potential association with antimicrobial usage (AMU). We investigated mortality, disease and weekly antimicrobial use (AMU) in 124 cycles of meat chicken flocks raised in 88 farms in the Mekong Delta of Vietnam (with a median cycle duration of 18 weeks [inter-quartile range IQR 17–20]). We visited each farm 4 times per cycle to review data collected weekly by the farmers on clinical signs, mortality, and AMU. The overall probability of disease and AMU were 0.31 (95% CI 0.29–0.32) and 0.26 (95% CI 0.24–0.28), respectively. The average weekly incidence of mortality was 2.6 (95% CI 2.2–3.0) per 100 birds. Both the probabilities of a flock experiencing disease and mortality, as well as of using antimicrobials decreased with the flock’s age. However, mortality peaked at the 5–10 week period. The only significant explanatory factors associated with presence of disease was the stage of production ≥5 weeks (protective) (OR ≤ 0.51). Factors independently associated with AMU (p < 0.05) were: (1) Number of chickens (log) (OR=1.46), (2) Stage of production ≥5 weeks (OR≤0.67) (protective), (3) Cao Lanh district (OR=2.23), (4) Density of veterinary drug shops at commune level (log) (OR=1.58), and (5) Disease in flocks (OR=1.80). Factors independently associated with overall increased weekly incidence of mortality (p < 0.05) were: (1) High level of education attainment (secondary education or higher) (Hazard rate Ratio [HR]=1.70), (2) number of chickens (log) (HR=1.39), and (3) Stage of production >5 weeks (HR≤2.14). In flocks reporting disease, AMU significantly reduced the incidence of mortality (HR=0.90). These results confirm an exceptionally high mortality in chicken flocks in the area, jeopardizing the profitability and sustainability of these small-scale farming systems. The data also suggest an association between nearby access to antimicrobials and AMU, and a high correlation of AMU over consecutive cycles. The atomized farming landscape of the Mekong Delta, the high incidence of disease and mortality, and the unrestricted and easy access to antimicrobials present major challenges to the implementation of policies aimed at AMU reductions.
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Affiliation(s)
- Juan Carrique-Mas
- Oxford University Clinical Research Unit, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.
| | | | | | - Bao Dinh Truong
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh, Vietnam
| | - Bach Tuan Kiet
- Sub-Department of Animal Health, Cao Lanh, Dong Thap, Vietnam
| | | | - Nguyen Ngoc Lon
- Sub-Department of Animal Health, Cao Lanh, Dong Thap, Vietnam
| | | | - Vo Be Hien
- Sub-Department of Animal Health, Cao Lanh, Dong Thap, Vietnam
| | - Pawin Padungtod
- Emergency Center for Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations, Green One UN House Building, 304 Kim Ma, Hanoi, Vietnam
| | - Marc Choisy
- Oxford University Clinical Research Unit, Vietnam; MIVEGEC, IRD, CNRS, University of Montpellier, France
| | - Erry Setyawan
- Food and Agriculture Organization of the United Nations, Jakarta, Indonesia
| | - Jonathan Rushton
- Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
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7
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Arai Y, Kawashita N, Hotta K, Hoang PVM, Nguyen HLK, Nguyen TC, Vuong CD, Le TT, Le MTQ, Soda K, Ibrahim MS, Daidoji T, Takagi T, Shioda T, Nakaya T, Ito T, Hasebe F, Watanabe Y. Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Sci Rep 2018; 8:13066. [PMID: 30166556 PMCID: PMC6117316 DOI: 10.1038/s41598-018-31397-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/15/2018] [Indexed: 12/31/2022] Open
Abstract
The role of the influenza virus polymerase complex in host range restriction has been well-studied and several host range determinants, such as the polymerase PB2-E627K and PB2-D701N mutations, have been identified. However, there may be additional, currently unknown, human adaptation polymerase mutations. Here, we used a database search of influenza virus H5N1 clade 1.1, clade 2.3.2.1 and clade 2.3.4 strains isolated from 2008-2012 in Southern China, Vietnam and Cambodia to identify polymerase adaptation mutations that had been selected in infected patients. Several of these mutations acted either alone or together to increase viral polymerase activity in human airway cells to levels similar to the PB2-D701N and PB2-E627K single mutations and to increase progeny virus yields in infected mouse lungs to levels similar to the PB2-D701N single mutation. In particular, specific mutations acted synergistically with the PB2-D701N mutation and showed synergistic effects on viral replication both in human airway cells and mice compared with the corresponding single mutations. Thus, H5N1 viruses in infected patients were able to acquire multiple polymerase mutations that acted cooperatively for human adaptation. Our findings give new insight into the human adaptation of AI viruses and help in avian influenza virus risk assessment.
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Affiliation(s)
- Yasuha Arai
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Norihito Kawashita
- Graduate School of Science and Engineering, Kindai University, Osaka, Japan.,Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
| | - Kozue Hotta
- Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Hanoi, Vietnam.,Laboratory of Veterinary Public Health, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Phuong Vu Mai Hoang
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hang Le Khanh Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thach Co Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Cuong Duc Vuong
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thanh Thi Le
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Mai Thi Quynh Le
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Kosuke Soda
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Madiha S Ibrahim
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Tomo Daidoji
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshihiro Ito
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Futoshi Hasebe
- Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Hanoi, Vietnam
| | - Yohei Watanabe
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan. .,Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
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8
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Jang JW, Lee CY, Kim IH, Choi JG, Lee YJ, Yuk SS, Lee JH, Song CS, Kim JH, Kwon HJ. Optimized clade 2.3.2.1c H5N1 recombinant-vaccine strains against highly pathogenic avian influenza. J Vet Sci 2018; 18:299-306. [PMID: 28859269 PMCID: PMC5583417 DOI: 10.4142/jvs.2017.18.s1.299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/06/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023] Open
Abstract
A/Puerto Rico/8/34 (PR8)-derived recombinant viruses have been used for seasonal flu vaccines; however, they are insufficient for vaccines against some human-fatal H5N1 highly pathogenic avian influenza (HPAI) viruses (HPAIV) due to low productivity. Additionally, the polymerase basic 2 (PB2) protein, an important mammalian-pathogenicity determinant, of PR8 possesses several mammalian-pathogenic mutations. We previously reported two avian PB2 genes (01310 and 0028) related to efficient replication in embryonated chicken eggs (ECEs) and nonpathogenicity in BALB/c mice. In this study, we generated PR8-derived H5N1 recombinant viruses harboring hemagglutinin (attenuated) and neuraminidase genes of a clade 2.3.2.1c H5N1 HPAIV (K10-483), as well as the 01310 or 0028 PB2 genes, and investigated their replication and immunogenicity. Compared with a control virus harboring six internal PR8 genes (rK10-483), the recombinant viruses possessing the 01310 and 0028 PB2 genes showed significantly higher replication efficiency in ECEs and higher antibody titers in chickens. In contrast to rK10-483, none of the viruses replicated in BALB/c mice, and all showed low titers in Madin-Darby canine kidney cells. Additionally, the recombinant viruses did not induce a neutralization antibody but elicited decreased protective immune responses against K10-483 in mice. Thus, the highly replicative and mammalian nonpathogenic recombinant H5N1 strains might be promising vaccine candidates against HPAI in poultry.
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Affiliation(s)
- Jin-Wook Jang
- Laboratory of Avian Diseases, Seoul National University, Seoul 88026, Korea.,College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 88026, Korea
| | - Chung-Young Lee
- Laboratory of Avian Diseases, Seoul National University, Seoul 88026, Korea.,College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 88026, Korea
| | - Il-Hwan Kim
- Center for Infectious Diseases, Korean National Institute of Health, Osong 28159, Korea
| | - Jun-Gu Choi
- Laboratory of Foreign Animal Disease, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Youn-Jeong Lee
- Laboratory of Avian Diseases, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Seong-Su Yuk
- Laboratory of Avian Diseases, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
| | - Ji-Ho Lee
- Laboratory of Avian Diseases, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
| | - Chang-Seon Song
- Laboratory of Avian Diseases, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
| | - Jae-Hong Kim
- Laboratory of Avian Diseases, Seoul National University, Seoul 88026, Korea.,College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 88026, Korea
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Production Medicine, Seoul National University, Seoul 88026, Korea.,College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 88026, Korea
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9
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Mutations in the PA Protein of Avian H5N1 Influenza Viruses Affect Polymerase Activity and Mouse Virulence. J Virol 2018; 92:JVI.01557-17. [PMID: 29212927 DOI: 10.1128/jvi.01557-17] [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: 09/04/2017] [Accepted: 11/28/2017] [Indexed: 01/09/2023] Open
Abstract
To study the influenza virus determinants of pathogenicity, we characterized two highly pathogenic avian H5N1 influenza viruses isolated in Vietnam in 2012 (A/duck/Vietnam/QT1480/2012 [QT1480]) and 2013 (A/duck/Vietnam/QT1728/2013 [QT1728]) and found that the activity of their polymerase complexes differed significantly, even though both viruses were highly pathogenic in mice. Further studies revealed that the PA-S343A/E347D (PA with the S-to-A change at position 343 and the E-to-D change at position 347) mutations reduced viral polymerase activity and mouse virulence when tested in the genetic background of QT1728 virus. In contrast, the PA-343S/347E mutations increased the polymerase activity of QT1480 and the virulence of a low-pathogenic H5N1 influenza virus. The PA-343S residue (which alone increased viral polymerase activity and mouse virulence significantly relative to viral replication complexes encoding PA-343A) is frequently found in H5N1 influenza viruses of several subclades; infection with a virus possessing this amino acid may pose an increased risk to humans.IMPORTANCE H5N1 influenza viruses cause severe infections in humans with a case fatality rate that exceeds 50%. The factors that determine the high virulence of these viruses in humans are not fully understood. Here, we identified two amino acid changes in the viral polymerase PA protein that affect the activity of the viral polymerase complex and virulence in mice. Infection with viruses possessing these amino acid changes may pose an increased risk to humans.
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10
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Liu M, Lu Q, Zhang S, Feng X, Hossain MS. Temporal and spatial characteristics of highly pathogenic avian influenza outbreaks in China during 2004 to 2015. Poult Sci 2017; 96:3113-3121. [PMID: 28453859 DOI: 10.3382/ps/pex097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Indexed: 11/20/2022] Open
Abstract
Identifying the temporal and spatial characteristics of highly pathogenic avian influenza (HPAI) outbreaks is very important for developing effective and appropriate countermeasures against HPAI and promoting sustainable development in the poultry industry. This study aimed to analyze four aspects of the temporal and spatial characteristics of HPAI outbreaks in China, including the frequency of HPAI outbreaks, numbers of dead animals (died or culled), types of HPAI viruses, and species of infected animals. Temporal characteristics showed that the frequency of HPAI outbreaks decreased and then increased, with some years deviating from the main trend in 2004 to 2010 and 2011 to 2015, while the largest number of dead animals due to HPAI outbreaks was in 2005. During 2004 to 2015, HPAI H5N1 was the major type of HPAI virus, and chickens had the greatest risk of being infected with HPAI, followed by ducks and geese. The HPAI outbreaks had obvious seasonal effects clustered in January to February, June, and November. Spatial characteristics revealed that outbreaks were more frequent in Xinjiang, Hubei, and Guangdong but caused a larger number of dead animals in Liaoning and Shanxi. HPAI H5N1 appeared in 25 provinces, while HPAI H5N2 was mainly localized in Hebei and Jiangsu, and HPAI H5N6 occurred in Heilongjiang, Jiangsu, Hunan, and Guangdong. HPAI viruses were most frequently detected in chickens and wild birds in northern China, while the majority of HPAI infections were identified in chickens, ducks, and geese in southern China. Regionally, HPAI outbreaks were most frequent in the western region but resulted in larger number of animals dying or being culled in the eastern region. These findings could provide a new understanding of the distributional characteristics of HPAI outbreaks and offer prospects for better prevention and control strategies.
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Affiliation(s)
- Mingyue Liu
- College of Economics and Management, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Qian Lu
- College of Economics and Management, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China.
| | - Shuxia Zhang
- College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Xiaolong Feng
- College of Economics and Management, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
| | - Md Shakhawat Hossain
- College of Economics and Management, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi, China
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11
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Takayama I, Hieu NT, Shirakura M, Nakauchi M, Fujisaki S, Takahashi H, Nagata S, Long NT, Odagiri T, Tashiro M, Kageyama T. Novel Reassortant Avian Influenza A(H5N1) Virus in Human, Southern Vietnam, 2014. Emerg Infect Dis 2016; 22:557-9. [PMID: 26889960 PMCID: PMC4766877 DOI: 10.3201/eid2203.151360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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12
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Naguib MM, Kinne J, Chen H, Chan KH, Joseph S, Wong PC, Woo PCY, Wernery R, Beer M, Wernery U, Harder TC. Outbreaks of highly pathogenic avian influenza H5N1 clade 2.3.2.1c in hunting falcons and kept wild birds in Dubai implicate intercontinental virus spread. J Gen Virol 2016; 96:3212-3222. [PMID: 26350163 DOI: 10.1099/jgv.0.000274] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5N1 have continued to perpetuate with divergent genetic variants in poultry within Asia since 2003. Further dissemination of Asian-derived H5 HPAIVs to Europe, Africa and, most recently, to the North American continent has occurred. We report an outbreak of HPAIV H5N1 among falcons kept for hunting and other wild bird species bred as falcon prey in Dubai, United Arab Emirates, during the autumn of 2014. The causative agent was identified as avian influenza virus subtype H5N1, clade 2.3.2.1c, by genetic and phylogenetic analyses. High mortality in infected birds was in accordance with systemic pathomorphological and histological alterations in affected falcons. Genetic analysis showed the HPAIV H5N1 of clade 2.3.2.1c is a reassortant in which the PB2 segment was derived from an Asian-origin H9N2 virus lineage. The Dubai H5N1 viruses were closely related to contemporary H5N1 HPAIVs from Nigeria, Burkina-Faso, Romania and Bulgaria. Median-joining network analysis of 2.3.2.1c viruses revealed that the Dubai outbreak was an episode of a westward spread of these viruses on a larger scale from unidentified Asian sources. The incursion into Dubai, possibly via infected captive hunting falcons returning from hunting trips to central Asian countries, preceded outbreaks in Nigeria and other West African countries. The alarmingly enhanced geographical mobility of clade 2.3.2.1.c and clade 2.3.4.4 viruses may represent another wave of transcontinental dissemination of Asian-origin HPAIV H5 viruses, such as the outbreak at Qinghai Lake caused by clade 2.2 (‘Qinghai’ lineage) in 2005.
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Affiliation(s)
- Mahmoud M Naguib
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald Insel-Riems, Germany
| | - Jörg Kinne
- Central Veterinary Research Laboratory, P.O. Box 597, Dubai, United Arab Emirates
| | - Honglin Chen
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, P.O. Box 597, Dubai, United Arab Emirates
| | - Po-Chun Wong
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Renate Wernery
- Central Veterinary Research Laboratory, P.O. Box 597, Dubai, United Arab Emirates
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald Insel-Riems, Germany
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, P.O. Box 597, Dubai, United Arab Emirates
| | - Timm C Harder
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald Insel-Riems, Germany
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13
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Nguyen TH, Than VT, Thanh HD, Hung VK, Nguyen DT, Kim W. Intersubtype Reassortments of H5N1 Highly Pathogenic Avian Influenza Viruses Isolated from Quail. PLoS One 2016; 11:e0149608. [PMID: 26900963 PMCID: PMC4765837 DOI: 10.1371/journal.pone.0149608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/03/2016] [Indexed: 11/18/2022] Open
Abstract
H5N1 highly pathogenic avian influenza (HPAI) viruses are considered a threat to national animal industries, causing production losses and high mortality in domestic poultry. In recent years, quail has become a popular terrestrial poultry species raised for production of meat and eggs in Asia. In this study, to better understand the roles of quail in H5N1 viral evolution, two H5N1-positive samples, designated A/quail/Vietnam/CVVI-49/2010 (CVVI-49/2010) and A/quail/Vietnam/CVVI-50/2014 (CVVI-50/2014), were isolated from quail during H5N1 outbreaks in Vietnam, and their whole genome were analyzed. The phylogenetic analysis reveals new evolutionary variation in the worldwide H5N1 viruses. The quail HA genes were clustered into clades 1.1.1 (CVVI-49/2010) and clade 2.3.2.1c (CVVI-50/2014), which may have evolved from viruses circulating from chickens and/or ducks in Cambodia, mainland of China, Taiwan, Indonesia, and South Korea in recent years. Interestingly, the M2 gene of the CVVI-49/2010 strain contained amino acid substitutions at position 26L-I and 31S-N that are related to amantadine-resistance. In particular, the CVVI-50/2014 strain revealed evidence of multiple intersubtype reassortment events between virus clades 2.3.2.1c, 2.3.2.1b, and 2.3.2.1a. Data from this study supports the possible role of quail as an important intermediate host in avian influenza virus evolution. Therefore, additional surveillance is needed to monitor these HPAI viruses both serologically and virologically in quail.
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Affiliation(s)
- Tinh Huu Nguyen
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Hien Dang Thanh
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Vu-Khac Hung
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Duc Tan Nguyen
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- * E-mail:
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14
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Saito T, Tanikawa T, Uchida Y, Takemae N, Kanehira K, Tsunekuni R. Intracontinental and intercontinental dissemination of Asian H5 highly pathogenic avian influenza virus (clade 2.3.4.4) in the winter of 2014-2015. Rev Med Virol 2015; 25:388-405. [DOI: 10.1002/rmv.1857] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/02/2015] [Accepted: 08/13/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Takehiko Saito
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
- United Graduate School of Veterinary Sciences; Gifu University; Gifu City Japan
| | - Taichiro Tanikawa
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Yuko Uchida
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Nobuhiro Takemae
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Katsushi Kanehira
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Ryota Tsunekuni
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
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