1
|
Zhi Y, Wei J, Liu Z, Zhang Q, Zhang T, Hu G. Inhibitory effects of Belamcanda extract on inflammatory response and antiviral mechanism in H9N2 Avian influenza virus: insights from in vitro and in vivo studies. Poult Sci 2024; 103:103885. [PMID: 38851182 PMCID: PMC11208944 DOI: 10.1016/j.psj.2024.103885] [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] [Revised: 05/02/2024] [Accepted: 05/18/2024] [Indexed: 06/10/2024] Open
Abstract
Avian influenza, particularly the H9N2 subtype, presents significant challenges to poultry health, underscoring the need for effective antiviral interventions. This study explores the antiviral capabilities of Belamcanda extract, a traditional Chinese medicinal herb, against H9N2 Avian influenza virus (AIV) in specific pathogen-free (SPF) chicks. Through a comprehensive approach, we evaluated the impact of the extract on cytokine modulation and crucial immunological signaling pathways, essential for understanding the host-virus interaction. Our findings demonstrate that Belamcanda extract significantly modulates the expression of key inflammatory cytokines, including tumor necrosis factor alpha (TNF-α), interleukin-1 (IL-1), interleukin-2 (IL-2), and interleukin-6 (IL-6), which are pivotal to the host's response to H9N2 AIV infection. Western blot analysis further revealed that the extract markedly reduces the expression of critical immune signaling molecules such as toll-like receptor 3 (TLR3), TIR-domain-containing adapter-inducing interferon-β (TRIF), and nuclear factor kappa B (NF-κB). These insights into the mechanisms by which Belamcanda extract influences host immune responses and hinders viral replication highlight its potential as an innovative antiviral agent for poultry health management. The study advances our comprehension of natural compounds' antiviral mechanisms and lays the groundwork for developing strategies to manage viral infections in poultry. The demonstrated ability of Belamcanda extract to modulate immune responses and inhibit viral replication establishes it as a promising candidate for future antiviral therapy development, especially in light of the need for effective treatments against evolving influenza virus strains and the critical demand for enhanced poultry health management strategies.
Collapse
Affiliation(s)
- Yan Zhi
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jingjie Wei
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhenyi Liu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Qian Zhang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Tao Zhang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Ge Hu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
| |
Collapse
|
2
|
Zhi Y, Zhao X, Liu Z, Shen G, Zhang T, Zhang T, Hu G. Oxymatrine Modulation of TLR3 Signaling: A Dual-Action Mechanism for H9N2 Avian Influenza Virus Defense and Immune Regulation. Molecules 2024; 29:1945. [PMID: 38731436 PMCID: PMC11085666 DOI: 10.3390/molecules29091945] [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: 03/15/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
In our research, we explored a natural substance called Oxymatrine, found in a traditional Chinese medicinal plant, to fight against a common bird flu virus known as H9N2. This virus not only affects birds but can also pose a threat to human health. We focused on how this natural compound can help in stopping the virus from spreading in cells that line the lungs of birds and potentially humans. Our findings show that Oxymatrine can both directly block the virus and boost the body's immune response against it. This dual-action mechanism is particularly interesting because it indicates that Oxymatrine might be a useful tool in developing new ways to prevent and treat this type of bird flu. Understanding how Oxymatrine works against the H9N2 virus could lead to safer and more natural ways to combat viral infections in animals and humans, contributing to the health and well-being of society. The H9N2 Avian Influenza Virus (AIV) is a persistent health threat because of its rapid mutation rate and the limited efficacy of vaccines, underscoring the urgent need for innovative therapies. This study investigated the H9N2 AIV antiviral properties of Oxymatrine (OMT), a compound derived from traditional Chinese medicine, particularly focusing on its interaction with pulmonary microvascular endothelial cells (PMVECs). Employing an array of in vitro assays, including 50% tissue culture infectious dose, Cell Counting Kit-8, reverse transcription-quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, and Western blot, we systematically elucidated the multifaceted effects of OMT. OMT dose-dependently inhibited critical antiviral proteins (PKR and Mx1) and modulated the expression of type I interferons and key cytokines (IFN-α, IFN-β, IL-6, and TNF-α), thereby affecting TLR3 signaling and its downstream elements (NF-κB and IRF-3). OMT's antiviral efficacy extended beyond TLR3-mediated responses, suggesting its potential as a versatile antiviral agent. This study not only contributes to the growing body of research on the use of natural compounds as antiviral agents but also underscores the importance of further investigating the broader application of OMT for combating viral infections.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ge Hu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China; (Y.Z.); (X.Z.); (Z.L.); (G.S.); (T.Z.); (T.Z.)
| |
Collapse
|
3
|
Cui M, Huang Y, Wang X, Bian X, Du L, Yan Y, Gu J, Dong W, Zhou J, Liao M. Genetic characterization and evolution of H6N6 subtype avian influenza viruses. Front Microbiol 2022; 13:963218. [PMID: 35979484 PMCID: PMC9376297 DOI: 10.3389/fmicb.2022.963218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
H6-subtype avian influenza virus (AIV) was prevalent in the world and could sporadically infect humans. Here, a new chicken-derived H6N6-subtype AIV strain A/chicken/Zhejiang/49/2021 (ZJ49) was isolated in Zhejiang Province, China in 2021. Phylogenetic analysis by Maximum likelihood methods showed that H6-subtype AIVs were classed into 13 groups according to HA gene. The ZJ49 strain belonged to the G12 group, which mainly consisted of strains from Asian and dominated in recent years. Based on NA gene, H6-subtype AIVs were divided into N6.1 and N6.2 clades according to the NA gene. The ZJ49 isolate was located in the N6.2e clade, which mainly consisted of the H5N6-subtype AIVs. Phylogenetic analysis by Bayesian methods showed that the effective quantity size of H6-subtype AIVs increased around 1990, reached a peak around 2015, declined after 2015, then kept in a stable level after 2018. The reassortment analysis predicted that the PB2, PA, and NA genes of ZJ49 may recombine with H5-subtype AIVs. The amino acid at 222 position of HA gene of ZJ49 strain mutated from A to V, suggesting that ZJ49 has a potential ability to cross species barriers. The four glycosylation sites were highly conserved, implying less impact on the fold and conception of HA stem structure. Our results revealed the complicated evolution, reassortment, and mutations of receptor binding sites of H6-subtype AIVs, which emphasize the importance to continuously monitor the epidemiology and evolution of H6-subtype AIVs.
Collapse
Affiliation(s)
- Mingxian Cui
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Yanming Huang
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Xingbo Wang
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Xiyi Bian
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Liuyang Du
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Yan Yan
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Jinyan Gu
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Weiren Dong
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center and State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Jiyong Zhou,
| | - Min Liao
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Center of Veterinary Medical Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Min Liao,
| |
Collapse
|
4
|
Hicks JT, Edwards K, Qiu X, Kim DK, Hixson JE, Krauss S, Webby RJ, Webster RG, Bahl J. Host diversity and behavior determine patterns of interspecies transmission and geographic diffusion of avian influenza A subtypes among North American wild reservoir species. PLoS Pathog 2022; 18:e1009973. [PMID: 35417497 PMCID: PMC9037922 DOI: 10.1371/journal.ppat.1009973] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/25/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Wild birds can carry avian influenza viruses (AIV), including those with pandemic or panzootic potential, long distances. Even though AIV has a broad host range, few studies account for host diversity when estimating AIV spread. We analyzed AIV genomic sequences from North American wild birds, including 303 newly sequenced isolates, to estimate interspecies and geographic viral transition patterns among multiple co-circulating subtypes. Our results show high transition rates within Anseriformes and Charadriiformes, but limited transitions between these orders. Patterns of transition between species were positively associated with breeding habitat range overlap, and negatively associated with host genetic distance. Distance between regions (negative correlation) and summer temperature at origin (positive correlation) were strong predictors of transition between locations. Taken together, this study demonstrates that host diversity and ecology can determine evolutionary processes that underlie AIV natural history and spread. Understanding these processes can provide important insights for effective control of AIV.
Collapse
Affiliation(s)
- Joseph T. Hicks
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Kimberly Edwards
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Do-Kyun Kim
- University of Texas Health Science Center at Houston School of Public Health, Houston, Texas, United States of America
| | - James E. Hixson
- University of Texas Health Science Center at Houston School of Public Health, Houston, Texas, United States of America
| | - Scott Krauss
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Richard J. Webby
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert G. Webster
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| |
Collapse
|
5
|
Alyas K, Wajid A, Dundon WG, Ather S, Batool T, Babar ME. Isolation and Characterization of Avian Influenza H9N2 Viruses from Different Avian Species in Pakistan 2016-17. Avian Dis 2020; 63:721-726. [PMID: 31865688 DOI: 10.1637/aviandiseases-d-19-00070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/27/2019] [Indexed: 11/05/2022]
Abstract
Avian influenza (AI) virus (AIV) subtype H9N2 continues to cause significant outbreaks among commercial and backyard poultry in Pakistan. Despite this, the characterization of H9N2 viruses in avian hosts other than chickens in Pakistan has not been thoroughly investigated. In this study, 12 low pathogenicity avian influenza viruses subtype H9N2 were isolated from peacocks (n = 4), ducks (n = 4), pheasants (n = 2), geese (n = 1), and black swans (n = 1) in Pakistan during 2016 and were characterized on the basis of the hemagglutinin (HA) and neuraminidase genes. All of the viruses possessed an amino acid substitution Q226L in the receptor-binding site of the HA protein, which is known to contribute to increased viral replication and virulence in mammals. In addition, phylogenetic studies showed that these H9N2 AIVs belonged to the Middle East B genetic group of sublineage G1 and were very similar to viruses isolated from an outbreak in chickens in Pakistan in 2017. This demonstrates an epidemiologic link between poultry and other avian species, which is a fact to consider in future H9N2 disease management programs.
Collapse
Affiliation(s)
- Kashaf Alyas
- Department of Biotechnology, Virtual University of Pakistan, 1-Davis Road, Lahore, Pakistan 54000.,The first two authors contributed equally to this work.,A. W. and K. A. conceived and designed the experiments. K. A., S. A., and T. B. performed the experiments. A. W., W. G. D., and M. E. B. analyzed the data. A. W. and W. G. D. wrote the paper that was approved by all authors
| | - Abdul Wajid
- Department of Biotechnology, Virtual University of Pakistan, 1-Davis Road, Lahore, Pakistan 54000, ; .,The first two authors contributed equally to this work.,A. W. and K. A. conceived and designed the experiments. K. A., S. A., and T. B. performed the experiments. A. W., W. G. D., and M. E. B. analyzed the data. A. W. and W. G. D. wrote the paper that was approved by all authors
| | - William G Dundon
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, Vienna, Austria 2444.,A. W. and K. A. conceived and designed the experiments. K. A., S. A., and T. B. performed the experiments. A. W., W. G. D., and M. E. B. analyzed the data. A. W. and W. G. D. wrote the paper that was approved by all authors
| | - Safa Ather
- Department of Molecular Biology, Virtual University of Pakistan, 1-Davis Road Lahore, Pakistan 54000.,A. W. and K. A. conceived and designed the experiments. K. A., S. A., and T. B. performed the experiments. A. W., W. G. D., and M. E. B. analyzed the data. A. W. and W. G. D. wrote the paper that was approved by all authors
| | - Tayyeba Batool
- Department of Molecular Biology, Virtual University of Pakistan, 1-Davis Road Lahore, Pakistan 54000.,A. W. and K. A. conceived and designed the experiments. K. A., S. A., and T. B. performed the experiments. A. W., W. G. D., and M. E. B. analyzed the data. A. W. and W. G. D. wrote the paper that was approved by all authors
| | - Masroor Ellahi Babar
- Department of Molecular Biology, Virtual University of Pakistan, 1-Davis Road Lahore, Pakistan 54000.,A. W. and K. A. conceived and designed the experiments. K. A., S. A., and T. B. performed the experiments. A. W., W. G. D., and M. E. B. analyzed the data. A. W. and W. G. D. wrote the paper that was approved by all authors
| |
Collapse
|
6
|
Li R, Adel A, Bohlin J, Lundkvist Å, Olsen B, Pettersson JHO, Naguib MM. Phylogeographic Dynamics of Influenza A(H9N2) Virus Crossing Egypt. Front Microbiol 2020; 11:392. [PMID: 32265861 PMCID: PMC7105594 DOI: 10.3389/fmicb.2020.00392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/25/2020] [Indexed: 11/23/2022] Open
Abstract
Low pathogenic avian influenza (LPAI) virus of subtype H9N2 is the most frequently detected subtype among domestic poultry and is a public health concern because of its zoonotic potential. Due to the multiple and complex routes of LPAIV H9N2 between geographic regions, little is known about the spatial diffusion of H9N2 virus to, within, and from Egypt, where it is endemic among poultry since 2011. Using close to 800 publicly available hemagglutinin (HA) segment nucleotide sequences, associated location and temporal data, we conducted a Bayesian discrete phylogeographic analysis. Here, we reconstructed and traced the origin, spread and principal transmission routes of H9N2 across large geographical regions, in addition to the transmission between Egypt and the rest of the world and between different Egyptian governorates. Our analysis suggests that during the last few decades, H9N2 has been introduced back and forth continuously between the countries where it is endemic. Amongst these regions, Saudi Arabia, United Arab Emirates and Iraq act as main distribution hubs and drive the viral migration worldwide, with bi-directional and long-distance diffusions. It is noteworthy that H9N2 was introduced once to Egypt via Israel in mid 2009, and that the descendants of the Egyptian LAIVs H9N2 were back-transmitted to Israel in 2015. Additionally, governorates in middle Egypt (Giza, Fayoum and Bani Souwaif) are major hubs in the LPAIV H9N2 transmission network in Egypt. This knowledge highlights that H9N2 is both a global and a national concern and can aid in updating the surveillance program and vaccine strain selection.
Collapse
Affiliation(s)
- Ruiyun Li
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Amany Adel
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Jon Bohlin
- Department of Infectious Disease Epidemiology and Modelling, Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Björn Olsen
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Mahmoud M Naguib
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| |
Collapse
|
7
|
Youk SS, Lee DH, Jeong JH, Pantin-Jackwood MJ, Song CS, Swayne DE. Live bird markets as evolutionary epicentres of H9N2 low pathogenicity avian influenza viruses in Korea. Emerg Microbes Infect 2020; 9:616-627. [PMID: 32183621 PMCID: PMC7144223 DOI: 10.1080/22221751.2020.1738903] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Live bird markets (LBMs) in Korea have been recognized as a reservoir, amplifier, and source of avian influenza viruses (AIVs); however, little was known about the role of LBMs in the epidemiology of AIVs in Korea until recently. Through 10 years of surveillance (2006–2016) we have isolated and sequenced H9N2 viruses in Korean LBMs. To understand how H9N2 evolves and spreads in Korea, a statistical Bayesian phylogenetic model was used. Phylogenetic analysis suggests that three separate introductions of progenitor gene pools, Korean domestic duck-origin and two wild aquatic bird-origin AIVs, contributed to the generation of the five genotypes of H9N2 viruses in Korea. Phylogenetic reconstruction of ecological states infer that the LBMs are where chickens become infected with the virus, with domestic ducks playing a major role in the transmission and evolution of the H9N2 viruses. Three increases in the genetic diversity of H9N2 viruses were observed and coincided with transitions in host species and the locations (domestic farm, LBM, slaughterhouse, and wild aquatic bird habitat) where the viruses were isolated, accompanying genetic reassortment. Following the introduction of a wild aquatic bird-origin AIVs in 2008, six genes of the Korean lineage H9N2 virus were replaced with genes originating from wild aquatic birds, and viruses with this new genotype became predominant in Korean LBMs.
Collapse
Affiliation(s)
- Sung-Su Youk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA.,Avian Diseases Laboratory, College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Dong-Hun Lee
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA.,Department of Pathobiology & Veterinary Science, University of Connecticut, Storrs, CT, USA
| | - Jei-Hyun Jeong
- Avian Diseases Laboratory, College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Mary J Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
| | - Chang-Seon Song
- Avian Diseases Laboratory, College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - David E Swayne
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
| |
Collapse
|
8
|
Inferring host roles in bayesian phylodynamics of global avian influenza A virus H9N2. Virology 2019; 538:86-96. [DOI: 10.1016/j.virol.2019.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 12/26/2022]
|
9
|
Jin X, Zha Y, Hu J, Li X, Chen J, Xie S, Dai Y, Li Z, Wang X, Wang F, Qi W, Liao M, Jia W. New molecular evolutionary characteristics of H9N2 avian influenza virus in Guangdong Province, China. INFECTION GENETICS AND EVOLUTION 2019; 77:104064. [PMID: 31618691 DOI: 10.1016/j.meegid.2019.104064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/16/2019] [Accepted: 10/06/2019] [Indexed: 12/31/2022]
Abstract
To understand the evolution of H9N2 avian influenza virus genotype and its molecular evolution rate, we systematically analyzed 72 H9N2 avian influenza virus sequences isolated from Guangdong province from 2014 to 2018. We found three genotypes (G57, G68, and G118) of the H9N2 avian influenza virus, of which G118 is a newly discovered genotype and G57 is the dominant genotype. The internal gene cassette of the G57 genotype H9N2 avian influenza virus is a stable combination that can easily transport internal genes to other novel avian influenza viruses, and the internal gene cassettes of the G68 and G118 are identical to those of G57.In addition, we estimated the nucleotide substitution rate of the HA and NA genes of the H9N2 influenza virus from 2014 to 2018.The nucleotide substitution rate of HA and NA genes showed an upward trend in 2015 and 2016. In the past two years, H9N2 avian influenza virus recombination has produced genotype G68, which disappeared in 2014 for one year. And very coincidentally, in 2015, there was a new genotype G118. We observed that the emergence of new genotypes was accompanied by a slight increase in overall nucleotide substitution rate. Therefore we hypothesize that the emergence of new genotypes could accelerate the molecular evolution rate of genes. Our research shows that the H9N2 avian influenza virus in Guangdong province has been undergoing intense evolution, demonstrating the need to strengthen influenza surveillance in the region.
Collapse
Affiliation(s)
- Xuanjiang Jin
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China
| | - Yunfeng Zha
- Guangdong Provincial Center for Animal Disease Control and Prevention, Guangzhou 510230, China
| | - Jingkai Hu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China
| | - Xiao Li
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China
| | - Jianglin Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China
| | - Shumin Xie
- Experimental Animal Center, South China agricultural university,Guangzhou,China
| | - Yixue Dai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China
| | - Zhixian Li
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China
| | - Xiao Wang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China
| | - Fuguang Wang
- Guangdong Provincial Center for Animal Disease Control and Prevention, Guangzhou 510230, China
| | - Wenbao Qi
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China; Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture,Guangzhou, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China; Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture,Guangzhou, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
| | - Weixin Jia
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, College of Veterinary Medicine, South China Agricultural University, China; Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
10
|
Scotch M, Tahsin T, Weissenbacher D, O'Connor K, Magge A, Vaiente M, Suchard MA, Gonzalez-Hernandez G. Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Virus Evol 2019; 5:vey043. [PMID: 30838129 PMCID: PMC6395475 DOI: 10.1093/ve/vey043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Discrete phylogeography using software such as BEAST considers the sampling location of each taxon as fixed; often to a single location without uncertainty. When studying viruses, this implies that there is no possibility that the location of the infected host for that taxa is somewhere else. Here, we relaxed this strong assumption and allowed for analytic integration of uncertainty for discrete virus phylogeography. We used automatic language processing methods to find and assign uncertainty to alternative potential locations. We considered two influenza case studies: H5N1 in Egypt; H1N1 pdm09 in North America. For each, we implemented scenarios in which 25 per cent of the taxa had different amounts of sampling uncertainty including 10, 30, and 50 per cent uncertainty and varied how it was distributed for each taxon. This includes scenarios that: (i) placed a specific amount of uncertainty on one location while uniformly distributing the remaining amount across all other candidate locations (correspondingly labeled 10, 30, and 50); (ii) assigned the remaining uncertainty to just one other location; thus ‘splitting’ the uncertainty among two locations (i.e. 10/90, 30/70, and 50/50); and (iii) eliminated uncertainty via two predefined heuristic approaches: assignment to a centroid location (CNTR) or the largest population in the country (POP). We compared all scenarios to a reference standard (RS) in which all taxa had known (absolutely certain) locations. From this, we implemented five random selections of 25 per cent of the taxa and used these for specifying uncertainty. We performed posterior analyses for each scenario, including: (a) virus persistence, (b) migration rates, (c) trunk rewards, and (d) the posterior probability of the root state. The scenarios with sampling uncertainty were closer to the RS than CNTR and POP. For H5N1, the absolute error of virus persistence had a median range of 0.005–0.047 for scenarios with sampling uncertainty—(i) and (ii) above—versus a range of 0.063–0.075 for CNTR and POP. Persistence for the pdm09 case study followed a similar trend as did our analyses of migration rates across scenarios (i) and (ii). When considering the posterior probability of the root state, we found all but one of the H5N1 scenarios with sampling uncertainty had agreement with the RS on the origin of the outbreak whereas both CNTR and POP disagreed. Our results suggest that assigning geospatial uncertainty to taxa benefits estimation of virus phylogeography as compared to ad-hoc heuristics. We also found that, in general, there was limited difference in results regardless of how the sampling uncertainty was assigned; uniform distribution or split between two locations did not greatly impact posterior results. This framework is available in BEAST v.1.10. In future work, we will explore viruses beyond influenza. We will also develop a web interface for researchers to use our language processing methods to find and assign uncertainty to alternative potential locations for virus phylogeography.
Collapse
Affiliation(s)
- Matthew Scotch
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Tasnia Tahsin
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA
| | - Davy Weissenbacher
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| | - Karen O'Connor
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| | - Arjun Magge
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Matteo Vaiente
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, 621 Charles E. Young Dr. South, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Dr. South, Los Angeles, CA, USA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA, USA
| | - Graciela Gonzalez-Hernandez
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| |
Collapse
|