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Huang C, Yu L, Xu Y, Huang J, Qin Y, Guo X, Zeng Y, Qin Y, Ouyang K, Wei Z, Huang W, García-Sastre A, Chen Y. Long-term co-circulation of multiple influenza A viruses in pigs, Guangxi, China. Emerg Microbes Infect 2024; 13:2337673. [PMID: 38572517 PMCID: PMC11005871 DOI: 10.1080/22221751.2024.2337673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Influenza A viruses (IAVs) pose a persistent potential threat to human health because of the spillover from avian and swine infections. Extensive surveillance was performed in 12 cities of Guangxi, China, during 2018 and 2023. A total of 2540 samples (including 2353 nasal swabs and 187 lung tissues) were collected from 18 pig farms with outbreaks of respiratory disease. From these, 192 IAV-positive samples and 19 genomic sequences were obtained. We found that the H1 and H3 swine influenza A viruses (swIAVs) of multiple lineages and genotypes have continued to co-circulate during that time in this region. Genomic analysis revealed the Eurasian avian-like H1N1 swIAVs (G4) still remained predominant in pig populations. Strikingly, the novel multiple H3N2 genotypes were found to have been generated through the repeated introduction of the early H3N2 North American triple reassortant viruses (TR H3N2 lineage) that emerged in USA and Canada in 1998 and 2005, respectively. Notably, when the matrix gene segment derived from the H9N2 avian influenza virus was introduced into endemic swIAVs, this produced a novel quadruple reassortant H1N2 swIAV that could pose a potential risk for zoonotic infection.
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Affiliation(s)
- Chongqiang Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Liangzheng Yu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Yi Xu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Jiamo Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Yibin Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Institute of Veterinary Medicine, Nanning, People’s Republic of China
| | - Xuan Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Nongken Yongxin Animal Husbandry Group Co. Ltd., Nanning, People’s Republic of China
| | - Yongfang Zeng
- Nanning Zhufulai Animal Health Management Co. Ltd., Nanning, People’s Republic of China
| | - Yifeng Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Kang Ouyang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Zuzhang Wei
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
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Du Y, Xia J, Wang Z, Xu J, Ji Y, Jin Y, Pu L, Xu S. Evolution of H6N6 viruses in China between 2014 and 2019 involves multiple reassortment events. Emerg Microbes Infect 2024; 13:2341142. [PMID: 38581279 DOI: 10.1080/22221751.2024.2341142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/04/2024] [Indexed: 04/08/2024]
Abstract
H6N6 avian influenza viruses (AIVs) have been widely detected in wild birds, poultry, and even mammals. Recently, H6N6 viruses were reported to be involved in the generation of H5 and H7 subtype viruses. To investigate the emergence, evolutionary pattern, and potential for an epidemic of H6N6 viruses, the complete genomes of 198 H6N6 viruses were analyzed, including 168 H6N6 viruses deposited in the NCBI and GISAID databases from inception to January 2019 and 30 isolates collected from China between November 2014 and January 2019. Using phylogenetic analysis, the 198 strains of H6N6 viruses were identified as 98 genotypes. Molecular clock analysis indicated that the evolution of H6N6 viruses in China was constant and not interrupted by selective pressure. Notably, the laboratory isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events. These results suggested that H6N6 viruses can act as an intermediary in the evolution of H5N6, H6N6, and H7N9 viruses. Animal experiments demonstrated that the 10 representative H6N6 viruses showed low pathogenicity in chickens and were capable of infecting mice without prior adaptation. Our findings suggest that H6N6 viruses play an important role in the evolution of AIVs, and it is necessary to continuously monitor and evaluate the potential epidemic of the H6N6 subtype viruses.
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Affiliation(s)
- Yingying Du
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Jun Xia
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, People's Republic of China
| | - Zhengxiang Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Jie Xu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Yanhong Ji
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Yinghong Jin
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, People's Republic of China
| | - Ling Pu
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guizhou, People's Republic of China
| | - Shuai Xu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
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Mao Q, Zhou S, Liu S, Peng C, Yin X, Li J, Zhang Y, Zhou W, Hou G, Jiang W, Liu H. Emergence of novel reassortant H3N3 avian influenza viruses with increased pathogenicity in chickens in 2023. Emerg Microbes Infect 2024; 13:2287683. [PMID: 37990831 PMCID: PMC10795584 DOI: 10.1080/22221751.2023.2287683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Affiliation(s)
- Qiuyan Mao
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
- College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, People’s Republic of China
| | - Shuning Zhou
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
| | - Shuo Liu
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
| | - Cheng Peng
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
| | - Xin Yin
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
| | - Jinping Li
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
| | - Yaxin Zhang
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Wanting Zhou
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
- College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, People’s Republic of China
| | - Guangyu Hou
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
| | - Wenming Jiang
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
| | - Hualei Liu
- China Animal Health and Epidemiology Center, Qingdao, People’s Republic of China
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Szablewski CM, McBride DS, Trock SC, Habing GG, Hoet AE, Nelson SW, Nolting JM, Bowman AS. Evolution of influenza A viruses in exhibition swine and transmission to humans, 2013-2015. Zoonoses Public Health 2024; 71:281-293. [PMID: 38110691 PMCID: PMC10994755 DOI: 10.1111/zph.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/14/2023] [Accepted: 12/09/2023] [Indexed: 12/20/2023]
Abstract
AIMS Swine are a mixing vessel for the emergence of novel reassortant influenza A viruses (IAV). Interspecies transmission of swine-origin IAV poses a public health and pandemic risk. In the United States, the majority of zoonotic IAV transmission events have occurred in association with swine exposure at agricultural fairs. Accordingly, this human-animal interface necessitates mitigation strategies informed by understanding of interspecies transmission mechanisms in exhibition swine. Likewise, the diversity of IAV in swine can be a source for novel reassortant or mutated viruses that pose a risk to both swine and human health. METHODS AND RESULTS In an effort to better understand those risks, here we investigated the epidemiology of IAV in exhibition swine and subsequent transmission to humans by performing phylogenetic analyses using full genome sequences from 272 IAV isolates collected from exhibition swine and 23 A(H3N2)v viruses from human hosts during 2013-2015. Sixty-seven fairs (24.2%) had at least one pig test positive for IAV with an overall estimated prevalence of 8.9% (95% CI: 8.3-9.6, Clopper-Pearson). Of the 19 genotypes found in swine, 5 were also identified in humans. There was a positive correlation between the number of human cases of a genotype and its prevalence in exhibition swine. Additionally, we demonstrated that A(H3N2)v viruses clustered tightly with exhibition swine viruses that were prevalent in the same year. CONCLUSIONS These data indicate that multiple genotypes of swine-lineage IAV have infected humans, and highly prevalent IAV genotypes in exhibition swine during a given year are also the strains detected most frequently in human cases of variant IAV. Continued surveillance and rapid characterization of IAVs in exhibition swine can facilitate timely phenotypic evaluation and matching of candidate vaccine strains to those viruses present at the human-animal interface which are most likely to spillover into humans.
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Affiliation(s)
- Christine M Szablewski
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Dillon S McBride
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Susan C Trock
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gregory G Habing
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Armando E Hoet
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Sarah W Nelson
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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Cao L, Xia D, Chen YY, Zhou TF, Yin SH, Liu YH, Li KB, Di B, Zhang ZB, Qin PZ. [The identification of a novel reassortant H3N2 avian influenza virus based on nanopore sequencing technology and genetic characterization]. Zhonghua Liu Xing Bing Xue Za Zhi 2024; 45:574-578. [PMID: 38678355 DOI: 10.3760/cma.j.cn112338-20230828-00105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Objective: To identify a novel reassortant H3N2 avian influenza virus using nanopore sequencing technology and analyze its genetic characteristics. Methods: The positive samples of the H3N2 avian influenza virus, collected from the external environment in the farmers' market of Guangzhou, were cultured in chicken embryos. The whole genome was sequenced by targeted amplification and nanopore sequencing technology. The genetic characteristics were analyzed using bioinformatics software. Results: The phylogenetic trees showed that each gene fragment of the strain belonged to the Eurasian evolutionary branch, and the host source was of avian origin. The HA gene was closely related to the origin of the H3N6 virus. The NA gene was closely related to the H3N2 avian influenza virus from 2017 to 2020. The PB1 gene was closely related to the H5N6 avian influenza virus in Guangxi Zhuang Autonomous Region and Fujian Province from 2016 to 2022 and was not related to the PB1 gene of the H5N6 avian influenza epidemic strain in Guangzhou. The other internal gene fragments had complex sources with significant genetic diversity. Molecular characteristics indicated that the strain exhibited the molecular characteristics of a typical low pathogenic avian influenza virus and tended to bind to the receptors of avian origin. On important protein sites related to biological characteristics, this strain had mutations of PB2-L89V, PB1-L473V, NP-A184K, M1-N30D/T215A, and NS1-P42S/N205S. Conclusions: This study identified a novel reassortant H3N2 avian influenza virus by nanopore sequencing, with the PB1 gene derived from the H5N6 avian influenza virus. The virus had a low ability to spread across species, but further exploration was needed to determine whether its pathogenicity to the host was affected.
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Affiliation(s)
- L Cao
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - D Xia
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - Y Y Chen
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - T F Zhou
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - S H Yin
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - Y H Liu
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - K B Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - B Di
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - Z B Zhang
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - P Z Qin
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
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Feoktistova S, Sayganova M, Trutneva K, Glazova O, Blagodatski AS, Shevkova L, Navoikova A, Anisimov Y, Albert E, Mityaeva O, Volchkov P, Deviatkin A. Abundant Intra-Subtype Reassortment Revealed in H13N8 Influenza Viruses. Viruses 2024; 16:568. [PMID: 38675910 DOI: 10.3390/v16040568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Influenza A viruses (IAVs) pose a serious threat to global health. On the one hand, these viruses cause seasonal flu outbreaks in humans. On the other hand, they are a zoonotic infection that has the potential to cause a pandemic. The most important natural reservoir of IAVs are waterfowl. In this study, we investigated the occurrence of IAV in birds in the Republic of Buryatia (region in Russia). In 2020, a total of 3018 fecal samples were collected from wild migratory birds near Lake Baikal. Of these samples, 11 were found to be positive for the H13N8 subtype and whole-genome sequencing was performed on them. All samples contained the same virus with the designation A/Unknown/Buryatia/Arangatui-1/2020. To our knowledge, virus A/Unknown/Buryatia/Arangatui-1/2020 is the first representative of the H13N8 subtype collected on the territory of Russia, the sequence of which is available in the GenBank database. An analysis of reassortments based on the genome sequences of other known viruses has shown that A/Unknown/Buryatia/Arangatui-1/2020 arose as a result of reassortment. In addition, a reassortment most likely occurred several decades ago between the ancestors of the viruses recently collected in China, the Netherlands, the United States and Chile. The presence of such reassortment emphasizes the ongoing evolution of the H13N8 viruses distributed in Europe, North and East Asia, North and South America and Australia. This study underscores the importance of the continued surveillance and research of less-studied influenza subtypes.
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Affiliation(s)
- Sofia Feoktistova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
| | - Marya Sayganova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
| | - Kseniya Trutneva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
| | - Olga Glazova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
| | - Artem S Blagodatski
- Federal State Budget Institution of Science Institute of Theoretical and Experimental Biophysics, 142290 Pushchino, Russia
| | - Liudmila Shevkova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
| | - Anna Navoikova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
| | - Yuriy Anisimov
- Baikalsky State Nature Biosphere Reserve, 671220 Tankhoi, Russia
| | - Eugene Albert
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
| | - Olga Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Pavel Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The Moscow Clinical Scientific Center (MCSC) Named after A.S. Loginov, 111123 Moscow, Russia
| | - Andrey Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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Valusenko-Mehrkens R, Schilling-Loeffler K, Johne R, Falkenhagen A. VP4 Mutation Boosts Replication of Recombinant Human/Simian Rotavirus in Cell Culture. Viruses 2024; 16:565. [PMID: 38675907 DOI: 10.3390/v16040565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Rotavirus A (RVA) is the leading cause of diarrhea requiring hospitalization in children and causes over 100,000 annual deaths in Sub-Saharan Africa. In order to generate next-generation vaccines against African RVA genotypes, a reverse genetics system based on a simian rotavirus strain was utilized here to exchange the antigenic capsid proteins VP4, VP7 and VP6 with those of African human rotavirus field strains. One VP4/VP7/VP6 (genotypes G9-P[6]-I2) triple-reassortant was successfully rescued, but it replicated poorly in the first cell culture passages. However, the viral titer was enhanced upon further passaging. Whole genome sequencing of the passaged virus revealed a single point mutation (A797G), resulting in an amino acid exchange (E263G) in VP4. After introducing this mutation into the VP4-encoding plasmid, a VP4 mono-reassortant as well as the VP4/VP7/VP6 triple-reassortant replicated to high titers already in the first cell culture passage. However, the introduction of the same mutation into the VP4 of other human RVA strains did not improve the rescue of those reassortants, indicating strain specificity. The results show that specific point mutations in VP4 can substantially improve the rescue and replication of recombinant RVA reassortants in cell culture, which may be useful for the development of novel vaccine strains.
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Affiliation(s)
- Roman Valusenko-Mehrkens
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Katja Schilling-Loeffler
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Reimar Johne
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Alexander Falkenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
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Solarte-Murillo L, Reyes H, Ojeda L, Cárcamo JG, Pontigo JP, Loncoman CA. Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Piscine orthoreovirus Evolution. Viruses 2024; 16:556. [PMID: 38675898 DOI: 10.3390/v16040556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate.
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Affiliation(s)
- Laura Solarte-Murillo
- Laboratorio de Virología Molecular, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Humberto Reyes
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Loreto Ojeda
- Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Interdisciplinary Center for Aquaculture Research, INCAR, Concepción 4030000, Chile
| | - Juan G Cárcamo
- Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Interdisciplinary Center for Aquaculture Research, INCAR, Concepción 4030000, Chile
| | - Juan Pablo Pontigo
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt 5400000, Chile
| | - Carlos A Loncoman
- Laboratorio de Virología Molecular, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
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9
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Tapia R, Brito B, Saavedra M, Mena J, García-Salum T, Rathnasinghe R, Barriga G, Tapia K, García V, Bucarey S, Jang Y, Wentworth D, Torremorell M, Neira V, Medina RA. Novel influenza A viruses in pigs with zoonotic potential, Chile. Microbiol Spectr 2024; 12:e0218123. [PMID: 38446039 DOI: 10.1128/spectrum.02181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Novel H1N2 and H3N2 swine influenza A viruses (IAVs) have recently been identified in Chile. The objective of this study was to evaluate their zoonotic potential. We perform phylogenetic analyses to determine the genetic origin and evolution of these viruses, and a serological analysis to determine the level of cross-protective antibodies in the human population. Eight genotypes were identified, all with pandemic H1N1 2009-like internal genes. H1N1 and H1N2 were the subtypes more commonly detected. Swine H1N2 and H3N2 IAVs had hemagglutinin and neuraminidase lineages genetically divergent from IAVs reported worldwide, including human vaccine strains. These genes originated from human seasonal viruses were introduced into the swine population since the mid-1980s. Serological data indicate that the general population is susceptible to the H3N2 virus and that elderly and young children also lack protective antibodies against the H1N2 strains, suggesting that these viruses could be potential zoonotic threats. Continuous IAV surveillance and monitoring of the swine and human populations is strongly recommended.IMPORTANCEIn the global context, where swine serve as crucial intermediate hosts for influenza A viruses (IAVs), this study addresses the pressing concern of the zoonotic potential of novel reassortant strains. Conducted on a large scale in Chile, it presents a comprehensive account of swine influenza A virus diversity, covering 93.8% of the country's industrialized swine farms. The findings reveal eight distinct swine IAV genotypes, all carrying a complete internal gene cassette of pandemic H1N1 2009 origin, emphasizing potential increased replication and transmission fitness. Genetic divergence of H1N2 and H3N2 IAVs from globally reported strains raises alarms, with evidence suggesting introductions from human seasonal viruses since the mid-1980s. A detailed serological analysis underscores the zoonotic threat, indicating susceptibility in the general population to swine H3N2 and a lack of protective antibodies in vulnerable demographics. These data highlight the importance of continuous surveillance, providing crucial insights for global health organizations.
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Affiliation(s)
| | - Bárbara Brito
- Universidad de Chile, Santiago, Chile
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- University of Technology Sydney, Sydney, New South Wales, Australia
| | - Marco Saavedra
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan Mena
- Universidad de Chile, Santiago, Chile
| | - Tamara García-Salum
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Raveen Rathnasinghe
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo Barriga
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karla Tapia
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Yunho Jang
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - David Wentworth
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | | | | | - Rafael A Medina
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Pathology and Experimental Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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10
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Yang J, Lan R, Chang H, Li H, Yu H, Tong Q, Liu J, Sun H. Isolation and characterization of genotype 4 Eurasian avian-like H1N1 influenza virus in pigs suffering from pneumonia. Virology 2024; 592:110009. [PMID: 38330852 DOI: 10.1016/j.virol.2024.110009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/28/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Swine influenza viruses pose ongoing threat to pork industry throughout the world. In 2023, fattening pigs from a swine farm in Inner Mongolia of China experienced influenza-like symptoms. Co-infection of influenza A virus with Pasteurella multocida was diagnosed in lung tissues of diseased pigs and a genotype 4 (G4) Eurasian avian-like (EA) H1N1 virus was isolated, which was named as A/swine/Neimenggu/0326/2023. We demonstrated the virus preferentially bound human-like SAα2,6Gal receptor. It was noteworthy that the virus possessed multiple genetic markers for mammalian adaptation in the internal genes. Animal studies showed that compared with genotype 1 (G1) EA H1N1 virus and early prevalent G4 EA H1N1 virus, A/swine/Neimenggu/0326/2023 virus exhibited increased virus shedding, enhanced replication in lungs, and caused more severe lung lesions in pigs. These findings indicate that the G4 EA H1N1 virus poses increased threat to pork industry, controlling the prevailing viruses in pigs should be promptly implemented.
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Affiliation(s)
- Jizhe Yang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Riguo Lan
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Haoyu Chang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Han Li
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Haili Yu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Qi Tong
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Honglei Sun
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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11
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Thomas MN, Zanella GC, Cowan B, Caceres CJ, Rajao DS, Perez DR, Gauger PC, Vincent Baker AL, Anderson TK. Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine. J Virol 2024; 98:e0170323. [PMID: 38353535 PMCID: PMC10949443 DOI: 10.1128/jvi.01703-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/22/2024] [Indexed: 03/20/2024] Open
Abstract
The increased detection of H3 C-IVA (1990.4.a) clade influenza A viruses (IAVs) in US swine in 2019 was associated with a reassortment event to acquire an H1N1pdm09 lineage nucleoprotein (pdmNP) gene, replacing a TRIG lineage NP (trigNP). We hypothesized that acquiring the pdmNP conferred a selective advantage over prior circulating H3 viruses with a trigNP. To investigate the role of NP reassortment in transmission, we identified two contemporary 1990.4.a representative strains (NC/19 and MN/18) with different evolutionary origins of the NP gene. A reverse genetics system was used to generate wild-type (wt) strains and swap the pdm and TRIG lineage NP genes, generating four viruses: wtNC/19-pdmNP, NC/19-trigNP, wtMN/18-trigNP, and MN/18-pdmNP. The pathogenicity and transmission of the four viruses were compared in pigs. All four viruses infected 10 primary pigs and transmitted to five indirect contact pigs per group. Pigs infected via contact with MN/18-pdmNP shed virus 2 days earlier than pigs infected with wtMN/18-trigNP. The inverse did not occur for wtNC/19-pdmNP and NC/19-trigNP. This suggests that pdmNP reassortment resulted in a combination of genes that improved transmission efficiency when paired with the 1990.4.a hemagglutinin (HA). This is likely a multigenic trait, as replacing the trigNP gene did not diminish the transmission of a wild-type IAV in swine. This study demonstrates how reassortment and evolutionary change of internal genes can result in more transmissible viruses that influence HA clade detection frequency. Thus, rapidly identifying novel reassortants paired with dominant hemagglutinin/neuraminidase may improve the prediction of strains to include in vaccines.IMPORTANCEInfluenza A viruses (IAVs) are composed of eight non-continuous gene segments that can reassort during coinfection of a host, creating new combinations. Some gene combinations may convey a selective advantage and be paired together preferentially. A reassortment event was detected in swine in the United States that involved the exchange of two lineages of nucleoprotein (NP) genes (trigNP to pdmNP) that became a predominant genotype detected in surveillance. Using a transmission study, we demonstrated that exchanging the trigNP for a pdmNP caused the virus to shed from the nose at higher levels and transmit to other pigs more rapidly. Replacing a pdmNP with a trigNP did not hinder transmission, suggesting that transmission efficiency depends on interactions between multiple genes. This demonstrates how reassortment alters IAV transmission and that reassortment events can provide an explanation for why genetically related viruses with different internal gene combinations experience rapid fluxes in detection frequency.
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Affiliation(s)
- Megan N. Thomas
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
| | - Giovana Ciacci Zanella
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Brianna Cowan
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - C. Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Phillip C. Gauger
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Amy L. Vincent Baker
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
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12
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Ke YK, Han XY, Lin SR, Wu HG, Li YX, Liu RQ, Liao M, Jia WX. Emergence of a triple reassortment avian influenza virus (A/H5N6) from wild birds. J Infect 2024; 88:106106. [PMID: 38242367 DOI: 10.1016/j.jinf.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/14/2024] [Indexed: 01/21/2024]
Affiliation(s)
- Yan-Kun Ke
- Shenzhen Center for Animal Disease Control and Prevention, Shenzhen, China
| | - Xin-Yu Han
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Si-Ru Lin
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Han-Guang Wu
- Shenzhen Center for Animal Disease Control and Prevention, Shenzhen, China
| | - Ying-Xin Li
- Shenzhen Center for Animal Disease Control and Prevention, Shenzhen, China
| | - Rong-Qi Liu
- Shenzhen Center for Animal Disease Control and Prevention, Shenzhen, China
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Wei-Xin Jia
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China; Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
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13
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Naiqing X, Tang X, Wang X, Cai M, Liu X, Lu X, Hu S, Gu M, Hu J, Gao R, Liu K, Chen Y, Liu X, Wang X. Hemagglutinin affects replication, stability and airborne transmission of the H9N2 subtype avian influenza virus. Virology 2024; 589:109926. [PMID: 37952465 DOI: 10.1016/j.virol.2023.109926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
H9N2 subtype avian influenza virus (AIV) can transmit by direct as well as airborne contacts. It has been widespread in poultry and continued to contribute to zoonotic spillover events by providing its six internal genes for the reassortment of novel influenza viruses (eg, H7N9) that infect poultry and humans. Compared to H7N9, H9N2 virus displays an efficient airborne transmissibility in poultry, but the mechanisms of transmission difference have been insufficiently studied. The Hemagglutinin (HA) and viral polymerase acidic protein (PA) have been implicated in the airborne transmission of influenza A viruses. Accordingly, we generated the reassortant viruses of circulating airborne transmissible H9N2 and non-airborne transmissible H7N9 viruses carrying HA and/or PA gene. The introduction of the PA gene from H7N9 into the genome of H9N2 virus resulted in a reduction in airborne transmission among chickens, while the isolated introduction of the HA gene segment completely eliminated airborne transmission among chickens. We further showed that introduction of HA gene of non-transmissible H7N9 did not influence the HA/NA balance of H9N2 virus, but increased the threshold for membrane fusion and decreased the acid stability. Thus, our results indicate that HA protein plays a key role in replication, stability, and airborne transmission of the H9N2 subtype AIV.
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Affiliation(s)
- Xu Naiqing
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Xinen Tang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Xin Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Miao Cai
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Xiaolong Lu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Min Gu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Jiao Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Ruyi Gao
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Kaituo Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.
| | - Yu Chen
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.
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14
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Zhu M, Zeng H, He J, Zhu Y, Wang P, Guo J, Guo J, Zhou H, Qin Y, Ouyang K, Wei Z, Huang W, Chen Y. Reassortant H9N2 canine influenza viruses containing the pandemic H1N1/2009 ribonucleoprotein complex circulating in pigs acquired enhanced virulence in mice. Virology 2024; 589:109927. [PMID: 37951087 DOI: 10.1016/j.virol.2023.109927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/08/2023] [Accepted: 10/30/2023] [Indexed: 11/13/2023]
Abstract
The reassortment between avian H9N2 and Eurasian avian-like (EA) H1N1 viruses may have potentially changed from avian-to-mammals adaptation. This study generated 20 reassortant viruses with the introduction of H1N1/2009 internal genes from EA H1N1 virus into H9N2 virus. 12 of these recovered the replication capability both in the lungs and turbinate samples. 10 of 12 obtained PA gene segments from the ribonucleoprotein (RNP) complexes of the EA H1N1 virus, and 3 exhibited extreme virulence. Specially, the combination of PB2, PA and NP genes could overcome the species-specific restriction in human cells. Analysis of the polymerase activities found that introduction of the PA gene resulted in increased polymerase activity. These findings indicated that RNP complexes from EA H1N1 virus could confer an adaptation advantage and high compatibility to avian H9N2 virus. This raises new concerns for public health due to the possible coexistence of H9N2 and EA H1N1 viruses in dogs.
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Affiliation(s)
- Min Zhu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Hao Zeng
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Jianqiao He
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Yaohui Zhu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Pingping Wang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Jianing Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Jinfan Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Huabo Zhou
- Huabo Pet Hospital, Nanning, 530004, PR China
| | - Yifeng Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Kang Ouyang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Zuzhang Wei
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Ying Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China.
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Doan YH, Dennis FE, Takemae N, Haga K, Shimizu H, Appiah MG, Lartey BL, Damanka SA, Hayashi T, Suzuki T, Kageyama T, Armah GE, Katayama K. Emergence of Intergenogroup Reassortant G9P[4] Strains Following Rotavirus Vaccine Introduction in Ghana. Viruses 2023; 15:2453. [PMID: 38140694 PMCID: PMC10747750 DOI: 10.3390/v15122453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023] Open
Abstract
Rotavirus (RVA) is a leading cause of childhood gastroenteritis. RVA vaccines have reduced the global disease burden; however, the emergence of intergenogroup reassortant strains is a growing concern. During surveillance in Ghana, we observed the emergence of G9P[4] RVA strains in the fourth year after RVA vaccine introduction. To investigate whether Ghanaian G9P[4] strains also exhibited the DS-1-like backbone, as seen in reassortant G1/G3/G8/G9 strains found in other countries in recent years, this study determined the whole genome sequences of fifteen G9P[4] and two G2P[4] RVA strains detected during 2015-2016. The results reveal that the Ghanaian G9P[4] strains exhibited a double-reassortant genotype, with G9-VP7 and E6-NSP4 genes on a DS-1-like backbone (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2). Although they shared a common ancestor with G9P[4] DS-1-like strains from other countries, further intra-reassortment events were observed among the original G9P[4] and co-circulating strains in Ghana. In the post-vaccine era, there were significant changes in the distribution of RVA genotype constellations, with unique strains emerging, indicating an impact beyond natural cyclical fluctuations. However, reassortant strains may exhibit instability and have a limited duration of appearance. Current vaccines have shown efficacy against DS-1-like strains; however, ongoing surveillance in fully vaccinated children is crucial for addressing concerns about long-term effectiveness.
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Affiliation(s)
- Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - Francis Ekow Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nobuhiro Takemae
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - Kei Haga
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Michael Gyasi Appiah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Belinda Larteley Lartey
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Susan Afua Damanka
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Takaya Hayashi
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Infection and Host Response, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
| | - Tsutomu Kageyama
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (Y.H.D.)
| | - George Enyimah Armah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Kazuhiko Katayama
- Laboratory of Viral Infection, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
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16
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Kristensen C, Laybourn HA, Crumpton JC, Martiny K, Webb A, Ryt-Hansen P, Trebbien R, Jensen HE, Nissen JN, Skovgaard K, Webby RJ, Larsen LE. Experimental infection of pigs and ferrets with "pre-pandemic," human-adapted, and swine-adapted variants of the H1N1pdm09 influenza A virus reveals significant differences in viral dynamics and pathological manifestations. PLoS Pathog 2023; 19:e1011838. [PMID: 38048355 PMCID: PMC10721187 DOI: 10.1371/journal.ppat.1011838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/14/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
Influenza A viruses are RNA viruses that cause epidemics in humans and are enzootic in the pig population globally. In 2009, pig-to-human transmission of a reassortant H1N1 virus (H1N1pdm09) caused the first influenza pandemic of the 21st century. This study investigated the infection dynamics, pathogenesis, and lesions in pigs and ferrets inoculated with natural isolates of swine-adapted, human-adapted, and "pre-pandemic" H1N1pdm09 viruses. Additionally, the direct-contact and aerosol transmission properties of the three H1N1pdm09 isolates were assessed in ferrets. In pigs, inoculated ferrets, and ferrets infected by direct contact with inoculated ferrets, the pre-pandemic H1N1pdm09 virus induced an intermediary viral load, caused the most severe lesions, and had the highest clinical impact. The swine-adapted H1N1pdm09 virus induced the highest viral load, caused intermediary lesions, and had the least clinical impact in pigs. The human-adapted H1N1pdm09 virus induced the highest viral load, caused the mildest lesions, and had the least clinical impact in ferrets infected by direct contact. The discrepancy between viral load and clinical impact presumably reflects the importance of viral host adaptation. Interestingly, the swine-adapted H1N1pdm09 virus was transmitted by aerosols to two-thirds of the ferrets. Further work is needed to assess the risk of human-to-human aerosol transmission of swine-adapted H1N1pdm09 viruses.
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Affiliation(s)
- Charlotte Kristensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Helena A. Laybourn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jeri-Carol Crumpton
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Karen Martiny
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Ashley Webb
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Pia Ryt-Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Ramona Trebbien
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Henrik E. Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Jakob N. Nissen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Lars E. Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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17
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Moon SH, Na W, Shin S, Kim H, Noh JY, Jang SS, Kim MC, Lim HA, Kim HY, Mun DY, Yoon SW, Kim HK. Evidence for the circulation of genotype 4 Eurasian avian-like lineage swine H1N1 influenza A viruses on Korean swine farms, obtained using a newly developed one-step multiplex RT-qPCR assay. Arch Virol 2023; 168:267. [PMID: 37801138 DOI: 10.1007/s00705-023-05887-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023]
Abstract
Genotype 4 (G4) Eurasian avian-like lineage swine H1N1 influenza A viruses, which are reassortants containing sequences from the pandemic 2009 H1N1 virus lineage, triple-reassortant-lineage internal genes, and EA-lineage external genes, have been reported in China since 2013. These have been predominant in pig populations since 2016 and have exhibited pandemic potential. In this study, we developed a one-step multiplex RT-qPCR assay targeting the M, HA1, and PB2 genes to detect G4 and related EA H1N1 viruses, with detection limits of 1.5 × 101 copies/μL and 1.15 × 10-2 ng/μL for the purified PCR products and RNA templates, respectively. The specificity of the detection method was confirmed using various influenza virus subtypes. When the one-step multiplex RT-qPCR assay was applied to swine respiratory samples collected between 2020 and 2022 in Korea, a virus related to G4 EA H1N1 strains was detected. Phylogenetic analysis based on portions of all eight genome segments showed that the positive sample contained HA, NA, PB2, NS, and NP genes closely related to those of G4 EA H1N1 viruses, confirming the ability of our assay to accurately detect G4 EA H1N1 viruses in the field.
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Affiliation(s)
- Soo Hyun Moon
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea
| | - Woonsung Na
- College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, South Korea
| | - Seongho Shin
- Optipharm Animal Disease Diagnostic Center, Cheongju, 28158, South Korea
| | - Hyunil Kim
- Optipharm, Inc., Cheongju, 28158, South Korea
| | - Ji Yeong Noh
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea
| | - Seong Sik Jang
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea
| | - Min Chan Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea
| | - Hyun A Lim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea
| | - Ha Yeon Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea
| | - Da Young Mun
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea
| | - Sun-Woo Yoon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea.
- Department of Vaccine Biotechnology, Andong National University, Andong, 36729, South Korea.
| | - Hye Kwon Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, South Korea.
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18
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Yao XY, Lian CY, Lv ZH, Zhang XL, Shao JW. Emergence of a novel reassortant H5N6 subtype highly pathogenic avian influenza virus in farmed dogs in China. J Infect 2023; 87:e70-e72. [PMID: 37507094 DOI: 10.1016/j.jinf.2023.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023]
Affiliation(s)
- Xin-Yan Yao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Chun-Yang Lian
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zhi-Hang Lv
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Xue-Lian Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China.
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19
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Yang Y, Huang Y, Huang K, Zhang Y, Hu X, Zou W, Wu C, Hui X, Li C, Zhao Y, Sun X, Zou Z, Jin M. Isolation and identification of Eurasian avian-like H1N1 swine influenza virus and evaluation of their pathogenicity and immune protective effects in pigs. Vet Microbiol 2023; 284:109827. [PMID: 37542928 DOI: 10.1016/j.vetmic.2023.109827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 08/07/2023]
Abstract
Swine influenza (SI) is a severe disease affecting pigs, with a huge economic impact on pig farmers. Currently, available SIV vaccines do not meet the requirements for Swine influenza prevention and control, indicating the need for vaccine development using predominant strains. Here, we isolated and identified the swine influenza virus in farms and slaughterhouses in nine provinces in China to determine the most prevalent strain. A total of 8383 samples were collected between 2013 and 2022, from which 87 swine influenza virus strains were isolated. Genome sequencing identified 62 strains of the H1N1 subtype, three strains of the H1N2 subtype, and 22 strains of the H3N2 subtype. The 521# strain virus possesses the viral ribonucleoprotein (vRNP) and matrix (M) genes from the pdm/09 lineage, the HA, NA from the original Eurasian avian-like (EA) H1N1 lineage, and the nonstructural (NS) gene from the triple-reassortant (TR) lineage. The 431# strain was also a TR, except its M-gene was derived from the original EA H1N1 lineage. The pathogenicity of two 431# strains and one typical 521# strain was evaluated in mice, and the 431# strain exhibited higher pathogenicity. Therefore, a new 521# strain was selected for vaccine production because it is the current circulating strain. The vaccine produced using the 521# strain and pre-evaluated adjuvants was effective against the homologous H05 strain, as evidenced by the normal body temperature of vaccinated pigs and low virus titer of nasal swabs. In contrast, infection with the H05 strain significantly increased the body temperature of unvaccinated pigs and increased the virus titer of nasal swabs. Notably, vaccination with the 521#-based vaccine conferred some level of protection against the heterologous B15 strain (H3N2 subtype), thus reducing the viral load in pigs.
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Affiliation(s)
- Ying Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China; Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Yunfu Huang
- Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China
| | - Kun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yufei Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaotong Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weihua Zou
- Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China
| | - Chao Wu
- Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China
| | - Xianfeng Hui
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengfei Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ya Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaomei Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhong Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China; Hubei Jiangxia Laboratory, Wuhan 430200, China.
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China; Hubei Jiangxia Laboratory, Wuhan 430200, China.
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20
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Zeller MA, Ma J, Wong FY, Tum S, Hidano A, Holt H, Chhay T, Sorn S, Koeut D, Seng B, Chao S, Ng GGK, Yan Z, Chou M, Rudge JW, Smith GJD, Su YCF. The genomic landscape of swine influenza A viruses in Southeast Asia. Proc Natl Acad Sci U S A 2023; 120:e2301926120. [PMID: 37552753 PMCID: PMC10438389 DOI: 10.1073/pnas.2301926120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/07/2023] [Indexed: 08/10/2023] Open
Abstract
Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza A virus (swIAV). Effective surveillance is essential to uncover emerging virus strains; however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. More than 4,000 nasal swabs were collected from pigs in Cambodia, yielding 72 IAV-positive samples by RT-qPCR and 45 genomic sequences. We unmasked the cocirculation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swIAV reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two and 15 B.P., indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.
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Affiliation(s)
- Michael A. Zeller
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Jordan Ma
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Sothyra Tum
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Arata Hidano
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Hannah Holt
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Ty Chhay
- Livestock Development for Community Livelihood, Phnom Penh120108, Cambodia
| | - San Sorn
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Dina Koeut
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Bunnary Seng
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Sovanncheypo Chao
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Giselle G. K. Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Zhuang Yan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Monidarin Chou
- University of Health Sciences, Phnom Penh120210, Cambodia
| | - James W. Rudge
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore169857, Singapore
- SingHealth Duke-NUS Global Health Institute,SingHealth Duke-NUS Academic Medical Centre, Singapore169857, Singapore
- Duke Global Health Institute, Duke University, Durham, NC27708
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
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21
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Sashina TA, Velikzhanina EI, Morozova OV, Epifanova NV, Novikova NA. Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia. Arch Virol 2023; 168:215. [PMID: 37524885 DOI: 10.1007/s00705-023-05838-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - E I Velikzhanina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - O V Morozova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
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22
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López-Valiñas Á, Valle M, Wang M, Darji A, Cantero G, Chiapponi C, Segalés J, Ganges L, Núñez JI. Vaccination against swine influenza in pigs causes different drift evolutionary patterns upon swine influenza virus experimental infection and reduces the likelihood of genomic reassortments. Front Cell Infect Microbiol 2023; 13:1111143. [PMID: 36992684 PMCID: PMC10040791 DOI: 10.3389/fcimb.2023.1111143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
Influenza A viruses (IAVs) can infect a wide variety of bird and mammal species. Their genome is characterized by 8 RNA single stranded segments. The low proofreading activity of their polymerases and the genomic reassortment between different IAVs subtypes allow them to continuously evolve, constituting a constant threat to human and animal health. In 2009, a pandemic of an IAV highlighted the importance of the swine host in IAVs adaptation between humans and birds. The swine population and the incidence of swine IAV is constantly growing. In previous studies, despite vaccination, swine IAV growth and evolution were proven in vaccinated and challenged animals. However, how vaccination can drive the evolutionary dynamics of swine IAV after coinfection with two subtypes is poorly studied. In the present study, vaccinated and nonvaccinated pigs were challenged by direct contact with H1N1 and H3N2 independent swine IAVs seeder pigs. Nasal swab samples were daily recovered and broncho-alveolar lavage fluid (BALF) was also collected at necropsy day from each pig for swine IAV detection and whole genome sequencing. In total, 39 swine IAV whole genome sequences were obtained by next generation sequencing from samples collected from both experimental groups. Subsequently, genomic, and evolutionary analyses were carried out to detect both, genomic reassortments and single nucleotide variants (SNV). Regarding the segments found per sample, the simultaneous presence of segments from both subtypes was much lower in vaccinated animals, indicating that the vaccine reduced the likelihood of genomic reassortment events. In relation to swine IAV intra-host diversity, a total of 239 and 74 SNV were detected within H1N1 and H3N2 subtypes, respectively. Different proportions of synonymous and nonsynonymous substitutions were found, indicating that vaccine may be influencing the main mechanism that shape swine IAV evolution, detecting natural, neutral, and purifying selection in the different analyzed scenarios. SNV were detected along the whole swine IAV genome with important nonsynonymous substitutions on polymerases, surface glycoproteins and nonstructural proteins, which may have an impact on virus replication, immune system escaping and virulence of virus, respectively. The present study further emphasized the vast evolutionary capacity of swine IAV, under natural infection and vaccination pressure scenarios.
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Affiliation(s)
- Álvaro López-Valiñas
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- *Correspondence: José I. Núñez, ; Álvaro López-Valiñas,
| | - Marta Valle
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Miaomiao Wang
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Ayub Darji
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Guillermo Cantero
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
| | - Chiara Chiapponi
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia-Romagna, Brescia, Italy
| | - Joaquim Segalés
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Llilianne Ganges
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain
| | - José I. Núñez
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, Spain
- *Correspondence: José I. Núñez, ; Álvaro López-Valiñas,
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23
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Taylor KY, Agu I, José I, Mäntynen S, Campbell AJ, Mattson C, Chou TW, Zhou B, Gresham D, Ghedin E, Díaz Muñoz SL. Influenza A virus reassortment is strain dependent. PLoS Pathog 2023; 19:e1011155. [PMID: 36857394 PMCID: PMC10010518 DOI: 10.1371/journal.ppat.1011155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/13/2023] [Accepted: 01/26/2023] [Indexed: 03/02/2023] Open
Abstract
RNA viruses can exchange genetic material during coinfection, an interaction that creates novel strains with implications for viral evolution and public health. Influenza A viral genetic exchange can occur when genome segments from distinct strains reassort in coinfected cells. Predicting potential genomic reassortment between influenza strains has been a long-standing goal. Experimental coinfection studies have shed light on factors that limit or promote reassortment. However, determining the reassortment potential between diverse Influenza A strains has remained elusive. To address this challenge, we developed a high throughput genotyping approach to quantify reassortment among a diverse panel of human influenza virus strains encompassing two pandemics (swine and avian origin), three specific epidemics, and both circulating human subtypes A/H1N1 and A/H3N2. We found that reassortment frequency (the proportion of reassortants generated) is an emergent property of specific pairs of strains where strain identity is a predictor of reassortment frequency. We detect little evidence that antigenic subtype drives reassortment as intersubtype (H1N1xH3N2) and intrasubtype reassortment frequencies were, on average, similar. Instead, our data suggest that certain strains bias the reassortment frequency up or down, independently of the coinfecting partner. We observe that viral productivity is also an emergent property of coinfections, but uncorrelated to reassortment frequency; thus viral productivity is a separate factor affecting the total number of reassortants produced. Assortment of individual segments among progeny and pairwise segment combinations within progeny generally favored homologous combinations. These outcomes were not related to strain similarity or shared subtype but reassortment frequency was closely correlated to the proportion of both unique genotypes and of progeny with heterologous pairwise segment combinations. We provide experimental evidence that viral genetic exchange is potentially an individual social trait subject to natural selection, which implies the propensity for reassortment is not evenly shared among strains. This study highlights the need for research incorporating diverse strains to discover the traits that shift the reassortment potential to realize the goal of predicting influenza virus evolution resulting from segment exchange.
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Affiliation(s)
- Kishana Y. Taylor
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Ilechukwu Agu
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Ivy José
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Sari Mäntynen
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - A. J. Campbell
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Courtney Mattson
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Tsui-Wen Chou
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - Bin Zhou
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - Elodie Ghedin
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States of America
| | - Samuel L. Díaz Muñoz
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
- Genome Center University of California, Davis Davis, California
- * E-mail:
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24
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Sun H, Liu H, Liu Y, Pang Z, Jiang Y, Liu Q, Liao M. Genetic characterization of a novel quadruple reassortant influenza A (H1N2) virus from swine, China, 2021. J Infect 2023; 86:66-117. [PMID: 36100112 DOI: 10.1016/j.jinf.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Hailiang Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China.
| | - Hanlin Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China.
| | - Yanwei Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China.
| | - Zifeng Pang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China.
| | - Yinglin Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China.
| | - Quan Liu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China.
| | - Ming Liao
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China.
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25
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Mabasa VV, van Zyl WB, Ismail A, Allam M, Taylor MB, Mans J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022; 14:v14122732. [PMID: 36560736 PMCID: PMC9788511 DOI: 10.3390/v14122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.
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Affiliation(s)
- Victor Vusi Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Walda Brenda van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0002, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Maureen Beatrice Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Correspondence: ; Tel.: +27-12-319-2660
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26
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Ganti K, Bagga A, Carnaccini S, Ferreri LM, Geiger G, Joaquin Caceres C, Seibert B, Li Y, Wang L, Kwon T, Li Y, Morozov I, Ma W, Richt JA, Perez DR, Koelle K, Lowen AC. Influenza A virus reassortment in mammals gives rise to genetically distinct within-host subpopulations. Nat Commun 2022; 13:6846. [PMID: 36369504 PMCID: PMC9652339 DOI: 10.1038/s41467-022-34611-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) genetic exchange through reassortment has the potential to accelerate viral evolution and has played a critical role in the generation of multiple pandemic strains. For reassortment to occur, distinct viruses must co-infect the same cell. The spatio-temporal dynamics of viral dissemination within an infected host therefore define opportunity for reassortment. Here, we used wild type and synonymously barcoded variant viruses of a pandemic H1N1 strain to examine the within-host viral dynamics that govern reassortment in guinea pigs, ferrets and swine. The first two species are well-established models of human influenza, while swine are a natural host and a frequent conduit for cross-species transmission and reassortment. Our results show reassortment to be pervasive in all three hosts but less frequent in swine than in ferrets and guinea pigs. In ferrets, tissue-specific differences in the opportunity for reassortment are also evident, with more reassortants detected in the nasal tract than the lower respiratory tract. While temporal trends in viral diversity are limited, spatial patterns are clear, with heterogeneity in the viral genotypes detected at distinct anatomical sites revealing extensive compartmentalization of reassortment and replication. Our data indicate that the dynamics of viral replication in mammals allow diversification through reassortment but that the spatial compartmentalization of variants likely shapes their evolution and onward transmission.
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Affiliation(s)
- Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anish Bagga
- Emory College of Arts and Sciences, Atlanta, GA, USA
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Lucas M Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - C Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Yonghai Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Liping Wang
- Department of Veterinary Pathobiology, and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Taeyong Kwon
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yuhao Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Igor Morozov
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wenjun Ma
- Department of Veterinary Pathobiology, and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
- St. Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, TN, USA
| | - Juergen A Richt
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
- St. Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, TN, USA
| | - Daniel R Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- The Center for Research on Influenza Pathogenesis and Transmission (CRIPT CEIRR), New York, NY, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, GA, USA.
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27
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Barrat-Charlaix P, Vaughan TG, Neher RA. TreeKnit: Inferring ancestral reassortment graphs of influenza viruses. PLoS Comput Biol 2022; 18:e1010394. [PMID: 35984845 PMCID: PMC9447925 DOI: 10.1371/journal.pcbi.1010394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 09/06/2022] [Accepted: 07/15/2022] [Indexed: 11/28/2022] Open
Abstract
When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments. Influenza viruses evolve quickly and escape immune defenses which requires frequent update of vaccines. Understanding this evolution is key to an effective public health response. The genome of influenza viruses is made up of 8 pieces called segments, each coding for different viral proteins. Within each segment, evolution is an asexual process in which genetic diversity is generated by mutations. But influenza also diversifies through reassortment which can occur when two different viruses infect the same cell: offsprings can then contain a combination of segments from both viruses. Reassortment is akin to sexual reproduction and can generate viruses that combine segments from diverged viral lineages. Reassortment is a crucial component of viral evolution, but it is challenging to reconstruct where reassortments happened and which segments share history. Here, we develop a method called TreeKnit to detect reassortment events. TreeKnit is based on genealogical trees of single segments that can be reconstructed using standard bioinformatics tools. Inconsistencies between these trees are then used as signs of reassortment. We show that TreeKnit is as accurate as other recent methods, but runs much faster. Our method will facilitate the study of reassortment and its consequences for influenza evolution.
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Affiliation(s)
- Pierre Barrat-Charlaix
- Biozentrum, Universität Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Timothy G. Vaughan
- Swiss Institute of Bioinformatics, Basel, Switzerland
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Richard A. Neher
- Biozentrum, Universität Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
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28
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Gu M, Chen K, Ge Z, Jiao J, Cai T, Liu S, Wang X, Jiao X, Peng D, Liu X. Zoonotic Threat of G4 Genotype Eurasian Avian-Like Swine Influenza A(H1N1) Viruses, China, 2020. Emerg Infect Dis 2022; 28:1664-1668. [PMID: 35876682 PMCID: PMC9328894 DOI: 10.3201/eid2808.212530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated genetic and biologic characteristics of 2 Eurasian avian-like H1N1 swine influenza viruses from pigs in China that belong to the predominant G4 genotype. One swine isolate exhibited strikingly great homology to contemporaneous human Eurasian avian-like H1N1 isolates, preferential binding to the human-type receptor, and vigorous replication in mice without adaptation.
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29
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Chen J, Xu L, Liu T, Xie S, Li K, Li X, Zhang M, Wu Y, Wang X, Wang J, Shi K, Niu B, Liao M, Jia W. Novel Reassortant Avian Influenza A(H5N6) Virus, China, 2021. Emerg Infect Dis 2022; 28:1703-1707. [PMID: 35820171 PMCID: PMC9328904 DOI: 10.3201/eid2808.212241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Although reports of human infection with influenza A(H5N6) increased in 2021, reports of similar H5N6 virus infection in poultry are few. We detected 10 avian influenza A(H5N6) clade 2.3.4.4b viruses in poultry from 4 provinces in China. The viruses showed strong immune-escape capacity and complex genetic reassortment, suggesting further transmission risk.
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30
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Wang SY, Wen F, Yu LX, Wang J, Wang MZ, Yan JC, Zhou YJ, Tong W, Shan TL, Li GX, Zheng H, Liu CL, Kong N, Tong GZ, Yu H. Potential Threats to Human Health from Eurasian Avian-Like Swine Influenza A(H1N1) Virus and Its Reassortants. Emerg Infect Dis 2022; 28:1489-1493. [PMID: 35680129 PMCID: PMC9239861 DOI: 10.3201/eid2807.211822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 2018-2020, we isolated 32 Eurasian avian-like swine influenza A(H1N1) viruses and their reassortant viruses from pigs in China. Genomic testing identified a novel reassortant H3N1 virus, which emerged in late 2020. Derived from G4 Eurasian H1N1 and H3N2 swine influenza viruses. This virus poses a risk for zoonotic infection.
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31
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Sun W, Cheng SSM, Lam KNT, Kwan TC, Wong RWK, Lau LHK, Liu GYZ, Luk LLH, Li JKC, Gu H, Peiris M, Poon LLM. Natural Reassortment of Eurasian Avian-Like Swine H1N1 and Avian H9N2 Influenza Viruses in Pigs, China. Emerg Infect Dis 2022; 28:1509-1512. [PMID: 35731193 PMCID: PMC9239857 DOI: 10.3201/eid2807.220642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Several zoonotic influenza A viruses detected in humans contain genes derived from avian H9N2 subtypes. We uncovered a Eurasian avian-like H1N1 swine influenza virus with polymerase basic 1 and matrix gene segments derived from the H9N2 subtype, suggesting that H9N2 viruses are infecting pigs and reassorting with swine influenza viruses in China.
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32
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Berhane Y, Joseph T, Lung O, Embury-Hyatt C, Xu W, Cottrell P, Raverty S. Isolation and Characterization of Novel Reassortant Influenza A(H10N7) Virus in a Harbor Seal, British Columbia, Canada. Emerg Infect Dis 2022; 28:1480-1484. [PMID: 35731188 PMCID: PMC9239883 DOI: 10.3201/eid2807.212302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We isolated a novel reassortant influenza A(H10N7) virus from a harbor seal in British Columbia, Canada, that died from bronchointerstitial pneumonia. The virus had unique genome constellations involving lineages from North America and Eurasia and polymerase basic 2 segment D701N mutation, associated with adaptation to mammals.
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33
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Zhu W, Li X, Dong J, Bo H, Liu J, Yang J, Zhang Y, Wei H, Huang W, Zhao X, Chen T, Yang J, Li Z, Zeng X, Li C, Tang J, Xin L, Gao R, Liu L, Tan M, Shu Y, Yang L, Wang D. Epidemiologic, Clinical, and Genetic Characteristics of Human Infections with Influenza A(H5N6) Viruses, China. Emerg Infect Dis 2022; 28:1332-1344. [PMID: 35476714 PMCID: PMC9239879 DOI: 10.3201/eid2807.212482] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The recent rise in the frequency of influenza A(H5N6) infections in China has raised serious concerns about whether the risk for human infection has increased. We surveyed epidemiologic, clinical, and genetic data of human infections with A(H5N6) viruses. Severe disease occurred in 93.8% of cases, and the fatality rate was 55.4%. Median patient age was 51 years. Most H5N6 hemagglutinin (HA) genes in human isolates in 2021 originated from subclade 2.3.4.4b; we estimated the time to most recent common ancestor as June 16, 2020. A total of 13 genotypes with HA genes from multiple subclades in clade 2.3.4.4 were identified in human isolates. Of note, 4 new genotypes detected in 2021 were the major causes of increased H5N6 virus infections. Mammalian-adapted mutations were found in HA and internal genes. Although we found no evidence of human-to-human transmission, continuous evolution of H5N6 viruses may increase the risk for human infections.
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34
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He D, Wang X, Wu H, Wang X, Yan Y, Li Y, Zhan T, Hao X, Hu J, Hu S, Liu X, Ding C, Su S, Gu M, Liu X. Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013-2019. Viruses 2022; 14:v14061256. [PMID: 35746727 PMCID: PMC9230085 DOI: 10.3390/v14061256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/29/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Reassortment with the H9N2 virus gave rise to the zoonotic H7N9 avian influenza virus (AIV), which caused more than five outbreak waves in humans, with high mortality. The frequent exchange of genomic segments between H7N9 and H9N2 has been well-documented. However, the reassortment patterns have not been described and are not yet fully understood. Here, we used phylogenetic analyses to investigate the patterns of intersubtype and intrasubtype/intralineage reassortment across the eight viral segments. The H7N9 virus and its progeny frequently exchanged internal genes with the H9N2 virus but rarely with the other AIV subtypes. Before beginning the intrasubtype/intralineage reassortment analyses, five Yangtze River Delta (YRD A-E) and two Pearl River Delta (PRD A-B) clusters were divided according to the HA gene phylogeny. The seven reset segment genes were also nomenclatured consistently. As revealed by the tanglegram results, high intralineage reassortment rates were determined in waves 2–3 and 5. Additionally, the clusters of PB2 c05 and M c02 were the most dominant in wave 5, which could have contributed to the onset of the largest H7N9 outbreak in 2016–2017. Meanwhile, a portion of the YRD-C cluster (HP H7N9) inherited their PB2, PA, and M segments from the co-circulating YRD-E (LP H7N9) cluster during wave 5. Untanglegram results revealed that the reassortment rate between HA and NA was lower than HA with any of the other six segments. A multidimensional scaling plot revealed a robust genetic linkage between the PB2 and PA genes, indicating that they may share a co-evolutionary history. Furthermore, we observed relatively more robust positive selection pressure on HA, NA, M2, and NS1 proteins. Our findings demonstrate that frequent reassortment, particular reassorted patterns, and adaptive mutations shaped the H7N9 viral genetic diversity and evolution. Increased surveillance is required immediately to better understand the current state of the HP H7N9 AIV.
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Affiliation(s)
- Dongchang He
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Xiyue Wang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Huiguang Wu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Yayao Yan
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Yang Li
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Tiansong Zhan
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Xiaoli Hao
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Jiao Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Chan Ding
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shuo Su
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
| | - Min Gu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (M.G.); (X.L.)
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (M.G.); (X.L.)
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Jiang W, Dong C, Liu S, Peng C, Yin X, Liang S, Zhang L, Li J, Yu X, Li Y, Wang J, Hou G, Zeng Z, Liu H. Emerging Novel Reassortant Influenza A(H5N6) Viruses in Poultry and Humans, China, 2021. Emerg Infect Dis 2022; 28:1064-1066. [PMID: 35447059 PMCID: PMC9045449 DOI: 10.3201/eid2805.212163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A novel highly pathogenic avian influenza A(H5N6) clade 2.3.4.4b virus was isolated from a poultry market in China that a person with a confirmed case had visited. Most genes of the avian and human H5N6 isolates were closely related. The virus also exhibited distinct antigenicity to the Re-11 vaccine strain.
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36
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Abstract
The continuous emergence and reemergence of diverse subtypes of influenza A viruses, which are known as "HxNy" and are mediated through the reassortment of viral genomes, account for seasonal epidemics, occasional pandemics, and zoonotic outbreaks. We summarize and discuss the characteristics of historic human pandemic HxNy viruses and diverse subtypes of HxNy among wild birds, mammals, and live poultry markets. In addition, we summarize the key molecular features of emerging infectious HxNy influenza viruses from the perspectives of the receptor binding of Hx, the inhibitor-binding specificities and drug-resistance features of Ny, and the matching of the gene segments. Our work enhances our understanding of the potential threats of novel reassortant influenza viruses to public health and provides recommendations for effective prevention, control, and research of this pathogen.
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Affiliation(s)
- William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Yan Wu
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Weifeng Shi
- Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an 271016, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China
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37
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Abstract
The structured coalescent allows inferring migration patterns between viral subpopulations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can undergo reassortment this assumption is broken. Reassortment reshuffles the segments of different parent lineages upon a coinfection event, which means that the shared history of viruses has to be represented by a network instead of a tree. Therefore, full genome analyses of such viruses are complex or even impossible. Although this problem has been addressed for unstructured populations, it is still impossible to account for population structure, such as induced by different host populations, whereas also accounting for reassortment. We address this by extending the structured coalescent to account for reassortment and present a framework for investigating possible ties between reassortment and migration (host jump) events. This method can accurately estimate subpopulation dependent effective populations sizes, reassortment, and migration rates from simulated data. Additionally, we apply the new model to avian influenza A/H5N1 sequences, sampled from two avian host types, Anseriformes and Galliformes. We contrast our results with a structured coalescent without reassortment inference, which assumes independently evolving segments. This reveals that taking into account segment reassortment and using sequencing data from several viral segments for joint phylodynamic inference leads to different estimates for effective population sizes, migration, and clock rates. This new model is implemented as the Structured Coalescent with Reassortment package for BEAST 2.5 and is available at https://github.com/jugne/SCORE.
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Affiliation(s)
- Ugnė Stolz
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Nicola F Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Timothy G Vaughan
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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Li F, Liu J, Yang J, Sun H, Jiang Z, Wang C, Zhang X, Yu Y, Zhao C, Pu J, Sun Y, Chang KC, Liu J, Sun H. H9N2 virus-derived M1 protein promotes H5N6 virus release in mammalian cells: Mechanism of avian influenza virus inter-species infection in humans. PLoS Pathog 2021; 17:e1010098. [PMID: 34860863 PMCID: PMC8641880 DOI: 10.1371/journal.ppat.1010098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 11/05/2021] [Indexed: 11/18/2022] Open
Abstract
H5N6 highly pathogenic avian influenza virus (HPAIV) clade 2.3.4.4 not only exhibits unprecedented intercontinental spread in poultry, but can also cause serious infection in humans, posing a public health threat. Phylogenetic analyses show that 40% (8/20) of H5N6 viruses that infected humans carried H9N2 virus-derived internal genes. However, the precise contribution of H9N2 virus-derived internal genes to H5N6 virus infection in humans is unclear. Here, we report on the functional contribution of the H9N2 virus-derived matrix protein 1 (M1) to enhanced H5N6 virus replication capacity in mammalian cells. Unlike H5N1 virus-derived M1 protein, H9N2 virus-derived M1 protein showed high binding affinity for H5N6 hemagglutinin (HA) protein and increased viral progeny particle release in different mammalian cell lines. Human host factor, G protein subunit beta 1 (GNB1), exhibited strong binding to H9N2 virus-derived M1 protein to facilitate M1 transport to budding sites at the cell membrane. GNB1 knockdown inhibited the interaction between H9N2 virus-derived M1 and HA protein, and reduced influenza virus-like particles (VLPs) release. Our findings indicate that H9N2 virus-derived M1 protein promotes avian H5N6 influenza virus release from mammalian, in particular human cells, which could be a major viral factor for H5N6 virus cross-species infection.
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Affiliation(s)
- Fangtao Li
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiyu Liu
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jizhe Yang
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Haoran Sun
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhimin Jiang
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chenxi Wang
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xin Zhang
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yinghui Yu
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chuankuo Zhao
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yipeng Sun
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kin-Chow Chang
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, United Kingdom
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
- * E-mail: (JL); (HS)
| | - Honglei Sun
- Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
- * E-mail: (JL); (HS)
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El-Shesheny R, Turner JCM, Walker D, Franks J, Seiler P, Barman S, Feeroz MM, Hasan MK, Akhtar S, Mukherjee N, Kercher L, McKenzie P, Webster RG, Webby RJ. Detection of a Novel Reassortant H9N9 Avian Influenza Virus in Free-Range Ducks in Bangladesh. Viruses 2021; 13:v13122357. [PMID: 34960626 PMCID: PMC8704232 DOI: 10.3390/v13122357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 01/10/2023] Open
Abstract
Wild aquatic birds are the primary natural reservoir for influenza A viruses (IAVs). In this study, an A(H9N9) influenza A virus (A/duck/Bangladesh/44493/2020) was identified via routine surveillance in free-range domestic ducks in Bangladesh. Phylogenetic analysis of hemagglutinin showed that the H9N9 virus belonged to the Y439-like lineage. The HA gene had the highest nucleotide identity to A/Bean Goose (Anser fabalis)/South Korea/KNU 2019-16/2019 (H9N2). The other seven gene segments clustered within the Eurasian lineage.
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Affiliation(s)
- Rabeh El-Shesheny
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Jasmine C. M. Turner
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - David Walker
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - John Franks
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - Patrick Seiler
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - Subrata Barman
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - Mohammed M. Feeroz
- Department of Zoology, Jahangirnagar University, Savar 1342, Bangladesh; (M.M.F.); (M.K.H.); (S.A.)
| | - Md Kamrul Hasan
- Department of Zoology, Jahangirnagar University, Savar 1342, Bangladesh; (M.M.F.); (M.K.H.); (S.A.)
| | - Sharmin Akhtar
- Department of Zoology, Jahangirnagar University, Savar 1342, Bangladesh; (M.M.F.); (M.K.H.); (S.A.)
| | - Nabanita Mukherjee
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - Lisa Kercher
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - Pamela McKenzie
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - Robert G. Webster
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (R.E.-S.); (J.C.M.T.); (D.W.); (J.F.); (P.S.); (S.B.); (N.M.); (L.K.); (P.M.); (R.G.W.)
- Correspondence:
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40
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Nissen JN, George SJ, Hjulsager CK, Krog JS, Nielsen XC, Madsen TV, Andersen KM, Krause TG, Vestergaard LS, Larsen LE, Trebbien R. Reassortant Influenza A(H1N1)pdm09 Virus in Elderly Woman, Denmark, January 2021. Emerg Infect Dis 2021; 27:3202-3205. [PMID: 34808097 PMCID: PMC8632190 DOI: 10.3201/eid2712.211361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
A case of human infection with influenza A(H1N1)pdm09 virus containing a nonstructural gene highly similar to Eurasian avian-like H1Nx swine influenza virus was detected in Denmark in January 2021. We describe the clinical case and report testing results of the genetic and antigenic characterizations of the virus.
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41
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Duong BT, Bal J, Sung HW, Yeo SJ, Park H. Molecular Analysis of the Avian H7 Influenza Viruses Circulating in South Korea during 2018-2019: Evolutionary Significance and Associated Zoonotic Threats. Viruses 2021; 13:v13112260. [PMID: 34835066 PMCID: PMC8623559 DOI: 10.3390/v13112260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/18/2022] Open
Abstract
Avian influenza virus (AIV) subtypes H5 and H7, possessing the ability to mutate spontaneously from low pathogenic (LP) to highly pathogenic (HP) variants, are major concerns for enormous socio-economic losses in the poultry industry, as well as for fatal human infections. Through antigenic drift and shift, genetic reassortments of the genotypes pose serious threats of increased virulence and pathogenicity leading to potential pandemics. In this study, we isolated the H7-subtype AIVs circulating in the Republic of Korea during 2018–2019, and perform detailed molecular analysis to study their circulation, evolution, and possible emergence as a zoonotic threat. Phylogenetic and nucleotide sequence analyses of these isolates revealed their distribution into two distinct clusters, with the HA gene sharing the highest nucleotide identity with either the A/common teal/Shanghai/CM1216/2017, isolated from wild birds in Shanghai, China, or the A/duck/Shimane/2014, isolated from Japan. Mutations were found in HA (S138A (H3 numbering)), M1 (N30D and T215A), NS1 (P42S), PB2 (L89V), and PA (H266R and F277S) proteins—the mutations had previously been reported to be related to mammalian adaptation and changes in the virulence of AIVs. Taken together, the results firmly put forth the demand for routine surveillance of AIVs in wild birds to prevent possible pandemics arising from reassortant AIVs.
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Affiliation(s)
- Bao Tuan Duong
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (B.T.D.); (J.B.)
| | - Jyotiranjan Bal
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (B.T.D.); (J.B.)
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon-si 24341, Korea
- Correspondence: (H.W.S.); (S.-J.Y.); (H.P.)
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul 03080, Korea
- Correspondence: (H.W.S.); (S.-J.Y.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (B.T.D.); (J.B.)
- Correspondence: (H.W.S.); (S.-J.Y.); (H.P.)
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Lee YN, Lee DH, Shin JI, Si YJ, Lee JH, Baek YG, Hong SY, Bunnary S, Tum S, Park M, Kye SJ, Lee MH, Lee YJ. Pathogenesis and genetic characteristics of a novel reassortant low pathogenic avian influenza A(H7N6) virus isolated in Cambodia in 2019. Transbound Emerg Dis 2021; 68:3180-3186. [PMID: 34347386 DOI: 10.1111/tbed.14256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/12/2021] [Indexed: 12/01/2022]
Abstract
The first human case of zoonotic A(H7N4) avian influenza virus (AIV) infection was reported in early 2018 in China. Two months after this case, novel A(H7N4) viruses phylogenetically related to the Jiangsu isolate emerged in ducks from live bird markets in Cambodia. During active surveillance in Cambodia, a novel A(H7N6) reassortant of the zoonotic low pathogenic AIV (LPAIV) A(H7N4) was detected in domestic ducks at a slaughterhouse. Complete genome sequencing and phylogenetic analysis showed that the novel A(H7N6) AIV is a reassortant, in which four gene segments originated from Cambodia A(H7N4) viruses and four gene segments originated from LPAIVs in Eurasia. Animal infection experiments revealed that chickens transmitted the A(H7N6) virus via low-level direct contacts, but ducks did not. Although avian-origin A(H7Nx) LPAIVs do not contain the critical mammalian-adaptive substitution (E627K) in PB2, the lethality and morbidity of the A(H7N6) virus in BALB/c mice were similar to those of A(H7N9) viruses, suggesting potential for interspecies transmission. Our study reports the emergence of a new reassortant of zoonotic A(H7N4) AIVs with novel viral characteristics and emphasizes the need for ongoing surveillance of avian-origin A(H7Nx) viruses.
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Affiliation(s)
- Yu-Na Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, Connecticut, USA
| | - Jae-In Shin
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Young-Jae Si
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Ji-Ho Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Yoon-Gi Baek
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Seo Yun Hong
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Seng Bunnary
- Department of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Sothyra Tum
- Department of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Minji Park
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Soo-Jeong Kye
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Myoung-Heon Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Youn-Jeong Lee
- Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
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43
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Waters K, Gao C, Ykema M, Han L, Voth L, Tao YJ, Wan XF. Triple reassortment increases compatibility among viral ribonucleoprotein genes of contemporary avian and human influenza A viruses. PLoS Pathog 2021; 17:e1009962. [PMID: 34618879 PMCID: PMC8525756 DOI: 10.1371/journal.ppat.1009962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 10/19/2021] [Accepted: 09/20/2021] [Indexed: 12/21/2022] Open
Abstract
Compatibility among the influenza A virus (IAV) ribonucleoprotein (RNP) genes affects viral replication efficiency and can limit the emergence of novel reassortants, including those with potential pandemic risks. In this study, we determined the polymerase activities of 2,451 RNP reassortants among three seasonal and eight enzootic IAVs by using a minigenome assay. Results showed that the 2009 H1N1 RNP are more compatible with the tested enzootic RNP than seasonal H3N2 RNP and that triple reassortment increased such compatibility. The RNP reassortants among 2009 H1N1, canine H3N8, and avian H4N6 IAVs had the highest polymerase activities. Residues in the RNA binding motifs and the contact regions among RNP proteins affected polymerase activities. Our data indicates that compatibility among seasonal and enzootic RNPs are selective, and enzoosis of multiple strains in the animal-human interface can facilitate emergence of an RNP with increased replication efficiency in mammals, including humans.
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Affiliation(s)
- Kaitlyn Waters
- Missouri University Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Cheng Gao
- Missouri University Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, United States of America
| | - Matthew Ykema
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Lei Han
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Lynden Voth
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Xiu-Feng Wan
- Missouri University Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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Yang F, Xiao Y, Liu F, Yao H, Wu N, Wu H. Molecular characterization and antigenic analysis of reassortant H9N2 subtype avian influenza viruses in Eastern China in 2016. Virus Res 2021; 306:198577. [PMID: 34560182 DOI: 10.1016/j.virusres.2021.198577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/31/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022]
Abstract
H9N2 avian influenza viruses (AIVs) can cause respiratory symptoms and decrease the egg production. Additionally, H9N2 AIVs can provide internal genes for reassortment with other subtypes. During the monitoring of live poultry markets in 2016, a total of 32 (32/179, 17.88%) H9N2 AIVs were isolated from poultry in Eastern China, and seven representative strains were selected based on the isolation time, isolation location and sequence homology for further characterization. Phylogenetic analysis of hemagglutinin and neuraminidase showed that these H9N2 AIVs clustered into the Y280 sublineage. And the phylogenetic trees of six internal genes showed that the source of these gene fragments was more abundant, suggesting that extensive reassortment has occurred in these H9N2 viruses. Molecular analysis showed that multiple specific amino acid mutations occurred that increased H9N2 AIVs' infectivity, transmissibility, and affinity to mammals, including Q226L and Q227M in hemagglutinin, E627K in polymerase basic protein 2 (PB2), L13P in polymerase basic protein 1 (PB1), and A70V and S409N in polymerase acidic protein (PA). Pathogenicity tests in mice showed these H9N2 AIVs could replicate in lungs and exhibited slight to moderate virulence. The continuous circulation of these H9N2 viruses suggests the necessity for persistent surveillance of the H9N2 AIVs in poultry.
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Affiliation(s)
- Fan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, Zhejiang, China
| | - Yixin Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, Zhejiang, China
| | - Fumin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, Zhejiang, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, Zhejiang, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, Zhejiang, China
| | - Haibo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, and National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, Zhejiang, China.
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Ropiak HM, King S, Busquets MG, Newbrook K, Pullinger GD, Brown H, Flannery J, Gubbins S, Batten C, Rajko-Nenow P, Darpel KE. Identification of a BTV-Strain-Specific Single Gene That Increases Culicoides Vector Infection Rate. Viruses 2021; 13:1781. [PMID: 34578362 PMCID: PMC8472919 DOI: 10.3390/v13091781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/27/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Since the 2000s, the distribution of bluetongue virus (BTV) has changed, leading to numerous epidemics and economic losses in Europe. Previously, we found a BTV-4 field strain with a higher infection rate of a Culicoides vector than a BTV-1 field strain has. We reverse-engineered parental BTV-1 and BTV-4 strains and created BTV-1/BTV-4 reassortants to elucidate the influence of individual BTV segments on BTV replication in both C. sonorensis midges and in KC cells. Substitution of segment 2 (Seg-2) with Seg-2 from the rBTV-4 significantly increased vector infection rate in reassortant BTV-14S2 (30.4%) in comparison to reverse-engineered rBTV-1 (1.0%). Replacement of Seg-2, Seg-6 and Seg-7 with those from rBTV-1 in reassortant BTV-41S2S6S7 (2.9%) decreased vector infection rate in comparison to rBTV-4 (30.2%). However, triple-reassorted BTV-14S2S6S7 only replicated to comparatively low levels (3.0%), despite containing Seg-2, Seg-6 and Seg-7 from rBTV-4, indicating that vector infection rate is influenced by interactions of multiple segments and/or host-mediated amino acid substitutions within segments. Overall, these results demonstrated that we could utilize reverse-engineered viruses to identify the genetic basis influencing BTV replication within Culicoides vectors. However, BTV replication dynamics in KC cells were not suitable for predicting the replication ability of these virus strains in Culicoides midges.
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Wang Y, Jiang N, Fan L, Niu X, Zhang W, Huang M, Gao L, Li K, Gao Y, Liu C, Cui H, Liu A, Pan Q, Zhang Y, Wang X, Qi X. Identification and Pathogenicity Evaluation of a Novel Reassortant Infectious Bursal Disease Virus (Genotype A2dB3). Viruses 2021; 13:v13091682. [PMID: 34578267 PMCID: PMC8472943 DOI: 10.3390/v13091682] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/26/2023] Open
Abstract
Infectious bursal disease virus (IBDV) is a non-enveloped, bi-segmented double-stranded RNA virus and the causative agent of a poultry immunosuppressive disease known as infectious bursal disease (IBD). The novel variant IBDV (nVarIBDV) recently posed a great threat to the development of the poultry industry. In this study, we identified a novel segment-reassortant IBDV strain, IBDV-JS19-14701 (Genotype A2dB3). Phylogenic analysis showed that Segments A and B of IBDV-JS19-14701 were derived from emerging nVarIBDV (Genotype A2dB1) and long-prevalent HLJ0504-like strains (Genotype A3B3) in China, respectively. The pathogenicity of IBDV-JS19-14701 was further evaluated via animal experiments. IBDV-JS19-14701 exhibited a similar virulence to chickens with the nVarIBDV. The identification of this reassortment event is beneficial for understanding the epidemiology of nVarIBDV and will contribute to the efficient prevention and control of IBD.
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Affiliation(s)
- Yulong Wang
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Nan Jiang
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Linjin Fan
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xinxin Niu
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wenying Zhang
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Mengmeng Huang
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Li Gao
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Kai Li
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
| | - Yulong Gao
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Changjun Liu
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
| | - Hongyu Cui
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Aijing Liu
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Qing Pan
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
| | - Yanping Zhang
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
| | - Xiaomei Wang
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
- Jiangsu Co-Innovation Centre for Prevention and Control of Important Animal Infectious Disease and Zoonosis, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xiaole Qi
- State Key Laboratory of Veterinary Biotechnology, Avian Immunosuppressive Diseases Division, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.W.); (N.J.); (L.F.); (X.N.); (W.Z.); (M.H.); (L.G.); (K.L.); (Y.G.); (C.L.); (H.C.); (A.L.); (Q.P.); (Y.Z.); (X.W.)
- OIE Reference Laboratory for Infectious Bursal Disease, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
- Correspondence: ; Tel.: +86-0451-5105-1692
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Sobolev I, Sharshov K, Dubovitskiy N, Kurskaya O, Alekseev A, Leonov S, Yushkov Y, Irza V, Komissarov A, Fadeev A, Danilenko D, Mine J, Tsunekuni R, Uchida Y, Saito T, Shestopalov A. Highly Pathogenic Avian Influenza A(H5N8) Virus Clade 2.3.4.4b, Western Siberia, Russia, 2020. Emerg Infect Dis 2021; 27:2224-2227. [PMID: 34287138 PMCID: PMC8314819 DOI: 10.3201/eid2708.204969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Two variants of highly pathogenic avian influenza A(H5N8) virus were detected in dead poultry in Western Siberia, Russia, during August and September 2020. One variant was represented by viruses of clade 2.3.4.4b and the other by a novel reassortant between clade 2.3.4.4b and Eurasian low pathogenicity avian influenza viruses circulating in wild birds.
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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Postnikova Y, Treshchalina A, Boravleva E, Gambaryan A, Ishmukhametov A, Matrosovich M, Fouchier RAM, Sadykova G, Prilipov A, Lomakina N. Diversity and Reassortment Rate of Influenza A Viruses in Wild Ducks and Gulls. Viruses 2021; 13:v13061010. [PMID: 34072256 PMCID: PMC8230314 DOI: 10.3390/v13061010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 01/18/2023] Open
Abstract
Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. The complete genomes of 38 IAVs of H1N1, H1N2, H3N1, H3N2, H3N6, H3N8, H4N6, H5N3, H6N2, H11N6, and H11N9 subtypes isolated from wild mallard ducks and gulls resting in a city pond in Moscow, Russia were sequenced. The analysis of phylogenetic trees showed that stable viral genotypes do not persist from year to year in ducks owing to frequent gene reassortment. For comparison, similar analyses were carried out using sequences of IAVs isolated in the same period from ducks and gulls in The Netherlands. Our results revealed a significant difference in diversity and rates of reassortment of IAVs in ducks and gulls.
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Affiliation(s)
- Yulia Postnikova
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Anastasia Treshchalina
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Elizaveta Boravleva
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
- Correspondence: ; Tel.: +7-985-136-3586
| | - Aydar Ishmukhametov
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Mikhail Matrosovich
- Institute of Virology, Philipps University, Hans-Meerwein-Str. 2, D-35043 Marburg, Germany;
| | - Ron A. M. Fouchier
- Department of Virology, Erasmus Medical Centre, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands;
| | - Galina Sadykova
- The Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia; (G.S.); (A.P.); (N.L.)
| | - Alexey Prilipov
- The Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia; (G.S.); (A.P.); (N.L.)
| | - Natalia Lomakina
- The Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia; (G.S.); (A.P.); (N.L.)
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