1
|
Cheung JTL, Tsang TK, Yen HL, Perera RAPM, Mok CKP, Lin YP, Cowling BJ, Peiris M. Determining Existing Human Population Immunity as Part of Assessing Influenza Pandemic Risk. Emerg Infect Dis 2022; 28:977-985. [PMID: 35447069 PMCID: PMC9045452 DOI: 10.3201/eid2805.211965] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Zoonotic influenza infections continue to threaten human health. Ongoing surveillance and risk assessment of animal viruses are needed for pandemic preparedness, and population immunity is an important component of risk assessment. We determined age-stratified hemagglutinin inhibition seroprevalence against 5 swine influenza viruses circulating in Hong Kong and Guangzhou in China. Using hemagglutinin inhibition seroprevalence and titers, we modeled the effect of population immunity on the basic reproduction number (R0) if each virus were to become transmissible among humans. Among 353 individual serum samples, we reported low seroprevalence for triple-reassortant H1N2 and Eurasian avian-like H1N1 influenza viruses, which would reduce R0 by only 18%–20%. The smallest R0 needed to cause a pandemic was 1.22–1.24, meaning existing population immunity would be insufficient to block the spread of these H1N1 or H1N2 variants. For human-origin H3N2, existing population immunity could suppress R0 by 47%, thus reducing pandemic risk.
Collapse
|
2
|
Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019. Sci Rep 2021; 11:11276. [PMID: 34050216 PMCID: PMC8163766 DOI: 10.1038/s41598-021-90512-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
Surveillance of swine influenza A viruses (swIAV) allows timely detection and identification of new variants with potential zoonotic risks. In this study, we aimed to identify swIAV subtypes that circulated in pigs in Belgium and the Netherlands between 2014 and 2019, and characterize their genetic and antigenic evolution. We subtyped all isolates and analyzed hemagglutinin sequences and hemagglutination inhibition assay data for H1 swIAV, which were the dominant HA subtype. We also analyzed whole genome sequences (WGS) of selected isolates. Out of 200 samples, 89 tested positive for swIAV. swIAV of H1N1, H1N2 and H3N2 subtypes were detected. Analysis of WGS of 18 H1 swIAV isolates revealed three newly emerged genotypes. The European avian-like H1 swIAV (lineage 1C) were predominant and accounted for 47.2% of the total isolates. They were shown to evolve faster than the European human-like H1 (1B lineage) swIAV, which represented 27% of the isolates. The 2009 pandemic H1 swIAV (lineage 1A) accounted for only 5.6% of the isolates and showed divergence from their precursor virus. These results point to the increasing divergence of swIAV and stress the need for continuous surveillance of swIAV.
Collapse
|
3
|
Anderson TK, Chang J, Arendsee ZW, Venkatesh D, Souza CK, Kimble JB, Lewis NS, Davis CT, Vincent AL. Swine Influenza A Viruses and the Tangled Relationship with Humans. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038737. [PMID: 31988203 PMCID: PMC7919397 DOI: 10.1101/cshperspect.a038737] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Influenza A viruses (IAVs) are the causative agents of one of the most important viral respiratory diseases in pigs and humans. Human and swine IAV are prone to interspecies transmission, leading to regular incursions from human to pig and vice versa. This bidirectional transmission of IAV has heavily influenced the evolutionary history of IAV in both species. Transmission of distinct human seasonal lineages to pigs, followed by sustained within-host transmission and rapid adaptation and evolution, represent a considerable challenge for pig health and production. Consequently, although only subtypes of H1N1, H1N2, and H3N2 are endemic in swine around the world, extensive diversity can be found in the hemagglutinin (HA) and neuraminidase (NA) genes, as well as the remaining six genes. We review the complicated global epidemiology of IAV in swine and the inextricably entangled implications for public health and influenza pandemic planning.
Collapse
Affiliation(s)
- Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Jennifer Chang
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Zebulun W. Arendsee
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Divya Venkatesh
- Department of Pathology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire AL9 7TA, United Kingdom
| | - Carine K. Souza
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - J. Brian Kimble
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Nicola S. Lewis
- Department of Pathology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire AL9 7TA, United Kingdom
| | - C. Todd Davis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Amy L. Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| |
Collapse
|
4
|
Ma W. Swine influenza virus: Current status and challenge. Virus Res 2020; 288:198118. [PMID: 32798539 PMCID: PMC7587018 DOI: 10.1016/j.virusres.2020.198118] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022]
Abstract
Since swine influenza virus was first isolated in 1930, it has become endemic in pigs worldwide. Although large amount of swine influenza vaccines has been used in swine industry, swine influenza still cannot be efficiently controlled and has been an important economic disease for swine industry. The high diversity and varied distribution of different subtypes and genotypes of swine influenza viruses circulating in pigs globally is a major challenge to produce broadly effective vaccines and control disease. Importantly, swine influenza virus is able to cross species barrier to infect humans and even caused influenza pandemic in 2009. Herein, current status and challenge of swine influenza viruses is reviewed and discussed.
Collapse
Affiliation(s)
- Wenjun Ma
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, United States.
| |
Collapse
|
5
|
Genetic Characterization of Influenza A Viruses in Japanese Swine in 2015 to 2019. J Virol 2020; 94:JVI.02169-19. [PMID: 32350072 PMCID: PMC7343197 DOI: 10.1128/jvi.02169-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/10/2020] [Indexed: 11/20/2022] Open
Abstract
Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies. To assess the current status of influenza A viruses of swine (IAVs-S) throughout Japan and to investigate how these viruses persisted and evolve on pig farms, we genetically characterized IAVs-S isolated during 2015 to 2019. Nasal swab samples collected through active surveillance and lung tissue samples collected for diagnosis yielded 424 IAVs-S, comprising 78 H1N1, 331 H1N2, and 15 H3N2 viruses, from farms in 21 sampled prefectures in Japan. Phylogenetic analyses of surface genes revealed that the 1A.1 classical swine H1 lineage has evolved uniquely since the late 1970s among pig populations in Japan. During 2015 to 2019, A(H1N1)pdm09 viruses repeatedly became introduced into farms and reassorted with endemic H1N2 and H3N2 IAVs-S. H3N2 IAVs-S isolated during 2015 to 2019 formed a clade that originated from 1999–2000 human seasonal influenza viruses; this situation differs from previous reports, in which H3N2 IAVs-S derived from human seasonal influenza viruses were transmitted sporadically from humans to swine but then disappeared without becoming established within the pig population. At farms where IAVs-S were frequently isolated for at least 3 years, multiple introductions of IAVs-S with phylogenetically distinct hemagglutinin (HA) genes occurred. In addition, at one farm, IAVs-S derived from a single introduction persisted for at least 3 years and carried no mutations at the deduced antigenic sites of the hemagglutinin protein, except for one at the antigenic site (Sa). Our results extend our understanding regarding the status of IAVs-S currently circulating in Japan and how they genetically evolve at the farm level. IMPORTANCE Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies.
Collapse
|
6
|
Mon PP, Thurain K, Janetanakit T, Nasamran C, Bunpapong N, Aye AM, San YY, Tun TN, Amonsin A. Swine influenza viruses and pandemic H1N1-2009 infection in pigs, Myanmar. Transbound Emerg Dis 2020; 67:2653-2666. [PMID: 32385913 DOI: 10.1111/tbed.13616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 11/28/2022]
Abstract
Swine influenza virus (SIV) causes respiratory diseases in pigs and has impacts on both animal and human health. In this study, we conducted swine influenza surveillance in pig farms in the Yangon and Bago regions, Myanmar, during 2017-2019. Nasal swabs (n = 500) were collected from pigs in 10 swine farms. Our results showed that 11 out of 100 pooled samples (11%) were positive for influenza A virus (IAV) by real-time RT-PCR. Five SIVs could be isolated and could be subtyped as SIV-H1N1 (n = 4) or SIV-H3N2 (n = 1). The viruses were further characterized by whole-genome sequencing and classified as pdmH1N1-2009 (n = 3), reassortant H1N1 (n = 1) or reassortant H3N2 (n = 1). Phylogenetic analysis of Myanmar SIVs showed that all genes of the three SIV-H1N1 (pdmH1N1-2009) were clustered with viruses of the pdm/09 lineage. For one SIV-H1N1 (rH1N1), the HA1 gene was clustered with those of endemic SIVs of the classical swine lineage, and seven genes were clustered with those of viruses of the pdm/09 lineage. For SIV-H3N2 (rH3N2), the HA3 and NA2 genes were clustered with those of endemic SIVs of the human-like swine lineage, while six internal genes were clustered with those of viruses of the pdm/09 lineage. Genetic analysis indicated that all the Myanmar SIVs possessed amino acids that favour binding to the human receptor. All the Myanmar SIVs contained amino acids related to amantadine resistance but not oseltamivir resistance. Notably, the pdmH1N1-2009 virus might have been circulating in the Myanmar pig population for a period of time after pdmH1N1-2009 outbreaks in humans. Then, reassortment between endemic SIV-H1N1 or SIV-H3N2 and pdmH1N1-2009 in pig farms in Myanmar could have occurred. Our findings ascertained the genetic diversity of SIVs, especially pdmH1N1-2009, in the pig population in Myanmar, with zoonotic and reverse zoonotic potentials.
Collapse
Affiliation(s)
- Pont Pont Mon
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Khin Thurain
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Taveesak Janetanakit
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Chanakarn Nasamran
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Napawan Bunpapong
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Aung Myo Aye
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Yin Yin San
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Than Naing Tun
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Alongkorn Amonsin
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
7
|
Park MS, Kim JI, Bae JY, Park MS. Animal models for the risk assessment of viral pandemic potential. Lab Anim Res 2020; 36:11. [PMID: 32337177 PMCID: PMC7175453 DOI: 10.1186/s42826-020-00040-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Pandemics affect human lives severely and globally. Experience predicts that there will be a pandemic for sure although the time is unknown. When a viral epidemic breaks out, assessing its pandemic risk is an important part of the process that characterizes genomic property, viral pathogenicity, transmission in animal model, and so forth. In this review, we intend to figure out how a pandemic may occur by looking into the past influenza pandemic events. We discuss interpretations of the experimental evidences resulted from animal model studies and extend implications of viral pandemic potentials and ingredients to emerging viral epidemics. Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses.
Collapse
Affiliation(s)
- Mee Sook Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| |
Collapse
|
8
|
Zhao Y, Sun F, Li L, Chen T, Cao S, Ding G, Cong F, Liu J, Qin L, Liu S, Xiao Y. Evolution and Pathogenicity of the H1 and H3 Subtypes of Swine Influenza Virus in Mice between 2016 and 2019 in China. Viruses 2020; 12:v12030298. [PMID: 32182849 PMCID: PMC7150921 DOI: 10.3390/v12030298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 02/08/2023] Open
Abstract
Pigs are considered a “mixing vessel” that can produce new influenza strains through genetic reassortments, which pose a threat to public health and cause economic losses worldwide. The timely surveillance of the epidemiology of the swine influenza virus is of importance for prophylactic action. In this study, 15 H1N1, one H1N2, and four H3N2 strains were isolated from a total of 4080 nasal swabs which were collected from 20 pig farms in three provinces in China between 2016 and 2019. All the isolates were clustered into four genotypes. A new genotype represented by the H1N2 strain was found, whose fragments came from the triple reassortant H1N2 lineage, classical swine influenza virus (cs-H1N1) lineage, and 2009 H1N1 pandemic virus lineage. A/Sw/HB/HG394/2018(H1N1), which was clustered into the cs-H1N1 lineage, showed a close relationship with the 1918 pandemic virus. Mutations determining the host range specificity were found in the hemagglutinin of all isolates, which indicated that all the isolates had the potential for interspecies transmission. To examine pathogenicity, eight isolates were inoculated into 6-week-old female BALB/c mice. The isolates replicated differently, producing different viral loadings in the mice; A/Swine/HB/HG394/2018(H1N1) replicated the most efficiently. This suggested that the cs-H1N1 reappeared, and more attention should be given to the new pandemic to pigs. These results indicated that new reassortments between the different strains occurred, which may increase potential risks to human health. Continuing surveillance is imperative to monitor swine influenza A virus evolution.
Collapse
Affiliation(s)
- Yuzhong Zhao
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Fachao Sun
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Li Li
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Ting Chen
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao 266100, China; (T.C.); (L.Q.)
| | - Shengliang Cao
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Guofei Ding
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Fangyuan Cong
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Jiaqi Liu
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Liting Qin
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao 266100, China; (T.C.); (L.Q.)
| | - Sidang Liu
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
| | - Yihong Xiao
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (Y.Z.); (F.S.); (L.L.); (S.C.); (G.D.); (F.C.); (J.L.); (S.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China
- Correspondence:
| |
Collapse
|
9
|
Identification, Genetic Analysis, and Pathogenicity of Classical Swine H1N1 and Human-Swine Reassortant H1N1 Influenza Viruses from Pigs in China. Viruses 2020; 12:v12010055. [PMID: 31906591 PMCID: PMC7019673 DOI: 10.3390/v12010055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/22/2019] [Accepted: 12/31/2019] [Indexed: 12/20/2022] Open
Abstract
Swine influenza virus causes a substantial disease burden to swine populations worldwide and poses an imminent threat to the swine industry and humans. Given its importance, we characterized two swine influenza viruses isolated from Shandong, China. The homology and phylogenetic analyses showed that all eight gene segments of A/swine/Shandong/AV1522/2011(H1N1) were closely related to A/Maryland/12/1991(H1N1) circulating in North America. The HA, NA, M, and NS genes of the isolate were also confirmed to have a high homology to A/swine/Hubei/02/2008(H1N1) which appeared in China in 2008, and the virus was clustered into the classical swine lineage. The gene segments of A/swine/Shandong/AV1523/2011(H1N1) were highly homologous to the early human H1N1 and H2N2 influenza viruses, except for the HA gene, and the virus was a reassortant H1N1 virus containing genes from the classical swine (HA) and human (NA, PB2, PB1, PA, NP, M, and NS) lineages. Both the viruses could cause lethal infection and replicate efficiently in the lungs, brains, spleens, and kidneys of mice. Histopathological examinations showed that AV1522 and AV1523 viruses caused a spectrum of marked pneumonia and meningoencephalitis according to the duration of infection, demonstrating a progression of respiratory disease and neurological disease over the course of infection that ultimately resulted in lethality for the infected mice. The changes in the pathogenicity of swine influenza viruses to mammals, accompanied with the continuous reassortment and evolution of the viruses, highlights the importance of ongoing epidemiological investigation.
Collapse
|
10
|
Abstract
Influenza A viruses (IAVs) of the Orthomyxoviridae virus family cause one of the most important respiratory diseases in pigs and humans. Repeated outbreaks and rapid spread of genetically and antigenically distinct IAVs represent a considerable challenge for animal production and public health. Bidirection transmission of IAV between pigs and people has altered the evolutionary dynamics of IAV, and a "One Health" approach is required to ameliorate morbidity and mortality in both hosts and improve control strategies. Although only subtypes of H1N1, H1N2, and H3N2 are endemic in swine around the world, considerable diversity can be found not only in the hemagglutinin (HA) and neuraminidase (NA) genes but in the remaining six genes as well. Human and swine IAVs have demonstrated a particular propensity for interspecies transmission, leading to regular and sometimes sustained incursions from man to pig and vice versa. The diversity of IAVs in swine remains a critical challenge in the diagnosis and control of this important pathogen for swine health and in turn contributes to a significant public health risk.
Collapse
Affiliation(s)
- Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA.
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA
| | - Kelly M Lager
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA
| |
Collapse
|
11
|
Baudon E, Peyre M, Tung DD, Thi Nga P, Khong NV, Cowling BJ, Peiris M. Surveillance of swine influenza viruses in sentinel familial farms in Hung Yen province in Northern Vietnam in 2013-2014. Zoonoses Public Health 2019; 67:213-221. [PMID: 31855326 DOI: 10.1111/zph.12671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/05/2019] [Accepted: 11/19/2019] [Indexed: 11/30/2022]
Abstract
From May 2013 to April 2014, 15 swine family-run farms (17 pig litters) in two districts in Hung Yen province, near Hanoi, were virologically and epizootiologically monitored for swine influenza viruses (SIV) monthly. No SIV was isolated from nasal swabs. Maternal antibodies were detected in 10 litters, and seroconversion against SIV was detected in six litters. There was a marked difference in patterns of SIV transmission in the two districts. Van Lam district which has low density of swine with mainly smallholder farms had low intensity of SIV, with much of the infection caused by H1N1 2009 pandemic-like viruses A(H1N1)pdm09, likely originated from humans. In contrast, Van Giang district, which has high swine density and larger farms, had high levels of typical SIV (triple reassortants H3N2 and H3N2 Binh Duong lineage viruses) circulating within swine. With one exception, the SIV lineages detected were those we concurrently isolated from studies in a large central abattoir in Hanoi. Influenza-like illness symptoms reported by farmers were poorly correlated with serological evidence of SIV infection.
Collapse
Affiliation(s)
- Eugénie Baudon
- The University of Hong Kong, Hong Kong, China.,French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Marisa Peyre
- French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Dao Duy Tung
- National Institute of Veterinary Research, Hanoi, Vietnam
| | - Pham Thi Nga
- National Institute of Veterinary Research, Hanoi, Vietnam
| | | | | | | |
Collapse
|
12
|
Rajao DS, Vincent AL, Perez DR. Adaptation of Human Influenza Viruses to Swine. Front Vet Sci 2019; 5:347. [PMID: 30723723 PMCID: PMC6349779 DOI: 10.3389/fvets.2018.00347] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022] Open
Abstract
A large diversity of influenza A viruses (IAV) within the H1N1/N2 and H3N2 subtypes circulates in pigs globally, with different lineages predominating in specific regions of the globe. A common characteristic of the ecology of IAV in swine in different regions is the periodic spillover of human seasonal viruses. Such human viruses resulted in sustained transmission in swine in several countries, leading to the establishment of novel IAV lineages in the swine host and contributing to the genetic and antigenic diversity of influenza observed in pigs. In this review we discuss the frequent occurrence of reverse-zoonosis of IAV from humans to pigs that have contributed to the global viral diversity in swine in a continuous manner, describe host-range factors that may be related to the adaptation of these human-origin viruses to pigs, and how these events could affect the swine industry.
Collapse
Affiliation(s)
- Daniela S Rajao
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Amy L Vincent
- Virus and Prion Research Unit, USDA-ARS, National Animal Disease Center, Ames, IA, United States
| | - Daniel R Perez
- Department of Population Health, University of Georgia, Athens, GA, United States
| |
Collapse
|
13
|
Eurasian Avian-Like Swine Influenza A Viruses Escape Human MxA Restriction through Distinct Mutations in Their Nucleoprotein. J Virol 2019; 93:JVI.00997-18. [PMID: 30355693 DOI: 10.1128/jvi.00997-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To cross the human species barrier, influenza A viruses (IAV) of avian origin have to overcome the interferon-induced host restriction factor MxA by acquiring distinct mutations in their nucleoprotein (NP). We recently demonstrated that North American classical swine IAV are able to partially escape MxA restriction. Here we investigated whether the Eurasian avian-like swine IAV lineage currently circulating in European swine would likewise evade restriction by human MxA. We found that the NP of the influenza virus isolate A/Swine/Belzig/2/2001 (Belzig-NP) exhibits increased MxA escape, similar in extent to that with human IAV NPs. Mutational analysis revealed that the MxA escape mutations in Belzig-NP differ from the known MxA resistance cluster of the North American classical swine lineage and human-derived IAV NPs. A mouse-adapted avian IAV of the H7N7 subtype encoding Belzig-NP showed significantly greater viral growth in both MxA-expressing cells and MxA-transgenic mice than control viruses lacking the MxA escape mutations. Similarly, the growth of the recombinant Belzig virus was only marginally affected in MxA-expressing cells and MxA-transgenic mice, in contrast to that of Belzig mutant viruses lacking MxA escape mutations in the NP. Phylogenetic analysis of the Eurasian avian-like swine IAV revealed that the NP amino acids required for MxA escape were acquired successively and were maintained after their introduction. Our results suggest that the circulation of IAV in the swine population can result in the selection of NP variants with a high degree of MxA resistance, thereby increasing the zoonotic potential of these viruses.
IMPORTANCE The human MxA protein efficiently blocks the replication of IAV from nonhuman species. In rare cases, however, these IAV overcome the species barrier and become pandemic. All known pandemic viruses have acquired and maintained MxA escape mutations in the viral NP and thus are not efficiently controlled by MxA. Intriguingly, partial MxA resistance can also be acquired in other hosts that express antivirally active Mx proteins, such as swine. To perform a risk assessment of IAV circulating in the European swine population, we analyzed the degree of MxA resistance of Eurasian avian-like swine IAV. Our data demonstrate that these viruses carry formerly undescribed Mx resistance mutations in the NP that mediate efficient escape from human MxA. We conclude that Eurasian avian-like swine IAV possess substantial zoonotic potential.
Collapse
|
14
|
Genetic and antigenic dynamics of influenza A viruses of swine on pig farms in Thailand. Arch Virol 2018; 164:457-472. [PMID: 30415389 DOI: 10.1007/s00705-018-4091-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/18/2018] [Indexed: 12/29/2022]
Abstract
Surveillance studies of influenza A virus of swine (IAV-S) have accumulated information regarding IAVs-S circulating in Thailand, but how IAVs-S evolve within a farm remains unclear. In the present study, we isolated 82 A(H1N1)pdm09 and 87 H3N2 viruses from four farms from 2011 through 2017. We then phylogenetically and antigenically analyzed the isolates to elucidate their evolution within each farm. Phylogenetic analysis demonstrated multiple introductions of A(H1N1)pdm09 viruses that resembled epidemic A(H1N1)pdm09 strains in humans in Thailand, and they reassorted with H3N2 viruses as well as other A(H1N1)pdm09 viruses. Antigenic analysis revealed that the viruses had acquired antigenic diversity either by accumulating substitutions in the hemagglutinin protein or through the introduction of IAV-S strains with different antigenicity. Our results, obtained through continuous longitudinal surveillance, revealed that IAV-S can be maintained on a pig farm over several years through the generation of antigenic diversity due to the accumulation of mutations, introduction of new strains, and reassortment events.
Collapse
|
15
|
Baudon E, Chu DKW, Tung DD, Thi Nga P, Vu Mai Phuong H, Le Khanh Hang N, Thanh LT, Thuy NT, Khanh NC, Mai LQ, Khong NV, Cowling BJ, Peyre M, Peiris M. Swine influenza viruses in Northern Vietnam in 2013-2014. Emerg Microbes Infect 2018; 7:123. [PMID: 29967457 PMCID: PMC6028489 DOI: 10.1038/s41426-018-0109-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 12/31/2022]
Abstract
Swine are an important intermediate host for emergence of pandemic influenza. Vietnam is the largest swine producer in South East Asia. Systematic virological and serological surveillance of swine influenza viruses was carried out in Northern Vietnam from May 2013 to June 2014 with monthly sampling of pigs in local and large collective slaughterhouses and in a live pig market. Influenza A seroprevalence in the local slaughterhouses and in the large collective slaughterhouse was 48.7% and 29.1%, respectively. Seventy-seven influenza A viruses were isolated, all from the large collective slaughterhouse. Genetic analysis revealed six virus genotypes including H1N1 2009 pandemic (H1N1pdm09) viruses, H1N2 with H1 of human origin, H3N2 and H1N1pdm09 reassortants, and triple-reassortant H3N2 viruses. Phylogenetic analysis of swine and human H1N1pdm09 viruses showed evidence of repeated spill-over from humans to swine rather than the establishment of H1N1pdm09 as long-term distinct lineage in swine. Surveillance at the large collective slaughterhouse proved to be the most efficient, cost-effective, and sustainable method of surveillance for swine influenza viruses in Vietnam.
Collapse
Affiliation(s)
- Eugénie Baudon
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong-Hong Kong Special Administrative Region, Hong Kong, China
- Animal and Integrated Risk Management Research Unit (AGIRs), French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Daniel K W Chu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong-Hong Kong Special Administrative Region, Hong Kong, China
| | - Dao Duy Tung
- National Institute of Veterinary Research, Hanoi, Vietnam
| | - Pham Thi Nga
- National Institute of Veterinary Research, Hanoi, Vietnam
| | | | | | - Le Thi Thanh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | - Lê Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong-Hong Kong Special Administrative Region, Hong Kong, China
| | - Marisa Peyre
- Animal and Integrated Risk Management Research Unit (AGIRs), French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong-Hong Kong Special Administrative Region, Hong Kong, China.
| |
Collapse
|
16
|
Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes. J Virol 2017; 91:JVI.00745-17. [PMID: 28659482 PMCID: PMC5571239 DOI: 10.1128/jvi.00745-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/10/2017] [Indexed: 02/08/2023] Open
Abstract
Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, there is limited information on the genetic diversity of swine IAVs within farrow-to-wean farms, which is where most pigs are born. In this longitudinal study, we sampled 5 farrow-to-wean farms for a year and collected 4,190 individual nasal swabs from three distinct pig subpopulations. Of these, 207 (4.9%) samples tested PCR positive for IAV, and 124 IAVs were isolated. We sequenced the complete genomes of 123 IAV isolates and found 31 H1N1, 26 H1N2, 63 H3N2, and 3 mixed IAVs. Based on the IAV hemagglutinin, seven different influenza A viral groups (VGs) were identified. Most of the remaining IAV gene segments allowed us to differentiate the same VGs, although an additional viral group was identified for gene segment 3 (PA). Moreover, the codetection of more than one IAV VG was documented at different levels (farm, subpopulation, and individual pigs), highlighting the environment for potential IAV reassortment. Additionally, 3 out of 5 farms contained IAV isolates (n = 5) with gene segments from more than one VG, and 79% of all the IAVs sequenced contained a signature mutation (S31N) in the matrix gene that has been associated with resistance to the antiviral amantadine. Within farms, some IAVs were detected only once, while others were detected for 283 days. Our results illustrate the maintenance and subsidence of different IAVs within swine farrow-to-wean farms over time, demonstrating that pig subpopulation dynamics are important to better understand the diversity and epidemiology of swine IAVs. IMPORTANCE On a global scale, swine are one of the main reservoir species for influenza A viruses (IAVs) and play a key role in the transmission of IAVs between species. Additionally, the 2009 IAV pandemics highlighted the role of pigs in the emergence of IAVs with pandemic potential. However, limited information is available regarding the diversity and distribution of swine IAVs on farrow-to-wean farms, where novel IAVs can emerge. In this study, we studied 5 swine farrow-to-wean farms for a year and characterized the genetic diversity of IAVs among three different pig subpopulations commonly housed on this type of farm. Using next-generation-sequencing technologies, we demonstrated the complex distribution and diversity of IAVs among the pig subpopulations studied. Our results demonstrated the dynamic evolution of IAVs within farrow-to-wean farms, which is crucial to improve health interventions to reduce the risk of transmission between pigs and from pigs to people.
Collapse
|
17
|
Baudon E, Peyre M, Peiris M, Cowling BJ. Epidemiological features of influenza circulation in swine populations: A systematic review and meta-analysis. PLoS One 2017; 12:e0179044. [PMID: 28591202 PMCID: PMC5462427 DOI: 10.1371/journal.pone.0179044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/23/2017] [Indexed: 11/25/2022] Open
Abstract
Background The emergence of the 2009 influenza pandemic virus with a swine origin stressed the importance of improving influenza surveillance in swine populations. The objectives of this systematic review and meta-analysis were to describe epidemiological features of swine influenza (SI) across the world and identify factors impacting swine influenza virus surveillance. Methods The systematic review followed the PRISMA guidelines. Articles published after 1990 containing data on SI on pig and herd-level seroprevalence, isolation and detection rates, and risk factors were included. Meta-regression analyses using seroprevalence and virological rates were performed. Results A total of 217 articles were included. Low avian influenza (AI) seroprevalence (means pig = 4.1%; herd = 15%) was found, showing that AIV do not readily establish themselves in swine while SIV seroprevalence was usually high across continents (influenza A means pig = 32.6–87.8%; herd = 29.3–100%). Higher pig density and number of pigs per farm were shown by the meta-regression analyses and/or the risk factor articles to be associated with higher SI seroprevalence. Lower seroprevalence levels were observed for countries with low-to-medium GDP. These results suggest that larger industrial farms could be more at risk of SIV circulation. Sampling swine with influenza-like illness (ILI) was positively associated with higher isolation rates; most studies in Europe, Latin and North America were targeting swine with ILI. Conclusions To improve understanding of SI epidemiology, standardization of the design and reporting of SI epidemiological studies is desirable. Performance of SI surveillance systems in low-to-medium GDP countries should be evaluated to rule out technical issues linked to lower observed SIV prevalence. Targeting certain swine age groups, farming systems and swine with ILI may improve the surveillance cost-effectiveness. However, focusing on pigs with ILI may bias virus detection against strains less virulent for swine but which may be important as pandemic threats.
Collapse
Affiliation(s)
- Eugénie Baudon
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Animal and Integrated Risk Management Research Unit (AGIRs), French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Marisa Peyre
- Animal and Integrated Risk Management Research Unit (AGIRs), French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin John Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
- * E-mail:
| |
Collapse
|
18
|
Peteranderl C, Sznajder JI, Herold S, Lecuona E. Inflammatory Responses Regulating Alveolar Ion Transport during Pulmonary Infections. Front Immunol 2017; 8:446. [PMID: 28458673 PMCID: PMC5394420 DOI: 10.3389/fimmu.2017.00446] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/31/2017] [Indexed: 01/13/2023] Open
Abstract
The respiratory epithelium is lined by a tightly balanced fluid layer that allows normal O2 and CO2 exchange and maintains surface tension and host defense. To maintain alveolar fluid homeostasis, both the integrity of the alveolar–capillary barrier and the expression of epithelial ion channels and pumps are necessary to establish a vectorial ion gradient. However, during pulmonary infection, auto- and/or paracrine-acting mediators induce pathophysiological changes of the alveolar–capillary barrier, altered expression of epithelial Na,K-ATPase and of epithelial ion channels including epithelial sodium channel and cystic fibrosis membrane conductance regulator, leading to the accumulation of edema and impaired alveolar fluid clearance. These mediators include classical pro-inflammatory cytokines such as TGF-β, TNF-α, interferons, or IL-1β that are released upon bacterial challenge with Streptococcus pneumoniae, Klebsiella pneumoniae, or Mycoplasma pneumoniae as well as in viral infection with influenza A virus, pathogenic coronaviruses, or respiratory syncytial virus. Moreover, the pro-apoptotic mediator TNF-related apoptosis-inducing ligand, extracellular nucleotides, or reactive oxygen species impair epithelial ion channel expression and function. Interestingly, during bacterial infection, alterations of ion transport function may serve as an additional feedback loop on the respiratory inflammatory profile, further aggravating disease progression. These changes lead to edema formation and impair edema clearance which results in suboptimal gas exchange causing hypoxemia and hypercapnia. Recent preclinical studies suggest that modulation of the alveolar–capillary fluid homeostasis could represent novel therapeutic approaches to improve outcomes in infection-induced lung injury.
Collapse
Affiliation(s)
- Christin Peteranderl
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susanne Herold
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Emilia Lecuona
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
19
|
Influenza A Viruses of Swine (IAV-S) in Vietnam from 2010 to 2015: Multiple Introductions of A(H1N1)pdm09 Viruses into the Pig Population and Diversifying Genetic Constellations of Enzootic IAV-S. J Virol 2016; 91:JVI.01490-16. [PMID: 27795418 DOI: 10.1128/jvi.01490-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/03/2016] [Indexed: 12/18/2022] Open
Abstract
Active surveillance of influenza A viruses of swine (IAV-S) involving 262 farms and 10 slaughterhouses in seven provinces in northern and southern Vietnam from 2010 to 2015 yielded 388 isolates from 32 farms; these viruses were classified into H1N1, H1N2, and H3N2 subtypes. Whole-genome sequencing followed by phylogenetic analysis revealed that the isolates represented 15 genotypes, according to the genetic constellation of the eight segments. All of the H1N1 viruses were entirely A(H1N1)pdm09 viruses, whereas all of the H1N2 and H3N2 viruses were reassortants among 5 distinct ancestral viruses: H1 and H3 triple-reassortant (TR) IAV-S that originated from North American pre-2009 human seasonal H1, human seasonal H3N2, and A(H1N1)pdm09 viruses. Notably, 93% of the reassortant IAV-S retained M genes that were derived from A(H1N1)pdm09, suggesting some advantage in terms of their host adaptation. Bayesian Markov chain Monte Carlo analysis revealed that multiple introductions of A(H1N1)pdm09 and TR IAV-S into the Vietnamese pig population have driven the genetic diversity of currently circulating Vietnamese IAV-S. In addition, our results indicate that a reassortant IAV-S with human-like H3 and N2 genes and an A(H1N1)pdm09 origin M gene likely caused a human case in Ho Chi Minh City in 2010. Our current findings indicate that human-to-pig transmission as well as cocirculation of different IAV-S have contributed to diversifying the gene constellations of IAV-S in Vietnam. IMPORTANCE This comprehensive genetic characterization of 388 influenza A viruses of swine (IAV-S) isolated through active surveillance of Vietnamese pig farms from 2010 through 2015 provides molecular epidemiological insight into the genetic diversification of IAV-S in Vietnam after the emergence of A(H1N1)pdm09 viruses. Multiple reassortments among A(H1N1)pdm09 viruses and enzootic IAV-S yielded 14 genotypes, 9 of which carried novel gene combinations. The reassortants that carried M genes derived from A(H1N1)pdm09 viruses became predominant, replacing those of the IAV-S that had been endemic in Vietnam since 2011. Notably, one of the novel reassortants likely caused a human case in Vietnam. Given that Vietnam is the second-largest pig-producing country in Asia, continued monitoring of IAV-S is highly important from the viewpoints of both the swine industry and human public health.
Collapse
|
20
|
Song Y, Wu X, Wang N, Ouyang G, Qu N, Cui J, Qi Y, Liao M, Jiao P. A Novel H1N2 Influenza Virus Related to the Classical and Human Influenza Viruses from Pigs in Southern China. Front Microbiol 2016; 7:1068. [PMID: 27458456 PMCID: PMC4937032 DOI: 10.3389/fmicb.2016.01068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/24/2016] [Indexed: 01/26/2023] Open
Abstract
Southern China has long been considered to be an epicenter of pandemic influenza viruses. The special environment, breeding mode, and lifestyle in southern China provides more chances for wild aquatic birds, domestic poultry, pigs, and humans to be in contact. This creates the opportunity for interspecies transmission and generation of new influenza viruses. In this study, we reported a novel reassortant H1N2 influenza virus from pigs in southern China. According to the phylogenetic trees and homology of the nucleotide sequence, the virus was confirmed to be a novel triple-reassortant H1N2 virus containing genes from classical swine (PB2, PB1, HA, NP, and NS genes), triple-reassortant swine (PA and M genes), and recent human (NA gene) lineages. It indicated that the novel reassortment virus among human and swine influenza viruses occurred in pigs in southern China. The isolation of the novel reassortant H1N2 influenza viruses provides further evidence that pigs are “mixing vessels,” and swine influenza virus surveillance in southern China will provide important information about genetic evaluation and antigenic variation of swine influenza virus to formulate the prevention and control measures for the viruses.
Collapse
Affiliation(s)
- Yafen Song
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and ControlGuangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of AgricultureGuangzhou, China; Key Laboratory of Zoonosis Prevention and Control of GuangdongGuangzhou, China
| | - Xiaowei Wu
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Entry-Exit Inspection and Quarantine BureauGuangzhou, China
| | - Nianchen Wang
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and ControlGuangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of AgricultureGuangzhou, China; Key Laboratory of Zoonosis Prevention and Control of GuangdongGuangzhou, China
| | - Guowen Ouyang
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and ControlGuangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of AgricultureGuangzhou, China; Key Laboratory of Zoonosis Prevention and Control of GuangdongGuangzhou, China
| | - Nannan Qu
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and ControlGuangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of AgricultureGuangzhou, China; Key Laboratory of Zoonosis Prevention and Control of GuangdongGuangzhou, China
| | - Jin Cui
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and ControlGuangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of AgricultureGuangzhou, China; Key Laboratory of Zoonosis Prevention and Control of GuangdongGuangzhou, China
| | - Yan Qi
- China Animal Husbandry Group Beijing, China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and ControlGuangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of AgricultureGuangzhou, China; Key Laboratory of Zoonosis Prevention and Control of GuangdongGuangzhou, China
| | - Peirong Jiao
- College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and ControlGuangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of AgricultureGuangzhou, China; Key Laboratory of Zoonosis Prevention and Control of GuangdongGuangzhou, China
| |
Collapse
|
21
|
Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, Castro-Peralta F, Cunha LF, Trovão NS, Lozano-Dubernard B, Rambaut A, van Bakel H, García-Sastre A. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. eLife 2016; 5. [PMID: 27350259 PMCID: PMC4957980 DOI: 10.7554/elife.16777] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of the Americas, and to date the most closely related ancestor viruses were identified in Asian swine. Here, we use 58 new whole-genome sequences from IAVs collected in Mexican swine to establish that the swine virus responsible for the 2009 pandemic evolved in central Mexico. This finding highlights how the 2009 pandemic arose from a region not considered a pandemic risk, owing to an expansion of IAV diversity in swine resulting from long-distance live swine trade. DOI:http://dx.doi.org/10.7554/eLife.16777.001 In 2009 a new influenza virus jumped from pigs to humans and spread very rapidly, causing an initial outbreak in Mexico and becoming a global pandemic in just a few months. Although the most straightforward explanation is that the virus originated in swine in Mexico, several studies suggested that this was unlikely because key genetic components of the virus had never been detected in the Americas. Determining the source of the disease is critical for predicting and preparing for future influenza pandemics. Mena, Nelson et al. sought to better characterize the genetic diversity of influenza viruses in Mexican swine by obtaining the entire genetic sequences of 58 viruses collected from swine in Mexico, including some from previously unsampled regions in central Mexico. The sequences revealed extensive diversity among the influenza viruses circulating in Mexican swine. Several viruses included genetic segments that originated from viruses from Eurasia (the landmass containing Europe and Asia) and had not previously been detected in the Americas. The new sequences contained key genetic components of the 2009 pandemic virus. Furthermore, the sequences suggest that viruses with a similar genetic composition to the 2009 pandemic virus have been circulating in pigs in central-west Mexico for more than a decade. Thus, this region is the most likely source of the virus that started the 2009 pandemic. Mena, Nelson et al. also found that the movement of viruses from Eurasia and the United States into Mexico closely follows the direction of the global trade of live swine. This highlights the critical role that animal trading plays in bringing together diverse viruses from different continents, which can then combine and generate new pandemic viruses. A potential next step is to perform experiments that investigate how well the swine viruses can replicate and pass between different animal models. Comparing the results of such experiments with the findings presented by Mena, Nelson et al. could identify factors that make the viruses more likely to spread to humans and produce a pandemic. DOI:http://dx.doi.org/10.7554/eLife.16777.002
Collapse
Affiliation(s)
- Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States
| | | | - Jayeeta Dutta
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | | | | | | | - Luis F Cunha
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nídia S Trovão
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.,Department of Microbiology and Immunology, Rega Institute, University of Leuven, Leuven, Belgium
| | | | - Andrew Rambaut
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Harm van Bakel
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, United States
| |
Collapse
|
22
|
Lewis NS, Russell CA, Langat P, Anderson TK, Berger K, Bielejec F, Burke DF, Dudas G, Fonville JM, Fouchier RA, Kellam P, Koel BF, Lemey P, Nguyen T, Nuansrichy B, Peiris JM, Saito T, Simon G, Skepner E, Takemae N, Webby RJ, Van Reeth K, Brookes SM, Larsen L, Watson SJ, Brown IH, Vincent AL. The global antigenic diversity of swine influenza A viruses. eLife 2016; 5:e12217. [PMID: 27113719 PMCID: PMC4846380 DOI: 10.7554/elife.12217] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/23/2016] [Indexed: 12/11/2022] Open
Abstract
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the risk profile of swine influenza viruses in terms of their epizootic and pandemic potential. Here, using the most comprehensive set of swine influenza virus antigenic data compiled to date, we quantify the antigenic diversity of swine influenza viruses on a multi-continental scale. The substantial antigenic diversity of recently circulating viruses in different parts of the world adds complexity to the risk profiles for the movement of swine and the potential for swine-derived infections in humans. DOI:http://dx.doi.org/10.7554/eLife.12217.001 Influenza viruses, commonly called flu, infect millions of people and animals every year and occasionally causes pandemics in humans. The immune system can neutralise flu viruses by recognising the proteins on the virus surface, generically referred to as antigens. These antigens change as flu viruses evolve to escape detection by the immune system. These changes tend to be relatively small such that exposure to one flu virus generates immunity that is still effective against other related flu viruses. However, over time, the accumulation of these small changes can result in larger differences such that prior infections no longer provide protection against the new virus. Influenza A viruses infect a wide variety of birds and mammals. Viruses can also transmit from one species to another, which may result in the introduction of viruses with antigens that are new to the recipient species and which have the potential to cause substantial outbreaks. Pig flu viruses have long been considered to be a potential risk for human pandemic viruses and were the source of the 2009 pandemic H1N1 virus. Importantly, humans often transmit flu viruses to pigs. Understanding the dynamics and consequences of this two-way transmission is important for designing effective strategies to detect and respond to new strains of flu. Influenza A viruses of the H1 and H3 subtypes circulate widely in pigs. However, it was poorly understood how closely related swine and human viruses circulating in different regions were to one another and how much the antigens varied between the different viruses. Lewis, Russell et al. have now analysed the antigenic variation of hundreds of H1 and H3 viruses from pigs on multiple continents. The antigenic diversity of recent swine flu viruses resembles the diversity of H1 and H3 viruses observed in humans over the last 40 years. A key factor driving the diversity of the H1 and H3 viruses in pigs is the frequent introduction of human viruses to pigs. In contrast, only one flu virus from a bird had contributed to the observed antigenic diversity in pigs in a substantial way. Once in pigs, human-derived flu viruses continue to evolve their antigens. This results in a tremendous diversity of flu viruses that can be transmitted to other pigs and also to humans. These flu viruses could pose a serious risk to public health because they are no longer similar to the current human flu strains. These findings have important implications not only for developing flu vaccines for pigs but also for informing the development of more-effective surveillance and disease-control strategies to prevent the spread of new flu variants. DOI:http://dx.doi.org/10.7554/eLife.12217.002
Collapse
Affiliation(s)
- Nicola S Lewis
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Pinky Langat
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, United States
| | - Kathryn Berger
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Filip Bielejec
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - David F Burke
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Judith M Fonville
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Ron Am Fouchier
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Bjorn F Koel
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Philippe Lemey
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Tung Nguyen
- Department of Animal Health, National Centre for Veterinary Diagnostics, Hanoi, Vietnam
| | | | - Js Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | - Gaelle Simon
- Swine Virology Immunology Unit, Anses, Ploufragan-Plouzané Laboratory, Ploufragan, France
| | - Eugene Skepner
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Richard J Webby
- St Jude Children's Research Hospital, Memphis, United States
| | - Kristien Van Reeth
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | | | - Lars Larsen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Simon J Watson
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian H Brown
- Animal Health and Plant Agency, Weybridge, United Kingdom
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, United States
| |
Collapse
|
23
|
Novel reassortant influenza viruses between pandemic (H1N1) 2009 and other influenza viruses pose a risk to public health. Microb Pathog 2015; 89:62-72. [PMID: 26344393 DOI: 10.1016/j.micpath.2015.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/21/2022]
Abstract
Influenza A virus (IAV) is characterized by eight single-stranded, negative sense RNA segments, which allows for gene reassortment among different IAV subtypes when they co-infect a single host cell simultaneously. Genetic reassortment is an important way to favor the evolution of influenza virus. Novel reassortant virus may pose a pandemic among humans. In history, three human pandemic influenza viruses were caused by genetic reassortment between avian, human and swine influenza viruses. Since 2009, pandemic (H1N1) 2009 (pdm/09 H1N1) influenza virus composed of two swine influenza virus genes highlighted the genetic reassortment again. Due to wide host species and high transmission of the pdm/09 H1N1 influenza virus, many different avian, human or swine influenza virus subtypes may reassert with it to generate novel reassortant viruses, which may result in a next pandemic among humans. So, it is necessary to understand the potential threat of current reassortant viruses between the pdm/09 H1N1 and other influenza viruses to public health. This study summarized the status of the reassortant viruses between the pdm/09 H1N1 and other influenza viruses of different species origins in natural and experimental conditions. The aim of this summarization is to facilitate us to further understand the potential threats of novel reassortant influenza viruses to public health and to make effective prevention and control strategies for these pathogens.
Collapse
|
24
|
Abstract
To assess the potential transmission for zoonotic influenza, sero-antibodies against two kinds of influenza viruses—classical swine H1N1 and human H1N1pdm09 virus were detected in persons whose profession involved contact with swine in Guangdong province, China. Compared to the non-exposed control group, a significantly higher proportion of subjects with occupational contact to pigs exhibited positive seroreaction against the classical H1N1 SIV. Participants aged 26–50 years were at high risk of classic swine H1N1 infections. Seropositive rate to 2009 pandemic H1N1 virus among swine workers was similar with controls. The major impact of age was apparent for younger populations. Our present study has documented evidence for swine influenza virus infection among persons with occupational swine exposures. The differences of seroreactivity for the two tested influenza subtypes emphasize the necessity of regular surveillance both in pigs and human.
Collapse
|
25
|
Sandbulte MR, Spickler AR, Zaabel PK, Roth JA. Optimal Use of Vaccines for Control of Influenza A Virus in Swine. Vaccines (Basel) 2015; 3:22-73. [PMID: 26344946 PMCID: PMC4494241 DOI: 10.3390/vaccines3010022] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/09/2015] [Accepted: 01/19/2015] [Indexed: 12/29/2022] Open
Abstract
Influenza A virus in swine (IAV-S) is one of the most important infectious disease agents of swine in North America. In addition to the economic burden of IAV-S to the swine industry, the zoonotic potential of IAV-S sometimes leads to serious public health concerns. Adjuvanted, inactivated vaccines have been licensed in the United States for over 20 years, and there is also widespread usage of autogenous/custom IAV-S vaccines. Vaccination induces neutralizing antibodies and protection against infection with very similar strains. However, IAV-S strains are so diverse and prone to mutation that these vaccines often have disappointing efficacy in the field. This scientific review was developed to help veterinarians and others to identify the best available IAV-S vaccine for a particular infected herd. We describe key principles of IAV-S structure and replication, protective immunity, currently available vaccines, and vaccine technologies that show promise for the future. We discuss strategies to optimize the use of available IAV-S vaccines, based on information gathered from modern diagnostics and surveillance programs. Improvements in IAV-S immunization strategies, in both the short term and long term, will benefit swine health and productivity and potentially reduce risks to public health.
Collapse
Affiliation(s)
- Matthew R Sandbulte
- Center for Food Security and Public Health, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
| | - Anna R Spickler
- Center for Food Security and Public Health, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
| | - Pamela K Zaabel
- Center for Food Security and Public Health, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
| | - James A Roth
- Center for Food Security and Public Health, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
26
|
Nelson MI, Vincent AL. Reverse zoonosis of influenza to swine: new perspectives on the human-animal interface. Trends Microbiol 2015; 23:142-53. [PMID: 25564096 DOI: 10.1016/j.tim.2014.12.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 01/09/2023]
Abstract
The origins of the 2009 influenza A (H1N1) pandemic in swine are unknown, highlighting gaps in our understanding of influenza A virus (IAV) ecology and evolution. We review how recently strengthened influenza virus surveillance in pigs has revealed that influenza virus transmission from humans to swine is far more frequent than swine-to-human zoonosis, and is central in seeding swine globally with new viral diversity. The scale of global human-to-swine transmission represents the largest 'reverse zoonosis' of a pathogen documented to date. Overcoming the bias towards perceiving swine as sources of human viruses, rather than recipients, is key to understanding how the bidirectional nature of the human-animal interface produces influenza threats to both hosts.
Collapse
Affiliation(s)
- Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, US Department of Agriculture (USDA) Agricultural Research Service (ARS), Ames, IA 50010, USA
| |
Collapse
|
27
|
Zumla A, Memish ZA, Maeurer M, Bates M, Mwaba P, Al-Tawfiq JA, Denning DW, Hayden FG, Hui DS. Emerging novel and antimicrobial-resistant respiratory tract infections: new drug development and therapeutic options. THE LANCET. INFECTIOUS DISEASES 2014; 14:1136-1149. [PMID: 25189352 PMCID: PMC7106460 DOI: 10.1016/s1473-3099(14)70828-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence and spread of antimicrobial-resistant bacterial, viral, and fungal pathogens for which diminishing treatment options are available is of major global concern. New viral respiratory tract infections with epidemic potential, such as severe acute respiratory syndrome, swine-origin influenza A H1N1, and Middle East respiratory syndrome coronavirus infection, require development of new antiviral agents. The substantial rise in the global numbers of patients with respiratory tract infections caused by pan-antibiotic-resistant Gram-positive and Gram-negative bacteria, multidrug-resistant Mycobacterium tuberculosis, and multiazole-resistant fungi has focused attention on investments into development of new drugs and treatment regimens. Successful treatment outcomes for patients with respiratory tract infections across all health-care settings will necessitate rapid, precise diagnosis and more effective and pathogen-specific therapies. This Series paper describes the development and use of new antimicrobial agents and immune-based and host-directed therapies for a range of conventional and emerging viral, bacterial, and fungal causes of respiratory tract infections.
Collapse
Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Centre, University College London Hospitals, London, UK; University of Zambia-University College London Research and Training Project, University Teaching Hospital, Lusaka, Zambia; Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Ziad A Memish
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia; Al-Faisal University, Riyadh, Saudi Arabia
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Matthew Bates
- Division of Infection and Immunity, University College London, London, UK; University of Zambia-University College London Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Peter Mwaba
- University of Zambia-University College London Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Jaffar A Al-Tawfiq
- Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indianapolis, IN, USA
| | - David W Denning
- National Aspergillosis Centre, University Hospital South Manchester, University of South Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - David S Hui
- Division of Respiratory Medicine and Stanley Ho Center for Emerging Infectious Diseases, Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong.
| |
Collapse
|
28
|
Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, Muller MA, Hui D, Maeurer M, Bates M, Mwaba P, Al-Hakeem R, Gray G, Gautret P, Al-Rabeeah AA, Memish ZA, Gant V. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections--needs, advances, and future prospects. THE LANCET. INFECTIOUS DISEASES 2014; 14:1123-1135. [PMID: 25189349 PMCID: PMC7106435 DOI: 10.1016/s1473-3099(14)70827-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory tract infections rank second as causes of adult and paediatric morbidity and mortality worldwide. Respiratory tract infections are caused by many different bacteria (including mycobacteria) and viruses, and rapid detection of pathogens in individual cases is crucial in achieving the best clinical management, public health surveillance, and control outcomes. Further challenges in improving management outcomes for respiratory tract infections exist: rapid identification of drug resistant pathogens; more widespread surveillance of infections, locally and internationally; and global responses to infections with pandemic potential. Developments in genome amplification have led to the discovery of several new respiratory pathogens, and sensitive PCR methods for the diagnostic work-up of these are available. Advances in technology have allowed for development of single and multiplexed PCR techniques that provide rapid detection of respiratory viruses in clinical specimens. Microarray-based multiplexing and nucleic-acid-based deep-sequencing methods allow simultaneous detection of pathogen nucleic acid and multiple antibiotic resistance, providing further hope in revolutionising rapid point of care respiratory tract infection diagnostics.
Collapse
Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK; Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia.
| | | | - Virve I Enne
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Kidd
- Division of Infection and Immunity, University College London, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marcel A Muller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - David Hui
- Division of Respiratory Medicine and Stanley Ho Center for emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Matthew Bates
- Division of Infection and Immunity, University College London, London, UK; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Peter Mwaba
- UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Rafaat Al-Hakeem
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Gregory Gray
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Philippe Gautret
- Assistance Publique Hôpitaux de Marseille, CHU Nord, Pôle Infectieux, Institut Hospitalo-Universitaire Méditerranée Infection & Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), Marseille, France
| | - Abdullah A Al-Rabeeah
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Ziad A Memish
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; Al-Faisal University, Riyadh, Saudi Arabia
| | - Vanya Gant
- Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| |
Collapse
|
29
|
Ebrahimi M, Aghagolzadeh P, Shamabadi N, Tahmasebi A, Alsharifi M, Adelson DL, Hemmatzadeh F, Ebrahimie E. Understanding the undelaying mechanism of HA-subtyping in the level of physic-chemical characteristics of protein. PLoS One 2014; 9:e96984. [PMID: 24809455 PMCID: PMC4014573 DOI: 10.1371/journal.pone.0096984] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/07/2014] [Indexed: 01/05/2023] Open
Abstract
The evolution of the influenza A virus to increase its host range is a major concern worldwide. Molecular mechanisms of increasing host range are largely unknown. Influenza surface proteins play determining roles in reorganization of host-sialic acid receptors and host range. In an attempt to uncover the physic-chemical attributes which govern HA subtyping, we performed a large scale functional analysis of over 7000 sequences of 16 different HA subtypes. Large number (896) of physic-chemical protein characteristics were calculated for each HA sequence. Then, 10 different attribute weighting algorithms were used to find the key characteristics distinguishing HA subtypes. Furthermore, to discover machine leaning models which can predict HA subtypes, various Decision Tree, Support Vector Machine, Naïve Bayes, and Neural Network models were trained on calculated protein characteristics dataset as well as 10 trimmed datasets generated by attribute weighting algorithms. The prediction accuracies of the machine learning methods were evaluated by 10-fold cross validation. The results highlighted the frequency of Gln (selected by 80% of attribute weighting algorithms), percentage/frequency of Tyr, percentage of Cys, and frequencies of Try and Glu (selected by 70% of attribute weighting algorithms) as the key features that are associated with HA subtyping. Random Forest tree induction algorithm and RBF kernel function of SVM (scaled by grid search) showed high accuracy of 98% in clustering and predicting HA subtypes based on protein attributes. Decision tree models were successful in monitoring the short mutation/reassortment paths by which influenza virus can gain the key protein structure of another HA subtype and increase its host range in a short period of time with less energy consumption. Extracting and mining a large number of amino acid attributes of HA subtypes of influenza A virus through supervised algorithms represent a new avenue for understanding and predicting possible future structure of influenza pandemics.
Collapse
Affiliation(s)
- Mansour Ebrahimi
- Department of Biology, School of Basic Sciences, University of Qom, Qom, Iran
| | - Parisa Aghagolzadeh
- Department of Nephrology, Hypertension, and Clinical Pharmacology, University of Bern, Bern, Switzerland
| | - Narges Shamabadi
- Department of Biology, School of Basic Sciences, University of Qom, Qom, Iran
| | | | - Mohammed Alsharifi
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
| | - David L. Adelson
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Science, The University of Adelaide, Adelaide, Australia
- * E-mail: (FH); (EE)
| | - Esmaeil Ebrahimie
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
- * E-mail: (FH); (EE)
| |
Collapse
|
30
|
Hoschler K, Thompson C, Casas I, Ellis J, Galiano M, Andrews N, Zambon M. Population susceptibility to North American and Eurasian swine influenza viruses in England, at three time points between 2004 and 2011. ACTA ACUST UNITED AC 2013; 18:pii=20578. [PMID: 24079379 DOI: 10.2807/1560-7917.es2013.18.36.20578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Age-stratified sera collected in 2004, 2008 and 2010 in England were evaluated for antibody to swine influenza A(H3N2) and A(H1N1) viruses from the United States or Europe as a measure of population susceptibility to the emergence of novel viruses. Children under 11 years of age had little or no measurable antibody to recent swine H3N2 viruses despite their high levels of antibody to recent H3N2 seasonal human strains. Adolescents and young adults (born 1968–1999) had higher antibody levels to swine H3N2 viruses. Antibody levels to swine H3N2 influenza show little correlation with exposure to recent seasonal H3N2 (A/Perth/16/2009) strains, but with antibody to older H3N2 strains represented by A/Wuhan/359/1995. Children had the highest seropositivity to influenza A(H1N1)pdm09 virus, and young adults had the lowest antibody levels to A/Perth/16/2009. No age group showed substantial antibody levels to A/Aragon/RR3218/2008, a European swine H1N1 virus belonging to the Eurasian lineage. After vaccination with contemporary trivalent vaccine we observed evidence of boosted reactivity to swine H3N2 viruses in children and adults, while only a limited boosting effect on antibody levels to A/Aragon/RR3218/2008 was observed in both groups. Overall, our results suggest that different vaccination strategies may be necessary according to age if swine viruses emerge as a significant pandemic threat.
Collapse
Affiliation(s)
- K Hoschler
- Public Health England, Microbiology Services Colindale, London, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
31
|
Qi X, Pan Y, Qin Y, Zu R, Tang F, Zhou M, Wang H, Song Y. Molecular characterization of avian-like H1N1 swine influenza a viruses isolated in Eastern China, 2011. Virol Sin 2012; 27:292-8. [PMID: 23055004 DOI: 10.1007/s12250-012-3262-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 09/06/2012] [Indexed: 11/29/2022] Open
Abstract
Currently, three predominant subtypes of influenza virus are prevalent in pig populations worldwide: H1N1, H3N2, and H1N2. European avian-like H1N1 viruses, which were initially detected in European pig populations in 1979, have been circulating in pigs in eastern China since 2007. In this study, six influenza A viruses were isolated from 60 swine lung samples collected from January to April 2011 in eastern China. Based on whole genome sequencing, molecular characteristics of two isolates were determined. Phylogenetic analysis showed the eight genes of the two isolates were closely related to those of the avian-like H1N1 viruses circulating in pig populations, especially similar to those found in China. Four potential glycosylation sites were observed at positions 13, 26, 198, 277 in the HA1 proteins of the two isolates. Due to the presence of a stop codon at codon 12, the isolates contained truncated PB1-F2 proteins. In this study, the isolates contained 591Q, 627E and 701N in the polymerase subunit PB2, which had been shown to be determinants of virulence and host adaptation. The isolates also had a D rather than E at position 92 of the NS1, a marker of mammalian adaptation. Both isolates contained the GPKV motif at the PDZ ligand domain of the 3' end of the NS1, a characteristic marker of the European avian-like swine viruses since about 1999, which is distinct from those of avian, human and classical swine viruses. The M2 proteins of the isolates have the mutation (S31N), a characteristic marker of the European avian-like swine viruses since about 1987, which may confer resistance to amantadine and rimantadine antivirals. Our findings further emphasize the importance of surveillance on the genetic diversity of influenza A viruses in pigs, and raise more concerns about the occurrence of cross-species transmission events.
Collapse
Affiliation(s)
- Xian Qi
- Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Qi X, Cui L, Jiao Y, Pan Y, Li X, Zu R, Huo X, Wu B, Tang F, Song Y, Zhou M, Wang H, Cardona CJ, Xing Z. Antigenic and genetic characterization of a European avian-like H1N1 swine influenza virus from a boy in China in 2011. Arch Virol 2012; 158:39-53. [PMID: 22935945 DOI: 10.1007/s00705-012-1423-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/11/2012] [Indexed: 10/27/2022]
Abstract
Cross-species transmission of influenza A viruses from swine to human occurs occasionally. In 2011, an influenza A H1N1 virus, A/Jiangsu/ALS1/2011 (JS/ALS1/2011), was isolated from a boy who suffered from severe pneumonia in China. The virus is closely related antigenically and genetically to avian-like swine H1N1 viruses that have recently been circulating in pigs in China and that were initially detected in European pig populations in 1979. The isolation of JS/ALS1/2011 provides additional evidence that swine influenza viruses can occasionally infect humans and emphasizes the importance of reinforcing influenza virus surveillance in both pigs and humans.
Collapse
MESH Headings
- Animals
- Antibodies, Viral/immunology
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Child, Preschool
- China
- Genetic Variation
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza, Human/immunology
- Influenza, Human/virology
- Male
- Molecular Sequence Data
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/virology
- Phylogeny
- Swine
- Swine Diseases/immunology
- Swine Diseases/virology
Collapse
Affiliation(s)
- Xian Qi
- Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Fan X, Zhu H, Zhou B, Smith DK, Chen X, Lam TTY, Poon LLM, Peiris M, Guan Y. Emergence and dissemination of a swine H3N2 reassortant influenza virus with 2009 pandemic H1N1 genes in pigs in China. J Virol 2012; 86:2375-8. [PMID: 22171260 PMCID: PMC3302387 DOI: 10.1128/jvi.06824-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 12/02/2011] [Indexed: 11/20/2022] Open
Abstract
The 2009 pandemic influenza virus (pdm/09) has been frequently introduced to pigs and has reassorted with other swine viruses. Recently, H3N2 reassortants with pdm/09-like internal genes were isolated in Guangxi and Hong Kong, China. Genetic and epidemiological analyses suggest that these viruses have circulated in swine for some time. This is the first evidence that swine reassortant viruses with pdm/09-like genes may have become established in the field, altering the landscape of human and swine influenza.
Collapse
Affiliation(s)
- Xiaohui Fan
- Department of Microbiology, Guangxi Medical University, Nanning, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Boping Zhou
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - David K. Smith
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xinchun Chen
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Tommy T.-Y. Lam
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo L. M. Poon
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|