1
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Poon AFY. Prospects for a sequence-based taxonomy of influenza A virus subtypes. Virus Evol 2024; 10:veae064. [PMID: 39247559 PMCID: PMC11378807 DOI: 10.1093/ve/veae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 05/03/2024] [Accepted: 08/09/2024] [Indexed: 09/10/2024] Open
Abstract
Hemagglutinin (HA) and neuraminidase (NA) proteins are the primary antigenic targets of influenza A virus (IAV) infections. IAV infections are generally classified into subtypes of HA and NA proteins, e.g. H3N2. Most of the known subtypes were originally defined by a lack of antibody cross-reactivity. However, genetic sequencing has played an increasingly important role in characterizing the evolving diversity of IAV. Novel subtypes have recently been described solely by their genetic sequences, and IAV infections are routinely subtyped by molecular assays, or the comparison of sequences to references. In this study, I carry out a comparative analysis of all available IAV protein sequences in the Genbank database (over 1.1 million, reduced to 272,292 unique sequences prior to phylogenetic reconstruction) to determine whether the serologically defined subtypes can be reproduced with sequence-based criteria. I show that a robust genetic taxonomy of HA and NA subtypes can be obtained using a simple clustering method, namely, by progressively partitioning the phylogeny on its longest internal branches. However, this taxonomy also requires some amendments to the current nomenclature. For example, two IAV isolates from bats previously characterized as a divergent lineage of H9N2 should be separated into their own subtype. With the exception of these small and highly divergent lineages, the phylogenies relating each of the other six genomic segments do not support partitions into major subtypes.
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Affiliation(s)
- Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044, London, Ontario N6A 5C1, Canada
- Department of Microbiology & Immunology, Western University, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
- Department of Computer Science, Western University, Room 355, Middlesex College, London N6A 5B7, Canada
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2
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Zeller MA, Ma J, Wong FY, Tum S, Hidano A, Holt H, Chhay T, Sorn S, Koeut D, Seng B, Chao S, Ng GGK, Yan Z, Chou M, Rudge JW, Smith GJD, Su YCF. The genomic landscape of swine influenza A viruses in Southeast Asia. Proc Natl Acad Sci U S A 2023; 120:e2301926120. [PMID: 37552753 PMCID: PMC10438389 DOI: 10.1073/pnas.2301926120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/07/2023] [Indexed: 08/10/2023] Open
Abstract
Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza A virus (swIAV). Effective surveillance is essential to uncover emerging virus strains; however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. More than 4,000 nasal swabs were collected from pigs in Cambodia, yielding 72 IAV-positive samples by RT-qPCR and 45 genomic sequences. We unmasked the cocirculation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swIAV reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two and 15 B.P., indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.
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Affiliation(s)
- Michael A. Zeller
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Jordan Ma
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Sothyra Tum
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Arata Hidano
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Hannah Holt
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Ty Chhay
- Livestock Development for Community Livelihood, Phnom Penh120108, Cambodia
| | - San Sorn
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Dina Koeut
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Bunnary Seng
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Sovanncheypo Chao
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Giselle G. K. Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Zhuang Yan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Monidarin Chou
- University of Health Sciences, Phnom Penh120210, Cambodia
| | - James W. Rudge
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore169857, Singapore
- SingHealth Duke-NUS Global Health Institute,SingHealth Duke-NUS Academic Medical Centre, Singapore169857, Singapore
- Duke Global Health Institute, Duke University, Durham, NC27708
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
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Layton DS, Butler J, Stewart C, Stevens V, Payne J, Rootes C, Deffrasnes C, Walker S, Shan S, Gough TJ, Cowled C, Bruce K, Wang J, Kedzierska K, Wong FYK, Bean AGD, Bingham J, Williams DT. H7N9 bearing a mutation in the nucleoprotein leads to increased pathology in chickens. Front Immunol 2022; 13:974210. [PMID: 36275684 PMCID: PMC9583263 DOI: 10.3389/fimmu.2022.974210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
The zoonotic H7N9 avian influenza (AI) virus first emerged in 2013 as a low pathogenic (LPAI) strain, and has repeatedly caused human infection resulting in severe respiratory illness and a mortality of ~39% (>600 deaths) across five epidemic waves. This virus has circulated in poultry with little to no discernible clinical signs, making detection and control difficult. Contrary to published data, our group has observed a subset of specific pathogen free chickens infected with the H7N9 virus succumb to disease, showing clinical signs consistent with highly pathogenic AI (HPAI). Viral genome sequencing revealed two key mutations had occurred following infection in the haemagglutinin (HA 226 L>Q) and nucleoprotein (NP 373 A>T) proteins. We further investigated the impact of the NP mutation and demonstrated that only chickens bearing a single nucleotide polymorphism (SNP) in their IFITM1 gene were susceptible to the H7N9 virus. Susceptible chickens demonstrated a distinct loss of CD8+ T cells from the periphery as well as a dysregulation of IFNγ that was not observed for resistant chickens, suggesting a role for the NP mutation in altered T cell activation. Alternatively, it is possible that this mutation led to altered polymerase activity, as the mutation occurs in the NP 360-373 loop which has been previously show to be important in RNA binding. These data have broad ramifications for our understanding of the pathobiology of AI in chickens and humans and provide an excellent model for investigating the role of antiviral genes in a natural host species.
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Affiliation(s)
- Daniel S. Layton
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
- *Correspondence: Daniel S. Layton, ; David T. Williams,
| | - Jeffrey Butler
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Cameron Stewart
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Vicky Stevens
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Jean Payne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Christina Rootes
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Celine Deffrasnes
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Som Walker
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Songhua Shan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Parkville, VIC, Australia
| | - Tamara J. Gough
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Christopher Cowled
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Kerri Bruce
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Jianning Wang
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Parkville, VIC, Australia
| | - Frank Y. K. Wong
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Andrew G. D. Bean
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - John Bingham
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - David T. Williams
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
- *Correspondence: Daniel S. Layton, ; David T. Williams,
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Kuroda M, Usui T, Shibata C, Nishigaki H, Yamaguchi T. Possible bidirectional human-swine and subsequent human-human transmission of influenza virus A(H1N1)/2009 in Japan. Zoonoses Public Health 2022; 69:721-728. [PMID: 35538641 DOI: 10.1111/zph.12960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 11/27/2022]
Abstract
In 2019, sows at a swine farm in Japan showed influenza-like illness (ILI) shortly after contact with an employee that exhibited ILI. Subsequently, a veterinarian became sick shortly after examining the sows and was diagnosed with influenza A virus (IAV) infection. Then, her family also contracted the infection. Subsequently, Pandemic A(H1N1)2009 viruses were isolated from all samples obtained from the sows, veterinarian and her family. Whole-genome analysis of the isolates confirmed that the viruses belonged to the same lineage (6B.1A) and the genome sequences obtained from all of the isolates were almost identical to each other. Furthermore, an epidemiological survey revealed no contact between veterinarians or their families and influenza patients prior to the onset of illness. These results strongly indicated a case of bidirectional infection between humans and sows. At the same time, we found a few unique mutations in the IAV genomes corresponding to the host species. The mutations that occurred in the virus after it was transferred from the farm worker to the sows were not observed in the humans infected from the sows, probably as a result of the mutations reverting to the original nucleotides. These results demonstrate that the bidirectional transmission of IAV is a potential risk for the next pandemic outbreak due to the emergence of new mutant strains.
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Affiliation(s)
- Moegi Kuroda
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Tatsufumi Usui
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Chiharu Shibata
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Haruka Nishigaki
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Tsuyoshi Yamaguchi
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan
- Laboratory of Veterinary Hygiene, Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Japan
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5
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Subbarao K. What influenza activity can we anticipate in 2022? Med J Aust 2022; 216:239-241. [DOI: 10.5694/mja2.51437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza Doherty Institute Melbourne VIC
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6
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Chauhan RP, Gordon ML. Review of genome sequencing technologies in molecular characterization of influenza A viruses in swine. J Vet Diagn Invest 2022; 34:177-189. [PMID: 35037523 PMCID: PMC8921814 DOI: 10.1177/10406387211068023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The rapidly evolving antigenic diversity of influenza A virus (IAV) genomes in swine makes it imperative to detect emerging novel strains and track their circulation. We analyzed in our review the sequencing technologies used for subtyping and characterizing swine IAV genomes. Google Scholar, PubMed, and International Nucleotide Sequence Database Collaboration (INSDC) database searches identified 216 studies that have utilized Sanger, second-, and third-generation sequencing techniques to subtype and characterize swine IAV genomes up to 31 March 2021. Sanger dideoxy sequencing was by far the most widely used sequencing technique for generating either full-length (43.0%) or partial (31.0%) IAV genomes in swine globally; however, in the last decade, other sequencing platforms such as Illumina have emerged as serious competitors for the generation of whole-genome sequences of swine IAVs. Although partial HA and NA gene sequences were sufficient to determine swine IAV subtypes, whole-genome sequences were critical for determining reassortments and identifying unusual or less frequently occurring IAV subtypes. The combination of Sanger and second-generation sequencing technologies also greatly improved swine IAV characterization. In addition, the rapidly evolving third-generation sequencing platform, MinION, appears promising for on-site, real-time sequencing of complete swine IAV genomes. With a higher raw read accuracy, the use of the MinION could enhance the scalability of swine IAV testing in the field and strengthen the swine IAV disease outbreak response.
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Affiliation(s)
| | - Michelle L. Gordon
- Michelle L. Gordon, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Rd, Durban 4001, South Africa.
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7
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Encinas P, del Real G, Dutta J, Khan Z, van Bakel H, del Burgo MÁM, García-Sastre A, Nelson MI. Evolution of influenza A virus in intensive and free-range swine farms in Spain. Virus Evol 2022; 7:veab099. [PMID: 35039784 PMCID: PMC8754697 DOI: 10.1093/ve/veab099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/21/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Swine harbor genetically diverse influenza A viruses (IAVs) with the capacity to host-switch to humans, causing global pandemics. Spain is the largest swine producer in Europe and has a mixed production system that includes 'white coat' pigs raised intensively in modern buildings and free-range Iberian pigs that interface differently with humans, wildlife, and other swine. Through active longitudinal IAV surveillance in nine Spanish provinces during 2015-9, we generated forty-seven complete or near-complete genome sequences from IAVs collected from swine in both systems. Genetically diverse IAVs were identified in intensively raised white pigs and free-range Iberian pigs, including new H3N1 reassortants. Both systems are dynamic environments for IAV evolution, but driven by different processes. IAVs in white pigs were genetically related to viruses found in swine raised intensively in other European countries, reflecting high rates of viral introduction following European trade routes. In contrast, IAVs in Iberian pigs have a genetic makeup shaped by frequent introductions of human IAVs, reflecting rearing practices with high rates of human contact. Transmission between white and Iberian pigs also occurred. In conclusion, Iberian swine with high rates of human contact harbor genetically diverse IAVs and potentially serve as intermediary hosts between white pigs and humans, presenting an understudied zoonotic risk that requires further investigation.
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Affiliation(s)
- Paloma Encinas
- Department of Biotechnology, National Institute of Agricultural and Food Research and Technology (INIA, CSIC), Ctra. de La Coruña Km 7.5, Madrid 28040, Spain
| | - Gustavo del Real
- Department of Biotechnology, National Institute of Agricultural and Food Research and Technology (INIA, CSIC), Ctra. de La Coruña Km 7.5, Madrid 28040, Spain
| | - Jayeeta Dutta
- Genetics and Genomic Sciences, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Zenab Khan
- Genetics and Genomic Sciences, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Harm van Bakel
- Genetics and Genomic Sciences, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - M Ángeles Martín del Burgo
- Department of Biotechnology, National Institute of Agricultural and Food Research and Technology (INIA, CSIC), Ctra. de La Coruña Km 7.5, Madrid 28040, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Martha I Nelson
- Laboratory of Parasitic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
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Mancera Gracia JC, Pearce DS, Masic A, Balasch M. Influenza A Virus in Swine: Epidemiology, Challenges and Vaccination Strategies. Front Vet Sci 2020; 7:647. [PMID: 33195504 PMCID: PMC7536279 DOI: 10.3389/fvets.2020.00647] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023] Open
Abstract
Influenza A viruses cause acute respiratory infections in swine that result in significant economic losses for global pig production. Currently, three different subtypes of influenza A viruses of swine (IAV-S) co-circulate worldwide: H1N1, H3N2, and H1N2. However, the origin, genetic background and antigenic properties of those IAV-S vary considerably from region to region. Pigs could also have a role in the adaptation of avian influenza A viruses to humans and other mammalian hosts, either as intermediate hosts in which avian influenza viruses may adapt to humans, or as a “mixing vessel” in which influenza viruses from various origins may reassort, generating novel progeny viruses capable of replicating and spreading among humans. These potential roles highlight the importance of controlling influenza A viruses in pigs. Vaccination is currently the main tool to control IAV-S. Vaccines containing whole inactivated virus (WIV) with adjuvant have been traditionally used to generate highly specific antibodies against hemagglutinin (HA), the main antigenic protein. WIV vaccines are safe and protect against antigenically identical or very similar strains in the absence of maternally derived antibodies (MDAs). Yet, their efficacy is reduced against heterologous strains, or in presence of MDAs. Moreover, vaccine-associated enhanced respiratory disease (VAERD) has been described in pigs vaccinated with WIV vaccines and challenged with heterologous strains in the US. This, together with the increasingly complex epidemiology of SIVs, illustrates the need to explore new vaccination technologies and strategies. Currently, there are two different non-inactivated vaccines commercialized for swine in the US: an RNA vector vaccine expressing the HA of a H3N2 cluster IV, and a bivalent modified live vaccine (MLV) containing H1N2 γ-clade and H3N2 cluster IV. In addition, recombinant-protein vaccines, DNA vector vaccines and alternative attenuation technologies are being explored, but none of these new technologies has yet reached the market. The aim of this article is to provide a thorough review of the current epidemiological scenario of IAV-S, the challenges faced in the control of IAV-S infection and the tools being explored to overcome those challenges.
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Affiliation(s)
| | - Douglas S Pearce
- Zoetis Inc., Veterinary Medicine Research and Development, Kalamazoo, MI, United States
| | - Aleksandar Masic
- Zoetis Inc., Veterinary Medicine Research and Development, Kalamazoo, MI, United States
| | - Monica Balasch
- Zoetis Manufacturing & Research Spain S.L. Ctra., Girona, Spain
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Prakash S, Roy S, Srivastava R, Coulon PG, Dhanushkodi NR, Vahed H, Jankeel A, Geertsema R, Amezquita C, Nguyen L, Messaoudi I, Burkhardt AM, BenMohamed L. Unique molecular signatures of antiviral memory CD8 + T cells associated with asymptomatic recurrent ocular herpes. Sci Rep 2020; 10:13843. [PMID: 32796943 PMCID: PMC7427992 DOI: 10.1038/s41598-020-70673-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
The nature of antiviral CD8+ T cells associated with protective and pathogenic herpes simplex virus type 1 (HSV-1) infections remains unclear. We compared the transcriptome, phenotype, and function of memory CD8+ T cells, sharing the same HSV-1 epitope-specificities, from infected HLA-A*0201 positive symptomatic (SYMP) vs. asymptomatic (ASYMP) individuals and HLA-A*0201 transgenic rabbits. Compared to higher frequencies of multifunctional effector memory CD8+ TEM cells in ASYMP individuals, the SYMP individuals presented dysfunctional CD8+ TEM cells, expressing major exhaustion pathways. Compared to protected ASYMP HLA transgenic rabbits, the trigeminal ganglia of non-protected SYMP HLA transgenic rabbits had higher frequencies of dysfunctional tissue-resident CD8+ TRM cells. Moreover, blockade of T cell exhaustion pathways restored the function of CD8+ T cells, reduced virus reactivation, and diminished recurrent disease in HLA transgenic rabbits. These findings reveal unique molecular signatures of protective CD8+ T cells and pave the way for T-cell-based immunotherapy to combat recurrent ocular herpes.
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Affiliation(s)
- Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Soumyabrata Roy
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Ruchi Srivastava
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Pierre-Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Nisha R Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Hawa Vahed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Allen Jankeel
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Roger Geertsema
- University Laboratory Animal Resources, University of California Irvine, Irvine, CA, 92697, USA
| | - Cassandra Amezquita
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Lan Nguyen
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Amanda M Burkhardt
- Vaccine Research and Development Center, Department of Physiology & Biophysics, University of California, Irvine, CA, 92617, USA
- Institute for Immunology, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, School of Medicine, University of California Irvine, Hewitt Hall, Room 2032; 843 Health Sciences Rd, Irvine, CA, 92697, USA.
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
- Vaccine Research and Development Center, Department of Physiology & Biophysics, University of California, Irvine, CA, 92617, USA.
- Institute for Immunology, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA.
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10
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Chauhan RP, Gordon ML. A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide. Pathogens 2020; 9:pathogens9050355. [PMID: 32397138 PMCID: PMC7281378 DOI: 10.3390/pathogens9050355] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023] Open
Abstract
The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics.
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Affiliation(s)
- Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martha I. Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Deng YM, Wong FYK, Spirason N, Kaye M, Beazley R, Grau MLL, Shan S, Stevens V, Subbarao K, Sullivan S, Barr IG, Dhanasekaran V. Locally Acquired Human Infection with Swine-Origin Influenza A(H3N2) Variant Virus, Australia, 2018. Emerg Infect Dis 2020; 26:143-147. [PMID: 31661057 PMCID: PMC6924914 DOI: 10.3201/eid2601.191144] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 2018, a 15-year-old female adolescent in Australia was infected with swine influenza A(H3N2) variant virus. The virus contained hemagglutinin and neuraminidase genes derived from 1990s-like human seasonal viruses and internal protein genes from influenza A(H1N1)pdm09 virus, highlighting the potential risk that swine influenza A virus poses to human health in Australia.
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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.
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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
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14
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Deng YM, Wong FY, Spirason N, Kaye M, Beazley R, Grau M, Shan S, Stevens V, Subbarao K, Sullivan S, Barr IG, Dhanasekaran V. Locally Acquired Human Infection with Swine-Origin Influenza A(H3N2) Variant Virus, Australia, 2018. Emerg Infect Dis 2020. [DOI: 10.3201/2601.191144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Smith DW, Barr IG, Loh R, Levy A, Tempone S, O'Dea M, Watson J, Wong FYK, Effler PV. Respiratory Illness in a Piggery Associated with the First Identified Outbreak of Swine Influenza in Australia: Assessing the Risk to Human Health and Zoonotic Potential. Trop Med Infect Dis 2019; 4:tropicalmed4020096. [PMID: 31242646 PMCID: PMC6632059 DOI: 10.3390/tropicalmed4020096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 12/15/2022] Open
Abstract
Australia was previously believed to be free of enzootic swine influenza viruses due strict quarantine practices and use of biosecure breeding facilities. The first proven Australian outbreak of swine influenza occurred in Western Australian in 2012, revealing an unrecognized zoonotic risk, and a potential future pandemic threat. A public health investigation was undertaken to determine whether zoonotic infections had occurred and to reduce the risk of further transmission between humans and swine. A program of monitoring, testing, treatment, and vaccination was commenced, and a serosurvey of workers was also undertaken. No acute infections with the swine influenza viruses were detected. Serosurvey results were difficult to interpret due to previous influenza infections and past and current vaccinations. However, several workers had elevated haemagglutination inhibition (HI) antibody levels to the swine influenza viruses that could not be attributed to vaccination or infection with contemporaneous seasonal influenza A viruses. However, we lacked a suitable control population, so this was inconclusive. The experience was valuable in developing better protocols for managing outbreaks at the human–animal interface. Strict adherence to biosecurity practices, and ongoing monitoring of swine and their human contacts is important to mitigate pandemic risk. Strain specific serological assays would greatly assist in identifying zoonotic transmission.
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Affiliation(s)
- David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA 6009, Australia.
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA 6009, Australia.
| | - Ian G Barr
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Richmond Loh
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth, WA 6151, Australia.
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA 6009, Australia.
| | - Simone Tempone
- Communicable Disease Control Directorate, Department of Health Western Australia, Perth, WA 6004, Australia.
| | - Mark O'Dea
- School of Veterinary Medicine, Murdoch University, Perth, WA 6150, Australia.
| | - James Watson
- CSIRO Australian Animal Health Laboratory, Geelong, VIC 3219, Australia.
| | - Frank Y K Wong
- CSIRO Australian Animal Health Laboratory, Geelong, VIC 3219, Australia.
| | - Paul V Effler
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA 6009, Australia.
- Communicable Disease Control Directorate, Department of Health Western Australia, Perth, WA 6004, Australia.
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