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Gonzalez-Obando J, Zuluaga-Cabrera A, Moreno I, Úsuga J, Ciuderis K, Forero JE, Diaz A, Rojas-Arbeláez C, Hernández-Ortiz JP, Ruiz-Saenz J. First Molecular Detection and Epidemiological Analysis of Equine Influenza Virus in Two Regions of Colombia, 2020-2023. Viruses 2024; 16:839. [PMID: 38932133 PMCID: PMC11209042 DOI: 10.3390/v16060839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Equine influenza is a viral disease caused by the equine influenza virus (EIV), and according to the WOAH, it is mandatory to report these infections. In Latin America and Colombia, EIV risk factors have not been analyzed. The objective of this research is to perform an epidemiological and molecular analysis of the EIV in horses with respiratory symptoms from 2020 to 2023 in Colombia. Molecular EIV detection was performed using RT-qPCR and nanopore sequencing. A risk analysis was also performed via the GEE method. A total of 188 equines with EIV respiratory symptoms were recruited. The positivity rate was 33.5%. The descriptive analysis showed that only 12.8% of the horses were vaccinated, and measures such as the quarantine and isolation of symptomatic animals accounted for 91.5% and 88.8%, respectively. The variables associated with the EIV were the non-isolation of positive individuals (OR = 8.16, 95% CI (1.52-43.67), p = 0.014) and sharing space with poultry (OR = 2.16, 95% CI (1.09-4.26), p = 0.027). In conclusion, this is the first EIV investigation in symptomatic horses in Colombia, highlighting the presence of the virus in the country and the need to improve preventive and control measures.
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Affiliation(s)
- Juliana Gonzalez-Obando
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia;
- Grupo de Epidemiología, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Angélica Zuluaga-Cabrera
- Grupo de Investigación GISCA, Facultad de Medicina Veterinaria y Zootecnia, Fundación Universitaria Vision de las Américas, Medellín 050031, Colombia;
| | - Isabel Moreno
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín 050036, Colombia; (I.M.); (J.Ú.); (K.C.); (J.P.H.-O.)
| | - Jaime Úsuga
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín 050036, Colombia; (I.M.); (J.Ú.); (K.C.); (J.P.H.-O.)
| | - Karl Ciuderis
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín 050036, Colombia; (I.M.); (J.Ú.); (K.C.); (J.P.H.-O.)
| | - Jorge E. Forero
- Grupo de Investigación en Microbiología Ambiental, Escuela de Microbiología, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Andrés Diaz
- Pig Improvement Company Hendersonville, Hendersonville, TN 37075, USA;
| | | | - Juan P. Hernández-Ortiz
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín 050036, Colombia; (I.M.); (J.Ú.); (K.C.); (J.P.H.-O.)
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia;
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Kleij L, Bruder E, Raoux-Barbot D, Lejal N, Nevers Q, Deloizy C, Da Costa B, Legrand L, Barrey E, Chenal A, Pronost S, Delmas B, Dhorne-Pollet S. Genomic characterization of equine influenza A subtype H3N8 viruses by long read sequencing and functional analyses of the PB1-F2 virulence factor of A/equine/Paris/1/2018. Vet Res 2024; 55:36. [PMID: 38520035 PMCID: PMC10960481 DOI: 10.1186/s13567-024-01289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/16/2024] [Indexed: 03/25/2024] Open
Abstract
Equine influenza virus (EIV) remains a threat to horses, despite the availability of vaccines. Strategies to monitor the virus and prevent potential vaccine failure revolve around serological assays, RT-qPCR amplification, and sequencing the viral hemagglutinin (HA) and neuraminidase (NA) genes. These approaches overlook the contribution of other viral proteins in driving virulence. This study assesses the potential of long-read nanopore sequencing for fast and precise sequencing of circulating equine influenza viruses. Therefore, two French Florida Clade 1 strains, including the one circulating in winter 2018-2019 exhibiting more pronounced pathogenicity than usual, as well as the two currently OIE-recommended vaccine strains, were sequenced. Our results demonstrated the reliability of this sequencing method in generating accurate sequences. Sequence analysis of HA revealed a subtle antigenic drift in the French EIV strains, with specific substitutions, such as T163I in A/equine/Paris/1/2018 and the N188T mutation in post-2015 strains; both substitutions were in antigenic site B. Antigenic site E exhibited modifications in post-2018 strains, with the N63D substitution. Segment 2 sequencing also revealed that the A/equine/Paris/1/2018 strain encodes a longer variant of the PB1-F2 protein when compared to other Florida clade 1 strains (90 amino acids long versus 81 amino acids long). Further biological and biochemistry assays demonstrated that this PB1-F2 variant has enhanced abilities to abolish the mitochondrial membrane potential ΔΨm and permeabilize synthetic membranes. Altogether, our results highlight the interest in rapidly characterizing the complete genome of circulating strains with next-generation sequencing technologies to adapt vaccines and identify specific virulence markers of EIV.
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Affiliation(s)
- Lena Kleij
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Elise Bruder
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dorothée Raoux-Barbot
- CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Nathalie Lejal
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Quentin Nevers
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Charlotte Deloizy
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Bruno Da Costa
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Loïc Legrand
- LABÉO Frank Duncombe, 14280, Saint-Contest, France
- BIOTARGEN, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Eric Barrey
- AgroParisTech, Unité de Génétique Animale et Biologie Intégrative, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Alexandre Chenal
- CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Stéphane Pronost
- LABÉO Frank Duncombe, 14280, Saint-Contest, France
- BIOTARGEN, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Bernard Delmas
- Unité de Virologie et Immunologie Moléculaires, INRAE, UVSQ, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Sophie Dhorne-Pollet
- AgroParisTech, Unité de Génétique Animale et Biologie Intégrative, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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3
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Trovão NS, Khan SM, Lemey P, Nelson MI, Cherry JL. Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species. mBio 2024; 15:e0264923. [PMID: 38078770 PMCID: PMC10886446 DOI: 10.1128/mbio.02649-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE For decades, researchers have studied the rapid evolution of influenza A viruses for vaccine design and as a useful model system for the study of host/parasite evolution. By performing an exhaustive analysis of hemagglutinin protein (HA) sequences from 49 lineages independently evolving in birds, swine, canines, equines, and humans over the last century, our work uncovers surprising features of HA evolution. In particular, the canine H3 stalk, unlike human H3 and H1 stalk domains, is not evolving slowly, suggesting that evolution in the stalk domain is not universally constrained across all host species. Therefore, a broader multi-host perspective on HA evolution may be useful during the evaluation and design of stalk-targeted vaccine candidates.
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Affiliation(s)
- Nidia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Sairah M Khan
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua L Cherry
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evol 2023; 9:vead052. [PMID: 37692894 PMCID: PMC10484056 DOI: 10.1093/ve/vead052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Evin Rothschild
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Stephanie E Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, Scotland
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Laura B Goodman
- Baker Institute for Animal Health, Department of Public and Ecosystems Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James C Kile
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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5
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Pellegrini F, Buonavoglia A, Omar AH, Diakoudi G, Lucente MS, Odigie AE, Sposato A, Augelli R, Camero M, Decaro N, Elia G, Bányai K, Martella V, Lanave G. A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing. Animals (Basel) 2023; 13:ani13071153. [PMID: 37048408 PMCID: PMC10093709 DOI: 10.3390/ani13071153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Massive sequencing techniques have allowed us to develop straightforward approaches for the whole genome sequencing of viruses, including influenza viruses, generating information that is useful for improving the levels and dimensions of data analysis, even for archival samples. Using the Nanopore platform, we determined the whole genome sequence of an H3N8 equine influenza virus, identified from a 2005 outbreak in Apulia, Italy, whose origin had remained epidemiologically unexplained. The virus was tightly related (>99% at the nucleotide level) in all the genome segments to viruses identified in Poland in 2005–2008 and it was seemingly introduced locally with horse trading for the meat industry. In the phylogenetic analysis based on the eight genome segments, strain ITA/2005/horse/Bari was found to cluster with sub-lineage Florida 2 in the HA and M genes, whilst in the other genes it clustered with strains of the Eurasian lineage, revealing a multi-reassortant nature.
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Affiliation(s)
- Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Alessio Buonavoglia
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Ahmed H. Omar
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Maria S. Lucente
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Amienwanlen E. Odigie
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Alessio Sposato
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | | | - Michele Camero
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Gabriella Elia
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Krisztián Bányai
- Veterinary Medical Research Institute, 1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, 1400 Budapest, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
- Correspondence:
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
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6
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Ahmed BM, Bayoumi MM, Farrag MA, Elgamal MA, Daly JM, Amer HM. Emergence of equine influenza virus H3Nx Florida clade 2 in Arabian racehorses in Egypt. Virol J 2022; 19:185. [PMID: 36371185 PMCID: PMC9652821 DOI: 10.1186/s12985-022-01917-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background Equine influenza is an important cause of respiratory disease in equids. The causative virus; EIV, is highly variable and can evolve by accumulation of mutations, particularly in the haemagglutinin (HA) gene. Currently, H3N8 is the sole subtype circulating worldwide with Florida clade 1 (FC1) is most prevalent in the Americas and FC2 in Asia and Europe. In Egypt, EIV was detected in two occasions: subtype H7N7 in 1989 and subtype H3N8 (FC1) in 2008. No data is available on the circulation pattern of EIV during the last decade despite frequent observation of suspected cases.
Methods Twenty-two nasal swabs were collected from vaccinated and non-vaccinated horses showing respiratory signs suggestive of EIV infection in 2017–18. Three additional swabs were retrieved during a national race event in January 2018 from Arabian mares with high fever, gait stiffness and dry cough. Samples were screened by RT-qPCR and HA1 domain of the hemagglutinin gene was amplified and sequenced for sequence and phylogenetic analysis. Results RT-qPCR screening revealed that only the 3 samples from the race were positive with cycle thresholds ranging from 16 to 21 indicating high viral load. Isolation attempts in hen’s eggs were unsuccessful. Sequence analysis of the HA1 domain gene has revealed two identical nucleotide sequences, while the third contained 3 synonymous mutations. Phylogenetic analysis clustered study sequences with recent FC2 sequences from Europe. Amino acid alignments revealed 14 and 13 amino acid differences in the study sequences compared to A/equine/Egypt/6066NANRU-VSVRI/08 (H3N8) and A/equine/Kentucky/1997 (H3N8), respectively, available as EIV vaccines in Egypt. Nine amino acids were different from A/equine/Richmond/1/2007 (H3N8), the recommended FC2 vaccine strain by the world organization of animal health expert surveillance panel (OIE-ESP), two of which were unique to the Egyptian sequences while the remaining 7 changes were shared with the FC2-144V subgroup detected in the United Kingdom from late 2015 to 2016. Conclusions The study represents the first reported detection of FC2-144V related EIV from Arabian mares in Egypt, and probably from the entire middle east region. The presented information about EIV epidemiology and spread may require reconsideration of the vaccine strains used in the national vaccination programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01917-9.
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7
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Gonzalez-Obando J, Forero JE, Zuluaga-Cabrera AM, Ruiz-Saenz J. Equine Influenza Virus: An Old Known Enemy in the Americas. Vaccines (Basel) 2022; 10:vaccines10101718. [PMID: 36298583 PMCID: PMC9610386 DOI: 10.3390/vaccines10101718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Equine influenza is a highly contagious disease caused by the H3N8 equine influenza virus (EIV), which is endemically distributed throughout the world. It infects equids, and interspecies transmission to dogs has been reported. The H3N8 Florida lineage, which is divided into clades 1 and 2, is the most representative lineage in the Americas. The EIV infects the respiratory system, affecting the ciliated epithelial cells and preventing the elimination of foreign bodies and substances. Certain factors related to the disease, such as an outdated vaccination plan, age, training, and close contact with other animals, favor the presentation of equine influenza. This review focuses on the molecular, pathophysiological, and epidemiological characteristics of EIV in the Americas to present updated information to achieve prevention and control of the virus. We also discuss the need for monitoring the disease, the use of vaccines, and the appropriate application of those biologicals, among other biosecurity measures that are important for the control of the virus.
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Affiliation(s)
- Juliana Gonzalez-Obando
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia
| | - Jorge Eduardo Forero
- Grupo de Investigación en Microbiología Veterinaria, Escuela de Microbiología, Universidad de Antioquia, Medellín 050010, Colombia
| | - Angélica M Zuluaga-Cabrera
- Facultad de Medicina Veterinaria y Zootecnia, Fundación Universitaria Autónoma de las Américas, Circular 73 N°35-04, Medellín 050010, Colombia
| | - Julián Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia
- Correspondence:
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8
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Alaql FA, Alhafufi AN, Kasem S, Alhammad YMO, Albaqshi H, Alyousaf A, Alsubaie FM, Alghamdi AN, Abdel-Moneim AS, Alharbi SA. Full-Length Genome of the Equine Influenza A Virus Subtype H3N8 from 2019 Outbreak in Saudi Arabia. Animals (Basel) 2022; 12:ani12192720. [PMID: 36230462 PMCID: PMC9558945 DOI: 10.3390/ani12192720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022] Open
Abstract
Simple Summary Equine influenza is a highly contagious respiratory viral disease. The current study is the first to provide a description of the full-length genome sequence and surveillance of recent exposure to the equine influenza virus (EIV) during the 2019 epidemic in Saudi Arabia. This epidemic was benign, since it resulted in low case fatality (0.45%, 1/224). The viruses detected in the current study were found to be related to subtype H73N8 clade 1 of the Florida sublineage. Full-length genome sequencing revealed no evidence of major genetic changes or of reassortment among the eight segments of the viral genome. However, the Saudi strains showed a considerable number of amino acid substitutions in the signal peptide (2 amino acid substitutions), HA1 (10 amino acid substitutions) and HA2 (4 amino acid substitutions) in the haemagglutinin glycoprotein in comparison to clade 1 Florida sublineage vaccinal strains. These findings should be considered during selection of the equine influenza vaccine strains approved for use in Saudi Arabia. Abstract Equine influenza is a major cause of respiratory infections in horses and can spread rapidly despite the availability of commercial vaccines. This study aimed to screen the incidence of equine influenza virus (EIV) and molecularly characterize the haemagglutinin and neuraminidase from positive EIV field samples collected from Saudi Arabia. Six-hundred twenty-one horses from 57 horse barns were screened for the presence of the clinical signs, suggestive for equine influenza, from different parts of Saudi Arabia. Nasopharyngeal swabs were collected from each horse showing respiratory distress. Samples from the same horse barn were pooled together and screened for the presence of the influenza A virus using quantitative real time reverse transcriptase polymerase chain reaction (qRT-PCR). Selective positive samples were subjected to full-length genome sequencing using MiSeq Illumina. Out of the total 57 pools, 39 were found positive to EIV using qRT-PCR. Full-length gene sequences were compared with representative EIV strains selected from the GenBank database. Phylogenetic analysis of the HA and NA genes revealed that the identified virus strains belong to H3N8 clade 1 of the Florida sublineage and were very similar to viruses identified in USA in 2019, with no current evidence for reassortment. This is one of the first reports providing detailed description and characterization of EIVs in Saudi Arabia. Detailed surveillance and genetic information sharing could allow genetic evolution of equine influenza viruses to be monitored more effectively on a global basis and aid in refinement of vaccine strain selection for EIV.
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Affiliation(s)
- Fanan A. Alaql
- Virology and Genome Department in Central Veterinary Laboratory (CVL), Ministry of Environment, Water and Agriculture (MEWA), P.O. Box 15831, Riyadh 11454, Saudi Arabi
- Botany & Microbiology Department, College of Science, King Saud University, Riyadh 12372, Saudi Arabia
| | - Ali N. Alhafufi
- Virology and Genome Department in Central Veterinary Laboratory (CVL), Ministry of Environment, Water and Agriculture (MEWA), P.O. Box 15831, Riyadh 11454, Saudi Arabi
| | - Samy Kasem
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, El Geish Street, Kafrelsheikh 33516, Egypt
- Correspondence: (S.K.); (A.S.A.-M.)
| | - Yousef M. O. Alhammad
- Virology and Genome Department in Central Veterinary Laboratory (CVL), Ministry of Environment, Water and Agriculture (MEWA), P.O. Box 15831, Riyadh 11454, Saudi Arabi
| | - Hassan Albaqshi
- Virology and Genome Department in Central Veterinary Laboratory (CVL), Ministry of Environment, Water and Agriculture (MEWA), P.O. Box 15831, Riyadh 11454, Saudi Arabi
| | - Ameen Alyousaf
- Virology and Genome Department in Central Veterinary Laboratory (CVL), Ministry of Environment, Water and Agriculture (MEWA), P.O. Box 15831, Riyadh 11454, Saudi Arabi
| | - Faisal M. Alsubaie
- Virology and Genome Department in Central Veterinary Laboratory (CVL), Ministry of Environment, Water and Agriculture (MEWA), P.O. Box 15831, Riyadh 11454, Saudi Arabi
| | - Ahmed N. Alghamdi
- Department of Microbiology, College of Medicine, Taif University, Taif 21944, Saudi Arabia
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif 21944, Saudi Arabia
- Correspondence: (S.K.); (A.S.A.-M.)
| | - Sulaiman A. Alharbi
- Botany & Microbiology Department, College of Science, King Saud University, Riyadh 12372, Saudi Arabia
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9
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Whitlock F, Murcia PR, Newton JR. A Review on Equine Influenza from a Human Influenza Perspective. Viruses 2022; 14:v14061312. [PMID: 35746783 PMCID: PMC9229935 DOI: 10.3390/v14061312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/12/2022] Open
Abstract
Influenza A viruses (IAVs) have a main natural reservoir in wild birds. IAVs are highly contagious, continually evolve, and have a wide host range that includes various mammalian species including horses, pigs, and humans. Furthering our understanding of host-pathogen interactions and cross-species transmissions is therefore essential. This review focuses on what is known regarding equine influenza virus (EIV) virology, pathogenesis, immune responses, clinical aspects, epidemiology (including factors contributing to local, national, and international transmission), surveillance, and preventive measures such as vaccines. We compare EIV and human influenza viruses and discuss parallels that can be drawn between them. We highlight differences in evolutionary rates between EIV and human IAVs, their impact on antigenic drift, and vaccine strain updates. We also describe the approaches used for the control of equine influenza (EI), which originated from those used in the human field, including surveillance networks and virological analysis methods. Finally, as vaccination in both species remains the cornerstone of disease mitigation, vaccine technologies and vaccination strategies against influenza in horses and humans are compared and discussed.
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Affiliation(s)
- Fleur Whitlock
- Medical Research Council, University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, UK; (F.W.); (P.R.M.)
- Equine Infectious Disease Surveillance (EIDS), Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Pablo R. Murcia
- Medical Research Council, University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, UK; (F.W.); (P.R.M.)
| | - J. Richard Newton
- Equine Infectious Disease Surveillance (EIDS), Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
- Correspondence:
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10
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El-Hage C, Hartley C, Savage C, Watson J, Gilkerson J, Paillot R. Assessment of Humoral and Long-Term Cell-Mediated Immune Responses to Recombinant Canarypox-Vectored Equine Influenza Virus Vaccination in Horses Using Conventional and Accelerated Regimens Respectively. Vaccines (Basel) 2022; 10:vaccines10060855. [PMID: 35746463 PMCID: PMC9229645 DOI: 10.3390/vaccines10060855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 02/05/2023] Open
Abstract
During Australia's first and only outbreak of equine influenza (EI), which was restricted to two northeastern states, horses were strategically vaccinated with a recombinant canarypox-vectored vaccine (rCP-EIV; ProteqFlu™, Merial P/L). The vaccine encoded for haemagglutinin (HA) belonging to two equine influenza viruses (EIVs), including an American and Eurasian lineage subtype that predated the EIV responsible for the outbreak (A/equine/Sydney/07). Racehorses in Victoria (a southern state that remained free of EI) were vaccinated prophylactically. Although the vaccine encoded for (HA) belonged to two EIVs of distinct strains of the field virus, clinical protection was reported in vaccinated horses. Our aim is to assess the extent of humoral immunity in one group of vaccinated horses and interferon-gamma ((EIV)-IFN-γ)) production in the peripheral blood mononuclear cells (PBMCs) of a second population of vaccinated horses. Twelve racehorses at work were monitored for haemagglutination inhibition antibodies to three antigenically distinct equine influenza viruses (EIVs) The EIV antigens included two H3N8 subtypes: A/equine/Sydney/07) A/equine/Newmarket/95 (a European lineage strain) and an H7N7 subtype (A/equine/Prague1956). Cell-mediated immune responses of: seven racehorses following an accelerated vaccination schedule, two horses vaccinated using a conventional regimen, and six unvaccinated horses were evaluated by determining (EIV)-IFN-γ levels. Antibody responses following vaccination with ProteqFlu™ were cross-reactive in nature, with responses to both H3N8 EIV strains. Although (EIV)IFN-γ was clearly detected following the in vitro re-stimulation of PBMC, there was no significant difference between the different groups of horses. Results of this study support reports of clinical protection of Australian horses following vaccination with Proteq-Flu™ with objective evidence of humoral cross-reactivity to the outbreak viral strain A/equine/Sydney/07.
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Affiliation(s)
- Charles El-Hage
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (C.H.); (C.S.); (J.G.)
- Correspondence: ; Tel.: +61-417166029
| | - Carol Hartley
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (C.H.); (C.S.); (J.G.)
| | - Catherine Savage
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (C.H.); (C.S.); (J.G.)
| | - James Watson
- Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC 3216, Australia;
| | - James Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (C.H.); (C.S.); (J.G.)
| | - Romain Paillot
- School of Equine and Veterinary Physiotherapy, Writtle University College, Lordship Road, Writtle, Chelmsford CM1 3RR, UK;
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11
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Xu W, Navarro-López R, Solis-Hernandez M, Liljehult-Fuentes F, Molina-Montiel M, Lagunas-Ayala M, Rocha-Martinez M, Ferrara-Tijera E, Pérez de la Rosa J, Berhane Y. Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses. Viruses 2022; 14:v14050958. [PMID: 35632700 PMCID: PMC9146523 DOI: 10.3390/v14050958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
We have demonstrated for the first time a comprehensive evolutionary analysis of the Mexican lineage H5N2 avian influenza virus (AIV) using complete genome sequences (n = 189), from its first isolation in 1993 until 2019. Our study showed that the Mexican lineage H5N2 AIV originated from the North American wild bird gene pool viruses around 1990 and is currently circulating in poultry populations of Mexico, the Dominican Republic, and Taiwan. Since the implementation of vaccination in 1995, the highly pathogenic AIV (HPAIV) H5N2 virus was eradicated from Mexican poultry in mid-1995. However, the low pathogenic AIV (LPAIV) H5N2 virus has continued to circulate in domestic poultry populations in Mexico, eventually evolving into five distinct clades. In the current study, we demonstrate that the evolution of Mexican lineage H5N2 AIVs involves gene reassortments and mutations gained over time. The current circulating Mexican lineage H5N2 AIVs are classified as LPAIV based on the amino acid sequences of the hemagglutinin (HA) protein cleavage site motif as well as the results of the intravenous pathogenicity index (IVPI). The immune pressure from vaccinations most likely has played a significant role in the positive selection of antigenic drift mutants within the Mexican H5N2 AIVs. Most of the identified substitutions in these viruses are located on the critical antigenic residues of the HA protein and as a result, might have contributed to vaccine failures. This study highlights and stresses the need for vaccine updates while emphasizing the importance of continued molecular monitoring of the HA protein for its antigenic changes compared to the vaccines used.
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Affiliation(s)
- Wanhong Xu
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada;
| | - Roberto Navarro-López
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Mario Solis-Hernandez
- United States-Mexico Commission for the Prevention of Foot-and-Mouth Disease and Other Exotic Diseases of Animals, Mexico City 64590, Mexico; (M.S.-H.); (F.L.-F.)
| | - Francisco Liljehult-Fuentes
- United States-Mexico Commission for the Prevention of Foot-and-Mouth Disease and Other Exotic Diseases of Animals, Mexico City 64590, Mexico; (M.S.-H.); (F.L.-F.)
| | - Miguel Molina-Montiel
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - María Lagunas-Ayala
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Marisol Rocha-Martinez
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Eduardo Ferrara-Tijera
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Juan Pérez de la Rosa
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada;
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2S2, Canada
- Correspondence: ; Tel.: +1-204-789-7062
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12
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Lee K, Pusterla N, Barnum SM, Lee DH, Martínez-López B. Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling. Transbound Emerg Dis 2022; 69:e1734-e1748. [PMID: 35263501 DOI: 10.1111/tbed.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States (US) and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread and evolutionary characteristics at US and global scales using Bayesian phylogeography with balanced subsampling based on regional horse population size. A total of 297 Haemagglutinin (HA) sequences of global EIV H3N8 were collected from 1963 to 2019 and subsampled to global subset (n = 67), raw US sequences (n = 100) and US subset (n = 44) datasets. Discrete trait phylogeography analysis was used to estimate the transmission history of EIV using four global and US genome datasets. The North American lineage was the major source of globally dominant EIV variants and spread to other global regions. The US EIV strains generally spread from the southern and midwestern regions to other regions. The EIV H3N8 accumulated approximately three nucleotide substitutions per year in the HA gene under heterogenous local positive selection. Our findings will guide better decision making of target intervention strategies of EIV H3N8 infection and provide the better scheme of genomic surveillance in the US and global equine health. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kyuyoung Lee
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Samantha M Barnum
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
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13
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Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:pathogens11020252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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14
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Abstract
Influenza A viruses (IAV) initiate infection by binding to glycans with terminal sialic acids on the cell surface. Hosts of IAV variably express two major forms of sialic acid, N-acetylneuraminic acid (NeuAc) and N-glycolylneuraminic acid (NeuGc). NeuGc is produced in most mammals including horses and pigs, but is absent in humans, ferrets, and birds. The only known naturally occurring IAVs that exclusively bind NeuGc are extinct highly pathogenic equine H7N7 viruses. We determined the crystal structure of a representative equine H7 hemagglutinin (HA) in complex with NeuGc and observed high similarity in the receptor-binding domain with an avian H7 HA. To determine the molecular basis for NeuAc and NeuGc specificity, we performed systematic mutational analyses, based on the structural insights, on two distant avian H7 HAs and an H15 HA. We found that mutation A135E is key for binding α2,3-linked NeuGc but does not abolish NeuAc binding. Additional mutations S128T, I130V, T189A, and K193R converted the specificity from NeuAc to NeuGc. We investigated the residues at positions 128, 130, 135, 189, and 193 in a phylogenetic analysis of avian and equine H7 HAs. This revealed a clear distinction between equine and avian residues. The highest variability was observed at key position 135, of which only the equine glutamic acid led to NeuGc binding. These results demonstrate that genetically distinct H7 and H15 HAs can be switched from NeuAc to NeuGc binding and vice versa after introduction of several mutations, providing insights into the adaptation of H7 viruses to NeuGc receptors. (250 words) Importance Influenza A viruses cause millions of cases of severe illness and deaths annually. To initiate infection and replicate, the virus first needs to bind to a structure on the cell surface, like a key fitting in a lock. For influenza A viruses, these 'keys' (receptors) on the cell surface are chains of sugar molecules (glycans). The terminal sugar on these glycans is often either N-acetylneuraminic acid (NeuAc) or N-glycolylneuraminic acid (NeuGc). Most influenza A viruses bind NeuAc, but a small minority binds NeuGc. NeuGc is present in species like horses, pigs, and mice, but not in humans, ferrets, and birds. Here, we investigated the molecular determinants of NeuGc specificity and the origin of viruses that bind NeuGc.
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15
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Abstract
Horses are the third major mammalian species, along with humans and swine, long known to be subject to acute upper respiratory disease from influenza A virus infection. The viruses responsible are subtype H7N7, which is believed extinct, and H3N8, which circulates worldwide. The equine influenza lineages are clearly divergent from avian influenza lineages of the same subtypes. Their genetic evolution and potential for interspecies transmission, as well as clinical features and epidemiology, are discussed. Equine influenza is spread internationally and vaccination is central to control efforts. The current mechanism of international surveillance and virus strain recommendations for vaccines is described.
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Affiliation(s)
- Thomas M Chambers
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
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16
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Amat JAR, Patton V, Chauché C, Goldfarb D, Crispell J, Gu Q, Coburn AM, Gonzalez G, Mair D, Tong L, Martinez-Sobrido L, Marshall JF, Marchesi F, Murcia PR. Long-term adaptation following influenza A virus host shifts results in increased within-host viral fitness due to higher replication rates, broader dissemination within the respiratory epithelium and reduced tissue damage. PLoS Pathog 2021; 17:e1010174. [PMID: 34919598 PMCID: PMC8735595 DOI: 10.1371/journal.ppat.1010174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/06/2022] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanisms and consequences of genome evolution on viral fitness following host shifts are poorly understood. In addition, viral fitness -the ability of an organism to reproduce and survive- is multifactorial and thus difficult to quantify. Influenza A viruses (IAVs) circulate broadly among wild birds and have jumped into and become endemic in multiple mammalian hosts, including humans, pigs, dogs, seals, and horses. H3N8 equine influenza virus (EIV) is an endemic virus of horses that originated in birds and has been circulating uninterruptedly in equine populations since the early 1960s. Here, we used EIV to quantify changes in infection phenotype associated to viral fitness due to genome-wide changes acquired during long-term adaptation. We performed experimental infections of two mammalian cell lines and equine tracheal explants using the earliest H3N8 EIV isolated (A/equine/Uruguay/63 [EIV/63]), and A/equine/Ohio/2003 (EIV/2003), a monophyletic descendant of EIV/63 isolated 40 years after the emergence of H3N8 EIV. We show that EIV/2003 exhibits increased resistance to interferon, enhanced viral replication, and a more efficient cell-to-cell spread in cells and tissues. Transcriptomics analyses revealed virus-specific responses to each virus, mainly affecting host immunity and inflammation. Image analyses of infected equine respiratory explants showed that despite replicating at higher levels and spreading over larger areas of the respiratory epithelium, EIV/2003 induced milder lesions compared to EIV/63, suggesting that adaptation led to reduced tissue pathogenicity. Our results reveal previously unknown links between virus genotype and the host response to infection, providing new insights on the relationship between virus evolution and fitness. As viruses are obligate intracellular pathogens, their ability to replicate and spread within their hosts is key for survival, even if it leads to severe disease or death of the host. Understanding the consequences of long-term virus adaptation after viral emergence is key for pandemic preparedness. H3N8 equine influenza virus (EIV) originated in birds and has circulated in horses since 1963, thus providing unique opportunities to study virus adaptation. We compared the replication kinetics of two EIVs of the same lineage but with different evolutionary histories: the earliest virus (EIV/63, isolated in 1963), and EIV/2003, which was isolated after 40 years of continuous circulation in horses. Experimental infections of cell lines (MDCK and E.Derm cells) and equine respiratory explants show that EIV evolved towards enhanced replication and cell-to-cell spread; but reduced tissue damage, confirming that viral fitness is adaptive and does not necessarily result in higher virulence.
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Affiliation(s)
- Julien A. R. Amat
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Veronica Patton
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Caroline Chauché
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Centre for Inflammation Research, University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh, Scotland, United Kingdom
| | - Daniel Goldfarb
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Joanna Crispell
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Alice M. Coburn
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Gaelle Gonzalez
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - John F. Marshall
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Francesco Marchesi
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- * E-mail:
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17
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Could Interleukin-33 (IL-33) Govern the Outcome of an Equine Influenza Virus Infection? Learning from Other Species. Viruses 2021; 13:v13122519. [PMID: 34960788 PMCID: PMC8704309 DOI: 10.3390/v13122519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/04/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Influenza A viruses (IAVs) are important respiratory pathogens of horses and humans. Infected individuals develop typical respiratory disorders associated with the death of airway epithelial cells (AECs) in infected areas. Virulence and risk of secondary bacterial infections vary among IAV strains. The IAV non-structural proteins, NS1, PB1-F2, and PA-X are important virulence factors controlling AEC death and host immune responses to viral and bacterial infection. Polymorphism in these proteins impacts their function. Evidence from human and mouse studies indicates that upon IAV infection, the manner of AEC death impacts disease severity. Indeed, while apoptosis is considered anti-inflammatory, necrosis is thought to cause pulmonary damage with the release of damage-associated molecular patterns (DAMPs), such as interleukin-33 (IL-33). IL-33 is a potent inflammatory mediator released by necrotic cells, playing a crucial role in anti-viral and anti-bacterial immunity. Here, we discuss studies in human and murine models which investigate how viral determinants and host immune responses control AEC death and subsequent lung IL-33 release, impacting IAV disease severity. Confirming such data in horses and improving our understanding of early immunologic responses initiated by AEC death during IAV infection will better inform the development of novel therapeutic or vaccine strategies designed to protect life-long lung health in horses and humans, following a One Health approach.
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18
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Review of Influenza Virus Vaccines: The Qualitative Nature of Immune Responses to Infection and Vaccination Is a Critical Consideration. Vaccines (Basel) 2021; 9:vaccines9090979. [PMID: 34579216 PMCID: PMC8471734 DOI: 10.3390/vaccines9090979] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023] Open
Abstract
Influenza viruses have affected the world for over a century, causing multiple pandemics. Throughout the years, many prophylactic vaccines have been developed for influenza; however, these viruses are still a global issue and take many lives. In this paper, we review influenza viruses, associated immunological mechanisms, current influenza vaccine platforms, and influenza infection, in the context of immunocompromised populations. This review focuses on the qualitative nature of immune responses against influenza viruses, with an emphasis on trained immunity and an assessment of the characteristics of the host–pathogen that compromise the effectiveness of immunization. We also highlight innovative immunological concepts that are important considerations for the development of the next generation of vaccines against influenza viruses.
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19
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Equine Influenza Virus and Vaccines. Viruses 2021; 13:v13081657. [PMID: 34452521 PMCID: PMC8402878 DOI: 10.3390/v13081657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 01/01/2023] Open
Abstract
Equine influenza virus (EIV) is a constantly evolving viral pathogen that is responsible for yearly outbreaks of respiratory disease in horses termed equine influenza (EI). There is currently no evidence of circulation of the original H7N7 strain of EIV worldwide; however, the EIV H3N8 strain, which was first isolated in the early 1960s, remains a major threat to most of the world's horse populations. It can also infect dogs. The ability of EIV to constantly accumulate mutations in its antibody-binding sites enables it to evade host protective immunity, making it a successful viral pathogen. Clinical and virological protection against EIV is achieved by stimulation of strong cellular and humoral immunity in vaccinated horses. However, despite EI vaccine updates over the years, EIV remains relevant, because the protective effects of vaccines decay and permit subclinical infections that facilitate transmission into susceptible populations. In this review, we describe how the evolution of EIV drives repeated EI outbreaks even in horse populations with supposedly high vaccination coverage. Next, we discuss the approaches employed to develop efficacious EI vaccines for commercial use and the existing system for recommendations on updating vaccines based on available clinical and virological data to improve protective immunity in vaccinated horse populations. Understanding how EIV biology can be better harnessed to improve EI vaccines is central to controlling EI.
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20
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Lee K, Pusterla N, Barnum SM, Lee DH, Martínez-López B. Genome-informed characterisation of antigenic drift in the haemagglutinin gene of equine influenza strains circulating in the United States from 2012 to 2017. Transbound Emerg Dis 2021; 69:e52-e63. [PMID: 34331828 DOI: 10.1111/tbed.14262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/14/2021] [Accepted: 07/24/2021] [Indexed: 01/14/2023]
Abstract
Equine influenza virus (EIV) is a major infectious pathogen causing significant respiratory signs in equids worldwide. Voluntary surveillances in the United States recently reported EIV detection in horses with respiratory signs even with adequate vaccine protocols and biosecurity programs and posed a concern about suboptimal effectiveness of EIV vaccine in the United States. This study aims to determine the genetic characteristics of 58 field EIV H3N8 strains in the United States from 2012 to 2017 using the phylogenetic analysis based on the haemagglutinin (HA) gene. Amino acid substitution and acquisition of N-glycosylation of the HA gene were also evaluated. Phylogenetic analysis identified that almost all US field strains belonged to the Florida clade 1 (FC1) except one Florida clade 2 strain from a horse imported in 2014. US EIV strains in 2017 shared 11 fixed amino acid substitutions in the HA gene, compared to the vaccine strain (A/equine/Ohio/2003), and two additional amino acid substitutions were detected in 2019. The introduction of foreign EIV strains into the United States was not detected, but antigenic drift without acquisition of N-glycosylation in the HA gene was observed in US field strains until 2017. Considering the global dominance of FC1 strains, subsequent antigenic drift of US EIV strains should be monitored for better effectiveness of the EIV vaccine in the United States and global equine industries.
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Affiliation(s)
- Kyuyoung Lee
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Samantha M Barnum
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, USA
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, the University of Connecticut, Storrs, Connecticut, USA
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, USA
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21
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Abstract
Influenza is an extremely contagious respiratory disease, which predominantly affects the upper respiratory tract. There are four types of influenza virus, and pigs and chickens are considered two key reservoirs of this virus. Equine influenza (EI) virus was first identified in horses in 1956, in Prague. The influenza A viruses responsible for EI are H7N7 and H3N8. Outbreaks of EI are characterized by their visible and rapid spread, and it has been possible to isolate and characterize H3N8 outbreaks in several countries. The clinical diagnosis of this disease is based on the clinical signs presented by the infected animals, which can be confirmed by performing complementary diagnostic tests. In the diagnosis of EI, in the field, rapid antigen detection tests can be used for a first approach. Treatment is based on the management of the disease and rest for the animal. Regarding the prognosis, it will depend on several factors, such as the animal's vaccination status. One of the important points in this disease is its prevention, which can be done through vaccination. In addition to decreasing the severity of clinical signs and morbidity during outbreaks, vaccination ensures immunity for the animals, reducing the economic impact of this disease.
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22
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Shen HX, Li X, Yang DQ, Ju HB, Ge FF, Wang J, Zhao HJ. Phylogenetic analysis and evolutionary dynamics of H3N2 canine and feline influenza virus strains from 2006 to 2019. J Med Virol 2021; 93:3496-3507. [PMID: 33386745 DOI: 10.1002/jmv.26767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 02/01/2023]
Abstract
H3N2 feline influenza virus (FIV) and canine influenza virus (CIV) are very common in cats and dogs. Due to the ability of the influenza virus to spread across hosts and frequent contact between pets and people, there exist huge public health problems. In this study, we collected H3N2 CIV and FIV genomes from 2006 to 2019 from NCBI and analyzed the evolutionary dynamics and molecular variation using a series of phylogenetic analysis methods. Results indicated that H3N2 FIVs were closely related to CIVs with high posterior probability and CIVs and FIVs have certain regional characteristics. However, compared with previous studies, the significance of geographical structure correlation decreased. Furthermore, we also found that the intrasubtypic reassortment between FIVs and CIVs were common during epidemics. The integrated analysis was also performed for different selection pressure acting on HA (566 codons), NA (469 codons), M1 (252 codons), and M2 (97 codons) proteins. One HA, two NA, three M1, and two M2 sites were found under positive selection. We subsequently performed the evolutionary dynamics of H3N2 CIV. The results indicated that the time of the most recent common ancestor of CIV H3N2 may have occurred earlier than indicated in a previous study. The Bayesian skyline plot analysis in this study showed the period of divergence of major H3N2 CIVs segments occurred between 2008 and 2010. Notably, according to our research, the PB1 has experienced two divergence periods (2006-2008 and 2009-2011).
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Affiliation(s)
- Hai-Xiao Shen
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Xin Li
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - De-Quan Yang
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Hou-Bin Ju
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Fei-Fei Ge
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Jian Wang
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
| | - Hong-Jin Zhao
- Shanghai Animal Disease Control Center, Shanghai, People's Republic of China
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23
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Zhou P, Xiao X, Hu X, Dong J, Zhang H, Li Y, Li S. Beagle Dogs Have Low Susceptibility to Florida Clade 2 H3N8 Equine Avian Influenza. Virol Sin 2021; 36:1248-1251. [PMID: 33860386 DOI: 10.1007/s12250-021-00366-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/25/2021] [Indexed: 11/27/2022] Open
Affiliation(s)
- Pei Zhou
- Guangdong Provincial Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Technological Engineering Research Center for Pets, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Xiangyu Xiao
- Guangdong Provincial Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Xinkai Hu
- Guangdong Provincial Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Dong
- Guangdong Provincial Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Haoyao Zhang
- Guangdong Provincial Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yanchao Li
- Guangdong Provincial Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Shoujun Li
- Guangdong Provincial Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Technological Engineering Research Center for Pets, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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24
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Bravo-Vasquez N, Yao J, Jimenez-Bluhm P, Meliopoulos V, Freiden P, Sharp B, Estrada L, Davis A, Cherry S, Livingston B, Danner A, Schultz-Cherry S, Hamilton-West C. Equine-Like H3 Avian Influenza Viruses in Wild Birds, Chile. Emerg Infect Dis 2020; 26:2887-2898. [PMID: 33219648 PMCID: PMC7706983 DOI: 10.3201/eid2612.202063] [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] [Indexed: 12/22/2022] Open
Abstract
Since their discovery in the United States in 1963, outbreaks of infection with equine influenza virus (H3N8) have been associated with serious respiratory disease in horses worldwide. Genomic analysis suggests that equine H3 viruses are of an avian lineage, likely originating in wild birds. Equine-like internal genes have been identified in avian influenza viruses isolated from wild birds in the Southern Cone of South America. However, an equine-like H3 hemagglutinin has not been identified. We isolated 6 distinct H3 viruses from wild birds in Chile that have hemagglutinin, nucleoprotein, nonstructural protein 1, and polymerase acidic genes with high nucleotide homology to the 1963 H3N8 equine influenza virus lineage. Despite the nucleotide similarity, viruses from Chile were antigenically more closely related to avian viruses and transmitted effectively in chickens, suggesting adaptation to the avian host. These studies provide the initial demonstration that equine-like H3 hemagglutinin continues to circulate in a wild bird reservoir.
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25
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Gao F, Kawakubo S, Ho SYW, Ohshima K. The evolutionary history and global spatio-temporal dynamics of potato virus Y. Virus Evol 2020; 6:veaa056. [PMID: 33324488 PMCID: PMC7724251 DOI: 10.1093/ve/veaa056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the phylodynamics of the virus by analysing 253 nucleotide sequences of the genes encoding the third protein (P3), cylindrical inclusion protein (CI), and the nuclear inclusion protein (NIb). Our Bayesian phylogenetic analyses showed that the mean substitution rates of different regions of the genome ranged from 8.50 × 10-5 to 1.34 × 10-4 substitutions/site/year, whereas the time to the most recent common ancestor of PVY varied with the length of the genomic regions and with the number of viral isolates being analysed. Our phylogeographic analysis showed that the PVY population originated in South America and was introduced into Europe in the 19th century, from where it spread around the globe. The migration pathways of PVY correlate well with the trade routes of potato tubers, suggesting that the global spread of PVY is associated with human activities.
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Affiliation(s)
- Fangluan Gao
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shusuke Kawakubo
- Laboratory of Plant Virology, Department of Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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26
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Abstract
Equine influenza virus (EIV) is a common respiratory pathogen of horses and other equids in most parts of the world. EIV are Type A influenza viruses and two subtypes are known: H3N8 and H7N7. Both are believed to have evolved from avian influenza virus ancestors. The H3N8 subtype circulates widely, but the H7N7 subtype is thought to be extinct. The clinical disease in horses, caused by either subtype, is an upper respiratory infection of varying severity depending upon the immune status of the individual animal. It is not normally life-threatening in itself except in very young foals; however it predisposes infected equids to secondary infections capable of producing life-threatening pneumonias. Vaccines are available and widely used in some horse populations, but their effectiveness is limited by antigenic drift and other factors, and vaccinated animals with subclinical infections have been responsible for introduction of EIV into susceptible populations. EIV has spread into canines.
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27
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Blanco-Lobo P, Rodriguez L, Reedy S, Oladunni FS, Nogales A, Murcia PR, Chambers TM, Martinez-Sobrido L. A Bivalent Live-Attenuated Vaccine for the Prevention of Equine Influenza Virus. Viruses 2019; 11:v11100933. [PMID: 31614538 PMCID: PMC6832603 DOI: 10.3390/v11100933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
Vaccination remains the most effective approach for preventing and controlling equine influenza virus (EIV) in horses. However, the ongoing evolution of EIV has increased the genetic and antigenic differences between currently available vaccines and circulating strains, resulting in suboptimal vaccine efficacy. As recommended by the World Organization for Animal Health (OIE), the inclusion of representative strains from clade 1 and clade 2 Florida sublineages of EIV in vaccines may maximize the protection against presently circulating viral strains. In this study, we used reverse genetics technologies to generate a bivalent EIV live-attenuated influenza vaccine (LAIV). We combined our previously described clade 1 EIV LAIV A/equine/Ohio/2003 H3N8 (Ohio/03 LAIV) with a newly generated clade 2 EIV LAIV that contains the six internal genes of Ohio/03 LAIV and the HA and NA of A/equine/Richmond/1/2007 H3N8 (Rich/07 LAIV). The safety profile, immunogenicity, and protection efficacy of this bivalent EIV LAIV was tested in the natural host, horses. Vaccination of horses with the bivalent EIV LAIV, following a prime-boost regimen, was safe and able to confer protection against challenge with clade 1 (A/equine/Kentucky/2014 H3N8) and clade 2 (A/equine/Richmond/2007) wild-type (WT) EIVs, as evidenced by a reduction of clinical signs, fever, and virus excretion. This is the first description of a bivalent LAIV for the prevention of EIV in horses that follows OIE recommendations. In addition, since our bivalent EIV LAIV is based on the use of reverse genetics approaches, our results demonstrate the feasibility of using the backbone of clade 1 Ohio/03 LAIV as a master donor virus (MDV) for the production and rapid update of LAIVs for the control and protection against other EIV strains of epidemiological relevance to horses.
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Affiliation(s)
- Pilar Blanco-Lobo
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
| | - Laura Rodriguez
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
- Agencia Española de Medicamentos y Productos Sanitarios, E28022 Madrid, Spain.
| | - Stephanie Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Fatai S Oladunni
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
- Center for Animal Health Research- National Institute for Agricultural and Food Research and Technology, Valdeolmos, 28130 Madrid, Spain.
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1AF, UK.
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
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28
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Equine Influenza Virus in Asia: Phylogeographic Pattern and Molecular Features Reveal Circulation of an Autochthonous Lineage. J Virol 2019; 93:JVI.00116-19. [PMID: 31019053 DOI: 10.1128/jvi.00116-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022] Open
Abstract
Equine influenza virus (EIV) causes severe acute respiratory disease in horses. Currently, the strains belonging to the H3N8 subtype are divided into two clades, Florida clade 1 (FC1) and Florida clade 2 (FC2), which emerged in 2002. Both FC1 and FC2 clades were reported in Asian and Middle East countries in the last decade. In this study, we described the evolution, epidemiology, and molecular characteristic of the EIV lineages, with focus on those detected in Asia from 2007 to 2017. The full genome phylogeny showed that FC1 and FC2 constituted separate and divergent lineages, without evidence of reassortment between the clades. While FC1 evolved as a single lineage, FC2 showed a divergent event around 2004 giving rise to two well-supported and coexisting sublineages, European and Asian. Furthermore, two different spread patterns of EIV in Asian countries were identified. The FC1 outbreaks were caused by independent introductions of EIV from the Americas, with the Asian isolates genetically similar to the contemporary American lineages. On the other hand, the FC2 strains detected in Asian mainland countries conformed to an autochthonous monophyletic group with a common ancestor dated in 2006 and showed evidence of an endemic circulation in a local host. Characteristic aminoacidic signature patterns were detected in all viral proteins in both Asian-FC1 and FC2 populations. Several changes were located at the top of the HA1 protein, inside or near antigenic sites. Further studies are needed to assess the potential impact of these antigenic changes in vaccination programs.IMPORTANCE The complex and continuous antigenic evolution of equine influenza viruses (EIVs) remains a major hurdle for vaccine development and the design of effective immunization programs. The present study provides a comprehensive analysis showing the EIV evolutionary dynamics, including the spread and circulation within the Asian continent and its relationship to global EIV populations over a 10-year period. Moreover, we provide a better understanding of EIV molecular evolution in Asian countries and its consequences on the antigenicity. The study underscores the association between the global horse movement and the circulation of EIV in this region. Understanding EIV evolution is imperative in order to mitigate the risk of outbreaks affecting the horse industry and to help with the selection of the viral strains to be included in the formulation of future vaccines.
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29
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Toh X, Soh ML, Ng MK, Yap SC, Harith N, Fernandez CJ, Huangfu T. Isolation and characterization of equine influenza virus (H3N8) from an equine influenza outbreak in Malaysia in 2015. Transbound Emerg Dis 2019; 66:1884-1893. [PMID: 31059176 PMCID: PMC6852086 DOI: 10.1111/tbed.13218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/20/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022]
Abstract
Equine influenza is a major cause of respiratory infections in horses and can spread rapidly despite the availability of commercial vaccines. In this study, we carried out molecular characterization of Equine Influenza Virus (EIV) isolated from the Malaysian outbreak in 2015 by sequencing of the HA and NA gene segments using Sanger sequencing. The nucleotide and amino acid sequences of HA and NA were compared with representative Florida clade 1 and clade 2 strains using phylogenetic analysis. The Florida clade 1 viruses identified in this outbreak revealed numerous amino acid substitutions in the HA protein as compared to the current OIE vaccine strain recommendations and representative strains of circulating Florida sub-lineage clade 1 and clade 2. Differences in HA included amino acids located within antigenic sites which could lead to reduced immune recognition of the outbreak strain and alter the effectiveness of vaccination against the outbreak strain. Detailed surveillance and genetic information sharing could allow genetic drift of equine influenza viruses to be monitored more effectively on a global basis and aid in refinement of vaccine strain selection for EIV.
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Affiliation(s)
- Xinyu Toh
- Centre for Animal and Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board, Singapore City, Singapore
| | - Moi Lien Soh
- Centre for Animal and Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board, Singapore City, Singapore
| | - Mee Keun Ng
- Centre for Animal and Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board, Singapore City, Singapore
| | - Shew Choo Yap
- Centre for Animal and Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board, Singapore City, Singapore
| | - Nurshilla Harith
- Centre for Animal and Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board, Singapore City, Singapore
| | - Charlene Judith Fernandez
- Centre for Animal and Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board, Singapore City, Singapore
| | - Taoqi Huangfu
- Centre for Animal and Veterinary Sciences, Professional and Scientific Services, Animal and Veterinary Service, National Parks Board, Singapore City, Singapore
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30
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Gahan J, Garvey M, Asmah Abd Samad R, Cullinane A. Whole Genome Sequencing of the First H3N8 Equine Influenza Virus Identified in Malaysia. Pathogens 2019; 8:E62. [PMID: 31083430 PMCID: PMC6630255 DOI: 10.3390/pathogens8020062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/23/2023] Open
Abstract
In August 2015, Malaysia experienced an outbreak of acute respiratory disease in racehorses. Clinical signs observed were consistent with equine influenza (EI) infection. The index cases were horses recently imported from New Zealand. Rapid control measures, including temporary cancellation of racing, were implemented to minimize the impact of the outbreak. By November, the disease outbreak was resolved, and movement restrictions were lifted. The aim of this study was to confirm the clinical diagnosis and characterize the causal virus. A pan-reactive influenza type A real-time RT-PCR was used for confirmatory diagnosis. Antigenic characterization by haemagglutinin inhibition using a panel of specific ferret antisera indicated that the causal virus belonged to clade 1 of the H3N8 Florida sub-lineage. The genetic characterization was achieved by the whole genome sequencing of positive nasal swabs from clinically affected animals. Pylogenetic analysis of the haemagglutinin (HA) and neuraminidase (NA) genes demonstrated ≥99% homology with several EI strains that had recently circulated in the USA and Japan. The antigenic and genetic characterization did not indicate that the current World Organisation for Animal Health (OIE) recommendations for EI vaccine composition required modification.
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Affiliation(s)
- Jacinta Gahan
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
| | - Marie Garvey
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
| | - Rozanah Asmah Abd Samad
- Department of Veterinary Services, Federal Government Administration Centre, 62630 Putrajaya, Malaysia.
| | - Ann Cullinane
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
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31
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Genetic Analysis of the M Gene of Equine Influenza Virus Strains Isolated in Poland, in the Context of the Asian-like Group Formation. J Vet Res 2019; 62:405-412. [PMID: 30729195 PMCID: PMC6364155 DOI: 10.2478/jvetres-2018-0057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/15/2018] [Indexed: 11/20/2022] Open
Abstract
Introduction Traditionally, evolutionary analysis of equine influenza virus (EIV) is based on the HA gene. However, the specificity of the influenza virus enables the classification of viral strains into different phylogenetic groups, depending on the gene being analysed. The aim of the study was to analyse phylogenetic paths of EIV based on M gene with reference to the HA gene. Material and Methods M gene of Polish isolates has been sequenced and analysed along with all M sequences of EIV available in GenBank database. Phylogenetic analysis was performed using BioEdit, ClustalW, and MEGA7 softwares. Results The clustering of the strains isolated not only from Asia but also from Europe into one common Asian-like group of EIV was observed. Twelve nucleotide substitutions in the M gene of strains from the Asian-like group were crucial for the evolutionary analysis. We also observed homology in the M gene of the Asian-like and H7N7 strains. Conclusions M gene specific for the Asian-like group is present in strains recently isolated in Europe and Asia, which were classified previously in the Florida 2 clade based on HA. Therefore, Asian-like group does not seem to be assigned to a specific geographical region. Traces of H7N7 strains in more conservative genes like M of some contemporary EIV strains may indicate the link between the old phylogenetic group and recent H3N8 strains. Analysis of conservative genes may be more useful in tracking the direction of virus evolution than in the genes where the high variability rate may blur the original relationships.
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32
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He W, Li G, Zhu H, Shi W, Wang R, Zhang C, Bi Y, Lai A, Gao GF, Su S. Emergence and adaptation of H3N2 canine influenza virus from avian influenza virus: An overlooked role of dogs in interspecies transmission. Transbound Emerg Dis 2019; 66:842-851. [PMID: 30520554 DOI: 10.1111/tbed.13093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022]
Abstract
H3N2 canine influenza virus (CIV) originated from avian species and emerged in dogs in Asia around 2005 where it became enzootic before reaching the USA in 2015. To investigate the key aspects of the evolution of H3N2 CIV regarding its emergence and adaptation in the canine host, we conducted an extensive analysis of all publicly available H3N2 CIV sequences spanning a 10-year period. We believe that H3N2 AIVs transferred to canines around 2002-2004. Furthermore, H3N2 CIVs could be divided into seven major clades with strong geographic clustering and some changed sites evidence of adaptive evolution. Most notably, the dN/dS of each H3N2 CIVs segment was higher than the correspondent of H3N2 AIVs and the U content of HA and NA was increasing over time, suggesting the idea that this avian-origin virus may be gradually adapting to the host. Our results provide a framework to elucidate a general mechanism for emergence of novel influenza viruses.
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Affiliation(s)
- Wanting He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Gairu Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Weifeng Shi
- Institute of Pathogen Biology, Taishan Medical College, Taian, China
| | - Ruyi Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Cheng Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuhai Bi
- Chinese Center for Disease Control and Prevention (China CDC), National Institute for Viral Disease Control and Prevention, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Alexander Lai
- College of Natural, Applied, and Health Sciences, Kentucky State University, Frankfort, Kentucky, USA
| | - George F Gao
- Chinese Center for Disease Control and Prevention (China CDC), National Institute for Viral Disease Control and Prevention, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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33
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RETRACTED: An epidemiological investigation of associated risk factors with equine influenza (H3N8) epidemic 2015-16 in Pakistan. Acta Trop 2018; 186:63-68. [PMID: 30003906 DOI: 10.1016/j.actatropica.2018.07.006] [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: 05/19/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 11/24/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the request of the Editors-in-Chief.
The article duplicates significant parts of a paper that had already appeared in Preventative Veterinary Medicine, 149, 132-139; https://doi.org/10.1016/j.prevetmed.2017.12.005.
One of the conditions of submission of a paper for publication is that authors declare explicitly that the paper has not been previously published and is not under consideration for publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a misuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.
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34
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Hemida MG, Perera RAPM, Chu DKW, Alnaeem AA, Peiris M. Evidence of equine influenza A (H3N8) activity in horses from Eastern and Central Saudi Arabia: 2013-2015. Equine Vet J 2018; 51:218-221. [PMID: 30074632 DOI: 10.1111/evj.13001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/29/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Equine influenza virus (EIV) is one of the main causes of viral respiratory affections in horses. Little is known about the prevalence of EIV in Saudi Arabia especially the H3N8 serotype. OBJECTIVES To assess prevalence of equine influenza in horse populations in Eastern and Central Saudi Arabia. STUDY DESIGN Cross-sectional study. METHODS We collected 145 sera, 323 nasal and 323 rectal swabs from horses from six major cities in Eastern and Central regions. None of the horses were vaccinated against EIV. Sera were tested in ELISA assays for influenza A type-specific antibodies and by haemagglutination inhibition (HI) tests using equine H3N8. The swabs were tested by RT-qPCR assay targeting a conserved region of the influenza A matrix gene that detects influenza A viruses of all subtypes. RESULTS None of the swabs had detectable influenza A virus RNA. Of the 145 serasamples tested by ELISA, 81 (55.9%) were positive and 98 (67.6%) of 145 sera tested by HI tests were positive for equine H3. MAIN LIMITATIONS Our failure to detect and sequence any EIV prevents identification of the lineage of virus that circulates in the Kingdom of Saudi Arabia. CONCLUSIONS These results confirm that EIV H3N8 is circulating in Saudi Arabia and should be considered as a possible cause when investigating horses with respiratory disease in Saudi Arabia.
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Affiliation(s)
- M G Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Alhufuf, Saudi Arabia.,Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr el-Sheikh, Egypt
| | - R A P M Perera
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - D K W Chu
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - A A Alnaeem
- Department of Clinical Studies, College of Veterinary Medicine, King Faisal University, Alhufuf, Saudi Arabia
| | - M Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
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Gahan J, Garvey M, Gildea S, Gür E, Kagankaya A, Cullinane A. Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. Influenza Other Respir Viruses 2018; 12:374-382. [PMID: 28940727 PMCID: PMC5907808 DOI: 10.1111/irv.12485] [Citation(s) in RCA: 8] [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] [Accepted: 07/26/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In 2013, there was an outbreak of acute respiratory disease in racehorses in Turkey. The clinical signs were consistent with equine influenza (EI). OBJECTIVE The aim was to confirm the cause of the outbreak and characterise the causal virus. METHODS A pan-reactive influenza type A real-time RT-PCR and a rapid antigen detection kit were used for confirmatory diagnosis of equine influenza virus (EIV). Immunological susceptibility to EIV was examined using single radial haemolysis and ELISA. Antigenic characterisation was completed by haemagglutinin inhibition using a panel of specific ferret antisera. Genetic characterisation was achieved by whole-genome sequencing using segment-specific primers with M13 tags. RESULTS A H3N8 EIV of the Florida clade 2 sublineage (FC2) was confirmed as the causal agent. The index cases were unvaccinated and immunologically susceptible. Phylogenetic analysis of the HA1 and NA genes demonstrated that A/equine/Ankara/1/2013 clustered with the FC2 strains circulating in Europe. Antigenic characterisation confirmed the FC2 classification and demonstrated the absence of significant drift. Whole-genome sequencing indicated that A/equine/Ankara/1/2013 is most closely related to the viruses described as the 179 group based on the substitution I179V in HA1, for example A/equine/East Renfrewshire/2/2011, A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015. The greatest diversity was observed in the NS1 segment and the polymerase complex. CONCLUSIONS The first recorded outbreak of EI in Turkey was caused by an FC2 virus closely related to viruses circulating in Europe. Antigenic and genetic characterisation gave no indication that the current OIE recommendations for EI vaccine composition require modification.
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Affiliation(s)
| | | | | | - Emre Gür
- Head of Equine Health and Veterinary Services DepartmentJockey Club of TurkeyIstanbulTurkey
| | - Anil Kagankaya
- Department of SurgeryAnkara University Faculty of Veterinary MedicineAnkaraTurkey
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Rodriguez L, Reedy S, Nogales A, Murcia PR, Chambers TM, Martinez-Sobrido L. Development of a novel equine influenza virus live-attenuated vaccine. Virology 2018; 516:76-85. [PMID: 29331866 PMCID: PMC5840510 DOI: 10.1016/j.virol.2018.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 11/16/2022]
Abstract
H3N8 equine influenza virus (EIV) is an important and significant respiratory pathogen of horses. EIV is enzootic in Europe and North America, mainly due to the suboptimal efficacy of current vaccines. We describe, for the first time, the generation of a temperature sensitive (ts) H3N8 EIV live-attenuated influenza vaccine (LAIV) using reverse-genetics approaches. Our EIV LAIV was attenuated (att) in vivo and able to induce, upon a single intranasal administration, protection against H3N8 EIV wild-type (WT) challenge in both a mouse model and the natural host, the horse. Notably, since our EIV LAIV was generated using reverse genetics, the vaccine can be easily updated against drifting or emerging strains of EIV using the safety backbone of our EIV LAIV as master donor virus (MDV). These results demonstrate the feasibility of implementing a novel EIV LAIV approach for the prevention and control of currently circulating H3N8 EIVs in horse populations.
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Affiliation(s)
- Laura Rodriguez
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, United States
| | - Stephanie Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, United States
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, United States.
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Mammalian Adaptation of an Avian Influenza A Virus Involves Stepwise Changes in NS1. J Virol 2018; 92:JVI.01875-17. [PMID: 29237841 PMCID: PMC5809720 DOI: 10.1128/jvi.01875-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
Influenza A viruses (IAVs) are common pathogens of birds that occasionally establish endemic infections in mammals. The processes and mechanisms that result in IAV mammalian adaptation are poorly understood. The viral nonstructural 1 (NS1) protein counteracts the interferon (IFN) response, a central component of the host species barrier. We characterized the NS1 proteins of equine influenza virus (EIV), a mammalian IAV lineage of avian origin. We showed that evolutionarily distinct NS1 proteins counteract the IFN response using different and mutually exclusive mechanisms: while the NS1 proteins of early EIVs block general gene expression by binding to cellular polyadenylation-specific factor 30 (CPSF30), NS1 proteins from more evolved EIVs specifically block the induction of IFN-stimulated genes by interfering with the JAK/STAT pathway. These contrasting anti-IFN strategies are associated with two mutations that appeared sequentially and were rapidly selected for during EIV evolution, highlighting the importance of evolutionary processes in immune evasion mechanisms during IAV adaptation. IMPORTANCE Influenza A viruses (IAVs) infect certain avian reservoir species and occasionally transfer to and cause epidemics of infections in some mammalian hosts. However, the processes by which IAVs gain the ability to efficiently infect and transmit in mammals remain unclear. H3N8 equine influenza virus (EIV) is an avian-origin virus that successfully established a new lineage in horses in the early 1960s and is currently circulating worldwide in the equine population. Here, we analyzed the molecular evolution of the virulence factor nonstructural protein 1 (NS1) and show that NS1 proteins from different time periods after EIV emergence counteract the host innate immune response using contrasting strategies, which are associated with two mutations that appeared sequentially during EIV evolution. The results shown here indicate that the interplay between virus evolution and immune evasion plays a key role in IAV mammalian adaptation.
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Jurado-Tarifa E, Daly JM, Pérez-Écija A, Barba-Recreo M, Mendoza FJ, Al-Shuwaikh AM, García-Bocanegra I. Epidemiological survey of equine influenza in Andalusia, Spain. Prev Vet Med 2018; 151:52-56. [PMID: 29496107 DOI: 10.1016/j.prevetmed.2018.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 11/18/2022]
Abstract
Equine influenza is a highly contagious respiratory disease considered the most important respiratory disease in equids. Although influenza A virus (IAV) has caused outbreaks in equids worldwide, surveillance in these species in Spain has not been conducted. A cross-sectional study was carried out to determine the individual and herd prevalence of antibodies against H3N8 and H7N7 IAV in equids in Andalusia (southern Spain). Antibodies againsts IAV were measured by the single radial haemolysis assay. A spatial scan statistical analysis was carried out using a Bernoulli model. Risk factors associated with IAV infection were assessed by multivariate analysis. Antibodies to H3N8 IAV were detected in 241 out of 464 unvaccinated equids (51.9%; 95% CI: 47.4-56.5). Seropositivity against the H7N7 subtype IAV was not found in any of the analysed animals. Significantly higher seropositivity was found in geriatric (OR = 6.1, P = 0.008, 95% CI = 1.6-23.1) and adult (OR = 4.8, P < 0.001, 95% CI = 2.5-9.0) equids compared to young animals. Specific antibodies against A/equine/Shropshire/2010 (H3N8) or A/equine/Newmarket/5/2003 (H3N8) only were confirmed in 11 and 45 of the animals, respectively. The spatial analysis showed a statistically significant cluster centred in the west part of Andalusia. The results confirmed widespread H3N8 subtype IAV exposure in equine species in Andalusia. Conversely, the absence of seropositivity against H7N7 IAV obtained in the present study suggests that this subtype has not circulated in southern Spain in recent years. Because of the animal health and economic consequences of IAV in equids, further surveillance and molecular studies are required to monitor and characterize the most prevalent IAV circulating in these species in Spain.
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Affiliation(s)
- E Jurado-Tarifa
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Córdoba-Agrifood Excellence International Campus (ceiA3), Córdoba, Spain
| | - J M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - A Pérez-Écija
- Departamento de Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad de Córdoba-Agrifood Excellence International Campus (ceiA3), Córdoba, Spain.
| | - M Barba-Recreo
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK; Departamento de Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - F J Mendoza
- Departamento de Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad de Córdoba-Agrifood Excellence International Campus (ceiA3), Córdoba, Spain
| | - A M Al-Shuwaikh
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK; Microbiology Department, College of Medicine, Al-Nahrain University, Baghdad, Iraq
| | - I García-Bocanegra
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Córdoba-Agrifood Excellence International Campus (ceiA3), Córdoba, Spain
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Sreenivasan CC, Jandhyala SS, Luo S, Hause BM, Thomas M, Knudsen DEB, Leslie-Steen P, Clement T, Reedy SE, Chambers TM, Christopher-Hennings J, Nelson E, Wang D, Kaushik RS, Li F. Phylogenetic Analysis and Characterization of a Sporadic Isolate of Equine Influenza A H3N8 from an Unvaccinated Horse in 2015. Viruses 2018; 10:v10010031. [PMID: 29324680 PMCID: PMC5795444 DOI: 10.3390/v10010031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 01/08/2023] Open
Abstract
Equine influenza, caused by the H3N8 subtype, is a highly contagious respiratory disease affecting equid populations worldwide and has led to serious epidemics and transboundary pandemics. This study describes the phylogenetic characterization and replication kinetics of recently-isolated H3N8 virus from a nasal swab obtained from a sporadic case of natural infection in an unvaccinated horse from Montana, USA. The nasal swab tested positive for equine influenza by Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR). Further, the whole genome sequencing of the virus confirmed that it was the H3N8 subtype and was designated as A/equine/Montana/9564-1/2015 (H3N8). A BLASTn search revealed that the polymerase basic protein 1 (PB1), polymerase acidic (PA), hemagglutinin (HA), nucleoprotein (NP), and matrix (M) segments of this H3N8 isolate shared the highest percentage identity to A/equine/Tennessee/29A/2014 (H3N8) and the polymerase basic protein 2 (PB2), neuraminidase (NA), and non-structural protein (NS) segments to A/equine/Malaysia/M201/2015 (H3N8). Phylogenetic characterization of individual gene segments, using currently available H3N8 viral genomes, of both equine and canine origin, further established that A/equine/Montana/9564-1/2015 belonged to the Florida Clade 1 viruses. Interestingly, replication kinetics of this H3N8 virus, using airway derived primary cells from multiple species, such as equine, swine, bovine, and human lung epithelial cells, demonstrated appreciable titers, when compared to Madin-Darby canine kidney epithelial cells. These findings indicate the broad host spectrum of this virus isolate and suggest the potential for cross-species transmissibility.
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Affiliation(s)
- Chithra C. Sreenivasan
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (C.C.S.); (S.S.J.); (S.L.); (D.W.); (R.S.K.)
| | - Sunayana S. Jandhyala
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (C.C.S.); (S.S.J.); (S.L.); (D.W.); (R.S.K.)
| | - Sisi Luo
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (C.C.S.); (S.S.J.); (S.L.); (D.W.); (R.S.K.)
| | - Ben M. Hause
- Cambridge Technologies, Oxford Street Worthington, MN 56187, USA;
| | - Milton Thomas
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
| | - David E. B. Knudsen
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
| | - Pamela Leslie-Steen
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
| | - Travis Clement
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
| | - Stephanie E. Reedy
- Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (S.E.R.); (T.M.C.)
| | - Thomas M. Chambers
- Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (S.E.R.); (T.M.C.)
| | - Jane Christopher-Hennings
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
| | - Eric Nelson
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
| | - Dan Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (C.C.S.); (S.S.J.); (S.L.); (D.W.); (R.S.K.)
- BioSNTR, Brookings, SD 57007, USA
| | - Radhey S. Kaushik
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (C.C.S.); (S.S.J.); (S.L.); (D.W.); (R.S.K.)
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
| | - Feng Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (C.C.S.); (S.S.J.); (S.L.); (D.W.); (R.S.K.)
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; (M.T.); (D.E.B.K.); (P.L.-S.); (T.C.); (J.C.-H.); (E.N.)
- BioSNTR, Brookings, SD 57007, USA
- Correspondence:
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Khan A, Mushtaq MH, Ahmad MUD, Nazir J, Fatima Z, Khan A, Farooqi SH. Investigating the epidemiology of EI epidemic spread in the Province of Khyber Pakhtunkhwa, Pakistan in 2015-16. Prev Vet Med 2018; 149:132-139. [PMID: 29290294 DOI: 10.1016/j.prevetmed.2017.12.005] [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: 02/08/2017] [Revised: 11/05/2017] [Accepted: 12/03/2017] [Indexed: 11/18/2022]
Abstract
EI in non-vaccinated population causes disruption and economic losses. To identify the risk factors associated with the EI epidemics in equids in Pakistan, a 1:1 matched case control study was conducted during 2015-2016. Including a total of 197 laboratory confirmed cases and negative controls, matched on the basis of geography, time of sampling, specie and age. A piloted questionnaire was used to collect data regarding risk factors associated with the occurrence of EI in face to face interviews. Conditional logistic regression was performed to analyze the data. A total of 16 out of 23 variables were found associated as risk factors in Univariable conditional logistic regression analysis. Multivariable conditional logistic-regression analysis was also performed. Monthly removal of manure doubles the risk of EI (EI) compared to its daily removal. Due to lack of vaccination; the spread of disease was favored by high equine density. Investigating the index-case it was recorded that infected cases were imported from Afghanistan. Most of these risk factors related to biosecurity and management were due to low awareness level regarding EI amongst the respondents. These findings are in line with the results of many other studies identifying similar risk factors for EI infection in various countries. Adopting protective practices, vaccination and controlling the risk factors identified in the present study could reduce the spread and future outbreaks of EI in Pakistan.
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Affiliation(s)
- Amjad Khan
- Department of Veterinary Sciences, The Maxwell H. Gluck Equine Research Centre, OIE Reference Lab for EI, University of Kentucky, Lexington, 40502, USA/Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Muhammad Hassan Mushtaq
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Mansur Ud Din Ahmad
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Jawad Nazir
- Department of Clinical Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Zahida Fatima
- Pakistan Agricultural Research Council, Islamabad, 33000, Pakistan
| | - Asghar Khan
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Shahid Hussain Farooqi
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
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Yang H, Xiao Y, Meng F, Sun F, Chen M, Cheng Z, Chen Y, Liu S, Chen H. Emergence of H3N8 equine influenza virus in donkeys in China in 2017. Vet Microbiol 2017; 214:1-6. [PMID: 29408020 DOI: 10.1016/j.vetmic.2017.11.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/26/2017] [Accepted: 11/26/2017] [Indexed: 11/26/2022]
Abstract
Equine influenza virus is a major respiratory pathogen in horses. Although both horses and donkeys belong to the genus Equus, donkey infection with influenza viruses is rare. In March 2017, an influenza outbreak occurred in donkeys in Shandong province, China. The causative virus, A/donkey/Shandong/1/2017(H3N8), was isolated from a dead donkey. Genetic analysis indicated that the virus originated from influenza A (H3N8) clade 2 of the Florida sub-lineage that has been circulating in Asian equine populations. Comparison of the deduced amino acid sequence of the HA gene of this causative virus with that of the A/equine/Richmond/1/2007 vaccine strain showed that substitutions had occurred in the antigenic regions A, B, and C. This study provides insight into the currently circulating and newly emerging H3N8 strains in donkeys in China.
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Affiliation(s)
- Huanliang Yang
- State Key Laboratory of Veterinary Biotechnology-Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yihong Xiao
- Department of Fundamental Veterinary Medicine, College of Animal Science and Veterinary Medicine-Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Shandong, China
| | - Fei Meng
- State Key Laboratory of Veterinary Biotechnology-Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Fachao Sun
- Department of Fundamental Veterinary Medicine, College of Animal Science and Veterinary Medicine-Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Shandong, China
| | - Meng Chen
- Department of Fundamental Veterinary Medicine, College of Animal Science and Veterinary Medicine-Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Shandong, China
| | - Zilong Cheng
- Department of Fundamental Veterinary Medicine, College of Animal Science and Veterinary Medicine-Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Shandong, China
| | - Yan Chen
- State Key Laboratory of Veterinary Biotechnology-Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Sidang Liu
- Department of Fundamental Veterinary Medicine, College of Animal Science and Veterinary Medicine-Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Shandong, China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology-Harbin Veterinary Research Institute, CAAS, Harbin, China.
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Harms D, Wang B, Papp CP, Bock CT. Capturing virus evolution by proteomic bioinformatics: Hunting for characteristic mutations in the hepatitis E virus genome. Virulence 2017; 9:13-16. [PMID: 28945510 PMCID: PMC5955182 DOI: 10.1080/21505594.2017.1384526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Dominik Harms
- a Division of Viral Gastroenteritis , Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute , Berlin , Germany
| | - Bo Wang
- a Division of Viral Gastroenteritis , Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute , Berlin , Germany
| | - C Patrick Papp
- a Division of Viral Gastroenteritis , Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute , Berlin , Germany
| | - C-Thomas Bock
- a Division of Viral Gastroenteritis , Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute , Berlin , Germany.,b Institute of Tropical Medicine, University of Tuebingen , Tuebingen , Germany
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Bera BC, Virmani N, Kumar N, Anand T, Pavulraj S, Rash A, Elton D, Rash N, Bhatia S, Sood R, Singh RK, Tripathi BN. Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution. BMC Genomics 2017; 18:652. [PMID: 28830350 PMCID: PMC5568313 DOI: 10.1186/s12864-017-4063-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. RESULTS The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2. CONCLUSIONS Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the codon usage patterns and evolution of polymerase genes of EIVs.
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Affiliation(s)
- Bidhan Ch Bera
- National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India
| | - Nitin Virmani
- National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India.
| | - Naveen Kumar
- National Institute of High Security Animal Diseases, Hathai Kheda Dam Road, Anand Nagar, Bhopal, Madhya Pradesh, India
| | - Taruna Anand
- National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India
| | - S Pavulraj
- National Research Centre on Equines, Sirsa Road, Hisar, Haryana, India
| | - Adam Rash
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK
| | - Debra Elton
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK
| | - Nicola Rash
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK
| | - Sandeep Bhatia
- National Institute of High Security Animal Diseases, Hathai Kheda Dam Road, Anand Nagar, Bhopal, Madhya Pradesh, India
| | - Richa Sood
- National Institute of High Security Animal Diseases, Hathai Kheda Dam Road, Anand Nagar, Bhopal, Madhya Pradesh, India
| | - Raj Kumar Singh
- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
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Fougerolle S, Legrand L, Lecouturier F, Sailleau C, Paillot R, Hans A, Pronost S. Genetic evolution of equine influenza virus strains (H3N8) isolated in France from 1967 to 2015 and the implications of several potential pathogenic factors. Virology 2017; 505:210-217. [DOI: 10.1016/j.virol.2017.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 11/15/2022]
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Joseph U, Su YCF, Vijaykrishna D, Smith GJD. The ecology and adaptive evolution of influenza A interspecies transmission. Influenza Other Respir Viruses 2017; 11:74-84. [PMID: 27426214 PMCID: PMC5155642 DOI: 10.1111/irv.12412] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 12/16/2022] Open
Abstract
Since 2013, there have been several alarming influenza-related events; the spread of highly pathogenic avian influenza H5 viruses into North America, the detection of H10N8 and H5N6 zoonotic infections, the ongoing H7N9 infections in China and the continued zoonosis of H5N1 viruses in parts of Asia and the Middle East. The risk of a new influenza pandemic increases with the repeated interspecies transmission events that facilitate reassortment between animal influenza strains; thus, it is of utmost importance to understand the factors involved that promote or become a barrier to cross-species transmission of Influenza A viruses (IAVs). Here, we provide an overview of the ecology and evolutionary adaptations of IAVs, with a focus on a review of the molecular factors that enable interspecies transmission of the various virus gene segments.
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MESH Headings
- Animals
- Animals, Wild
- Asia/epidemiology
- China/epidemiology
- Disease Reservoirs/virology
- Ducks/virology
- Evolution, Molecular
- Geese/virology
- Humans
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza A Virus, H5N1 Subtype/physiology
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/pathogenicity
- Influenza A Virus, H7N9 Subtype/physiology
- Influenza A virus/genetics
- Influenza A virus/pathogenicity
- Influenza A virus/physiology
- Influenza in Birds/virology
- Influenza, Human/transmission
- Influenza, Human/virology
- Orthomyxoviridae Infections/transmission
- Orthomyxoviridae Infections/virology
- Phylogeny
- Reassortant Viruses/genetics
- Reassortant Viruses/pathogenicity
- Reassortant Viruses/physiology
- Zoonoses
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Affiliation(s)
| | | | | | - Gavin J. D. Smith
- Duke‐NUS Medical SchoolSingapore
- Duke Global Health InstituteDuke UniversityDurhamNCUSA
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Olguin Perglione C, Golemba MD, Torres C, Barrandeguy M. Molecular Epidemiology and Spatio-Temporal Dynamics of the H3N8 Equine Influenza Virus in South America. Pathogens 2016; 5:E61. [PMID: 27754468 PMCID: PMC5198161 DOI: 10.3390/pathogens5040061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 01/24/2023] Open
Abstract
Equine influenza virus (EIV) is considered the most important respiratory pathogen of horses as outbreaks of the disease lead to substantial economic losses. The H3N8 EIV has caused respiratory disease in horses across the world, including South American countries. Nucleotide and deduced amino acid sequences for the complete haemagglutinin gene of the H3N8 EIV detected in South America since 1963 were analyzed. Phylogenetic and Bayesian coalescent analyses were carried out to study the origin, the time of the most recent common ancestors (tMRCA), the demographic and the phylogeographic patterns of the H3N8 EIV. The phylogenetic analysis demonstrated that the H3N8 EIV detected in South America grouped in 5 well-supported monophyletic clades, each associated with strains of different origins. The tMRCA estimated for each group suggested that the virus was circulating in North America at least one year before its effective circulation in the South American population. Phylogenetic and coalescent analyses revealed a polyphyletic behavior of the viruses causing the outbreaks in South America between 1963 and 2012, possibly due to the introduction of at least 4 different EIVs through the international movement of horses. In addition, phylodynamic analysis suggested South America as the starting point of the spread of the H3N8 EIV in 1963 and showed migration links from the United States to South America in the subsequent EIV irruptions. Further, an increase in the relative genetic diversity was observed between 2006 and 2007 and a subsequent decline since 2009, probably due to the co-circulation of different lineages and as a result of the incorporation of the Florida clade 2 strain in vaccines, respectively. The observed data highlight the importance of epidemiological surveillance and the implementation of appropriate quarantine procedures to prevent outbreaks of the disease.
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Affiliation(s)
- Cecilia Olguin Perglione
- Instituto de Virología CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Dr. Nicolás Repetto y De Los Reseros s/n Hurlingham B1686LQF, Buenos Aires, Argentina.
| | - Marcelo D Golemba
- Hospital de Pediatría S.A.M.I.C. "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, Ciudad Autónoma de Buenos Aires C1245AAM, Argentina.
| | - Carolina Torres
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina.
- CONICET, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina.
| | - Maria Barrandeguy
- Instituto de Virología CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Dr. Nicolás Repetto y De Los Reseros s/n Hurlingham B1686LQF, Buenos Aires, Argentina.
- Escuela de Veterinaria, Universidad del Salvador, Viamonte 1856, Ciudad Autónoma de Buenos Aires C1056ABB, Argentina.
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47
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Franzo G, Tucciarone CM, Blanco A, Nofrarías M, Biarnés M, Cortey M, Majó N, Catelli E, Cecchinato M. Effect of different vaccination strategies on IBV QX population dynamics and clinical outbreaks. Vaccine 2016; 34:5670-5676. [PMID: 27670071 PMCID: PMC7173296 DOI: 10.1016/j.vaccine.2016.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/05/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022]
Abstract
Two large scale molecular epidemiology studies performed in Italy and Spain. The population dynamics trends differed between the two countries. Relevant association between changes in vaccination strategies and viral population. Strong association between viral population dynamics and outbreak frequency. Hill’s criteria for causation were accomplished.
The extreme variability and rapid evolution of Infectious bronchitis virus (IBV) has always represented the key challenge for its control because of the limited cross-protection among different strains. Several experimental trials have proven a broadening of the protection spectrum when animals are vaccinated with multiple genotypes. Nevertheless, the conditions of vaccine administration in field are so different that the generalization of experimental results is, at least, questionable. In the present study a large scale epidemiological-phylodynamic approach was used to reconstruct the demographic history of the major field genotype (i.e. the QX one) circulating in Italy and Spain. These two countries were selected because, even if they share a comparable epidemiological scenario, the implemented vaccination protocols did not vary in Spain while changed dramatically in Italy over the time period considered. One hundred and ninety-five Italian and 98 Spanish non-recombinant sequences of the hyper-variable region of the S1 gene obtained between 2012 and 2016 were analyzed using a serial coalescent-based approach to reconstruct viral population history over time. While the IBV QX population dynamics remained constant in Spain, a much more complex pattern was evidenced in Italy; both in terms of viral population size and clinical outbreak frequency. Remarkably, a strong association with changes in vaccination strategies was recognized. This allowed demonstrating, by accomplishing all Hill’s criteria for causation, the cause-effect relationship between the vaccine administration/withdrawal and the variation in viral population dynamics and, above all, IBV related outbreaks. Thus, a robust confirmation about the efficacy of IBV vaccination in field conditions was provided. Additionally, the history herein reported testifies the primary importance of rigorously planning not only the intervention strategies but also their monitoring and evaluation.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy.
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Angela Blanco
- CESAC-Centre de Sanitat Avícola de Catalunya i Aragó, Ctra. Castellvell, s/n, 43206 Reus, Spain
| | - Miquel Nofrarías
- Centre de Recerca en Sanitat Animal, CReSA, UAB-IRTA, Campus de la UAB, edifici CReSA, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Mar Biarnés
- CESAC-Centre de Sanitat Avícola de Catalunya i Aragó, Ctra. Castellvell, s/n, 43206 Reus, Spain
| | - Marti Cortey
- Centre de Recerca en Sanitat Animal, CReSA, UAB-IRTA, Campus de la UAB, edifici CReSA, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Natàlia Majó
- Centre de Recerca en Sanitat Animal, CReSA, UAB-IRTA, Campus de la UAB, edifici CReSA, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Elena Catelli
- Dipartimento di Scienze Mediche Veterinarie, Alma Mater Studiorum - Università di Bologna, Via Tolara di Sopra, 50, 40064 Ozzano dell'Emilia (BO), Italy
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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48
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Wei K, Tang X, Li Y. Genome-scale phylodynamics and evolution analysis of global H7N7 influenza viruses. Vet Microbiol 2016; 193:83-92. [PMID: 27599934 DOI: 10.1016/j.vetmic.2016.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 07/23/2016] [Accepted: 08/03/2016] [Indexed: 11/18/2022]
Abstract
Previous studies lacked of comprehensive analysis about the evolutionary history and phylogeography of global H7N7 viruses. In this study, it is essential to undertake a genome-scale analysis to investigate the evolutionary processes in a global perspective. There was local phylogenetic divergence among eight trees based on individual segments of 132 strains. We detected four reassortments between four distinct groups of viruses divided by HA gene, suggesting intrasubtype reassortment could accelerate the emergence of highly pathogenic virus. The molecular clock estimated that H7N7 virus evolved at a slower evolutionary rate ranged from 1.03E-03 to 2.81E-03subs/site/year. And we also showed that all gene segments of the virus were under strong purifying selection. A total of 11 positively selected sites were detected by at least two out of three methods. We reconstructed the population dynamics of global H7N7 viruses spanning over a century, revealing that temporal trends of the effective population size were consistent with the major epidemics previously reported. Our study adopt a Bayesian phylogeographic approach to investigate the geographic spread of H7N7 viruses, which combined with temporal and spatial information of all sequences. We have confirmed several migration events between different geographic locations supported by higher values of Bayes factor. The diffusion patterns of H7N7 viruses reveal that the virus is more likely to evolve to expand their host ranges even cross the species.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China.
| | - Xiaoping Tang
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
| | - Yuhan Li
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
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Kumar N, Bera BC, Greenbaum BD, Bhatia S, Sood R, Selvaraj P, Anand T, Tripathi BN, Virmani N. Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses. PLoS One 2016; 11:e0154376. [PMID: 27119730 PMCID: PMC4847779 DOI: 10.1371/journal.pone.0154376] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts.
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MESH Headings
- Adaptation, Physiological/genetics
- Animals
- Biological Evolution
- Codon
- Gene Expression Regulation, Viral
- Genetic Code
- Genome, Viral
- Horse Diseases/virology
- Horses
- Host-Pathogen Interactions
- Influenza A Virus, H3N8 Subtype/genetics
- Influenza A Virus, H3N8 Subtype/metabolism
- Influenza A Virus, H7N7 Subtype/genetics
- Influenza A Virus, H7N7 Subtype/metabolism
- Models, Statistical
- Mutation Rate
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/virology
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Species Specificity
- Virus Replication
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Affiliation(s)
- Naveen Kumar
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Bidhan Chandra Bera
- Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | - Benjamin D. Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Pathology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sandeep Bhatia
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Richa Sood
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Pavulraj Selvaraj
- Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | - Taruna Anand
- Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | | | - Nitin Virmani
- Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India
- * E-mail:
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50
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Alves Beuttemmüller E, Woodward A, Rash A, Dos Santos Ferraz LE, Fernandes Alfieri A, Alfieri AA, Elton D. Characterisation of the epidemic strain of H3N8 equine influenza virus responsible for outbreaks in South America in 2012. Virol J 2016; 13:45. [PMID: 26993620 PMCID: PMC4799594 DOI: 10.1186/s12985-016-0503-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/11/2016] [Indexed: 01/26/2023] Open
Abstract
Background An extensive outbreak of equine influenza occurred across multiple countries in South America during 2012. The epidemic was first reported in Chile then spread to Brazil, Uruguay and Argentina, where both vaccinated and unvaccinated animals were affected. In Brazil, infections were widespread within 3months of the first reported cases. Affected horses included animals vaccinated with outdated vaccine antigens, but also with the OIE-recommended Florida clade 1 strain South Africa/4/03. Methods Equine influenza virus strains from infected horses were isolated in eggs, then a representative strain was subjected to full genome sequencing using segment-specific primers with M13 tags. Phylogenetic analyses of nucleotide sequences were completed using PhyML. Amino acid sequences of haemagglutinin and neuraminidase were compared against those of vaccine strains and recent isolates from America and Uruguay, substitutions were mapped onto 3D protein structures using PyMol. Antigenic analyses were completed by haemagglutination-inhibition assay using post-infection ferret sera. Results Nucleotide sequences of the haemaglutinin (HA) and neuraminidase (NA) genes of Brazilian isolate A/equine/Rio Grande do Sul/2012 were very similar to those of viruses belonging to Florida clade 1 and clustered with contemporary isolates from the USA. Comparison of their amino acid sequences against the OIE-recommended Florida clade 1 vaccine strain A/equine/South Africa/4/03 revealed five amino acid substitutions in HA and seven in NA. Changes in HA included one within antigenic site A and one within the 220-loop of the sialic acid receptor binding site. However, antigenic analysis by haemagglutination inhibition (HI) assay with ferret antisera raised against representatives of European, Kentucky and Florida sublineages failed to indicate any obvious differences in antigenicity. Conclusions An extensive outbreak of equine influenza in South America during 2012 was caused by a virus belonging to Florida clade 1, closely related to strains circulating in the USA in 2011. Despite reports of vaccine breakdown with products containing the recommended strain South Africa/03, no evidence was found of significant antigenic drift. Other factors may have contributed to the rapid spread of this virus, including poor control of horse movement. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0503-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edsel Alves Beuttemmüller
- Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Pr 445 Km 380, Campus Universitário, Londrina, Paraná, CEP 86057-970, Brazil
| | - Alana Woodward
- Animal Health Trust, Lanwades Park, Kentford, Suffolk, CB8 7UU, UK
| | - Adam Rash
- Animal Health Trust, Lanwades Park, Kentford, Suffolk, CB8 7UU, UK
| | | | - Alice Fernandes Alfieri
- Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Pr 445 Km 380, Campus Universitário, Londrina, Paraná, CEP 86057-970, Brazil
| | - Amauri Alcindo Alfieri
- Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Pr 445 Km 380, Campus Universitário, Londrina, Paraná, CEP 86057-970, Brazil
| | - Debra Elton
- Animal Health Trust, Lanwades Park, Kentford, Suffolk, CB8 7UU, UK.
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