1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
Affiliation(s)
- Thomas M Chambers
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky 40546, USA
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Abstract
Influenza A virus has long been known to encode 10 major polypeptides, produced, almost without exception, by every natural isolate of the virus. These polypeptides are expressed in readily detectable amounts during infection and are either fully essential or their loss severely attenuates virus replication. More recent work has shown that this core proteome is elaborated by expression of a suite of accessory gene products that tend to be expressed at lower levels through noncanonical transcriptional and/or translational events. Expression and activity of these accessory proteins varies between virus strains and is nonessential (sometimes inconsequential) for virus replication in cell culture, but in many cases has been shown to affect virulence and/or transmission in vivo. This review describes, when known, the expression mechanisms and functions of this influenza A virus accessory proteome and discusses its significance and evolution.
Collapse
Affiliation(s)
- Rute M Pinto
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Eleanor Gaunt
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| |
Collapse
|
5
|
Alnaeem A, Shawaf T, Ali AM, Hemida MG. Clinical observations and molecular detection of Type-A influenza virus in some of the family Equidae in eastern Saudi Arabia winter-2019. Vet Res Commun 2021; 45:423-430. [PMID: 34435308 DOI: 10.1007/s11259-021-09822-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVES In the current study, we are investigating the viral causes of some respiratory clinical signs in some animals belongs to the family Equidae in eastern Saudi Arabia (ESA) during winter- 2019. We observed the progression of severe respiratory clinical signs among some horses, donkeys, and ponies in the ESA. Animals showed rapid respiration, fever, nasal discharges (started as serous then changed into mucopurulent with the progression of the infection per some animals). We conducted a longitudinal study to monitor the progression of this outbreak. We conducted molecular surveillance for the influenza virus Type-A using real-time PCR and regular RT-PCR. We also conducted a serosurveillance of the virus in sera of the tested animals using the commercially available enzyme-linked immunosorbent assay (ELISA). RESULTS The molecular detection of the Influenza virus type-A virus from nasal swabs of the affected animals using the real-time PCR results clearly showing that 35.1% of the tested horses, donkeys, and ponies were positives. Further confirmation was achieved by reporting the seroconversion of some of the affected animals. Several attempts were conducted to isolate the circulating influenza strains using the embryonated chicken eggs were unsuccessful. This was based on the absence of any amplicons in the harvested embryonated egg fluids using some oligonucleotides for the common influenza virus genes (HA, NA, M, and N). Meanwhile, ELISA results revealed the detection of the antibodies in sera of horses and donkeys 72.9%. Seroconversion was reported in many animals several weeks after the onset of the outbreak. Taken together all these pieces of evidence, we confirm an influenza virus type-A outbreak among the tested animals during winter 2019.
Collapse
Affiliation(s)
- Abdelmohsen Alnaeem
- Department of Clinical Sciences, College of Veterinary Medicine, King Faisal University, Al Hofuf, Saudi Arabia
| | - Turke Shawaf
- Department of Clinical Sciences, College of Veterinary Medicine, King Faisal University, Al Hofuf, Saudi Arabia
| | - Ali M Ali
- Department of Biological Sciences, College of Science, King Faisal University, Al Hofuf, Saudi Arabia.,Department of Botany and Microbiology, Faculty of Science, Minia University, El-Minia, Egypt
| | - Maged Gomaa Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Ahasa, Saudi Arabia. .,Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr Elsheikh, Egypt.
| |
Collapse
|
6
|
Diallo AA, Souley MM, Issa Ibrahim A, Alassane A, Issa R, Gagara H, Yaou B, Issiakou A, Diop M, Ba Diouf RO, Lo FT, Lo MM, Bakhoum T, Sylla M, Seck MT, Meseko C, Shittu I, Cullinane A, Settypalli TBK, Lamien CE, Dundon WG, Cattoli G. Transboundary spread of equine influenza viruses (H3N8) in West and Central Africa: Molecular characterization of identified viruses during outbreaks in Niger and Senegal, in 2019. Transbound Emerg Dis 2020; 68:1253-1262. [PMID: 32770642 DOI: 10.1111/tbed.13779] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/13/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022]
Abstract
Since November 2018, several countries in West and Central Africa have reported mortalities in donkeys and horses. Specifically, more than 66,000 horses and donkeys have succumbed to disease in Burkina Faso, Chad, Cameroon, The Gambia, Ghana, Mali, Niger, Nigeria, and Senegal. Strangles caused by Streptococcus equi subsp equi, African Horse Sickness (AHS) virus, and Equine influenza virus (EIV) were all suspected as potential causative agents. This study reports the identification of EIV in field samples collected in Niger and Senegal. Phylogenetic analysis of the hemagglutinin and neuraminidase genes revealed that the identified viruses belonged to clade 1 of the Florida sublineage and were very similar to viruses identified in Nigeria in 2019. Interestingly, they were also more similar to EIVs from recent outbreaks in South America than to those in Europe and the USA. This is one of the first reports providing detailed description and characterization of EIVs in West and Central Africa region.
Collapse
Affiliation(s)
- Alpha Amadou Diallo
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal
| | | | | | - Abdou Alassane
- Laboratoire Central de l'Elevage (LABOCEL), Niamey, Niger
| | - Rahila Issa
- Laboratoire Central de l'Elevage (LABOCEL), Niamey, Niger
| | - Haladou Gagara
- Laboratoire Central de l'Elevage (LABOCEL), Niamey, Niger
| | - Bachir Yaou
- Laboratoire Central de l'Elevage (LABOCEL), Niamey, Niger
| | - Abdou Issiakou
- Direction Générale des Services Vétérinaires du Niger, Niamey, Niger
| | - Mariame Diop
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal
| | - Racky Oumar Ba Diouf
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal
| | - Fatou Tall Lo
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal
| | - Modou Moustapha Lo
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal
| | - Thierno Bakhoum
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal
| | - Mamadou Sylla
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal.,Direction du Développement des Equidés, MEPA, Dakar, Sénégal
| | - Momar Talla Seck
- Laboratoire National de l'Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), Dakar, Sénégal
| | - Clement Meseko
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Ismaila Shittu
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Ann Cullinane
- OIE Reference Laboratory for Equine influenza, Irish Equine Centre, Kildare, Ireland
| | - Tirumala B K Settypalli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Charles E Lamien
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| |
Collapse
|
7
|
Olguin-Perglione C, Vissani MA, Alamos F, Tordoya MS, Barrandeguy M. Multifocal outbreak of equine influenza in vaccinated horses in Argentina in 2018: Epidemiological aspects and molecular characterisation of the involved virus strains. Equine Vet J 2020; 52:420-427. [PMID: 31494962 DOI: 10.1111/evj.13176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Equine influenza is an important cause of respiratory disease of horses worldwide. The equine influenza virus (EIV) undergoes antigenic drift through the accumulation of amino acid substitutions in the viral proteins, which may lead to vaccine breakdown. OBJECTIVES To describe the epidemiological findings and the molecular characteristics of the EIV detected during the multifocal outbreak that occurred in Argentina between March and July 2018 and evidence a vaccine breakdown. STUDY DESIGN Observational, descriptive study. METHODS Virus was detected in nasopharyngeal swabs using real-time reverse transcriptase PCR (RT-PCR). Nucleotide and deduced amino acid sequences of the haemagglutinin (HA) and neuraminidase (NA) genes were obtained from EIV positive nasopharyngeal swabs, and phylogenetic analysis was undertaken. Amino acid sequences were compared against the current World Organisation for Animal Health (OIE)-recommended Florida clade 1 vaccine strain and strain components of vaccines used in Argentina. Serum samples were tested using haemagglutination inhibition test. RESULTS Equine influenza virus infection was confirmed using real-time RT-PCR and serological testing. The phylogenetic analysis of the HA and NA genes revealed that all the EIV identified during the outbreak belong to the H3N8 subtype, Florida clade 1. Multiple amino acid changes, some of them at antigenic sites, were observed in the circulating virus when compared with the strains included in the most commonly used vaccine in Argentina. Seventy-six percent of the affected horses had been vaccinated with this vaccine, suggesting the occurrence of vaccine breakdown. MAIN LIMITATIONS The study does not include antigenic characterisation and full genome sequencing of Argentinian strains, that could provide additional information. CONCLUSIONS The occurrence of this multifocal equine influenza outbreak in regularly vaccinated horses is a field evidence of vaccine breakdown, reinforcing the necessity of keeping vaccine strains updated according to OIE recommendations. It also underlines the importance of the implementation of appropriate quarantine measures and restriction of horse movement in the face of disease.
Collapse
Affiliation(s)
- C Olguin-Perglione
- Instituto de Virología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - M A Vissani
- Instituto de Virología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
- Escuela de Veterinaria, Universidad del Salvador, Pilar, Buenos Aires, Argentina
| | - F Alamos
- Instituto de Virología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - M S Tordoya
- Instituto de Virología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - M Barrandeguy
- Instituto de Virología, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
- Escuela de Veterinaria, Universidad del Salvador, Pilar, Buenos Aires, Argentina
| |
Collapse
|
8
|
Success and Limitation of Equine Influenza Vaccination: The First Incursion in a Decade of a Florida Clade 1 Equine Influenza Virus that Shakes Protection Despite High Vaccine Coverage. Vaccines (Basel) 2019; 7:vaccines7040174. [PMID: 31684097 PMCID: PMC6963532 DOI: 10.3390/vaccines7040174] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 11/21/2022] Open
Abstract
Every year, several epizooties of equine influenza (EI) are reported worldwide. However, no EI case has been identified in France between 2015 and late 2018, despite an effective field surveillance of the pathogen and the disease. Vaccination against equine influenza virus (EIV) remains to this day one of the most effective methods to prevent or limit EI outbreaks and the lack of detection of the pathogen could be linked to vaccination coverage. The aim of this study was to evaluate EI immunity and vaccine coverage in France through a large-scale serological study. A total of 3004 archived surplus serums from French horses of all ages, breeds and sexes were selected from four different geographical regions and categories (i.e., sanitary check prior to exportation, sale, breeding protocol or illness diagnosis). EIV-specific antibody response was measured by single radial hemolysis (SRH) and an EIV-nucleoprotein (NP) ELISA (used as a DIVA test). Overall immunity coverage against EIV infection (i.e., titers induced by vaccination and/or natural infection above the clinical protection threshold) reached 87.6%. The EIV NP ELISA results showed that 83% of SRH positive serum samples from young horses (≤3 years old) did not have NP antibodies, which indicates that the SRH antibody response was likely induced by EI vaccination alone (the HA recombinant canarypoxvirus-based EI vaccine is mostly used in France) and supports the absence of EIV circulation in French horse populations between 2015 and late 2018, as reported by the French equine infectious diseases surveillance network (RESPE). Results from this study confirm a strong EI immunity in a large cohort of French horses, which provides an explanation to the lack of clinical EI in France in recent years and highlights the success of vaccination against this disease. However, such EI protection has been challenged since late 2018 by the incursion in the EU of a Florida Clade 1 sub-lineage EIV (undetected in France since 2009), which is also reported here.
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
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
| | | |
Collapse
|
12
|
Gildea S, Garvey M, Lyons P, Lyons R, Gahan J, Walsh C, Cullinane A. Multifocal Equine Influenza Outbreak with Vaccination Breakdown in Thoroughbred Racehorses. Pathogens 2018; 7:pathogens7020043. [PMID: 29673169 PMCID: PMC6027538 DOI: 10.3390/pathogens7020043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 01/24/2023] Open
Abstract
Equine influenza (EI) outbreaks occurred on 19 premises in Ireland during 2014. Disease affected thoroughbred (TB) and non-TB horses/ponies on a variety of premises including four racing yards. Initial clinical signs presented on 16 premises within a two-month period. Extensive field investigations were undertaken, and the diagnostic effectiveness of a TaqMan RT-PCR assay was demonstrated in regularly-vaccinated and sub-clinically-affected horses. Epidemiological data and repeat clinical samples were collected from 305 horses, of which 40% were reported as clinically affected, 39% were identified as confirmed cases and 11% were sub-clinically affected. Multivariable analysis demonstrated a significant association between clinical signs and age, vaccination status and number of vaccine doses received. Vaccine breakdown was identified in 31% of horses with up to date vaccination records. This included 27 horses in four different racing yards. Genetic and antigenic analysis identified causal viruses as belonging to Clade 2 of the Florida sublineage (FCL2). At the time of this study, no commercially available EI vaccine in Ireland had been updated in line with World Organisation for Animal Health (OIE) recommendations to include a FCL2 virus. The findings of this study highlight the potential ease with which EI can spread among partially immune equine populations.
Collapse
Affiliation(s)
- Sarah Gildea
- 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.
| | - Pamela Lyons
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
| | - Rachel Lyons
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
| | - Jacinta Gahan
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
| | - Cathal Walsh
- Department of Mathematics and Statistics, University of Limerick, Castletroy, Limerick V94 T9PX, Ireland.
| | - Ann Cullinane
- Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare W91 RH93, Ireland.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| | | |
Collapse
|
15
|
Khan A, Mushtaq MH, Ahmad MUD, Nazir J, Farooqi SH, Khan A. Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16. Virus Res 2017; 240:56-63. [PMID: 28757141 DOI: 10.1016/j.virusres.2017.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/15/2017] [Accepted: 07/26/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND A widespread epidemic of equine influenza (EI) occurred in nonvaccinated equine population across multiple districts in Khyber Pakhtunkhwa Province of Pakistan during 2015-2016. OBJECTIVES AND METHODS An epidemiological surveillance study was conducted from Oct 2015 to April 2016 to investigate the outbreak. EI virus strains were isolated in embryonated eggs from suspected equines swab samples and were subjected to genome sequencing using M13 tagged segment specific primers. Phylogenetic analyses of the nucleotide sequences were concluded using Geneious. Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and nucleoprotein (NP) genes nucleotide and amino acid sequences of the isolated viruses were aligned with those of OIE recommended, FC-1, FC-2, and contemporary isolates of influenza A viruses from other species. RESULTS HA and NA genes amino acid sequences were very similar to Tennessee/14 and Malaysia/15 of FC-1 and clustered with the contemporary isolates recently reported in the USA. Phylogenetic analysis showed that these viruses were mostly identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing chicken/Pakistan/14 (H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes. Genetic analysis indicated that A/equine/Pakistan/16 viruses were most probably the result of several re-assortments between the co-circulating avian and equine viruses, and were genetically unlike the other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes. CONCLUSION Epidemiological data analysis indicated the potential chance of mixed, and management such as mixed farming system by keeping equine, canine and backyard poultry together in confined premises as the greater risk factors responsible for the re-assortments. Other factors might have contributed to the spread of the epidemic, including low awareness level, poor control of equine movements, and absence of border control disease strategies.
Collapse
Affiliation(s)
- Amjad Khan
- Department of Epidemiology and Public Health, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Muhammad Hassan Mushtaq
- Department of Epidemiology and Public Health, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Mansur Ud Din Ahmad
- Department of Epidemiology and Public Health, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Jawad Nazir
- Department of Veterinary Microbiology, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Shahid Hussain Farooqi
- Department of Clinical Medicine and Surgery, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Asghar Khan
- Department of Clinical Medicine, Arid Agricultural University, Rawalpindi, 44000, Pakistan.
| |
Collapse
|
16
|
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]
|
17
|
Evolution and Divergence of H3N8 Equine Influenza Viruses Circulating in the United Kingdom from 2013 to 2015. Pathogens 2017; 6:pathogens6010006. [PMID: 28208721 PMCID: PMC5371894 DOI: 10.3390/pathogens6010006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 12/18/2022] Open
Abstract
Equine influenza viruses (EIV) are a major cause of acute respiratory disease in horses worldwide and occasionally also affect vaccinated animals. Like other influenza A viruses, they undergo antigenic drift, highlighting the importance of both surveillance and virus characterisation in order for vaccine strains to be kept up to date. The aim of the work reported here was to monitor the genetic and antigenic changes occurring in EIV circulating in the UK from 2013 to 2015 and to identify any evidence of vaccine breakdown in the field. Virus isolation, reverse transcription polymerase chain reaction (RT-PCR) and sequencing were performed on EIV-positive nasopharyngeal swab samples submitted to the Diagnostic Laboratory Services at the Animal Health Trust (AHT). Phylogenetic analyses were completed for the haemagglutinin-1 (HA1) and neuraminidase (NA) genes using PhyML and amino acid sequences compared against the current World Organisation for Animal Health (OIE)-recommended Florida clade 2 vaccine strain. Substitutions between the new isolates and the vaccine strain were mapped onto the three-dimensional structure protein structures using PyMol. Antigenic analyses were carried out by haemagglutination inhibition assay using a panel of post-infection ferret antisera. Sixty-nine outbreaks of equine influenza in the UK were reported by the AHT between January 2013 and December 2015. Forty-seven viruses were successfully isolated in eggs from 41 of the outbreaks. Only three cases of vaccine breakdown were identified and in each case the vaccine used contained a virus antigen not currently recommended for equine influenza vaccines. Nucleotide sequencing of the HA and NA genes revealed that all of the viruses belonged to the Florida clade 2 sub-lineage of H3N8 EIV. Phylogenetic and sequence analyses showed that the two sub-populations, previously identified within clade 2, continued to circulate and had accrued further amino acid substitutions. Antigenic characterisation using post-infection ferret antisera in haemagglutination inhibition assays however, failed to detect any marked antigenic differences between the isolates. These findings show that Florida clade 2 EIV continue to circulate in the UK and support the current OIE recommendation to include an example of Florida clade 2 in vaccines.
Collapse
|
18
|
Lee J, Yu H, Li Y, Ma J, Lang Y, Duff M, Henningson J, Liu Q, Li Y, Nagy A, Bawa B, Li Z, Tong G, Richt JA, Ma W. Impacts of different expressions of PA-X protein on 2009 pandemic H1N1 virus replication, pathogenicity and host immune responses. Virology 2017; 504:25-35. [PMID: 28142079 DOI: 10.1016/j.virol.2017.01.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 01/20/2017] [Accepted: 01/21/2017] [Indexed: 12/16/2022]
Abstract
Although several studies have investigated the functions of influenza PA-X, the impact of different expressions of PA-X protein including full-length, truncated or PA-X deficient forms on virus replication, pathogenicity and host response remains unclear. Herein, we generated two mutated viruses expressing a full-length or deficient PA-X protein based on the A/California/04/2009 (H1N1) virus that expresses a truncated PA-X to understand three different expressions of PA-X protein on virus replication, pathogenicity and host immune responses. The results showed that expression of either full-length or truncated PA-X protein enhanced viral replication and pathogenicity as well as reduced host innate immune response in mice by host shutoff activity when compared to the virus expressing the deficient PA-X form. Furthermore, the full-length PA-X expression exhibited a greater effect on virus pathogenicity than the truncated PA-X form. Our results provide novel insights of PA-X on viral replication, pathogenicity and host immune responses.
Collapse
Affiliation(s)
- Jinhwa Lee
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Hai Yu
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA; Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yonghai Li
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Jingjiao Ma
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Yuekun Lang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Michael Duff
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Jamie Henningson
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Qinfang Liu
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA; Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yuhao Li
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Abdou Nagy
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Bhupinder Bawa
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Juergen A Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Wenjun Ma
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape. Sci Rep 2016; 6:18745. [PMID: 26738561 PMCID: PMC4704030 DOI: 10.1038/srep18745] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 11/23/2015] [Indexed: 12/28/2022] Open
Abstract
H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique 'escape' mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites "H9-A" and "H9-B". Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design.
Collapse
|
21
|
Bavagnoli L, Cucuzza S, Campanini G, Rovida F, Paolucci S, Baldanti F, Maga G. The novel influenza A virus protein PA-X and its naturally deleted variant show different enzymatic properties in comparison to the viral endonuclease PA. Nucleic Acids Res 2015; 43:9405-17. [PMID: 26384413 PMCID: PMC4627086 DOI: 10.1093/nar/gkv926] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/07/2015] [Indexed: 12/18/2022] Open
Abstract
The PA protein of Influenza A virus (IAV) encoded by segment 3 acts as a specialized RNA endonuclease in the transcription of the viral genome. The same genomic segment encodes for a second shorter protein, termed PA-X, with the first 191 N-terminal aminoacids (aa) identical to PA, but with a completely different C-ter domain of 61 aa, due to a ribosomal frameshifting. In addition, it has been shown that several IAV isolates encode for a naturally truncated PA-X variant, PAXΔC20, missing the last 20 aa. The biochemical properties of PA-X and PAXΔC20 have been poorly investigated so far. Here, we have carried out an enzymatic characterization of PA-X and its naturally deleted form, in comparison with PA from the human IAV strain A/WSN/33 (H1N1). Our results showed, to the best of our knowledge for the first time, that PA-X possesses an endonucleolytic activity. Both PA and PA-X preferentially cut single stranded RNA regions, but with some differences. In addition, we showed that PAXΔC20 has severely reduced nuclease activity. These results point to a previously undetected role of the last C-ter 20 aa for the catalytic activity of PA-X and support distinct roles for these proteins in the viral life cycle.
Collapse
Affiliation(s)
- Laura Bavagnoli
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Stefano Cucuzza
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giulia Campanini
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Francesca Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| |
Collapse
|
22
|
Using epidemics to map H3 equine influenza virus determinants of antigenicity. Virology 2015; 481:187-98. [DOI: 10.1016/j.virol.2015.02.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/08/2014] [Accepted: 02/14/2015] [Indexed: 01/25/2023]
|