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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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He W, Li G, Wang R, Shi W, Li K, Wang S, Lai A, Su S. Host-range shift of H3N8 canine influenza virus: a phylodynamic analysis of its origin and adaptation from equine to canine host. Vet Res 2019; 50:87. [PMID: 31666126 PMCID: PMC6822366 DOI: 10.1186/s13567-019-0707-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
Prior to the emergence of H3N8 canine influenza virus (CIV) and the latest avian-origin H3N2 CIV, there was no evidence of a circulating canine-specific influenza virus. Molecular and epidemiological evidence suggest that H3N8 CIV emerged from H3N8 equine influenza virus (EIV). This host-range shift of EIV from equine to canine hosts and its subsequent establishment as an enzootic CIV is unique because this host-range shift was from one mammalian host to another. To further understand this host-range shift, we conducted a comprehensive phylodynamic analysis using all the available whole-genome sequences of H3N8 CIV. We found that (1) the emergence of H3N8 CIV from H3N8 EIV occurred in approximately 2002; (2) this interspecies transmission was by a reassortant virus of the circulating Florida-1 clade H3N8 EIV; (3) once in the canine species, H3N8 CIV spread efficiently and remained an enzootic virus; (4) H3N8 CIV evolved and diverged into multiple clades or sublineages, with intra and inter-lineage reassortment. Our results provide a framework to understand the molecular basis of host-range shifts of influenza viruses and that dogs are potential “mixing vessels” for the establishment of novel influenza viruses.
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Affiliation(s)
- Wanting He
- Ministry of Education 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
- Ministry of Education 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
| | - Ruyi Wang
- Ministry of Education 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
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Taishan Medical College, Taian, 271000, China
| | - Kemang Li
- Ministry of Education 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
| | - Shilei Wang
- Ministry of Education 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
| | - Alexander Lai
- College of Natural, Applied, and Health Sciences, Kentucky State University, Frankfort, KY, USA.
| | - Shuo Su
- Ministry of Education 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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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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Singh RK, Dhama K, Karthik K, Khandia R, Munjal A, Khurana SK, Chakraborty S, Malik YS, Virmani N, Singh R, Tripathi BN, Munir M, van der Kolk JH. A Comprehensive Review on Equine Influenza Virus: Etiology, Epidemiology, Pathobiology, Advances in Developing Diagnostics, Vaccines, and Control Strategies. Front Microbiol 2018; 9:1941. [PMID: 30237788 PMCID: PMC6135912 DOI: 10.3389/fmicb.2018.01941] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/31/2018] [Indexed: 01/23/2023] Open
Abstract
Among all the emerging and re-emerging animal diseases, influenza group is the prototype member associated with severe respiratory infections in wide host species. Wherein, Equine influenza (EI) is the main cause of respiratory illness in equines across globe and is caused by equine influenza A virus (EIV-A) which has impacted the equine industry internationally due to high morbidity and marginal morality. The virus transmits easily by direct contact and inhalation making its spread global and leaving only limited areas untouched. Hitherto reports confirm that this virus crosses the species barriers and found to affect canines and few other animal species (cat and camel). EIV is continuously evolving with changes at the amino acid level wreaking the control program a tedious task. Until now, no natural EI origin infections have been reported explicitly in humans. Recent advances in the diagnostics have led to efficient surveillance and rapid detection of EIV infections at the onset of outbreaks. Incessant surveillance programs will aid in opting a better control strategy for this virus by updating the circulating vaccine strains. Recurrent vaccination failures against this virus due to antigenic drift and shift have been disappointing, however better understanding of the virus pathogenesis would make it easier to design effective vaccines predominantly targeting the conserved epitopes (HA glycoprotein). Additionally, the cold adapted and canarypox vectored vaccines are proving effective in ceasing the severity of disease. Furthermore, better understanding of its genetics and molecular biology will help in estimating the rate of evolution and occurrence of pandemics in future. Here, we highlight the advances occurred in understanding the etiology, epidemiology and pathobiology of EIV and a special focus is on designing and developing effective diagnostics, vaccines and control strategies for mitigating the emerging menace by EIV.
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Affiliation(s)
- Raj K. Singh
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Ashok Munjal
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | | | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, West Tripura, India
| | - Yashpal S. Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | | | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | | | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Johannes H. van der Kolk
- Division of Clinical Veterinary Medicine, Swiss Institute for Equine Medicine (ISME), Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
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Barba M, Daly JM. The Influenza NS1 Protein: What Do We Know in Equine Influenza Virus Pathogenesis? Pathogens 2016; 5:pathogens5030057. [PMID: 27589809 PMCID: PMC5039437 DOI: 10.3390/pathogens5030057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/22/2022] Open
Abstract
Equine influenza virus remains a serious health and potential economic problem throughout most parts of the world, despite intensive vaccination programs in some horse populations. The influenza non-structural protein 1 (NS1) has multiple functions involved in the regulation of several cellular and viral processes during influenza infection. We review the strategies that NS1 uses to facilitate virus replication and inhibit antiviral responses in the host, including sequestering of double-stranded RNA, direct modulation of protein kinase R activity and inhibition of transcription and translation of host antiviral response genes such as type I interferon. Details are provided regarding what it is known about NS1 in equine influenza, especially concerning C-terminal truncation. Further research is needed to determine the role of NS1 in equine influenza infection, which will help to understand the pathophysiology of complicated cases related to cytokine imbalance and secondary bacterial infection, and to investigate new therapeutic and vaccination strategies.
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Affiliation(s)
- Marta Barba
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
| | - Janet M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, UK.
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