Full-Length Genome of the Equine Influenza A Virus Subtype H3N8 from 2019 Outbreak in Saudi Arabia
Fanan A. Alaql,
Ali N. Alhafufi,
Samy Kasem,
Yousef M. O. Alhammad,
Hassan Albaqshi,
Ameen Alyousaf,
Faisal M. Alsubaie,
Ahmed N. Alghamdi,
Ahmed S. Abdel-Moneim,
Sulaiman A. Alharbi
Affiliations
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
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
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
Sulaiman A. Alharbi
Botany & Microbiology Department, College of Science, King Saud University, Riyadh 12372, Saudi Arabia
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.
