Abstract Title
Detection and whole-genome sequence-based analysis of highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses isolated from chickens and quails from 2022-2024 in the Philippines
Abstract
The Philippines sits along the East Asian-Australasian Flyway, one of the world's largest migratory bird flight paths in the world, making it a breeding and aggregation point for hundreds of millions of waterbirds from the northern and southern hemisphere. Unfortunately, this biogeographic setting has brought the country to an increased risk of outbreaks from avian influenza virus (AIV). Ever since its first report of highly pathogenic avian influenza (HPAI) in 2017, recurring outbreaks of HPAI H5 viruses have continued to devastate the domestic poultry industry. Furthermore, sources of these outbreaks have not been fully characterized. Using Oxford Nanopore Technologies’ MinION, we report the first whole-genome sequencing data of H5N1 subtype HPAIVs in the Philippines from four isolates detected from oropharyngeal swabs that were collected from 2022 to 2024 in chickens and quails. Clinical signs observed from chickens included lethargy and sudden death while quails exhibited lethargy and inappetence. A total of 515,834, 101,263, 42,871, and 465, 502 sequencing reads were obtained from the four isolates (BA-MHN, BA-PTY, BA-P3, BA-RM15, respectively) which were used for map-based assembly and consensus sequence determination of AIV. Moreover, phylogenetic analysis based on the hemagglutinin (HA) sequences showed that all isolates have high similarity to 2022-2024 clade 2.3.4.4b H5N1 isolates from Asia, Europe, North America, and South America.
Key words: highly pathogenic avian influenza (HPAI), H5N1, whole genome sequencing, phylogenetic analysis, chickens, quails
Key words: highly pathogenic avian influenza (HPAI), H5N1, whole genome sequencing, phylogenetic analysis, chickens, quails
Co-Author(s)
Zyne Baybay [1]
Andrew Montecillo [1,2]
Airish Pantua [1]
Jimwel Bryan Christopher Ferrer [1]
Milagros Mananggit [3]
Jun Romo [4]
Esmeraldo San Pedro [4]
Homer Pantua [1]
Christina Lora Leyson [1,5]
[1] BioAssets Corporation, Sto. Tomas, Batangas, Philippines
[2] University of the Philippines Los Baños, Laguna, Philippines
[3] Department of Agriculture Regional Field Office III, Philippines
[4] Philippine College of Poultry Practitioners, Inc., Philippines
[5] Department of Science and Technology Balik Scientist Program, Philippines
Abstract Category
Notable outbreaks, field and molecular epidemiology, and surveillance in poultry