An African Swine Fever (ASF) outbreak was first recorded in the Philippines in July 2019. Since then, the disease has spread across provinces in Luzon, Visayas, and Mindanao, causing severe economic consequences for the country’s swine industry. Here, we report the genome sequencing of ASF virus strains from outbreaks in several provinces of the Philippines between 2021 and 2023, using a long-read tiled amplicon sequencing approach. The coding-complete genomes generated ranged from 187,609 to 189,540 bp in length, with GC contents of 38.4% to 38.5%. Notably, a strain from the Bataan province had a 1.9 kb deletion at the 5′-end, affecting several coding regions. The strains were characterized using 13 genes and regions; namely the B646L gene, the CD2v serogroup, the central variable region (CVR) of the B602L gene, the intergenic region (IGR) between the I73R and I329L genes, the IGR between A179L and A137R, O174L, K145R, Bt/Sj, J268L, and ECO2, the multigene family (MGF) 505-5R, and the MGF 505-9R and 10R regions. The ASFV strains were mostly related to Asian and European p72 genotype II strains. Genetic profiling provides valuable information on the diversity of local strains of ASFV in the Philippines, which are useful for epidemiology, diagnostics, and vaccine development.

H5 subtype high-pathogenicity avian influenza (HPAI) viruses continue to devastate the poultry industry and threaten food security and public health. The first outbreak of H5 HPAI in the Philippines was reported in 2017. Since then, H5 HPAI outbreaks have been reported in 2020, 2022, and 2023. Here, we report the first publicly available complete whole-genome sequence of an H5N1 high-pathogenicity avian influenza virus from a case in Central Luzon. Samples were collected from a flock of layer chickens exhibiting signs of lethargy, droopy wings, and ecchymotic hemorrhages in trachea with excessive mucus exudates. A high mortality rate of 96–100% was observed within the week. Days prior to the high mortality event, migratory birds were observed around the chicken farm. Lungs, spleen, cloacal swabs, and oropharyngeal–tracheal swabs were taken from two chickens from this flock. These samples were positive in quantitative RT-PCR assays for influenza matrix and H5 hemagglutinin (HA) genes. To further characterize the virus, the same samples were subjected to whole-virus-genome amplification and sequencing using the Oxford Nanopore method with mean coverages of 19,190 and 2984, respectively. A phylogenetic analysis of the HA genes revealed that the H5N1 HPAI virus from Central Luzon belongs to the Goose/Guangdong lineage clade 2.3.4.4b viruses. Other segments also have high sequence identity and the same genetic lineages as other clade 2.3.4.4b viruses from Asia. Collectively, these data indicate that wild migratory birds are the likely source of H5N1 viruses from the 2022 outbreaks in the Philippines. Thus, biosecurity practices and surveillance for HPAI viruses in both domestic and wild birds should be increased to prevent and mitigate HPAI outbreaks.

African Swine Fever (ASF) outbreak was first recorded in the Philippines in July 2019. Since then, the disease has spread across provinces in Luzon, Visayas, and Mindanao causing severe economic consequences for the country’s swine industry. . Here, we report the genome sequencing of ASF virus strains from outbreaks in several provinces of the Philippines between 2021 to 2023, using a long-read tiled amplicon sequencing approach. The coding-complete genomes generated ranged from 187,609 to 189,540 bp in length, with GC content of 38.4% to 38.5%. Notably, a strain from Bataan province had a 1.9-kb deletion at the 5’-end affecting several coding regions. The strains were characterized using 13 genes and regions, namely, B646L gene, CD2v serogroup, central variable region (CVR) of B602L gene, intergenic region (IGR) between I73R and I329L genes, IGR between A179L and A137R, O174L, K145R, Bt/Sj, J268L, ECO2, and multigene family (MGF) 505-5R, and MGF 505-9R and 10R. The ASFV strains were most related to Asian and European p72 genotype II strains. Genetic profiling provides valuable information on the diversity of local strains of ASFV in the Philippines, which are useful for epidemiology, diagnostics, and in vaccine development.