Sequence analysis of new variants of porcine epidemic diarrhea virus in Luzon, Philippines, in 2017

Salamat, Saubel Ezrael A.; Collantes, Therese Marie A.; Lumbera, Wenchie Marie L.; Tablizo, Francis A.; Mutia, Christian Thomas M.; Ong, John Daniel P.; Bandoy, D J Darwin R.

Porcine epidemic diarrhea virus (PEDV) is a coronavirus that causes emaciation and watery diarrhea in pigs. First identified in Europe in 1977, it eventually spread to Asia and North America, causing deadly outbreaks in neonatal piglets. In the Philippines, PEDV has caused several recorded outbreaks since 2005. However, DNA sequencing studies of local PEDV strains remain few and are limited to gene and gene fragment sequencing. Therefore, to provide updated sequence information about recent PEDV strains in the country, we performed reverse transcription PCR and sequencing of PEDV from swab samples collected from swine farms in the Philippines in 2017. Here, we report the first published whole genome sequence of PEDV from the Philippines as well as CO-26K equivalent (COE) domain sequences of strains from three provinces in Luzon where PEDV was detected in 2017. Sequence analysis suggested that PEDV from both the classical (genotype 1) and pandemic (genotype 2) groups are present in the Philippines, with possible East Asian and North American origins.