Profiling of porcine reproductive and respiratory syndrome virus from pigs slaughtered in Laguna, Philippines and utilization of reverse-transcription loop-mediated isothermal amplification assay for its detection
2018
Parayao, A.M.
Detection of Porcine Reproductive and Respiratory Syndrome Virus (PRRS), using two RT-PCR based methods and ORF6 sequence analyses revealed that out of the 77 pooled serum samples, 19 (24.67%) were confirmed positive for type 2 (North American) PRRSV strain. No European and highly pathogenic-PRRSV strains were detected among the samples. PRRSV positive samples were traced to have originated from farms in Biñan [Laguna, Philippines](4), Nagcarlan [Laguna, Philippines](3), San Pedro [Laguna, Philippines](4), Siniloan [Laguna, Philippines](1), Sta Cruz [Laguna, Philippines](6) and Sta Maria [Laguna, Philippines](1). Higher number of positive samples was detected in commercial farms (14) than in backyard farms (5). No significant association was found among the positive samples with reference to different municipalities, farm types, age and sex of the animals in the sampling population. Monophyletic relationship was demonstrated by the local PRRSV strains using ORF6 sequences. Full-length genome sequence of 15,407 bases of PRRSV designated as PRRSV SCL37-P59 was obtained from a pooled sample (P59), which originated from a backyard farm in Barangay Palasan, Sta Cruz, Laguna using Illumina Miseq Sequencing System. Phylogenetic relationship of PRRSV SCL37-P59 strain with other Asian PRRSV strains strongly supported uniqueness of the local virus strain. This isolate is also the first local PRRSV strain with its full-length genome sequenced in the country. The optimization and utilization of RT-LAMP protocol demonstrated a detection system, which is sensitive and rapid was able to detect the virus in all of the PRRSV positive serum samples.
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