Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production
Porcine reproductive and respiratory syndrome virus (PRRSV) type II has become one of the most common viruses affecting swine population in Thailand. The perpetuation of PRRSV genetic diversity has become the main obstacle for the effective control of PRRSV infection by the current commercial vaccines. Therefore, the genetic surveillance is suggested to facilitate an appropriate implementation for disease prevention and control. Here we analyzed sequences of GP5 and Nsp2 gene of type II PRRSVs from pigs in different herds during annual herd surveillance from 2008 to January 2013. To investigate genetic variation at amino acid level, the DNA sequences of GP5 and Nsp2 were translated in to amino acid sequences which is them aligned using MegAlign program (DNAStar). The results indicated that GP5 of Thai PRRSVs type II display amino acid deletion and a single amino acid substitutions take place throughout the N-portion of the polypeptide; especially, GP5 of lineage 1 contains the highest number of amino acid substitutions. Furthermore, the glycosylation patterns of Thai PRRSV type II are more variable and the number of N-linked glycosylation sites are greater, especially, in lineage 1 and the HP-PRRSVs were grouped in sublineage 8.7. Alignment of the deduced amino acids of partial Nsp2 region revealed that all selected HP-PRRSV isolates possess the 30 amino acid discontinuous deletions, specific to HPPRRSV. The results confirm that most of Thai HP-PRRSVs have the common discontinuous deletion marker within Nsp2 region. This study provides comprehensive information on the current knowledge of genetic diversity of type II PRRSV in Thailand. This information could be the basic of genetic database of PRRSV for future study.