MOLECULAR CHARACTERIZATION AND IN SILICO EPITOPE PREDICTIONS OF NSP2-HVII, GP5, AND NP OF PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS FROM MYANMAR

Abstract

Porcine reproductive and respiratory syndrome, a severe reproductive and respiratory disease in pigs, continues to cause a problem in pig production worldwide including Myanmar. In this study, six PRRSV-infected clinical samples collected from five regions of Myanmar during outbreaks in 2011 were investigated, and genetic characteristics and phylogenetic relationship of Myanmar PRRSVs were determined based on Nsp2-HVII, ORF5, and ORF7 gene regions. Sequence analyses revealed that all Myanmar PRRSVs shared 96.8-100% nucleotide and 94.9-100% amino acid identities of all three genes to each other, and 69.5-94.4% nucleotide and 61.4-96.7% amino acid sequence identities with VR-2332, the NA prototype, implying their source of derivation. The 30 discontinuous amino acid deletions at position 481 and 533-561 were found in the Nsp2-HVII of all Myanmar PRRSVs, indicated that they were highly pathogenic (HP)-PRRSV. The nucleotide and amino acid sequence identities of each gene were highly similar to HP-PRRSV strains, especially from Thailand, Laos, and Cambodia. From phylogenetic analyses, Myanmar PRRSVs were clustered into the same subtype 3 of NA-genotypic group as other Southeast Asian HP-PRRSV strains from Thailand, Laos, and Cambodia, suggesting their close relationships. The unique amino acid mutations found only in Myanmar PRRSVs were L292F, P431S, and V621M in Nsp2-HVII and E170G in GP5, which may be useful as a marker for monitoring genetic diversity of newly emerging HP-PRRSV strains. In order to propose a reverse vaccinology approach for the development of novel PRRS vaccine design, B-cell and T-cell epitopes from three PRRSV proteins were predicted. By using different in silico bioinformatics tools, a total of 44 linear B-cell epitopes, 17 MHC I binding T-cell and 97 MHC II binding T-cell epitopes were predicted from Nsp2-HVII, GP5, and NP of Myanmar PRRSV (HP/MYANMAR/2303AM/2011). Of which, SB3 of Nsp2-HVII, GB5 of GP5, and NB6 of NP were selected as first-line linear B-cell potential candidates. Furthermore, S1T5, and S2T32, G1T2, and G2T39, N1T2, and N2T10 were selected as MHC I and MHC II binding T-cell potential candidates of Nsp2-HVII, GP5, and NP, respectively. The immunogenicity of these potential PRRSV epitope vaccine candidates needs to be further verified through in vivo testing. This study provides basic information for monitoring newly diverging strains, future epidemiological investigation, and development of effective strategies to control PRRS in Myanmar.

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