Indian porcine reproductive and respiratory syndrome virus bears discontinuous deletion of 30 amino acids in nonstructural protein 2

Abstract

Since its first outbreak in 2013, porcine reproductive and respiratory syndrome (PRRS) has established as an enzootic disease in pig population of Mizoram state, India. Our previous studies based on phylogenetic analysis of ORF5 and ORF7 gene sequences revealed close relationship of Indian PRRSV with the highly pathogenic variant of PRRSV (HP-PRRSV) of Chinese origin. Despite the control measures, second major outbreak of the disease was recorded in Aizawl district of Mizoram in 2015. The objective of the present study was to examine the origin of PRRSV isolates of 2015 outbreak, identification of deleted region in Nsp2 gene and determination of any genetic variation between 2013 and 2015 isolates of PRRSV. The outbreak was confirmed by the detection of PRRSV-specific antibodies in 57 out of 92 serum samples (61.96 %) and also by RT-PCR in 42 out of 42 necropsy samples (100 %). Nucleotide sequence analysis of Nsp2 coding region of Indian isolates and comparison with reference sequences revealed 90 nucleotides discontinuous deletion further establishes the closeness of Indian PRRSV to Chinese HP-PRRSV. Further, sequence and phylogenetic analysis of ORF5, ORF7 and Nsp2 genes of Indian PRRSV from both 2013 and 2015 revealed that the outbreaks were caused by two different strains of HP-PRRSV closely associated with the Chinese 10 HEB-3 isolate and 07QN isolates of Vietnam origin respectively. The present study confirms that the Indian PRRSV is a highly pathogenic variant of PRRSV and this study serves as the basis for developing practical and effective control measures against this disease.

Keywords: India; Nsp2; ORF5; ORF7; PRRS; Phylogeny; Pig.

Fig. 1

Phylogenetic tree based on the analysis of ORF5 gene (603 bp) constructed using MEGA5 software by neighbour-joining method. It shows two distinct groups of Indian PRRSV separating the outbreaks of 2013 and 2015 but grouped together with novel variant of Chinese HP-PRRSV

Fig. 2

Phylogenetic tree based on the analysis of ORF7 gene (372 bp) constructed using MEGA5 software by neighbour-joining method. It shows two distinct groups of Indian PRRSV separating the outbreaks of 2013 and 2015 but grouped together with novel variant of Chinese HP-PRRSV

Fig. 3

Phylogenetic tree based on the analysis of Nsp2 coding region (558 bp) constructed using MEGA5 software by neighbour-joining method. It shows the Indian PRRSV clustered together with Chinese HP-PRRSV

Fig. 4

Alignment of Nsp2 nucleotide sequences of Indian PRRSV with reference sequences of North American and Chinese classical PRRSV and Chinese HP-PRRSV. a Alignment showing 3 nucleotides deletion in Indian PRRSV and Chinese HP-PRRSV from 2778 to 2780 with reference to VR-2332. b Alignment showing 87 nucleotides deletion in Indian PRRSV and Chinese HP-PRRSV from 2931 to 3017 with reference to VR-2332

Fig. 4

Alignment of Nsp2 nucleotide sequences of Indian PRRSV with reference sequences of North American and Chinese classical PRRSV and Chinese HP-PRRSV. a Alignment showing 3 nucleotides deletion in Indian PRRSV and Chinese HP-PRRSV from 2778 to 2780 with reference to VR-2332. b Alignment showing 87 nucleotides deletion in Indian PRRSV and Chinese HP-PRRSV from 2931 to 3017 with reference to VR-2332