A pilot study was carried out to find out the seroprevalence of Porcine circovirus 2 (PCV2), classical swine fever virus (CSFV), and Porcine respiratory and reproductive syndrome virus (PRRS) in pig population of Meghalaya

CSF is enzootic in most of pig-producing states, particularly in the NorthEastern (NE) region of India. In this study, a total of 249 sera and 190 tissue samples were collected from different parts of Meghalaya. Samples were processed by ELISA and RT-PCR for serological and molecular diagnosis. Representative positive samples from the Khasi Hills region were selected for sequencing and “close grid” phylogenetic relationship using partial genomic regions of 5′UTR and E2. High seroprevalence (74.7%) of CSFV was recorded. Detection of the CSFV genome in serologically positive serum samples and tissue samples was 61.29% and 18.94%, respectively. BLAST and phylogenetic analyses indicate the clustering of all the field samples in subgroup 2.2, with high identity with EF014334 from China. Molecular structural modelling of the E2 partial sequence using representative sequences MG563797 from Meghalaya and EF014334 from China indicate potential changes in the protein motif and its conformation, which may explain the emergence of subgroup 2.2 CSFV replacing the predominant subgroup 1.1 viruses in NorthEast India. The epidemiological information presented in this study may be helpful for determination of disease incidence in this region, whereas the virus profile may be useful for framing disease control programs.