First Report on Co-isolation and Whole-genomic Characterization of Mammalian Orthorubulavirus 5 and Mammalian Orthoreovirus Type-3 From Domestic Pigs in India

Abstract

During a surveillance study to monitor porcine epidemic diarrohoea virus and transmissible gastroenteritis virus in India, a total of 1043 swine samples including faeces (n=264) and clotted blood (n=779) were collected and tested. Five samples (four faecal and one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infective cell supernatant revealed the presence of two types of virions. Next generation sequencing (de novo) enabled complete genome assembly of Mammalian orthorubulavirus 5 (MRuV5; 15246 bp) and all 10 gene segments of Mammalian orthoreovirus (MRV; 22219 bp and 20512 bp). Genetic analysis of the MRuV5 revealed grouping of the Indian MRuV5 with those isolated from various mammalian species in South Korea and China, sharing more than 99% nucleotide identity. Deduced amino acid sequences of the HN, NP and F genes of MRuV5 isolates showed three (92L, 111R, 447H), two (86S, 121S) and two (139T, 246T) amino acid substitutions, respectively, compared to previously reported virus strains. The Indian MRV isolates were identified as MRV type-3 based on genetic analysis of S1 gene, showing the highest nucleotide identity (97.73%) with the MRV3 strain ZJ2013 isolated from pigs in China. Deduced amino acid sequences of MRV3 S1 gene revealed amino acid residues 198-204NLAIRLP, 249I, 340D, 419E known for sialic acid binding and neurotropism. We report the co-isolation and whole-genomic characterization of MRuV5 and MRV3 recorded incidentally for the first time from domestic pigs in India. It attracts attention to perform detailed surveillance studies and continuous monitoring of evolution and spread of emerging viruses, which may have pathogenic potential in animal and human hosts.