First detection of a recombinant enterovirus G carrying a torovirus papain-like cysteine protease gene from India.

Abstract

Enterovirus G (EV-G) comprises 20 genotypes (G1-G20) associated with various disease conditions in pig populations. Recombination among homologous EV-G drives virus evolution; however, recombination with a virus from a heterologous family is a rare event. Currently, two types of recombinant EV-G strains containing torovirus papain-like cysteine protease (PLCP) at the 2C-3A junction (Type I) and in place of structural proteins (Type II) are reported. The present study was conducted to reveal the RNA virome in diarrheic piglet feces, retrieving the genome coding for a complete polyprotein of EV-G1. The detected EV-G1 strain represents the first Type I recombinant from India. The polyprotein of the strain exhibiting 97% amino acid identity was closely related to the Chinese strain. The molecular clock analysis estimated that EV-G1-PLCP likely emerged around 1989 in Japan (95% HPD), the inferred substitution rate in study strain was a mean evolutionary rate of 1.23 × 10⁻substitutions per site per year. Furthermore, the EV-G1-PLCP strain was found to originate from South Korean, Chinese, and Japanese strains with breakpoints at nucleotide (nt) positions 1323 and 4725. Genetic and phylogenetic analysis of VP1 and PLCP of the study strain demonstrated its closeness to EV-G1-PLCP strains from South Korea KOR/KNU-1811/2018/G1-PLCP. The present study advances the knowledge about the genetic evolution of EV-G from gaining virulence genes from different virus families.