Genetic analysis of rotavirus G2P[4] strains in Pune, Western India: circulation of a novel reassortant bearing E6 NSP4 genotype

Abstract

In India, G2P[4] strains are known to be the second most predominant group A rotaviruses causing acute gastroenteritis among children. This study was performed to determine the diversity within VP7(G), VP4(P), VP6(I) and NSP4(E) genes of 16 G2P[4] rotavirus strains detected in children hospitalized for acute gastroenteritis in Pune, Western India during 2009-2013. Fourteen strains showed G2-P[4]-I2-E2 and two strains showed G2-P[4]-I2-E6 genotype constellation. Phylogenetic analysis showed their clustering into G2-IV-a3, P[4]-5bi/ii, I2-3ii and E2-4i/ii or E6 genotypes/lineages. These data reveal inter- and/or intra-genotypic variations in a genogroup-2 constellation of G2P[4] rotavirus strains circulating in Pune, Western India, providing evidence of a novel G2P[4] reassortant bearing a rare NSP4 genotype, E6 during 2009-2013.

Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations

“…During the same year, it was reported from New Delhi, India in combination with G8P[6] [ 48 ]. Later in 2017, it was reported with G2P[4] strains from Pune, India, in samples from 2009 to 2013 [ 49 ]. E6-NSP4 has now been reported only from the human hosts and is emerging in different geographical locations among the DS-1 like strains mostly and Wa-like strains in rare occasions.…”

Driving forces of continuing evolution of rotaviruses

“…Genogroup 1 or Wa-like has a genotype constellation G1/3/4/9/12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 ; genogroup 2 or DS-1-like has the genotype constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 ; and genogroup 3 or AU-1-like has a genotype constellation G3-P[9]-I3-R3-C3-M3-A3-N3-T3-E3-H3 [ 12 ]. Reassortment that occurs in intra-genogroups will produce reassortants that have variations at the subgenotype level[ 39 , 40 ]. Rotavirus reassortment rarely occurs across genogroups because the viral progeny tends to have low survival.…”

“…Similar to other pathogenic RNA viruses, the incidence of rotaviruses in various countries which shows genotypic differences fluctuating over time has also shown its dynamic evolution. The evolution of rotavirus is influenced by a number of driving factors, such as vaccine introduction, the host immune responses, and antiviral drugs[ 17 , 21 , 39 , 40 , 42 , 43 ].…”