Complete genome analyses of G12P[8] rotavirus strains from hospitalized children in Surabaya, Indonesia, 2017–2018

Abstract

Rotavirus A (RVA) is a major viral cause of acute gastroenteritis (AGE) worldwide. G12 RVA strains have emerged globally since 2007. There has been no report of the whole genome sequences of G12 RVAs in Indonesia. We performed the complete genome analysis by the next‐generation sequencing of five G12 strains from hospitalized children with AGE in Surabaya from 2017 to 2018. All five G12 strains were Wa‐like strains (G12‐P[8]‐I1‐R1‐C1‐M1‐A1‐N1‐T1‐E1‐H1) and were clustered into lineage‐III of VP7 gene phylogenetic tree. STM430 sample was observed as a mixed‐infection between G12 and G1 strains: G12/G1‐P[8]‐I1‐R1‐C1‐M1‐A1‐N1‐T1‐E1‐H1. A phylogenetic tree analysis revealed that all five Indonesian G12 strains (SOEP379, STM371, STM413, STM430, and STM433) were genetically close to each other in all 11 genome segments with 98.0%–100% nucleotide identities, except VP3 and NSP4 of STM430, suggesting that these strains have originated from a similar ancestral G12 RVA. The VP3 and NSP4 genome segments of STM430‐G12P[8] were separated phylogenetically from those of the other four G12 strains, probably due to intra‐genotype reassortment between the G12 and G1 Wa‐like strains. The change from G12P[6] lineage‐II in 2007 to G12P[8] lineage‐III 2017–2018 suggests the evolution and diversity of G12 RVAs in Indonesia over the past approximately 10 years.