Genetic diversity of G3 rotavirus strains circulating among children with acute gastroenteritis in Nam Dinh and Thua Thien Hue provinces, Vietnam, 2016 - 2021

Abstract

Rotavirus (RV) is the most common cause of severe childhood diarrhea worldwide. Since 2006, the WHO has approved the use of two vaccines against Rotavirus (RotaTeq and Rotarix), which has contributed to a significant reduction in morbidity and mortality from this disease in children under 5 years of age. Beside of that, the presence of vaccines could also cause selective pressure among circulating RV strains. Diarrhea samples were a part of the study of the project “Evaluation of rotavirus vaccine effectiveness in Vietnam” and some diarrhea samples were randomly selected from 2010 - 2015 and were stored in our laboratory. Rotavirus antigen in diarrhea samples was detected using the Premier Rotaclone kit. G and P genotypes were determined by RT-PCR using type specific primers. The nucleotide sequence
was determined by next generation sequencing and phylogenetic analysis was performed by the neighbor-joining method. 375/1715 (21.9%) samples detected G3 strain include equine-like G3 (eG3) and human G3 (hG3). The prevalence of G3 strains decreased from 2016 to 2021. All eleven gene segments were typed among 34 samples and substantial diversity among the circulating strains was observed. The circulating G3 strains were also phylogenetically diverse and related to strains from several different countries, different origins such as human (20 samples), pig (1 sample), cat (3 samples) and equine (10 samples). Comparing with the vaccine strains, the antigenic epitopes present on VP7 of
G3 in Vietnam differed considerably, especially the K238N. With the genetic characteristics of the G3 strain, it could contribute to the vaccine effectiveness in Vietnam.