Epidemiological characteristics of viruses causing diarrhea and whole-genome features of rotavirus A in Gansu, 2018−2020

  Objective  To understand the circulation and whole-genome features of rotavirus A in Gansu province during 2018−2020.

  Methods  Stool samples were collected from children with diarrhea in 6 sentinel hospitals in Gansu for the extraction of viral nucleic acids of rotavirus A, adenovirus , norovirus, astrovirus and sapovirus with real-time PCR, and the DNA sequencing library of partial rotavirus positive samples were constructed following the instructions, the gene sequencing was conducted by the second generation sequencing method, and the sequencing data were analyzed by phylogenetic software.

  Results  In the 2 553 stool samples collected, 853 were positive in nucleic acid test of adenovirus, norovirus, astrovirus, sapovirus and rotavirus (33.41%). The detection rate of rotavirus was highest (17.43%), followed by norovirus (12.65%), adenovirus (6.58%), astrovirus (4.70%) and sapovirus (1.02%). In the gene sequencing of 50 rotavirus positive samples, the full sequences of 31 strains were obtained, including 24 G9P［8］ strains, 2 G2P［8］ strains, 3 G2P［4］ strains,1 G9P［6］ strain and 1 G9P［4］ strain. Whole genome analysis suggested that except the VP7 segment, the VP3 and NSP4 segments also had more obviously differences in all the 31 strains. This study obtained 21 G9P［8］ Wa-like strains (G9-P［8］-I1-R1-C1-M1-A1-N1-T1-E1-H1), 3 G9P［8］-E2 strains (G9-P［8］-I1-R1-C1-M1-A1-N1-T1-E2-H1), and G9P［8］-E2 strains accounted for12.5% (3/24) in 24 rotavirus G9P［8］ strains sequenced.

  Conclusion  Rotavirus was the major pathogen causing diarrhea in children in Gansu during 2018−2020, G9P［8］ was the most predominant genotype, and G9P［8］-E2 reassortant strain was detected for the first time . It is necessary to continue the surveillance for virus variation.