Whole genome analysis on rotavirus isolated in outbreak in Ninghe district of Tianjin, 2020

  Objective  To understand the whole genome characteristics of rotavirus A strains isolated from acute gastroenteritis cases in an outbreak in Ninghe district of Tianjin in 2020.

  Methods  The viral nucleic acids of rotavirus isolated from positive stool samples collected in Ninghai were extracted for real-time PCR confirmation, the sequencing library 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, and 11 gene fragments full-genome sequences were analyzed by homology and phylogenetic analyses.

  Results  Complete gene sequences of 4 strains of rotavirus were obtained successfully by the second generation sequencing method. All the strains shared >99% homology and showed the Wa-like constellation G9-P［8］-I1-R1-C1-M1-A1-N1-T1-E1-H1. Furthermore, phylogenetic analysis revealed that the VP7 genes belonged to lineage G9-VI and the VP4 sequences belonged to lineage P［8］-3. Amino acid substitutions were observed in the antigenic regions of the VP7 and VP4 gene. The nonstructural protein 4 (NSP4) genes contained multiple substitutions in antigenic sites Ⅰ and Ⅱ. The other NSP genes were conserved.

  Conclusion  The study revealed that rotavirus G9-VI and P［8］-3 were the pathogens of this outbreak. The variations of the 4 strains were minor compared with the circulating strain. The continuous surveillance and analysis of the whole genomic constellation of circulating rotavirus strains needs to be strengthened to provide evidence for the prevention and control of rotavirus infection.