Objective:To investigate the genetic characteristics of norovirus (NoV) in children with acute gastroenteritis in Shanghai.Methods:A total of 709 stool specimens were collected from outpatients with acute gastroenteritis in Children′s Hospital of Shanghai from October 2018 to September 2019. Real-time RT-PCR was used for qualitative detection of NoV, and RT-PCR was used to identify the genotypes of NoV with the primers of VP1 gene, RdRp region and RdRp-VP1 region. SPSS20.0 statistical software was used for data processing and bioinformatics software was used for homology, phylogenetic and recombination analysis of NoV gene sequences.Results:NoV was detected in 265 out of the 709 stool specimens with a positive rate of 37.4%. Sequence analysis of RdRp region and VP1 gene showed that seven different genotypes including GⅡ.P16-GⅡ.2, GⅡ.P12-GⅡ.3, GⅡ.Pe-GⅡ.4_Sydney 2012, GⅡ.P7-GⅡ.6, GⅡ.P8-GⅡ.8, GⅡ.P21-GⅡ.13 and GⅡ.P17-GⅡ.17 were detected from 111 NoV-positive specimens. The predominated genotype was GⅡ.P16-GⅡ.2 (30.6%, 34/111), followed by GⅡ.Pe-GⅡ.4_Sydney 2012 (27.0%, 30/111) and GⅡ.P12-GⅡ.3 (24.3%, 27/111). Two new NoV recombinant strains belonging to GⅡ.P21-GⅡ.13 genotype were identified and the recombination site was in the junction region of ORF1 and ORF2. NoV infection occurred every month, but the predominant genotype was different. No significant difference in the positive rates of NoV was found between male and female patients ( P=0.329). However, there were significant differences between different age groups ( P=0.011) and the children in the age groups of >11-12 years old and >2-3 years old had higher rates of NoV infection. Conclusions:The predominated recombinant NoV strains belonged to GⅡ.P16-GⅡ.2, GⅡ.Pe-GⅡ.4_Sydney 2012 and GⅡ.P12-GⅡ.3 genotypes, and two new recombinant NoV strains (GⅡ.P21-GⅡ.13) were found in Shanghai during October 2018 to September 2019. Gene sequencing across ORF1 and ORF2 was conducive to better understanding the NoV genotypes and recombination.

ObjectiveTo conduct the sequencing and preliminarily analysis of the whole genome of BCG Shanghai D₂PB302 strain （hereinafter referred to as BCG Shanghai D₂ strain）， which has been used exclusively for the vaccine production in China. MethodsThe DNA of of BCG Shanghai D₂ strain （D2-JIA12-1） was extracted， and the whole genome was sequenced by Pacbio-RS Ⅱ. The sequence data was assembled by Smrtlink and polished with the illumina data. Genes， tRNA and rRNA were predicted based on the sequence data. The functional annotation of predicted genes was performed through BLASTP. The IVE-TB antigen gene and MTBVAC were selected as the target sequences to be compared with Mycobacterium tuberculosis H37Rv （NC_000962.3）. ResultsThe sequence length of BCG Shanghai D₂ strain was 4 045 232 bp， and the GC content was 65.66%. A total of 4 259 protein-encoding genes were predicted， with an average gene size of 933 bp. 2 476 genes had biological functions and others were hypothetical proteins.144 virulence genes were obtained by comparing with the VFDB. There were 29 type Ⅶ secretion system genes and 10 PE/PPE protein family genes. ConclusionThe whole genome sequence of BCG Shanghai D₂ strain is clarified. It lays a broad foundation for subsequent detection of the stability of major antigen genes.