Genotype Identification and Genetic Characteristics of HCoV⁃NL63 Strains prevalent in Shanghai

Objective To identify the genotype of HCoV-NL63 strains prevalent in Shanghai and analyze the genetic characteristics of viral genome.Methods HCoV-NL63 positive samples were collected from Shanghai acute respiratory infection surveillance system from 2019 to 2024, whole genome sequences were obtained by next generation sequencing. Phylogenetic analysis based on S gene, orf1ab gene as well as whole genome sequence was conducted respectively. Sequence homology analysis of the whole genome and amino acid mutation site analysis of S gene were also conducted.Results Seven whole genome sequences of HCoV⁃NL63 were obtained from 16 positive samples. Compared to Guangzhou strains obtained in 2018, amino acid sequence identity of five B2 strains in this study was 99.3%-99.8%, and the nucleotide sequence identity was 99.6%-99.9% . Compared to Fukushima strains obtained in 2023, amino acid sequence identity of two C2 strains in this study was 99.8%~99.9%, the nucleotide sequence identity 99.9%. Compared with the original strain NC005831, there were 44 amino acid mutation sites located on S gene of five B2 strains, among which E572A was in the RBD region. There were 15 amino acid mutation sites in the S gene of C3 subtype, with I507L and E572A in the RBD region and I507L as the signature mutation of C3 subtype that was closely related to viral virulence.Conclusion Seven HCoV-NL63 sequences obtained in this study covered B2 subtype and C3 subtype. Five B2 strains appears on the same branch of the phylogenetic tree with Guangzhou strains that detected in 2018, and two C3 strains are on the same branch with Fukushima strains detected in 2023.