[Molecular epidemiological characteristics of human coronavirus NL63 in Shanghai City from 2019 to 2024]

Objective: To investigate the genotype and epidemiological characteristics of Human Coronavirus NL63 (HCoV-NL63) epidemic strains in Shanghai, China. Methods: Whole genome sequencing of HCoV-NL63 was performed with the nucleic acid-positive specimens collected from the acute respiratory infection surveillance system in Shanghai from 2019 to 2024. Phylogenetic, homology, and key mutation site analysis of the S gene were conducted in combination with international reference sequences. Results: Seven whole genome sequences of HCoV-NL63 were obtained, including five (2020-2022) of subtype B2 and two (2024) of subtype C3. The B2 subtype sequences were highly homologous to the Guangzhou 2018 strain, while the C3 subtype sequences were highly homologous to the Japanese 2023 strain. There were 44 amino acid mutation sites located on the S gene of five B2 strains, with E572A in the receptor binding domain (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, closely related to viral virulence. Conclusion: The B2 and C3 subtypes coexist among the prevalent strains in Shanghai, and the related strains are highly homologous to the domestic and international strains causing severe infections, indicating the need to strengthen continuous monitoring and functional research on HCoV-NL63 variants in Shanghai.