Whole-genome sequence analysis of four human coronavirus NL63 strains regionally prevalent in Shenzhen, 2020

ABSTRACT

In this study, the genomic RNA of HCoV-NL63 from throat swab samples obtained from cases of respiratory tract infection was sequenced. The cases were collected from clustered or sporadic epidemics in the Nanshan district of Shenzhen City in 2020. Four whole genomes of HCoV-NL63 strains were obtained and analyzed with phylogenetic tree reconstruction and other bioinformatics analyses. The sequence similarity among the four strains was 99.80%~99.98% for nucleotides and 99.64%~99.93% for amino acids. The four strains of HCoV-NL63 belonged to the B genotype, B2 subgenotype, which were on the same branch of the phylogenetic tree and were genetically closest to MK334046.1. Analysis of the amino acid variation sites of the S protein indicated that L196F was present in the strains obtained from sporadic epidemic cases, and A946S was present in the strains acquired from clustered epidemic cases. The prediction of N-glycosylation sites indicated ten N-glycosylation sites in S protein and two N-glycosylation sites in M protein. Through whole genome sequencing and feature analysis, we determined that the HCoV-NL63 obtained in this study probably originated from the Guangzhou virus strain. Our current results provide some clues as to the basis for biological traceability, and might facilitate future epidemic prevention and control.