ABSTRACT
In 2020, numerous fast-spreading severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been reported. These variants had unusually high genetic changes in the spike (S) protein. In an attempt to understand the genetic background of SARS-CoV-2 viruses in Hong Kong, especially before vaccination, the purpose of this study is to summarize the S protein mutations detected among coronavirus disease 2019 (COVID-19) patients in Hong Kong in 2020. COVID-19 cases were selected every month in 2020. One virus from each case was analyzed. The full encoding region of the S proteins was sequenced. From January 2020 to December 2020, a total of 340 COVID-19 viruses were sequenced. The amino acids of the S protein for 44 (12.9%) were identical to the reference sequence, WIV04 (GenBank accession MN996528). For the remaining 296 sequences (87.1%), a total of 43 nonsynonymous substitution patterns were found. Of the nonsynonymous substitutions found, some of them were only detected at specific time intervals and then they disappeared. The ongoing genetic surveillance system is important. It would facilitate early detection of mutations that can increase infectivity as well as mutations that are selected for the virus to escape immunological restraint.
