The surveillance of spike protein for patients with COVID‐19 detected in Hong Kong in 2020

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.

Comparison of analytical sensitivity of the eight rapid antigen detection kits for detecting SARS-CoV-2 virus

“…This local strain represented the peak of COVID-19 cases detected in Hong Kong between July-August 2020 which was characterized by the 12F amino acid in the spike protein. It was only detected in this specific time interval and then disappeared [12] .…”

“…They are different from the SARS-CoV-2 strains detected in Hong Kong. Our S gene surveillance [11] showed that these two variants harbored ≥10 non-synonymous substitutions, while the Hong Kong cases sequenced between Jan 2020 to Dec 2020 harbored only a maximum of four non-synonymous substitutions [12] . Since the viral load of clinical specimens for 501Y.V1 were high, serial dilution could be performed and hence, 501Y.V1 was selected in the present study.…”

The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia

“…For mapping and quantification of the contributions of D614 and G614 viruses in countries, we relied on the tracking Web site () and for the regional geographical distribution within and outside of India we consulted multiple sources. ,− ,− ,− ,, Our study followed the PRISMA guidelines for systematic reviews and meta-analyses . We searched the COVID-19 portfolio of the National Institutes of Health () with the keywords, “anosmia” or “smell” and “India”, “Bangladesh”, “Pakistan” on and before July 22, 2021, resulting in 598 records.…”

Assessment of SARS-CoV-2 viral loads in combined nasal-and-throat swabs collected from COVID-19 individuals under the Universal Community Testing Programme in Hong Kong

“…Early detection of SARS-CoV-2 within a population is important for controlling and preventing the spread of COVID-19. In Hong Kong, two peaks of COVID-19 cases were observed before August 2020, namely during March–April 2020 and July–August 2020 [ Mak et al, 2021a ]. In order to eliminate COVID-19 in the community, the Hong Kong Special Administrative Region (HKSAR) government launched the Universal Community Testing Programme (UCTP) on 1 September 2020.…”