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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. [ABSTRACT FROM AUTHOR]

We read with interest the recent article by Cassuto et al.1 about self-testing of rapid antigen detection (RAD) test from coronavirus disease 2019 (COVID-19) individuals. Although patient C was not tested for the RAD test, the Ct value of the throat saliva was 20.71. Under the mandatory quarantine program at the study period, reverse-transcription polymerase chain reaction (RT-PCR) tests were arranged for individuals upon arrival of QCs and the 12th day of quarantine. [Extracted from the article]

Background: Standardized and validated heat inactivation procedure for Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not available. For heat inactivation, various protocols were reported to prepare External Quality Assessment Programme (EQAP) samples without direct comparison between different durations., Objective: To assess the heat inactivation procedures against SARS-CoV-2. The efficacy of the optimized condition was reflected by the results from laboratories testing the EQAP samples., Study Design: The SARS-CoV-2 strain was exposed to 95 °C in a water bath for three different time intervals, 5 min, 10 min and 15 min, respectively. The efficacy of inactivation was confirmed by the absence of cytopathic effects and decreasing viral load in 3 successive cell line passages. The viral stock inactivated by the optimal time interval was dispatched to EQAP participants and the result returned were analyzed., Results: All of the three conditions were capable of inactivating the SARS-CoV-2 of viral load at around cycle threshold value of 10. When the 95 °C 10 min condition was chosen to prepare SARS-CoV-2 EQAP samples, they showed sufficient homogeneity and stability. High degree of consensus was observed among EQAP participants in all samples dispatched., Conclusions: The conditions evaluated in the present study could be helpful for laboratories in preparing SARS-CoV-2 EQAP samples., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

We describe our experiences in investigating the origin of non-specific signals during the development phase of a multiplex PCR assay for respiratory viruses. After ruling out various sources of error, eventually we discovered the non-specific signal was related to the particular lot of the PCR kit., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

Background: Combined nasal-and-throat swabs (CNTS) is less invasive and easy to execute. CNTS also induces lower risk to healthcare workers upon collection. However, there is a lack of data on viral load assessment for population-wide testing., Objective: This study assessed if CNTS is suitable as an alternative specimen type for the detection of SARS-CoV-2., Methods: We assessed the viral load of SARS-CoV-2 in CNTS collected from COVID-19 individuals through the 2-week period of the Universal Community Testing Programme (UCTP) conducted in Hong Kong. In addition, we compared viral loads of SARS-CoV-2 for the paired CNTS and non-CNTS specimens among these individuals., Results: This UCTP identified 48 COVID-19 individuals from nearly 2 million specimens collected. The viral loads of SARS-CoV-2 varied widely, cycle threshold values Ct 16.28-36.94, among symptoms and asymptomatic individuals. The viral loads for the paired CNTS and non-CNTS specimens were comparable., Conclusions: This study demonstrated that CNTS could be a specimen of choice for diagnosis of SARS-CoV-2., (Copyright © 2021 Elsevier B.V. All rights reserved.)

RT-PCR is the gold standard to detect SARS-CoV-2, however, its capacity is limited. We evaluated an automated antigen detection (AAD) test, Elecsys SARS-CoV-2 Antigen (Roche, Germany), for detecting SARS-CoV-2. We compared the limit of detection (LOD) between AAD test, rapid antigen detection (RAD) test; SARS-CoV-2 Rapid Antigen Test (SD Biosensor, Korea), and in-house RT-PCR test. LOD results showed that the AAD test was 100 fold more sensitive than the RAD test, while the sensitivity of the AAD test was comparable to the RT-PCR test. The AAD test detected between 85.7% and 88.6% of RT-PCR-positive specimens collected from COVID-19 patients, false negative results were observed for specimens with Ct values >30. Although clinical sensitivity for the AAD test was not superior or comparable to the RT-PCR test in the present study, the AAD test may be an alternative to RT-PCR test in terms of turn-around time and throughput., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Background: Prior to this report, variants of concern for SARS-CoV-2 were only detected from imported cases in Hong Kong., Objective: Multiple cases of SARS-CoV-2 lineage B.1.351 have been identified in local community. We reported the phylogenetic relationship of these cases., Study Design: SARS-CoV-2 cases were screened for the key non-synonymous substitutions in spike protein by different assays. Preliminary positive cases were further tested by whole genome sequencing., Results: From Dec 2020 to May 2021, 55 SARS-CoV-2 cases belonged to lineage B.1.351. Among them, eight genomes were clustered together, all of them were local cases with epidemiological link., Conclusions: To track variants of SARS-CoV-2 and to allow early implementation of control measures, SARS-CoV-2 genomic surveillance must be consistently performed., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)