key: cord-0941510-5wh7c02k authors: Tsang, Alan KL; Mak, Gannon CK; Cheng, Peter KC; Yip, Peter CW; Ng, Ken HL; Lam, Edman TK; Chan, Rickjason CW; Tsang, Dominic NC title: Early detection of community acquired of SARS-CoV-2 lineage B.1.351 in Hong Kong date: 2021-06-14 journal: Journal of clinical virology plus DOI: 10.1016/j.jcvp.2021.100029 sha: 47ee770b277f52cee7fedd0d96b79f7ce215c232 doc_id: 941510 cord_uid: 5wh7c02k Background : Prior to this report, variants of 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 S gene 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. The SARS-CoV-2 has been spreading around the world since 2019 and its variants harboring various mutations have been increasingly identified (henceforth: 'variant' stands for virus with one or more mutations that are different from Wuhan-Hu-1 reference sequence (GenBank accession no. MN908947.3) [1] . These variants share common features, notably a high genetic changes in the spike (S) protein [2] [3] [4] [5] [6] which is a key target for vaccine, virus entry and infectivity [7] . In Hong Kong, the Public Health Laboratory Services Branch (PHLSB) implemented intensive surveillance system targeting incoming travelers to Hong Kong in December 2020. Variants of SARS-CoV-2 B.1.1.7 (the PANGO lineage nomenclature system is used throughout the article) and B.1.351 were identified last year [8, 9] . These two variants demonstrated high non-synonymous substitutions in the S protein when compared with other SARS-CoV-2 viruses detected in Hong Kong in 2020 [10] . Although SARS-CoV-2 variants were identified worldwide, they were only detected from imported cases in Hong Kong. In early April 2021, 11 cases of the SARS-CoV-2 B.1.351 were identified in local community setting. Here, we report the early detection community acquired variants of SARS-CoV-2 cases in Hong Kong. In Hong Kong, all COVID-19 confirmed cases were either diagnosed or confirmed by PHLSB. Contact tracing investigations were conducted by Communicable Disease Branch. Epidemiological information of confirmed cases were announced to the public through daily press conference. Epidemiologic information described in the manuscript were retrieved from public datasets [11] [12] [13] . From December 2020, all SARS-CoV-2 cases were screened for the key non-synonymous substitutions in S gene by partial S gene sequencing and/or real-time RT-PCR assays. Majority worldwide circulating variants were screened out. These in-house developed protocols are available on request. In brief, the RNA of the original specimens were put to RT-PCR. Sanger sequencing of the partial length covering 400-530 amino acid positions of S protein were performed using a pair of primers. Four different SNP real-time RT-PCRs were designed with probes targeting 452R, 484K, 484Q and 501Y. All of them were located in the S gene. These four PCRs could screen out variants including B. Preliminary SARS-CoV-2 variants positive cases were then put to whole genome sequencing. For whole genome sequencing, extracted RNA was reverse transcribed to cDNA using LunaScript® RT SuperMix Kit followed by PCR amplification using the ARTIC BWA [14] . The iVar v1.3.1 was used to trim primer sequences from the aligned reads. Variant calling and consensus sequence generation were performed using SAMtools version v 1.12 and iVar v1.3.1 [15] . The consensus sequences generated in the present study have been deposited into GISAID (Appendix). Multiple sequence alignment was performed using MAFFT [16] . The maximum-likelihood whole genome phylogenetic tree was constructed using IQ-TREE v 2.1.2 using a GTR substitution model and the -czb option with 1000 bootstrap replicates (17). The first local SARS-CoV-2 case having 484K and 501Y was reported on 17 Apr 2021. The case was a 29-year-old male (Patient 1) who arrived in Hong Kong from Dubai on 19 March 2021 (Table) . SARS-CoV-2 tests were negative throughout the The Wuhan-Hu-1 strain was included as reference sequence (GenBank accession no. MN908947). Our data showed that during the six-month period of surveillance, we were capable of identifying the first local SARS-CoV-2 B. May 2021. It is expected that variant of different types will be encountered in future. To track variants, control measures and SARS-CoV-2 genomic surveillance must be regularly performed to provide early warning on potential origins of cases so that effective control measures can be implemented on time. We thank all staff of the Microbiology Division, Public Health Laboratory Services Branch, and Communicable Disease Branch, Centre for Health Protection, for technical assistance and epidemiological information during the current SARS-CoV-2 pandemic. The effects of virus variants on COVID-19 vaccines Investigation of novel SARS-CoV-2 variant Variant of Concern 202012/01. 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Government to gazette compulsory testing notice and specifications under Prevention and Control of Disease (Compulsory Testing for Certain Persons) Regulation ☒ 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.☐The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: