Early detection of community acquired of SARS-CoV-2 lineage B.1.351 in Hong Kong

WHO. The effects of virus variants on COVID-19 vaccines. Available at: https://www.who.int/news-room/feature-stories/detail/the-effects-of-virus-variants-on-covid-19-vaccines (Accessed 11 June 2021). Public Health England. Investigation of novel SARS-CoV-2 variant Variant of Concern 202012/01. Version 1, release date 21/122020. Available at: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/959438/Technical_Briefing_VOC_SH_NJL2_SH2.pdf (Accessed 11 June 2021). Tegally, 2020, Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa, bioRxivorg Voloch, 2021, Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil, J. Virol., JVI.00119 Zhang, 2021, Emergence of a novel SARS-CoV-2 variant in Southern California, JAMA, 10.1001/jama.2021.1612 Yadav, 2021, Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees, Clin. Infect. Dis., ciab411, 10.1093/cid/ciab411 Walls, 2020, Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein, Cell, 181, 281, 10.1016/j.cell.2020.02.058 Hong Kong Free Press. Covid-19: gov't barring Hongkongers returning from UK, despite earlier stance on returnees from China, 24 December 2020. Available at: https://hongkongfp.com/2020/12/24/covid-19-govt-barring-hongkongers-returning-from-uk-despite-earlier-stance-on-returnees-from-china/ (Accessed 11 June 2021). Radio Television Hong Kong. HK sees first mutant Covid strain from South Africa, 31 December 2020. Available at: https://news.rthk.hk/rthk/en/component/k2/1568042-20201231.htm (11 June 2021). Mak, 2021, The surveillance of spike protein for patients with COVID-19 detected in Hong Kong in 2020, J. Med. Virol., 10.1002/jmv.27063 Centre for Health Protection. Latest situation of cases of COVID-19. Available at: https://www.chp.gov.hk/files/pdf/local_situation_covid19_en.pdf (Accessed 11 June 2021). The Government of the Hong Kong Special Administrative Region. https://www.info.gov.hk/gia/general/today.htm (Accessed 11 June 2021). COVID-19 in HK (Accessed 11 June 2021). https://wars.vote4.hk/en/cases. Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2. Li, 2011, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, 27, 2987, 10.1093/bioinformatics/btr509 Katoh, 2002, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res., 30, 3059, 10.1093/nar/gkf436 Minh, 2020, IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era, Mol. Biol. Evol., 37, 1530, 10.1093/molbev/msaa015 The Government of the Hong Kong Special Administrative Region. Government to gazette compulsory testing notice and specifications under Prevention and Control of Disease (Compulsory Testing for Certain Persons) Regulation. Available at: https://www.info.gov.hk/gia/general/202105/01/P2021050100026.htm (Accessed 11 June 2021).