Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China

Leung, KY; Ng, Timothy Ting Leung; Wu, Alan; Yau, Miranda Chong Yee; Lao, Hiu Yin; Choi, Ming Pan; Tam, Kingsley King Gee; Lee, Lam-Kwong; Wong, Bpy; Ho, Alex Yat-Man; Yip, K. T.; Lung, Kwok-Cheung; Liu, Raymond Wai To; Tso, Eugene Yuk‐Keung; Leung, Wai Shing; Chan, Man Chun; Ng, Yuk Yung; Sin, Kit Man; Fung, Kitty Sau Chun; Chau, Sandy Ka Yee; To, Wing‐Kin; Que, Tak Lun; Shum, David; Yip, Shea Ping; Yam, Wing Cheong; Siu, Gilman Kit Hang

doi:10.3201/eid2701.201543

Cited by 14 publications

(12 citation statements)

References 22 publications

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“…Lockdown and travel restriction measures have varied from country to country, which has dictated the profile of local outbreaks. Through the sharing of SARS-CoV-2 sequences during this pandemic, including from one of the first cases in Wuhan, China (MN908947.3) 7 , genomic epidemiology investigations are playing a major role in characterizing and understanding this emerging virus [8][9][10][11][12][13] . SARS-CoV-2 has typically been classified into two main phylogenetic lineages: lineage A and lineage B.…”

mentioning

confidence: 99%

Sixteen novel lineages of SARS-CoV-2 in South Africa

Tegally

Wilkinson

Lessells

et al. 2021

Nat Med

354

374

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The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90) 1 . Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections 2 . In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3 ), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4 ), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5 ).

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mentioning

confidence: 99%

Sixteen novel lineages of SARS-CoV-2 in South Africa

Tegally

Wilkinson

Lessells

et al. 2021

Nat Med

354

374

View full text Add to dashboard Cite

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“…An epidemiological study showed that the cases of 8V were involved in two clusters, “Hotpot dinner gathering at Kwun Tong,” and “Fook Wai Ching She in Maylun Apartments in North Point.” 11 A research group in Hong Kong also detected the 8V viruses for the 50 viruses collected before March 2020. The 8V viruses accounted for 54% of genomes sequenced (27/50) 12 . The 12F was detected from July to September 2020, it coincided with the peak observed during July 2020.…”

Section: Discussionmentioning

confidence: 80%

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

Mak

Lau

Chan

et al. 2021

Journal of Medical Virology

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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.

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“…For WGS of SARS-CoV-2, human DNA was removed from the RNA elutes with the use of Turbo DNA-free Kit (ThermoFisher Scientific, Waltham, MA, USA) [ 8 ]. cDNA was synthesized by using LunaScript RT SuperMix Kit (New England BioLabs Inc. (NEB), Hitchin, UK) and was then amplified by multiplex PCR with Q5 Hot Start High-Fidelity 2X Master Mix Kit (NEB) and ARTIC nCoV-2019 V3 primer sets (Integrated DNA Technologies, Coralville, IA, USA).…”

Section: Methodsmentioning

confidence: 99%

“…Sequencing data were analysed by using the pipelines modified from the ARTIC network nCoV-2019 novel coronavirus bioinformatics protocol [ 8 , 9 ]. In brief, filtered reads with length between 400 and 700 bp were mapped to the reference genome Wuhan-Hu-1 (GenBank no.…”

Section: Methodsmentioning

confidence: 99%

“…1000× bootstrap replications were performed and Mega X version 10.0 ( https://megasoftware.net/ ) was used to plot phylogenetic tree and rooted on the reference genome Wuhan-Hu-1. Bayesian molecular clock analysis with Markov Chain Monte Carlo (MCMC) framework provided by BEAST version 2.6.2 was used to estimate the viral evolutionary rate in substitutions per site per year as published in our previous study [ 8 ].…”

Section: Methodsmentioning

confidence: 99%

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Healthcare workers acquired COVID-19 disease from patients? An investigation by phylogenomics

Wong

Lee

Siu

et al. 2021

Journal of Hospital Infection

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The increasing number of coronavirus disease 2019 cases in the community has posed a significant epidemic pressure on healthcare settings. When healthcare workers (HCWs) acquire COVID-19, contact tracing and epidemiological investigation might not be adequate for determining the source of transmission. Here, we report a phylogenetic investigation involving two infected HCWs and nine patients to determine whether patient-to-HCW transmission had occurred in a hospital without a previous COVID-19 outbreak. This is the first study to apply phylogenomics to investigate suspected nosocomial transmission in a region with low prevalence of COVID-19. Our results do not support the occurrence of direct patient-to-HCW transmission.

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Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China

Cited by 14 publications

References 22 publications

Sixteen novel lineages of SARS-CoV-2 in South Africa

Sixteen novel lineages of SARS-CoV-2 in South Africa

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

Healthcare workers acquired COVID-19 disease from patients? An investigation by phylogenomics

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