key: cord-1007826-v62hzpqj
authors: Chau, Dr Nguyen Van Vinh
title: Rapid whole-genome sequencing to inform COVID-19 outbreak response in Vietnam
date: 2021-03-25
journal: J Infect
DOI: 10.1016/j.jinf.2021.03.017
sha: 48a98ef58773d30d4e48ee7395b083e23fcdb95c
doc_id: 1007826
cord_uid: v62hzpqj

nan

The rapid expansion of the outbreak in the north, possibly caused by variant B.1.1.7, raised 27 concerns about a nationwide outbreak (Supplementary Figure 1A) . This prompted HCMC to 28 conduct enhanced surveillance for SARS-CoV-2, primarily focusing on high-risk groups, including 29 those working at Tan Son Nhat (TSN) international and domestic airport in HCMC. Subsequently, 30 a baggage handler (patient 2) working at the airport and his brother (not working at the airport) 31

were found positive for SARS-CoV-2 on 6 th February. The next day, four co-workers (patients 3-6) 32 of patient 2 also tested positive for SARS-CoV-2, while all contacts of patient 2's brother were 33 negative. At this time, the outbreak in the north had expanded to another 10 provinces/cities 34 (Supplementary Figure 1B) . 35

To dissect the epidemiological picture of the ongoing outbreak, we whole genome sequenced 36 SARS-CoV-2 from the NTS of patients 2-6 using the ARTIC protocol. We obtained 3 complete 37 genomes (1 from patient 2 on 8 th February, and 2 from patients 3 and 4 on 10 th February). All were 38 assigned to sub-lineage A.23.1 (Pangolin). 39

After the detection of these six confirmed cases, contact tracing and testing detected 30 additional 40 PCR confirmed cases, totaling 36 infected cases, including 9 members of TSN airport staff in total 41

[3]. The remaining cases were contacts of these 9 individuals (data not shown). Two additional 42 SARS-CoV-2 whole genomes were successfully obtained from a brother of patient 6 and one of the 43 airport staff; all belonged to A.23.1. 

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