A cluster of severe acute respiratory syndrome coronavirus 2 infections in Danang, Vietnam, began July 25, 2020, and resulted in 551 confirmed cases and 35 deaths as of February 2021. We analyzed 26 sequences from this cluster and identified a novel shared mutation in nonstructural protein 9, suggesting a single introduction into Vietnam.

Genome-wide population structure analyses showed the presence of linkage disequilibrium and low recombination rates in the SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing novel coronavirus disease 2019 (COVID-19) appeared in Wuhan, Hubei province, China in late December 2019 and has rapidly spread worldwide. In this study, a total of 267 genomes of SARS CoV-2 viruses collected from 28 Center for Diseases Controls and hospitals in different provinces in Northern and Central Vietnam from January 2020 to April 2021 were sequenced and analyzed their diversity using the iSeq 100 platform. Results showed that most of the virus samples originated from domestic community patients (84.3%). Variable variants of SARS CoV-2 virus were detected within the three pandemic waves. The very first variant of SARS-CoV-2 in Viet Nam in January 2020 was 19B (Nextstrain Clade), 3/8 of the variants were from the international arrival samples group. In the first and second pandemic waves, lineage 20B was the most prevalent and this variant was found in Da Nang, Hai Duong and Thai Binh with a large number of patients. In the third wave of the COVID-19 pandemic, lineage 20I was the most dominant and detected in all provinces where the outbreak occurred. Five COVID-19 clusters caused by SARS-CoV-2 variant 20I were also found during this time.

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From January to August 2020, Northern Viet Nam faced a COVID-19 outbreak, up to September 2020, there were 1122 confrmed cases of SARS-CoV-2, of which 465 cases were imported from Europe, America and Asia, 657 cases were identifed domestically. A total of 30,686 samples were collected during the SARS-CoV-2 outbreak in Northern Viet Nam and examined by Real-time RT-PCR using primers and probe from Charite - Berlin protocol. This study showed the initial results of SARS-CoV-2 detection and RNA quantitative in positive samples. The positive rate was 0.8%, ranging from 0.4 to 3.5% according to collection sites. Out of 251 positive samples, the mean Ct value was 28 (IQR: 22.3-32; range 14 - 38). The positive samples had a Ct value below 30 was 68.5%, there was no signifcant difference between the Ct value of the group ≤ 30 and > 30. The mean of the RNA copies/µl was 8.4.107, (IQR: 2.29.106 - 1.83.109 RNA copies/µl, range: 1.95.103 – 4.95.1011). In the group of imported COVID-19 cases, the rate of virus at low level was 29%, an average was 56% and at high level was 15%. In the community groups, the viral load data showed that the average rate at low, intermediate and high level were 20%, 63% and 17% respectively. The proportion of high-level viral load may raise an alert to start the quarantine process to reduce the transmission of SARS-CoV-2