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Randomized Controlled Trial
. 2023 Nov 17;23(1):806.
doi: 10.1186/s12879-023-08814-8.

Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020-2021

Anna S Gladkikh  1 , Thang M Cao  2 , Ekaterina O Klyuchnikova  3 , Manh H Dao  2 , Alena A Sharova  1 , Vasilina D Melnichenko  1 , Margarita R Popova  1 , Tatiana V Arbuzova  1 , Valeriya A Sbarzaglia  1 , Nadezhda A Tsyganova  1 , Edward Ramsay  1 , Vladimir G Dedkov  1   4
Affiliations
Randomized Controlled Trial

Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020-2021

Anna S Gladkikh et al. BMC Infect Dis. .

Erratum in

Abstract

Background: Since its beginnings in 2019, the COVID-19 pandemic is still a problem of global medical concern. Southern Vietnam is one of the country's vast regions, including 20 provinces and the densely populated metropolis Ho Chi Minh City. A randomized retrospective study was performed to investigate the epidemiology and genetic diversity of COVID-19. Whole-genome sequencing of 126 SARS-CoV-2 samples collected from Southern Vietnam between January 2020 and December 2021 revealed the main circulating variants and their distribution.

Methods: Epidemiological data were obtained from the Department of Preventive Medicine of the Vietnamese Ministry of Health. To identify circulating variants, RNA, extracted from 126 nasopharyngeal swabs of patients with suspected COVID-19 were sequenced on Illunina MiSeq to obtain near complete genomes SARS-CoV-2.

Results: Due to the effectiveness of restrictive measures in Vietnam, it was possible to keep incidence at a low level. The partial relaxation of restrictive measures, and the spread of Delta lineages, contributed to the beginning of a logarithmic increase in incidence. Lineages 20A-H circulated in Southern Vietnam during 2020. Spread of the Delta lineage in Southern Vietnam began in March 2021, causing a logarithmic rise in the number of COVID-19 cases.

Conclusions: Pandemic dynamics in Southern Vietnam feature specific variations in incidence, and these reflect the success of the restrictive measures put in place during the early stages of the pandemic.

Keywords: COVID-19; Morbidity; NGS; SARS-CoV-2 lineages; Vietnam.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
COVID-19 incidence rate in Southern Vietnamese regions in 2020. Due to restrictions on movement and border crossing under strict quarantine, the incidence in 2020 in Southern Vietnam was sporadic. The incidence did not exceed 0.2 per 100,000 population
Fig. 2
Fig. 2
COVID-19 incidence rate in Southern Vietnamese regions in 2021. During the first five months of 2021, the incidence rate remained at a consistently low level. In May 2021, the incidence rate increased to 0.8 per 100,000 population. Since June 2021, there has been an increase in the number of cases from 16.8 in June to 851.9 by December 2021
Fig. 3
Fig. 3
SARS-CoV-2 phylogenetic tree reconstruction based on Nextclade tools. Branches are labeled by lineage according to Nextstrain nomenclature (legend top left). Sequences obtained in this study are colored red. The scale bar at the bottom indicates the number of nucleotide differences between each sample and the Wuhan-Hu-1/2019 reference sequence (GenBank: MN908947)
Fig. 4
Fig. 4
Phylogenetic comparison and heatmap analysis of variations observed in clades 19A-B and 20A-H. The figure shows the phylogenetic diversity and analysis of variations observed in lineages 19AB and 20A-H based on S gene sequence. Mutations were found relative to the Wuhan-Hu-1/2019 (GenBank: MN908947) reference strain. SGSV – S gene sequence variants. Clades in which this pattern occurs are indicated in parentheses. The number of strains of the specified variant in the studied group is indicated by a colon
Fig. 5
Fig. 5
Phylogenetic comparison and heatmap analysis of variations observed in Delta clades. In 2021, most strains from domestic and imported cases were in the Delta VOC, major lineage 21I, and minor lineages 21A and 21J. The figure shows the phylogenetic diversity and analysis of variations based on S gene sequence. Mutations were found relative to the Wuhan-Hu-1/2019 (GenBank: MN908947) reference strain. SGSV – Sgene sequence variants. Clades in which this pattern occurs are indicated in parentheses. The number of strains of the specified variant in the studied group is indicated by a colon
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