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Abstract

We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions.

Keywords: Alpha variant; COVID-19; Delta variant; SARS-CoV-2; Vietnam; coronavirus disease; coronaviruses; outbreak; respiratory infections; severe acute respiratory syndrome coronavirus-2; spatiotemporal evolution; viruses; zoonoses.

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Figures

Figure 1
Figure 1
Maximum-likelihood tree of SARS-CoV-2 Alpha and Delta variants during large nationwide outbreak of COVID-19, Vietnam, 2021. Complete coding sequences of Alpha variant viruses circulating in Vietnam in 2021 are shown. Phylogenetic clusters were named accordingly to community clusters recorded during the study period shown in Appendix Figure 1). Numbers along branches are bootstrap values. Cluster II was linked with a traveler from Japan (Appendix Figure 1). Outgroup was the SARS-CoV-2 wild-type strain (GenBank accession no. NC_0455122).
Figure 2
Figure 2
Spatiotemporal evolution of SARS-CoV-2 Alpha and Delta variants during large nationwide outbreak of COVID-19, Vietnam, 2021. Maximum clade credibility tree illustrates the phylogeography of AY.57 lineage in Vietnam in 2021, Branches are color-coded according to locations of sampling shown on map. Numbers along branches are bootstrap values. Posterior probabilities >0.8% and state probabilities >75% (black circles) are indicated at all nodes.
Figure 3
Figure 3
Genetic diversity and distribution of SARS-CoV-2 AY.57 lineage during large nationwide outbreak of COVID-19, Vietnam, 2021. A) Bayesian skyride plot illustrating the relative genetic diversity of AY.57 lineage in Vietnam during 2021. Purple shading indicates 95% highest posterior density interval. B) Distribution of the number of AY.57 sequences used for analysis over the study period.
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References

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Supplementary concepts