SARS-CoV-2 viral dynamics of the first 1000 sequences from Vietnam and neighbouring ASEAN countries

Abstract

Objective: The regional distribution and transmissibility of existing COVID-19 variants of concern (VOC) has led to concerns about increasing transmission, given the ability of VOCs to evade immunity as breakthrough infections become more prevalent.

Methods: SARS-CoV-2 genomes (n = 277) were sequenced and analysed alongside all available genomes from Vietnam and ASEAN countries to understand the phylodynamics. The observed lineages were assigned using Pangolin nomenclature, and spread patterns were investigated.

Results: Between January and November 8, 2021, VOCs, including alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2), were observed across the ASEAN countries. While alpha and delta were the major VOCs in nine ASEAN countries, delta was predominant. The alpha VOC was first reported by Singapore, beta by Malaysia, gamma by the Philippines, and delta by Singapore. Of the first 1000 genomes analysed from Vietnam, alpha and delta were the most represented, with delta being the dominant VOC from May 2021. The delta variant was introduced in early January 2021, and formed a large cluster within the representative genomes.

Conclusion: Spatial and temporal monitoring of SARS-CoV-2 variants is critical to the understanding of viral phylodynamics, and will provide useful guidance to policy makers for infection prevention and control.

Keywords: ASEAN; B.1.614.2; COVID-19; SARS-CoV-2; VOC; Vietnam; delta variant; variants of concern.

Figure 1

Distribution of SARS-CoV-2 variants of concern in ASEAN countries between December 2020 and November 8, 2021.

Figure 2

Distribution of SARS-CoV-2 lineages and VOCs in Vietnam between January 2020 and November 8, 2021.

Figure 3

Phylogenetic tree representing SARS-CoV-2 variants over space and time from nine ASEAN countries represented by different colours, reconstructed using Nextstrain algorithms (https://nextstrain.org/).