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

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The first 1000 SARS-CoV-2 genome sequences from Vietnam were analyzed.

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Delta was the major VOC in nine ASEAN countries.

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There are limited sequencing capacities in Laos, Brunei, and Myanmar.

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Strong epidemiological patterns of virus spread were evident after the introduction of VOCs in ASEAN.

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.