Background: Tracking the emergence, introduction and spread of SARS-CoV-2 variants of concern are essential for informing public health strategies. In 2021, Cambodia faced two major epidemic waves of SARS-CoV-2 triggered by the successive rise of the Alpha and Delta variants.
Methods: Phylodynamic analysis of 1,163 complete SARS-CoV-2 genomes from Cambodia, along with global sequences, were conducted between February and September 2021 to infer viral introductions, molecular epidemiology and population dynamics. The relationship between epidemic trends and control strategies were evaluated. Bayesian phylogeographic reconstruction was employed to estimate and contrast the spatiotemporal dynamics of the Alpha and Delta variants over time.
Results: Here we reveal that the Alpha variant displays rapid lineage diversification, accompanied by the acquisition of a spike E484K mutation that coincides with the national implementation of mass COVID-19 vaccination. Despite nationwide control strategies and increased vaccination coverage, the Alpha variant was quickly displaced by Delta variants that exhibits a higher effective reproductive number. Phylogeographic inference indicates that the Alpha variant was introduced through south-central region of Cambodia, with strong diffusion rates from the capital of Phnom Penh to other provinces, while the Delta variant likely entered the country via the northern border provinces.
Conclusions: Continual genomic surveillance and sequencing efforts, in combination with public health strategies, play a vital role in effectively tracking and responding to the emergence, evolution and dissemination of future emerging variants.
Tracking how SARS-CoV-2, the virus that causes COVID-19, changes over time is important for public health. In Cambodia, there were two major COVID-19 waves in 2021, driven by the Alpha and Delta variants. We analyzed 1,163 virus samples from Cambodia, plus samples from other places, to understand how these variants spread. We found that the Alpha variant quickly spread and changed as Cambodia started a mass vaccination campaign. Despite efforts to control it, the Delta variant, which spreads more easily, soon took over. The Alpha variant likely came into Cambodia from the south, while the Delta variant probably entered from the north. Monitoring these changes helps us respond better to future outbreaks.
© 2024. The Author(s).