Résumé
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
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COVID-19Résumé
Here, we report two sequences of the new SARS-CoV-2 variant recently detected and designed as B.1.526. This variant carries the immune escape-associated mutation E484K and additional mutations in the S, N, NSP2, NSP3, NSP4, NSP6, NSP8, NSP12 and NSP13 genes. Viral sequences were obtained from an individual traveling from the US to Equator with a negative RT-PCR and from one of his closest contacts that became infected. These cases should be considered an alert for the potential circulation of a new variant of concern with the E484K mutation in South America