PMC8664343_01
The 17 mutations defining lineage B.1.1.7 or alpha (clade 501.YV1). All the mutations are shared between the genome assembled for the first record of this variant in Ecuador and the reference genome for the clade.
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Alpha VOC. Alignment with the reference genomes "isolate Wuhan-Hu-1" GenBank (ID: NC_045512.3) and "VOC Alpha 202012/01 first detected in the UK" GISAID (ID: EPI_ISL_601443) showed that the sequence obtained contains the 17 mutations defining the Alpha variant or 501.YV1 clade, as well as other 4 mutations shared with the Wuhan-Hu isolated (Figure 1).
Maximum likelihood phylogeny of a sample of B.1.1.7 Pango lineage/VOC Alpha genomes from Europe, Latin America and North America. Names of key sequences from Ecuador are featured; the first sequence from Ecuador is shown in red, a selection of additional sequences produced by the national genomic surveillance scheme are shown in blue, and genomes from international locations are shown in grey.
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Phylogenetic analysis with a selection of alpha genomes from Ecuador, North America, Latin America and Europe, using RAxML-NG under a GTR substitution model and 1000 bootstrap replicates, confirms the genome identity as a proximal descendant from EPI_ISL_601443, a genetically similar sequence reported in England in September 2020 (Figure 2), and show different clusters of the variant in Ecuador (Figure 2).
Number of SARS-CoV-2 =VOC and VOI submitted to GISAID from Ecuador from January 2021. The figure shows the number of cases detected by week.
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Following the detection of the index case different sequencing laboratories in Ecuador reported an increasing number of alpha genomes to GISAID, alpha variant was the most frequent VOC until June 2021, before gamma and delta were detected in the country (Figure 3).