First Report of SARS-CoV-2 Lineage B.1.1.7 (Alpha Variant) in Ecuador, January 2021

Figures & data

Table 1 SARS-CoV-2 RT-qPCR Commercial Kits and Ct Values for the First B.1.1.7 or Alpha Strain Identified in Ecuador

SARS-CoV-2 RT Kit	Gene Targets	Ct Values
Cobas SARS-CoV-2 test	E/Orf1ab	27.7/28.2
ECUGEN SARS-CoV-2 RT-PCR kit	N1/N2	25.1/25.6
Allplex TM 2019-nCoV Assay	E/RdRp	25.4/28.8
TaqMan 2019 nCov Assay Kit v1	S/Orf1ab/N	26.0/ 26.1/ 24.0
TaqMan 2019 SARS-CoV-2 Assay Kit v2	S/Orf1ab/N	NA/ 23.3/ 25.3
TaqPath COVID-19 RT-PCR Kit	S/Orf1ab/N	NA/ 25.9/24.6

Abbreviation: NA, Not Amplification.

Figure 1 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.

Figure 2 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.

Figure 3 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.