The Emergence of Sars-CoV-2 Variant Lambda (C.37) in South America

We report the emergence of a novel lineage of SARS-CoV-2 in South America, termed C.37. It presents seven nonsynonymous mutations in the Spike gene ({Delta}247-253, G75V, T76I, L452Q, F490S, T859N) and a deletion in the ORF1a gene ({Delta}3675-3677) also found in variants of concern (VOCs) Alpha, Beta, and Gamma. Initially reported in Lima, Peru, in late December 2020, it now accounts for 97% of Peruvian public genomes in April 2021. It is expanding in Chile and Argentina, and there is evidence of onward transmission in Colombia, Ecuador, Mexico, the USA, Germany, and Israel. On June 15, 2021, the World Health Organization designated C.37 as Variant of Interest (VOI) Lambda.

The earliest record of C.37 on GISAID is from Argentina in November 2020. By June 19, 2021, there were 1771 C.37 sequences from 25 countries, including Chile (n=670), USA (n=510), Peru (n=222), Argentina (n=86), Germany (n=79), Mexico (n=55), Spain (n=40), and Ecuador (n=39). Beyond Peru, C.37 has expanded rapidly in Chile and Argentina, reaching 33% and 12% of all sequenced genomes on GISAID by April 2021, respectively ( Figure 2). The emergence of this lineage in Peru and its export to other countries is a current hypothesis, given its earlier detection and rise to nearly 100% of public sequences by April. We are sequencing additional Peruvian samples from October to December 2020 to confirm and date the origin of C.37.
Expansion of C.37 has occurred in South America in the presence of hundreds of circulating lineages and VOCs Alpha and Gamma ( Figure 1B), suggesting increased transmissibility of this lineage. However, additional epidemiological data and analyses are needed to assess its transmission, virulence, and immune escape properties.
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The copyright holder for this preprint this version posted July 3, 2021. ; https://doi.org/10.1101/2021.06.26.21259487 doi: medRxiv preprint Peruvian genomes were generated at Universidad Peruana Cayetano Heredia and Instituto Nacional de Salud using the Illumina COVIDseq or the Qiagen SARS-Cov-2 panel and QIAseq FX DNA library kits. Libraries were sequenced on Illumina MiSeq and NextSeq 550 instruments. Reads were processed and assembled with the Illumina DRAGEN COVID pipeline or a custom pipeline based on MEGAHIT v1.2.9. Assemblies with an average base coverage higher than 1000x were submitted to GISAID.

Data availability
All analyzed sequences were publicly available in GISAID at the time of manuscript submission. Raw Illumina reads from 350 Peruvian genomes sequenced at UPCH are available at NCBI BioProject PRJNA667090.  (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.  Gene   Amino acid   N  P13L, R203K, G204R, G214C, T366I   ORF1a T1246I, P2287S, F2387V, L3201P, T3255I, G3278S,   (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.