Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

TORRES, CAROLINA; CERIANI, CAROLINA

Frontiers in Medicine

Frontiers

Año: 2021 vol. 8

SARS-CoV-2 variants with concerning characteristics have emerged since the end of2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samplesfrom the capital city and 10 provinces of Argentina, during 51 epidemiological weeks(EWs) that covered the end of the first wave and the ongoing second wave of theCOVID-19 pandemic in the country (EW 44/2020 to EW 41/2021). The surveillancestrategy wasmainly based on Sanger sequencing of a Spike coding region that allows theidentification of signature mutations associated with variants. In addition, whole-genomesequences were obtained from 637 samples. The main variants found were Gammaand Lambda, and to a lesser extent, Alpha, Zeta, and Epsilon, and more recently,Delta. Whereas, Gamma dominated in different regions of the country, both Gammaand Lambda prevailed in the most populated area, the metropolitan region of BuenosAires. The lineages that circulated on the first wave were replaced by emergent variantsin a term of a few weeks. At the end of the ongoing second wave, Delta began to bedetected, replacing Gamma and Lambda. This scenario is consistent with the LatinAmerican variant landscape, so far characterized by a concurrent increase in Deltacirculation and a stabilization in the number of cases. The cost-effective surveillanceprotocol presented here allowed for a rapid response in a resource-limited setting,added information on the expansion of Lambda in South America, and contributedto the implementation of public health measures to control the disease spreadin Argentina.