Abstract
SARS-CoV-2 variants with concerning characteristics have emerged since the end of 2020. Surveillance of SARS-CoV-2 variants was performed on a total of 4,851 samples from 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 the COVID-19 pandemic in the country (EW 44/2020 to EW 41/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the identification of signature mutations associated with variants. In addition, whole-genome sequences were obtained from 637 samples. The main variants found were Gamma and Lambda, and to a lesser extent, Alpha, Zeta, and Epsilon, and more recently, Delta. Whereas, Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires. The lineages that circulated on the first wave were replaced by emergent variants in a term of a few weeks. At the end of the ongoing second wave, Delta began to be detected, replacing Gamma and Lambda. This scenario is consistent with the Latin American variant landscape, so far characterized by a concurrent increase in Delta circulation and a stabilization in the number of cases. The cost-effective surveillance protocol presented here allowed for a rapid response in a resource-limited setting, added information on the expansion of Lambda in South America, and contributed to the implementation of public health measures to control the disease spread in Argentina.
Highlights
The emergence of SARS-CoV-2 variants with concerning characteristics to public health has attracted the attention of the scientific community and governments both regionally and globally since the end of 2020
Its frequency in the metropolitan area of Buenos Aires (MABA) region (the CABA, Great Buenos Aires (GBA), Great La Plata (GLP), and surrounding areas) reached 15.5% in epidemiological weeks (EWs) 15-16/2021 (April 11th−24th) but decreased to 0% by EW 37-38/2021 (September 12th−25th, 2021) (Supplemetary Tables 1, 2, Figure 2)
We show genomic evidence of the introduction and local transmission of the SARS-CoV-2 variants Gamma, Lambda, and Delta, and to a lesser extent, of Alpha, Epsilon, and Zeta in Argentina, the sporadic detection of Mu and the circulation of mutations of interests, in different geographical regions of the country
Summary
The emergence of SARS-CoV-2 variants with concerning characteristics to public health has attracted the attention of the scientific community and governments both regionally and globally since the end of 2020. The most relevant variants described so far include: Alpha (lineage B.1.1.7), first detected in the United Kingdom; Beta (lineage B.1.351), initially detected in South Africa; Gamma (lineage P.1), initially detected in Manaus, Brazil, and Japan; Delta (lineage B.1.627.2), initially detected in India; Lambda (lineage C.37), initially detected in Peru; Mu (lineage B.1.621), first detected in Colombia; Epsilon (lineages B.1.427 and B.1.429), initially detected in California, United States; and Zeta (lineage P.2), first detected in Rio de Janeiro, Brazil [1] Four of these variants (Alpha to Delta) have been defined as variants of concern (VOCs) given their increased transmissibility and other characteristics, while Lambda and Mu have been defined as variants of interest (VOIs). Some of these variants share mutations in the Spike protein—several of them in the receptor-binding domain region—that potentially affect transmissibility, pathogenesis, and/or response to vaccination and immune-based therapies [7, 8]
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