Surveillance of SARS-CoV-2 variants in Argentina: detection of Alpha, Gamma, Lambda, Epsilon and Zeta in locally transmitted and imported cases

Abstract

Molecular surveillance of SARS-CoV-2 variants was performed on a total of 2,406 samples from the capital city and nine provinces of Argentina, during 30 epidemiological weeks (EW) that covered the end of the first wave and the beginning of the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 20/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the simultaneous identification of signature mutations associated with worldwide circulating variants. In addition, whole SARS-CoV-2 genome sequences were obtained from 456 samples. The main variants found were Gamma, Lambda and Alpha, and to a lesser extent, Zeta and Epsilon. 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 (MABA), although showing a heterogeneous distribution along this region. This cost-effective surveillance protocol allowed for a rapid response in a limited access to resources scenario, added information on the expansion of the Lambda variant in South America and contributed to the implementation of public health measures to control the disease spread in Argentina.

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

“…A preliminary version of this manuscript has been posted as a preprint at medRxiv (35), doi: 10.1101/2021.07.19.21260779.…”

SARS-CoV-2 epidemic in the South American Southern cone: can combined immunity from vaccination and infection prevent the spread of Gamma and Lambda variants while easing restrictions?

“…HIT will move upwards when more transmissible SARS-CoV-2 variants circulates in a population, but differences in the circulating SARS-CoV-2 variants do not explain variations among South American countries. Differences in the mean HIT were observed between countries where Gamma was the most prevalent variant like Brazil (45%), Paraguay (36%) and Uruguay (33%), and also between countries where Gamma and Lambda cocirculated at high prevalence like Chile (43%) and Argentina (29%) [2,3,4,5]. Differences in vaccine platforms deployed in each country might also mod-ulate the HIT at the decoupling time.…”

“…Countries from the South America Southern cone experienced large COVID-19 epidemic waves during the first months of 2021 driven by the lack of stringent mitigation measures along with the emergence and regional spread of the Variant of Concern (VOC) Gamma and the Variant of Interest (VOI) Lambda [1]. The VOC Gamma was the predominant viral variant in Brazil, Paraguay and Uruguay; while both Gamma and Lambda circulated at similar prevalence in Argentina and Chile [2,3,4,5]. Changes in different epidemic indicators from mid-June to end of August, including declining numbers of new SARS-CoV-2 cases and deaths and viral effective reproduction number R t below one, support a relative control of the COVID-19 epidemic in all five countries [1].…”