Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay (preprint)

Uruguay was able to control the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. We previously identified a B.1.1.28 sublineage carrying mutations Q675H+Q677H in the viral Spike, with local transmission in Rocha, a department bordering Brazil. To understand whether these B.1.1.28+Q675H+Q677H sequences were part of an emergent SARS-CoV-2 lineage broadly disseminated in Uruguay, herein we analyzed the country-wide genetic diversity of viruses between November, 2020 and April, 2021. Our findings support that B.1.1.28+Q675H+Q677H probably arose around November 2020, in Montevideo, Uruguay's capital department. This clade spread to other Uruguayan departments, with evidence of further local transmission clusters. It also spread to the USA and Spain. The Q675H and Q677H mutations are in the proximity of the polybasic cleavage site at the S1/S2 boundary and also arose independently in many SARS-CoV-2 lineages circulating worldwide. Although in Uruguay the B.1.1.28+Q675H+Q677H lineage was dominated by the VOC P.1 since April 2021, the monitoring of the concurrent emergence of Q675H+Q677H in VOIs and/or VOCs should be of worldwide interest.

Implementation of a qPCR assay coupled with genomic surveillance for real-time monitoring of SARS-CoV-2 variants of concern. (preprint)

We developed a genomic surveillance program for real-time monitoring of SARS-CoV-2 variants of concern in Uruguay. Here, we present the first results, including the proposed qPCR-VOC method, the general workflow and the report of the introduction and community transmission of the VOC P.1 in Uruguay in multiple independent events.

An effective COVID-19 response in South America: the Uruguayan Conundrum (preprint)

Background: South America has become the new epicenter of the COVID-19 pandemic with more than 1.1M reported cases and >50,000 deaths (June 2020). Conversely, Uruguay stands out as an outlier managing this health crisis with remarkable success. Methods: We developed a molecular diagnostic test to detect SARS-CoV-2. This methodology was transferred to research institutes, public hospitals and academic laboratories all around the country, creating a COVID-19 diagnostic lab network. Uruguay also implemented active epidemiological surveillance following the Test, Trace and Isolate (TETRIS) strategy coupled to real-time genomic epidemiology. Results: Three months after the first cases were detected, the number of positive individuals reached 826 (23 deaths, 112 active cases and 691 recovered). The Uruguayan strategy was based in a close synergy established between the national health authorities and the scientific community. In turn, academia rapidly responded to develop national RT-qPCR tests. Consequently, Uruguay was able to perform ~1,000 molecular tests per day in a matter of weeks. The COVID-19 diagnostic lab network performed more than 54% of the molecular tests in the country. This, together with real-time genomics, were instrumental to implement the TETRIS strategy, helping to contain domestic transmission of the main outbreaks registered so far. Conclusions: Uruguay has successfully navigated the first trimester of the COVID-19 health crisis in South America. A rapid response by the scientific community to increase testing capacity, together with national health authorities seeking out the support from the academia were fundamental to successfully contain, until now, the COVID-19 outbreak in the country.