Abstract
Since early 2020, the COVID-19 pandemic has caused an excess in morbidity and mortality rates worldwide. Containment strategies rely firstly on rapid and sensitive laboratory diagnosis, with molecular detection of the viral genome in respiratory samples being the gold standard. The reliability of diagnostic protocols could be affected by SARS-CoV-2 genetic variability. In fact, mutations occurring during SARS-CoV-2 genomic evolution can involve the regions targeted by the diagnostic probes. Following a review of the literature and an in silico analysis of the most recently described virus variants (including the UK B 1.1.7 and the South Africa 501Y.V2 variants), we conclude that the described genetic variability should have minimal or no effect on the sensitivity of existing diagnostic protocols for SARS-CoV-2 genome detection. However, given the continuous emergence of new variants, the situation should be monitored in the future, and protocols including multiple targets should be preferred.
Highlights
In March 2020, the World Health Organization declared the severe respiratory disease caused by a new coronavirus, COVID-19 (Coronavirus Disease 2019), a global pandemic
Coronaviridae infecting humans belong to the following subgenera: Duvinacovirus and Setracovirus for Alphacoronavirus, and Embecovirus, Sarbecovirus, and Merbecovirus for Betacoronavirus
The same analysis was conducted with the EPI_ISL_660190 genome, representative of the South Africa 501Y.V2 variant, and we found only two mismatches involving the central parts of China CDC N forward primer and the Japan National Institute of Infectious Diseases N reverse primer
Summary
In March 2020, the World Health Organization declared the severe respiratory disease caused by a new coronavirus (initially named “novel coronavirus 2019”: 2019nCoV), COVID-19 (Coronavirus Disease 2019), a global pandemic (https://www.who.int/dg/spe eches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-1 9---11-march-2020). The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses designated the virus responsible for COVID-19 as SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) [1]. Thenceforth, COVID-19 has continued expanding globally, causing almost 80 million infections and claiming more than 1.5 million lives from January 2020, as reported by the World Health Organization (situation updated as of 29 December 2020)
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