SARS-CoV-2 Omicron Variant AI-based Primers

As the COVID-19 pandemic continues to affect the world, a new variant of concern, B.1.1.529 (Omicron), has been recently identified by the World Health Organization. At the time of writing, there are still no available primer sets specific to the Omicron variant, and its identification is only possi...

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Bibliographic Details
Published in:bioRxiv 2022-01
Main Authors: Perez-Romero, Carmina Angelica, Tonda, Alberto, Mendoza-Maldonado, Lucero, Macsharry, John, Szafran, Joanna, Claassen, Eric, Garssen, Johan, Kraneveld, Aletta D, Lopez-Rincon, Alejandro
Format: Article
Language:English
Subjects:
Artificial intelligence
COVID-19
Pandemics
Primers
Severe acute respiratory syndrome coronavirus 2
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Summary:As the COVID-19 pandemic continues to affect the world, a new variant of concern, B.1.1.529 (Omicron), has been recently identified by the World Health Organization. At the time of writing, there are still no available primer sets specific to the Omicron variant, and its identification is only possible by using multiple targets, checking for specific failures, amplifying the suspect samples, and sequencing the results. This procedure is considerably time-consuming, in a situation where time might be of the essence. In this paper we use an Artificial Intelligence (AI) technique to identify a candidate primer set for the Omicron variant. The technique, based on Evolutionary Algorithms (EAs), has been already exploited in the recent past to develop primers for the B.1.1.7/Alpha variant, that have later been successfully tested in the lab. Starting from available virus samples, the technique explores the space of all possible subsequences of viral RNA, evaluating them as candidate primers. The criteria used to establish the suitability of a sequence as primer includes its frequency of appearance in samples labeled as Omicron, its absence from samples labeled as other variants, a specific range of melting temperature, and its CG content. The resulting primer set has been validated in silico and proves successful in preliminary laboratory tests. Thus, these results prove further that our technique could be established as a working template for a quick response to the appearance of new SARS-CoV-2 variants. Competing Interest Statement J. Garssen is a part time employee at Danone Nutricia Research, Utrecht, the Netherlands. Footnotes * https://github.com/steppenwolf0/omicronVariant
DOI:10.1101/2022.01.21.475953