Fitness-valley crossing in the emergence of SARS-CoV-2 mutants*

As for Oct 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 240 millions infections and about 5 millions deaths worldwide [1]. 

Because of that, SARS-CoV-2 has received unprecedented attention with over 4 millions sequences available in Global Initiative on Sharing All Influenza Data (GISAID) database, as the first pandemic in post genome era [3].

This worldwide genomic resource provides sufficient information about the evolution of SARS-CoV-2’s mutants.

And yet, basic facts about its evolution remain mysterious.

More strikingly, with months of little significant adaption, three similar variants, Alpha, Beta and Gamma, arose independently around a short time range [4,5].

They showed a strong selection advantage and rapidly became Variants of Concerns (VOC) [4,5].

This dynamics has not yet been analysis before.

We will use approximate analysis, simulations, and the genetic data to explore the possible fitness landscape, under which the simulation results are consistent with this observation.

Our results show the underlying fitness-valley crossing of the mutants' emergence.

[1]. WHO. Coronavirus (COVID-19) Dashboard. https://covid19.who.int/ (2021).

[2]. Dorp L van, Houldcroft CJ, Richard D, and Balloux F (2021) COVID-19, the first pandemic in the post-genomic era. Current Opinion in Virology. doi: 10.1016/j.coviro. 2021.07.002.

[3]. GISAID (2021) hCoV-19 Submission Tracking. https://www.gisaid.org/submission-tracker-global/

[4]. Hodcroft EB (2021) CoVariants: SARS-CoV-2 Mutations and Variants of Interest. https://covariants.org

[5]. Nextstrain. Genomic epidemiology of novel coronavirus - Global subsampling. https://nextstrain.org/ncov/gisaid/global