SARS-CoV-2: Proof of recombination between strains, emergence of possibly more virulent ones

Dania Haddad, Sumi Elsa John, View ORCID ProfileAnwar Mohammad, View ORCID ProfileMaha M Hammad, View ORCID ProfilePrashantha Hebbar, Arshad Channanath, Rasheeba Nizam, Sarah Al-Qabandi, View ORCID ProfileAshraf Al Madhoun, View ORCID ProfileAbdullah Alshukry, View ORCID ProfileHamad Ali, Thangavel Alphonse Thanaraj, View ORCID ProfileFahd Al-Mulla

doi: https://doi.org/10.1101/2020.11.11.20229765

This article is a preprint and has not been certified by peer review [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

PDF: https://www.medrxiv.org/content/10.1101/2020.11.11.20229765v1.full.pdf

Abstract

COVID-19 is challenging healthcare preparedness, world economies, and livelihoods. The infection and death rates associated with this pandemic are strikingly variable in different countries. To elucidate this discrepancy, we analyzed 2431 early spread SARS-CoV-2 sequences from GISAID. We estimated continental-wise admixture proportions, assessed haplotype block estimation, and tested for the presence or absence of strains recombination. Herein, we identified 1010 unique missense mutations and seven different SARS-CoV-2 clusters. In samples from Asia, a small haplotype block was identified; whereas, samples from Europe and North America harbored large and different haplotype blocks with nonsynonymous variants. Variant frequency and linkage disequilibrium varied among continents, especially in North America. Recombination between different strains was only observed in North American and European sequences. Additionally, we structurally modeled the two most common mutations D614G and P314L which suggested that these linked mutations may enhance viral entry and stability. Overall, we propose that COVID-19 virulence may be more severe in Europe and North America due to coinfection with different SARS-CoV-2 strains leading to genomic recombination which might be challenging for current treatment regimens and vaccine development. Furthermore, our study provides a possible explanation for the more severe second wave of COVID-19 that many countries are currently experiencing presented as higher rates of infection and death.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

This work was supported by Coronavirus emergency resilience grant from Kuwait Foundation for the Advancement of Sciences.

https://www.medrxiv.org/content/10.1101/2020.11.11.20229765v1