Open AccessSARS-CoV-2: Possible recombination and emergence of potentially more virulent strains
Author(s) -
Dania Haddad,
Sumi Elsa John,
Anwar Mohammad,
Maha M. Hammad,
Prashantha Hebbar,
Arshad Channanath,
Rasheeba Nizam,
Sarah Al-Qabandi,
Ashraf Al Madhoun,
Abdullah Alshukry,
Hamad Ali,
Thangavel Alphonse Thanaraj,
Fahd Al-Mulla
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0251368
Subject(s) - nonsynonymous substitution , haplotype , biology , linkage disequilibrium , genetics , virulence , pandemic , recombination , lineage (genetic) , genome , missense mutation , evolutionary biology , virology , mutation , genotype , covid-19 , gene , disease , infectious disease (medical specialty) , medicine , pathology
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. In addition, we structurally modelled the two most common mutations, Spike_D614G and Nsp12_P314L, which suggested that these linked mutations may enhance viral entry and replication, respectively. Overall, we propose that genomic recombination between different strains may contribute to SARS-CoV-2 virulence and COVID-19 severity and may present additional challenges for current treatment regimens and countermeasures. Furthermore, our study provides a possible explanation for the substantial second wave of COVID-19 presented with higher infection and death rates in many countries.