TY - JOUR
T1 - SARS-CoV-2
T2 - Possible recombination and emergence of potentially more virulent strains
AU - Haddad, Dania
AU - John, Sumi Elsa
AU - Mohammad, Anwar
AU - Hammad, Maha M.
AU - Hebbar, Prashantha
AU - Channanath, Arshad
AU - Nizam, Rasheeba
AU - Al-Qabandi, Sarah
AU - Madhoun, Ashraf Al
AU - Alshukry, Abdullah
AU - Ali, Hamad
AU - Thanaraj, Thangavel Alphonse
AU - Al-Mulla, Fahd
N1 - Publisher Copyright:
© 2021 Haddad et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2021/5
Y1 - 2021/5
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85106626981&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0251368
DO - 10.1371/journal.pone.0251368
M3 - Article
C2 - 34033650
AN - SCOPUS:85106626981
VL - 16
JO - PLoS ONE
JF - PLoS ONE
IS - 5 May
M1 - e0251368
ER -
