SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains.
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 c...
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oai:doaj.org-article:05471e16754f40b9852a03dedc302cf22021-12-02T20:18:55ZSARS-CoV-2: Possible recombination and emergence of potentially more virulent strains.1932-620310.1371/journal.pone.0251368https://doaj.org/article/05471e16754f40b9852a03dedc302cf22021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0251368https://doaj.org/toc/1932-6203COVID-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.Dania HaddadSumi Elsa JohnAnwar MohammadMaha M HammadPrashantha HebbarArshad ChannanathRasheeba NizamSarah Al-QabandiAshraf Al MadhounAbdullah AlshukryHamad AliThangavel Alphonse ThanarajFahd Al-MullaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0251368 (2021) |
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Medicine R Science Q 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 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. |
| description |
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. |
| format |
article |
| author |
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 |
| author_facet |
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 |
| author_sort |
Dania Haddad |
| title |
SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. |
| title_short |
SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. |
| title_full |
SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. |
| title_fullStr |
SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. |
| title_full_unstemmed |
SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. |
| title_sort |
sars-cov-2: possible recombination and emergence of potentially more virulent strains. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/05471e16754f40b9852a03dedc302cf2 |
| work_keys_str_mv |
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