SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains

• Published in: PloS one Vol. 16; no. 5; p. e0251368
• Main Authors: Haddad, Dania, John, Sumi Elsa, Mohammad, Anwar, Hammad, Maha M, Hebbar, Prashantha, Channanath, Arshad, Nizam, Rasheeba, Al-Qabandi, Sarah, Al Madhoun, Ashraf, Alshukry, Abdullah, Ali, Hamad, Thanaraj, Thangavel Alphonse, Al-Mulla, Fahd
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25-05-2021; Public Library of Science (PLoS)
• Subjects: ACE2; Amino acids; Analysis; Angiotensin; Angiotensin-converting enzyme 2; Biochemistry; Bioinformatics; Biology and life sciences; Cell surface; Computer programs; Coronaviruses; COVID-19; COVID-19 - pathology; COVID-19 - virology; Crystal structure; Data analysis; Databases, Genetic; Datasets; Diabetes; Diabetes mellitus; Disease transmission; DNA-directed RNA polymerase; Editing; Electronic mail; Environmental factors; Genes; Genetic diversity; Genetic Variation; Genetics; Genomes; Haplotypes; Head and neck; Health sciences; Humans; Laboratories; Linkage Disequilibrium; Medicine and health sciences; Methodology; Molecular biology; Molecular Dynamics Simulation; Morbidity; Mutation; Mutation, Missense; Otolaryngology; People and Places; Peptidyl-dipeptidase A; Physical Sciences; Principal Component Analysis; Principal components analysis; Protein Structure, Tertiary; Proteins; Public awareness; Public health; Receptors; Recombination; Recombination, Genetic; Reviews; Ribonucleic acid; RNA; RNA polymerase; RNA-Dependent RNA Polymerase - chemistry; RNA-Dependent RNA Polymerase - genetics; RNA-Dependent RNA Polymerase - metabolism; RNA-directed RNA polymerase; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - metabolism; SARS-CoV-2 - pathogenicity; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Severity of Illness Index; Software; Spike Glycoprotein, Coronavirus - chemistry; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - metabolism; Structural analysis; Surgery; Tat protein; Viral diseases; Virulence; Virulence - physiology; Kuwait
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0251368

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.