Abstract
The devastating SARS-CoV2 pandemic is worsening with relapsing surges, emerging mutants, and increasing mortalities. Despite enormous efforts, it is not clear how SARS-CoV2 adapts and evolves in a clonal background. Laboratory research is hindered by high biosafety demands. However, the rapid sequence availability opened doors for bioinformatics. Using different bioinformatics programs, we investigated 6305 sequences for clonality, expressions strategies, and evolutionary dynamics. Results showed high nucleotide identity of 99.9% among SARS-CoV2 indicating clonal evolution and genome. High sequence identity and phylogenetic tree concordance were obtained with isolates from different regions. In any given tree topology, ~50% of isolates in a country formed country-specific sub-clusters. However, abundances of subtle overexpression strategies were found including transversions, signature-sequences and slippery-structures. Five different short tracks dominated with identical location patterns in all genomes where Slippery-4 AAGAA was the most abundant. Interestingly, transversion and transition substitutions mostly affected the same amino acid residues implying compensatory changes. To ensure these strategies were independent of sequence clonality, we simultaneously examined sequence homology indicators; tandem-repeats, restriction-site, and 3′UTR, 5′ UTR-caps and stem-loop locations in addition to stringent alignment parameters for 100% identity which all confirmed stability. Nevertheless, two rare events; a rearrangement in two SARS-CoV2 isolates against betacoronavirus ancestor and a polymorphism in S gene, were detected. Thus, we report on abundance of transversions, slippery sequences, and ON/OFF molecular structures, implying adaptive expressions had occurred, despite clonal evolution and genome stability. Furthermore, functional validation of the point mutations would provide insights into mechanisms of SARS-CoV2 virulence and adaptation.
Highlights
The global community is under siege due to the on-going devastating pandemic by one of the most serious zoonotic coronavirus lineages of all times
In spite of the high sequence homology, abundant transversions were detected throughout the genome sequences that slightly changed the topology (Figure 1b)
These results were in agreement with earlier finding [39,40,41] implying that SARS-CoV2 lineage continues to have a clonal evolution and genome as it spreads throughout the world, despite identifications of recent point mutations (Mercatelli and Giorgi 2020; https://www.bmj.com/content/bmj/371/bmj.m4857.full.pdf), accessed on
Summary
The global community is under siege due to the on-going devastating pandemic by one of the most serious zoonotic coronavirus lineages of all times. In a matter of months, Covid, the disease caused by the Severe Acute Respiratory Syndrome Coronavirus (SARSCoV2), has reached every corner on earth dramatically changing the way humans live. The unprecedented speed in the spread of SARS-CoV2 and the subsequent evolution of mutants have resulted in increased hospitalizations, mortality are rates, and paralyzed global healthcare systems. Significant gaps have been created in our knowledge of evolutionary dynamics, epidemicity, and adaptive transcriptomic of coronavirus pandemics. It is not fully clear how the recurring zoonotic coronavirus lineages of including SARS-CoV2, successfully adapted, evolved, host-jumped, and maintained transmissions into humans
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