Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2
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Abstract
Phylogenomic analysis of SARS-CoV-2 as available from publicly available repositories suggests the presence of 3 prevalent groups of viral episomes (super-clades), which are mostly associated with outbreaks in distinct geographic locations (China, USA and Europe). While levels of genomic variability between SARS-CoV-2 isolates are limited, to our knowledge, it is not clear whether the observed patterns of variability in viral super-clades reflect ongoing adaptation of SARS-CoV-2, or merely genetic drift and founder effects. Here, we analyze more than 1100 complete, high quality SARS-CoV-2 genome sequences, and provide evidence for the absence of distinct evolutionary patterns/signatures in the genomes of the currently known major clades of SARS-CoV-2. Our analyses suggest that the presence of distinct viral episomes at different geographic locations are consistent with founder effects, coupled with the rapid spread of this novel virus. We observe that while cross species adaptation of the virus is associated with hypervariability of specific protein coding regions (including the RDB domain of the spike protein), the more variable genomic regions between extant SARS-CoV-2 episomes correspond with the 3’ and 5’ UTRs, suggesting that at present viral protein coding genes should not be subjected to different adaptive evolutionary pressures in different viral strains. Although this study can not be conclusive, we believe that the evidence presented here is strongly consistent with the notion that the biased geographic distribution of SARS-CoV-2 isolates should not be associated with adaptive evolution of this novel pathogen.
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SciScore for 10.1101/2020.03.30.016790: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Determination of the optimal clustering solution was performed based on the Dunn Index metrics, as computed by the clValid R package (Brock et al, 2008). clValidsuggested: (clValid , RRID:SCR_014626)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Notwithstanding some limitations, our comparative analyses are consistent with the hypothesis that the biased geographic …
SciScore for 10.1101/2020.03.30.016790: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Determination of the optimal clustering solution was performed based on the Dunn Index metrics, as computed by the clValid R package (Brock et al, 2008). clValidsuggested: (clValid , RRID:SCR_014626)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Notwithstanding some limitations, our comparative analyses are consistent with the hypothesis that the biased geographic distribution, and the allelic differences observed between major viral SARS-CoV-2 clades are not the result of an adaptive evolutionary process, but are more consistent with founder effects on viral populations, coupled with the rapid spread of this novel virus. Although our analyses do not suggest distinct evolutionary patterns, it remains unclear whether the genetic variants that discriminate between major viral clades could be related with differences in the virulence/pathogenicity of these clades. To address this issue it will be crucial to collect patient metadata, to sequence more genomes, and to enable the execution of retrospective statistical analyses.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- No funding statement was detected.
- No protocol registration statement was detected.
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