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Comment
. 2022 Nov;94(11):5082-5085.
doi: 10.1002/jmv.27979. Epub 2022 Jul 11.

The complex evolutionary dynamics of SARS-CoV-2, a big challenge to control the pandemic of COVID-19

Lauro Velazquez-Salinas  1
Affiliations
Comment

The complex evolutionary dynamics of SARS-CoV-2, a big challenge to control the pandemic of COVID-19

Lauro Velazquez-Salinas. J Med Virol. 2022 Nov.
No abstract available

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Conflict of interest statement

The author declares no conflict of interest

Figures

Figure 1
Figure 1
Evolutionary profile of SARS‐CoV‐2 during the pandemic of COVID‐19. (A) Phylogenetic tree reconstructed by Maximum likelihood and the general time reversible model, illustrating the 14 clades (based on GISAID classification) predicted during the evolution of SARS‐CoV‐2. This tree was constructed using a total of 32 full‐length sequences representing different clades. Representative sequences were obtained from GISAID database (https://www.gisaid.org/). (B) Observed/expected ratio (obs/exp) of sites under positive selection at different genes sections of SARS‐CoV‐2 normalized by gene length. (C) obs/exp ratio of CTL epitopes at different gene sections of SARS‐CoV‐2 normalized by gene length. (Obs/exp = proportion of the total number of predicted positive selected sites or CTL epitopes found at specific genome sections/proportion of length at the overall coding region of SARS‐CoV‐2 represented by different gene sections). Red numbers on the bars represent the raw number of either sites under positive selection or CTL epitopes (predicted/validated) at different gene sections of SARS‐CoV‐2. Genes of SARS‐CoV‐2 where no information was available about sites under positive selection or epitopes were excluded from the graphics. The horizontal line at 1.0 indicate obs/exp values under the expected gene size. Information for (B) and (C) were obtained from the adaptive evolution server Datamonkey (https://observablehq.com/@spond/revised‐sars‐cov‐2‐analytics‐page). COVID‐19, coronavirus disease 2019; CTL, cytotoxic T lymphocyte; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2.
Figure 2
Figure 2
Lineage circulation dynamics of SARS‐CoV‐2 during the pandemic, and vaccine effectiveness of RNA vaccines against COVID‐19. (A) Relevance of different divergent clades of SARS‐CoV‐2 during the pandemic (based on GISAID classification). (B) Circulation dynamic of different variants during the pandemic. (C) Percentage of available sequences at the GISAID database associated with the lineages described by Magalis et al., representing the low circulation of these lineages during the pandemic around the world. However, it is important to consider the huge temporal and geographical biases in sequencing and the presence of locally dominant variants that might have predominated in a single region/or country for this reason the concept of low‐circulating lineage must be taken with caution. Information about the number of sequences associated with different clades and lineages was obtained from the GISAID database. (D) Summary of the effectiveness at different clinical conditions of Moderna and Pfizer BioNTech vaccines against SARS‐COV‐2. Information was obtained from the Centers of Disease Control and Prevention (https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/fully-vaccinated-people.html. COVID‐19, coronavirus disease 2019; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2.
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References

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