The evolutionary trend of SARS-CoV-2 provides insight into the process of adaptation to the human host.

Evolutionary genomics research has focused primarily on the transformation of ribonucleic acid (RNA) viruses over time. The data obtained from these studies are even more important in the light of the coronavirus disease 2019 (COVID-19) pandemic.

study: The emergence of mutants with increased fitness accelerates the slowdown of genomic sequence heterogeneity of SARS-CoV-2 coronavirus. Image Credits: Andy Shell / Shutterstock.com

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is thought to result from direct bat-to-human transmission. Spillover event..Previous studies have shown that bats are common natural reservoirs like SARS. coronavirus (CoV).

Recombinant events between bat coronavirus and Pangolin virus or CoV of unknown origin are most likely of SARS-CoV-2 origin. Both the bat RaTG13 virus and the pangoline P1E virus are closely matched to SARS-CoV-2, but other intermediate hosts have also been identified.

Since its emergence in late 2019, SARS-CoV-2 has already accumulated a significant amount of mutations, resulting in the emergence of mutants that show significant differences in both gene and genomic composition. In fact, several synonymous and non-synonymous, as well as mismatched and deleted mutations have been identified in the SARS-CoV-2 genomic sequence. Among them, the mutations responsible for increased viral compatibility, loss of epitopes, and the ability of the antibody to escape were of particular scientific importance.

Several studies have reported that SARS-CoV-2 acquired mutations more slowly than expected in neutral evolution, which may be the dominant mode of evolution in purification of choice. It suggests that there is sex. Studies on mutations in the SARS-CoV-2 mutant also highlighted convergent evolution. This may contribute to the adaptation of the virus to the human host.

The pressure of active or passive mutations can cause changes in base composition at all levels of the phylogenetic hierarchy and throughout the genome. The composition domain structure can also be changed by changing the nucleotides at the boundary separating the two domains or by changing the nucleotide frequency at any region.

This set of compositional domains with different nucleotides has been reported to be associated with different biological characteristics of many organisms. Therefore, changes in genomic heterogeneity may be useful for evolutionary and epidemiological studies, as they can reveal the adaptive process of CoV to human hosts.

New survey published on preprint server bioRxiv * We used sequence composition complexity (SCC) to measure genomic heterogeneity using appropriate segmentation algorithms. This study uses phylogenetic ridge regression to reveal a long-term tendency for SARS-CoV-2 genomic sequence heterogeneity to decrease.

About research

The current study included a random, high-quality CoV genomic sequence search followed by masking, alignment, and phylogenetic tree analysis. The composition segmentation algorithm was then used to divide the CoV genome into homogeneous and non-overlapping domains.

Genomic heterogeneity was measured using SCC, followed by phylogenetic ridge regression. Finally, we compared the effects of the SARS-CoV-2 variant with each other.

Survey results

The first SARS-CoV-2 genomic sequence obtained at the start of the COVID-19 pandemic was divided into eight compositional domains. Subsequent SARS-CoV-2 strains showed significant variations in the number and length of each domain and nucleotide composition.

The heterogeneity of the SARS-CoV-2 genomic sequence did not follow the SCC trend during the first year of the pandemic. However, its sequence heterogeneity began to diminish over time with the advent of mutants in December 2020. In addition, a trend towards faster evolution was identified throughout the study period.

The SARS-CoV-2 Omicron variant showed a strong reduction in SCC compared to other mutants. The evolution rate of Omicron was also higher than that of the previous SARS-CoV-2 mutant.

Conclusion

Loss of genomic heterogeneity at CoV is associated with an increase in mutants that are highly adaptable to the virus, which allows the virus to adapt to the human host. Further studies on the evolutionary trends of new SARS-CoV-2 mutants and recombinant lines help determine the extent to which evolution of SARS-CoV-2 genomic sequence heterogeneity affects human health. increase.

*Important Notices

bioRxiv Publish preliminary scientific reports that should not be considered definitive as they have not been peer-reviewed, guide clinical practice / health-related behaviors, and should not be treated as established information.