Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered "facilitating" intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human-human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.
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http://dx.doi.org/10.1371/journal.pbio.3001115 | DOI Listing |
Alzheimers Dement
December 2024
Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
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View Article and Find Full Text PDFAlzheimers Dement
December 2024
Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.
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View Article and Find Full Text PDFCharacterizing the complex relationships between animals and their habitats is essential for effective wildlife conservation and management. Wildlife-habitat selection is influenced by multiple life-history requirements, which act over varying spatial and temporal scales, and result in dispersion patterns that can differ across ecological levels. For example, sites that attract intense communal use (e.
View Article and Find Full Text PDFIn this study, we performed a comparative analysis based on a total of 255 spider mitogenomes and four outgroups, of which the mitogenomes of 39 species were assembled de novo, to explore the phylogenetic relationships and the adaptive evolution of mitogenomes. Results showed that had the longest mitochondrial length and the most pronounced codon preference to be UUA, followed by CCU. Codon usage frequencies were similar between families and codon usage in the mitogenome of spiders was mainly influenced by natural selection pressures rather than G/C mutation bias.
View Article and Find Full Text PDFFront Plant Sci
December 2024
Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
New genotypes of hybrid from the and sections, which encompass economically important species of L., have great potential to significantly enhance genetic gain from selection. Growth and its functional and structural determinants exhibiting a high level of variability are not only controlled by genetics, but also affected by environment, as well as genotype and environment interaction (G×E).
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