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Cell Papers Examine Rise of SARS-CoV-2 Variants, Kākāpō Genomes, Malaria Parasite Sequencing

The emergence of three SARS-CoV-2 variants in 2020 followed changes in selective pressures on the virus, a new analysis appearing in Cell reports. An international team of researchers led by the University of Cape Town's Darren Martin applied phylogenetics-based approaches to examine patterns of natural selection within the Alpha, Beta, and Gamma viral variants. They found evidence of convergent evolution in the three lineages — a set of convergent mutations at 35 genomic sites, which they have dubbed the 501Y meta-signature. The researchers add that viruses from other lineages also appear to be converging on this meta-signature. "We therefore anticipate that the culmination of the currently ongoing evolutionary convergence of 501Y lineage viruses will yield a succession of variants possessing increasing subsets of 501Y lineage meta-signature mutations," they add.

A Swedish-led team of researchers has sequenced and analyzed the genome of the kākāpō, a critically endangered parrot living in New Zealand. They generated a chromosome-level reference genome for the surviving island kākāpō population and compared the genomes of those existing birds to those of museum specimens collected from a now-extinct mainland population, as they report in Cell Genomics. From this, they found that the existing island kākāpō have a reduced mutational load, as compared to the extinct mainland population. This suggested to the researchers that the island population has experienced a "combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection" and that "small populations can survive even when isolated" for generations.

Using single-cell sequencing, researchers from the Texas Biomedical Research Institute analyzed the genomes of 406 Plasmodium vivax isolates from 11 patients with malaria. As they write in Cell Host & Microbe, the researchers uncovered hundreds of de novo mutations within the isolates under strong selection. This included recurrent mutations affecting the ApiAP2 gene family of transcription factors. "Examining genome sequence data from single infected blood cells clearly reveals that mutation and selection within hosts play a key role in malaria parasite evolution, as occurs in the case of bacterial and viral infections," the researchers write. "This approach will allow direct interrogation of host-parasite interactions and intrahost parasite evolution."