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PLOS Papers on Chronic Pain, Indigenous Populations in Mexico, SARS-CoV-2 Mutations

\Researchers from the UK, US, and Sweden present findings from a sex-stratified genome-wide association study focused on chronic pain for a paper in PLOS Genetics. Using genotyping data for more than 178,500 male and nearly 209,100 female UK Biobank participants, the team searched for variants with ties to a chronic pain phenotype known as multisite chronic pain (MCP), along with other traits or conditions. The initial analysis led to 123 MCP-related SNPs in male participants and 286 MCP-associated SNPs at 10 loci in female participants, while subsequent meta-analyses, gene-level analyses, and expression analyses pointed to additional chronic pain-linked SNPs and dozens of genes that appeared to have distinct ties to MCP depending on biological sex, as well as candidate genes over-expressed in some nervous tissue. These and other findings suggest "sex differences in chronic pain exist at the SNP, gene, and transcript abundance level, and highlight possible sex-specific pleiotropy for MCP," they suggest, adding that the data "support the proposition of a strong central nervous system component to chronic pain." GenomeWeb has more on this here.

For a paper in PLOS One, a Mexico team takes a look at population sequence data for representatives from more than two dozen Indigenous Mexican groups. The investigators focused on high-coverage whole-genome sequence data for 76 unrelated Indigenous individuals with 97 percent Native American ancestry, on average. The participants came from 27 Indigenous groups in Mexico and carried some 3.26 million variants apiece, they note, leading to more than 44,100 previously unappreciated SNPs. The study's full variant set included SNPs with apparent ties to drug responses, while providing clues to population relationships and past population selection. "There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history," the authors say, noting that the results reveal "previously undetected population level variation in Native Mexicans, helping to reduce the gap in genomic data representation of such groups."

In PLOS Pathogens, investigators from the University of Michigan track SARS-CoV-2 mutation dynamics in hospitalized COVID-19 patients and occupational health workers infected at a hospital in southeastern Michigan over a few months during the first pandemic wave last spring. Based on high-coverage sequences on more than 300 upper respiratory samples from 190 hospitalized patients and 135 symptomatic employees, along with follow-up variant calling by sequencing strategies, the team saw signs that SARS-CoV-2 diversity was quite low in each host individual, and do not usually ramp up before the virus is passed on to others. Even so, the authors note that "people who are not part of the same epidemic cluster can share the same within-host variants, due to chance or various evolutionary forces."