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Nucleic Acids Research Papers on Viral Recombination, Pan-Cancer Mutations, SARS-CoV-2 Variability

Investigators at the University of Texas Medical Branch, the Scripps Research Institute, Seattle Children's Research Institute, and elsewhere present an updated and expanded version of the "co-variation mapper" (CoVaMa) pipeline, designed to detect linkage disequilibrium between recombination events and SNPs in viral genomes. The team applied the approach to long-read sequence data for serially passaged Flock House virus isolates, along with short reads from HIV isolates collected over time from the same patient, uncovering variants or mutations linked to insertions, deletions, or other viral recombination events. "In both cases, we observed novel associations of SNVs with specific recombination events," the authors conclude. "Knowledge of these associations is necessary to understand how viruses adapt to their environments and to characterize the distribution of specific genomic variants within viral intra-host diversity."

Hainan Medical University researchers profile mutation patterns across "intrinsically disordered protein regions" (IDRs) in more than 10,000 tumor samples spanning nearly three dozen cancer types characterized for the Cancer Genome Atlas project. Using a computational method called ROI-Driver, the team searched for cancer mutation-enriched regions of interest, focusing on cancer-associated IDR mutation hotspots and suspected driver genes. "We found that mutations are prevalent in IDRs in cancer, and genes enriched with mutations in IDRs are associated with cancer development," the authors suggest, adding that "[f]unctional analysis revealed that the potential driver genes play important roles in cancer signaling pathways."

A team from India estimates within-host SARS-CoV-2 variability using more than 1,300 publicly available viral sequences from India, China, Malaysia, Germany, and the UK during early phases of the pandemic. Within these sequences, the investigators flagged more than 16,400 intra-host single nucleotide variants (iSNVs), including a slew of Spike protein-coding variants. A significant proportion of the iSNVs appear to have become more widespread over time in publicly available sequences and in viral genomes from isolates collected in India from late 2020 to the spring of 2021, the authors note, explaining that the "majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population."

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