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PLOS Papers on Variant Penetrance, Influenza A Strain Evolution, Tsetse Fly Gene Expansions

In PLOS Genetics, Vanderbilt University researchers describe a computational framework for estimating the disease penetrance of individual risk variants. That Bayesian Beta-Binomial-based mixture algorithm was built using disease risk information on variants reported in prior studies, the team says, noting that "[l]ack of evidence to estimate the probability of disease from identified genetic variants, especially rare variants, presents a major barrier to integrating genotype information into clinical care." For their proof-of-principle analyses, the authors applied the algorithm to variants in the cardiac sodium channel gene SCN5A, estimating the penetrance of these variants in the context of a heart arrhythmia condition called Brugada syndrome using insights from more than 750 prior studies. 

A team from China takes a look at seasonal influenza A(H1N1)pdm09 virus sources and evolution in southwestern China over several years for a paper in PLOS One. Using whole-genome sequencing and phylogenetic analyses, the researchers assessed 45 influenza A(H1N1)pdm09 isolates collected in the city of Lincang in Yunnan province between 2014 and 2018, placing those isolates in a clade called 6B. Their analysis also highlighted shifts in the influenza A(H1N1)pdm09 viruses collected in 2018, which contained new hemagglutinin mutations with potential antigenic and receptor binding site effects. The authors suggest that the study "verifies the need for constant molecular monitoring of the circulating strains to provide prompt supporting data for the better selection of the vaccine strain of influenza A(H1N1)pdm09." 

For a study in PLOS Neglected Tropical Diseases, Kenyan researchers report on chemosensory gene expansions in half a dozen tsetse fly species compared to Drosophila melanogaster fruit flies, focusing on those that may influence host specificity in tsetse flies, known for the transmitting trypanosomiasis-causing trypanosome parasites. Along with comparative genomic analysis using available gene sequences from tsetse and fruit flies, the team did RNA sequencing, differential expression, pathway enrichment, and other analyses on head and antennae tissue from the Glossina morsitans morsitanstsetse fly subspecies, exploring shared and species-specific expansions involving vision, odor sensing, and other chemosensory pathway genes. "The putative tsetse fly-specific chemosensory gene orthologs and their respective ligands provide candidate gene targets and [emitted chemical] kairomones for respective downstream functional genomic and field evaluations that can effectively expand [the] toolbox of species-specific tsetse fly attractants, repellents, and other tsetse fly behavioral modulators."