In PLOS One, researchers from China describe "immune-related gene pairs," or IRGPs, with apparent ties to outcomes for individuals with malignant melanoma. Using RNA sequencing data collected from almost 500 cutaneous melanoma cases for The Cancer Genome Atlas project, the team focused in on nearly three dozen IRGPs that appeared to correspond to overall survival in the melanoma cohort. The authors verified the proposed prognostic immune signature with data on additional cases considered for the Gene Expression Omnibus project, or for the uveal melanoma arm of the TCGA study. "[T]he expression levels of a range of immune-related genes in each tumor sample were compared in pairs, ultimately generating a score for each immune gene pair," they write, adding that "we confirmed the efficacy of this immunomarker in predicting tumor prognosis by comparing it with other clinicopathological information."
A team from the Icahn School of Medicine at Mount Sinai profiles paramyxovirus plasticity for a paper in PLOS Pathogens. With the help of whole-genome transposon mutagenesis screening, the researchers searched for sites that were vulnerable to insertion mutagenesis in three types of paramyxovirus, a group of single-stranded RNA viruses that appears to be relatively stable over time. Based on transposon mutagenesis sequencing profiles for the Sendai virus, mumps virus, and Newcastle disease virus, the authors suggest that "there are structural constraints on changing [paramyxovirus] antigenicity," despite the presence of other accessory proteins that appeared to be permissive to insertional mutagenesis.
Korean researchers report on Hantaan orthohantavirus (HTNV) prevalence and genetic diversity in South Korea's Gangwon province for a PLOS Neglected Tropical Diseases study. The team assessed a dozen HTNV isolates found in Apodemus agrarius striped field mice from 2015 to 2018 by whole-genome sequencing, before using phylogenetics to look at genetic diversity and relationships between viruses in the region — an area in which hemorrhagic fever with renal syndrome linked to HTNV is endemic. "The cline analysis revealed a remarkable hybrid zone by showing spatial contact regions of HTNV at two sites … and the spatial separation and sequence divergence across genome segments of HTNV in Gangwon Province," the authors report, noting that these and other findings "demonstrate the genetic diversity and hybrid zone of HTNV circulating in Gangwon Province."