In an effort to tease out microbial contributors to bovine respiratory disease (BRD), a team from Egypt, Saudi Arabia, Canada, and Hong Kong profile microbial communities in upper respiratory tract samples from non-vaccinated animals at cow-calf sites in Egypt. As they report in PLOS One, the researchers performed metagenomic sequencing on pooled nasal swab samples from dozens of animals at Egyptian cow-calf operations affected by acute bovine respiratory disease, uncovering a BRD-associated overrepresentation of bovine herpesviruses (BHV) and bovine parvoviruses (BPV) including newly detected versions of the viruses. "The current study shows the detection of BHV-1.1 genotype and the first detection of BHV-5 and BPV-3 from the investigated cattle herds," the authors write, cautioning that although such viruses appear associated with BRD, "further research, including collecting and investigating more animal samples from different locations, is needed to determine the prevalence of the detected viruses and their contributions to BRD in cattle in Egypt."
A University of Glasgow and University of Edinburgh team reporting in PLOS Pathogens shares results from a genomics-based lineage classification and surveillance effort designed to detect and get rid of rabies virus. The researchers identified nearly 100 lineages — up from fewer than two dozen reported in the clade in the past — using a lineage classification scheme informed by the evolving nomenclature around the SARS-CoV-2 virus. With genomic, phylogenetic, and other clues, they flagged 96 rabis virus lineages in a key rabies clade before combining the tool with data from a growing rabies virus sequence set. With such approaches, the authors note, it was possible to pick out "lineage dynamics relevant to control and elimination programs, such as identifying importation and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions."
Investigators in the US and Canada consider the fitness costs of hepatitis C virus (HCV) mutations with the help of a frequency-based analytical approach and deep sequence data for samples from 195 HCV-infected patients. Based on nearly 8,000 genome-wide mutations, the team identified mutation types with an outsized effect on viral fitness, including non-synonymous mutations and alterations involving adenine or thymine. On the other hand, the authors note that genome location had a "modest" fitness impact, while mutations boosting resistance seemed to come with a steeper fitness cost. "Our results show that in vivo fitness costs of mutations can be site and virus specific," they report, "reinforcing the utility of constructing in vivo fitness cost maps of viral genomes."