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Genome Biology Papers on Ancient Haemophilus Influenzae, Oligodendroglia Circular RNA, VirStrain

Investigators at the University of Tartu and elsewhere present evidence of an ancient co-infection involving the plague pathogen Yersinia pestis and a bacterial meningitis-causing microbe Haemophilus influenzae. Using metagenomic sequencing, targeted enrichment sequencing, phylogenetics, skeletal analyses, and other approaches, the team characterized an H. influenzae serotype b (Hib) isolate dubbed EDI064 from a six-year-old Anglo-Saxon child with plague found at an almost 1,500-year-old British burial site. The 6th century Hib strain clustered with invasive disease-causing forms of the meningitis pathogen, for example, but showed a distinct virulence pattern consistent with broader diversity within an Hib division II clade. "Our results demonstrate the potential of [ancient DNA] data to inform us on plague co-infections and the role of plague as a co-infectant," the authors write, adding that "[f]urther sampling will also be needed to explore the overall genetic diversity and prevalence of the species and the Hib-II clade in ancient populations."

An Emory University-led team considers circular RNA (circRNA) contributions in differentiating human oligodendroglia cells. With the help of RNA sequencing, circRNA enrichment, a computational method known as "circRNA identification using A-tailing RNase R approach and Pseudo-reference alignment" (CARP), the researchers mapped out and quantified oligodendroglia-specific circRNA patterns and related regulatory features, including microRNA and messenger RNA shifts. "Our results reveal dynamic regulation of human oligodendroglia circRNA landscapes during early differentiation," they report, "and suggest critical roles of the circRNA-miRNA-mRNA axis in advancing human oligodendroglia development."

City University of Hong Kong researchers describe a VirStrain tool for identifying viral strains based on short read sequencing data. "[A]lthough there are a number of haplotype reconstruction tools, they all have their limitations in reconstructing low-abundance strains, producing full-length haplotypes, or distinguishing highly similar haplotypes," they note. The approach had high sensitivity and accuracy when the team applied it to simulated and real viral sequence data, including sequences from SARS-CoV-2, influenza A H1N1, HIV, hepatitis B virus, and human cytomegalovirus. "VirStrain can be applied to identify strains from low-quality sequencing data, which is the hard case for assembly tools," the authors report, adding that the tool "has high accuracy in detecting multi-strain infection cases."

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