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PLOS Papers on SARS-CoV-2 Phylogenies, Swiss Influenza Spread, Infant Meningitis in Ethiopia

In PLOS Genetics, an international team led by investigators at the University of California, Santa Cruz, shares strategies for finding and accounting for systematic genome sequencing errors that can affect SARS-CoV-2 phylogenies and insights gleaned from them. Using SARS-CoV-2 genome sequences behind dozens of sequence alignments and phylogenies from late March and April, the team tracked down examples of lab-specific systematic errors in viral genomes and described tools for dealing with these and other potential issues across phylogenetic trees. "We demonstrate that many [lab-associated variants] can be identified and removed by cross-referencing patterns of recurrence against the source sequencing lab," the authors report, "and we provide automated methods for detecting spurious and highly recurrent mutations."

Researchers from ETH Zurich, the Swiss Institute of Bioinformatics, and elsewhere report on findings from a phylogenetics-based study of influenza A/H3N2 spread in Basel, Switzerland, over one flu season for a PLOS Pathogens paper. By sequencing influenza isolates from more than 650 individuals treated at two hospitals or at private clinics in Basel from 2016 to 2017, the researchers identified large-scale patterns such as influenza introductions to the city, along with factors influencing local transmission networks. "The genetic sequence data allows us to reconstruct how the transmission dynamics changed over the course of the season, which we then compare to trends in humidity and temperature and times when schools were open or closed," the authors report, adding that the genetic information "allows us to see how individual cases are connected."

Group B streptococcus (GBS) may contribute to a significant proportion of meningitis cases in Ethiopia, according to a prospective study by an Ethiopian team reporting in PLOS One. The researchers used PCR to fish for GBS in cerebrospinal fluid samples from infants being treated for apparent bacterial meningitis infections at a hospital in Addis Ababa, focusing on cases in which culture methods did not yield a suspicious microbe. They detected GBS in samples from 46 of the 72 newborns or infants considered over the course of a year, including five fatal meningitis cases. "[G]BS was found out to be the major etiologic agent of [bacterial meningitis] among neonates and young infants," the investigators write, adding that "the role of GBS can be underestimated by using culture detection techniques in contrast to molecular assays like PCR."