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This Week in PLOS: Jan 7, 2013

In PLOS One, an international team led by investigators in Australia and the UK outlines a strategy for sequencing the malaria-causing parasite Plasmodium vivax from clinical samples. The approach involves filtering out patient's white blood cells before a short parasite-culturing stint from the cells that remain, researchers say, steps that curb human DNA contamination while upping the proportion of parasite DNA available for sequencing. In the new study, for instance, the team demonstrated that it could sequence the notoriously difficult-to-culture P. vivax parasite to high coverage — both in terms of genome depth and breadth — using samples from nearly two dozen patients.

A team from Spain and the US — including representatives from Pacific Biosciences — used single-molecule real-time sequencing with the PacBio RS instrument to profile methylation patterns at single-base resolution in two human pathogens from the genus Mycoplasma. As they report in PLOS Genetics, the investigators focused on the non-gonococcal urethritis-causing pathogen M. genitalium and M. pneumoniae, a culprit in some pneumonia cases. Analyses of pathogens in exponential and stationary phases of growth uncovered two sequence motifs that are particularly prone to methylation in one or both of the species. Those involved say the study "demonstrates the unique capability of SMRT sequencing to directly sequence and profile the methylome of a whole microbial genome, allowing for unprecedented progress towards understanding the role of epigenomics in the world of prokaryotes."

Finally, the University of Michigan's Mercedes Pascual and colleagues from the US and the UK look at factors affecting genetic diversity and antigen profiles in influenza A from the H3N2 subtype in PLOS Pathogens. Using information on influenza A mutation rates, levels of competition, and so on, the researchers came up with models consistent with known influenza H3N2 phylodynamics. Within this framework, they found, "a limited antigenic space can explain the observed phylogenetic patterns and … a limited mutation rate is a key property underlying the dynamic of (H3N2) influenza."

The Scan

UK Funds to Stay Ahead of Variants

The UK has announced a further £29.3 million to stay on top of SARS-CoV-2 variants, the Guardian reports.

Push for Access

In a letter, researchers in India seek easier access to COVID-19 data, Science reports.

Not as Cold

Late-stage trial results are expected soon for an RNA-based vaccine that could help meet global demand as it does not require very cold storage, the New York Times writes.

Genome Research Papers on Microbes' Effects on Host Transfer RNA, Honeybee Evolution, Single-Cell Histones

In Genome Research this week: influence of microbes on transfer RNA patterns, evolutionary relationships of honeybees, and more.