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Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

By sequencing nearly 4,000 SARS-CoV-2 genomes collected in Washington State last year, a group led by Fred Hutchinson Cancer Research Center investigators has found that human behavior, rather than different viral lineages, was mostly responsible for shaping the course of the pandemic in the region. As reported in Science Translational Medicine, the researchers find that cases of infection with the 614D variant initially dominated in Washington State, but were later taken over the potentially more transmissible 614G variant. However, the trends for 614G and 614D cases appeared to be explained by differences in when action to curb the spread of SARS-CoV-2 were taken on a county level. Additionally, while higher viral loads were observed in patients infected with the 614G variant, the scientists did not find evidence that the variant impacts clinical severity or patient outcomes.

Using a novel hierarchical phylogenomic approach, a team led by scientists from the University of Bristol has identified the root of the bacteria tree and gained new insights into early bacterial evolution. In their study, which appears in this week's Science, the investigators note that tracing billions of years of bacterial evolution back to the root has been difficult because standard phylogenetic models do not account for the full range of evolutionary processes that shape bacterial genomes. Standard rooting approaches also typically use an outgroup, which act a reference point for evolutionary analyses but have the potential to distort within-species relationships. Using a technique that explicitly uses information from gene duplications and losses within a genome, as well as gene transfers between genomes, they were able to root the bacterial tree without including an archaeal outgroup. Their analysis puts the root of the bacteria tree between the major clades Terrabacteria and Gracilicutes and suggests that the last bacterial common ancestor was a complex double-membraned cell capable of motility and chemotaxis that possessed a CRISPR-Cas system. The researchers also uncover a major role for vertical gene transmission in bacterial evolution.

The Scan

Vaccine Update Recommended

A US Food and Drug Administration panel recommends booster vaccines be updated to target Omicron, CNBC reports.

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Sentence Appealed

The Associated Press reports that Swedish prosecutors are appealing the sentence given to a surgeon once lauded for transplanting synthetic tracheas but then convicted of causing bodily harm.

Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.