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Cell Studies on SARS-CoV-2 Selection, Meiotic Recombination, Gut Microbe Response to Diet

In a journal pre-proof article, investigators at Virginia Tech and elsewhere assess genome sequences for more than 182,000 SARS-CoV-2 isolates to find features linked to human host adaptation, focusing in on a selective sweep signature involving the receptor-binding domain of the Spike protein. Their analyses suggest that selection for a non-synonymous change in the RBD site may have bolstered SARS-CoV-2 binding to a human receptor called ACE2, enhancing human infection and spread — predictions supported by the team's subsequent binding assay, reverse genetics, and viral replication experiments. The RBD change in question "is present in all human SARS-CoV-2 sequences but not closely related viruses from bats and pangolins," the authors write, noting that their results "suggest that this mutation likely contributed to SARS-CoV-2's emergence from animal reservoirs or enabled sustained human-to-human transmission."

A team from the National Institutes of Health and Johns Hopkins University maps DNA replication during meiosis in human males to better understand the relationship between meiotic replication and recombination. Using a method for mapping replication origins, the researchers characterized meiosis-specific replication origin firing rates and other distinctive DNA replication features in the context of meiotic recombination events. "We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination of individual chromosomes," they write, adding that the "findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation."

Investigators at Stanford University, Chan Zuckerberg Biohub, and other centers consider the gut microbiome consequences of diets high in plant-based fiber or in fermented food. The team's prospective study included 18 individuals randomized to each of the dietary intervention arms. From the gut microbial community and host data collected over time in these individuals, the authors suggest that dietary interventions that include high levels of fermented food tend to boost the diversity of microbes in the host gut, while dialing down inflammatory features in the host immune system. On the other hand, the high fiber diet appeared to bump up the functional abilities of microbes in the gut, with immune effects that varied from one participant to the next. "The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight," they report, noting that fermented food-focused dietary interventions "may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in industrialized society."

The Scan

Back as Director

A court has reinstated Nicole Boivin as director of the Max Planck Institute for the Science of Human History, Science reports.

Research, But Implementation?

Francis Collins reflects on his years as the director of the US National Institutes of Health with NPR.

For the False Negatives

The Guardian writes that the UK Health Security Agency is considering legal action against the lab that reported thousands of false negative COVID-19 test results.

Genome Biology Papers Present Epigenetics Benchmarking Resource, Genomic Architecture Maps of Peanuts, More

In Genome Biology this week: DNA methylation data for seven reference cell lines, three-dimensional genome architecture maps of peanut lines, and more.