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Genomic Surveillance Picks Up Hidden SARS-CoV-2 Delta Variant Spread in New Zealand

In a paper in Nature Communications, investigators at the University of Otago and other centers in New Zealand and the US outline SARS-CoV-2 Delta variant patterns detected in New Zealand through genomic surveillance between mid-August of 2021 and early December of that year. With genome sequence data for more than 3,800 SARS-CoV-2 isolates, the team saw previously unappreciated Delta variant spread within the country, along with genomic shifts in the virus, including an uptick in isolates containing a predicted truncation to the ORF7a accessory protein. "This genomic surveillance identified numerous examples of cryptic virus transmission by the apparent extinction and reappearance of genomically linked clusters," the authors report, adding that "we identified the emergence and dominance of a lineage possessing a 10-nucleotide frameshift deletion, likely rendering an accessory protein, encoded by the ORF7a gene, functionally impaired, within this outbreak."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.