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PNAS Papers on SARS-CoV-2 Diversity, Viral Detection Assay, New Guinea Singing Dog Ancestry

Investigators at Walter Reed Army Institute of Research, Henry M. Jackson Foundation for the Advancement of Military Medicine, and the Fred Hutchinson Cancer Research Center take a look at SARS-CoV-2 genetic diversity using more than 18,500 genome sequences collected since late 2019. Based on phylogenetic, population genetic, structural bioinformatic, and selection analyses, the team found that relatively few SARS-CoV-2 genome sites contain frequent variation, though an alteration affecting the coronavirus spike protein sequence appears to have reached consensus compared to a reference sequence from Wuhan. For the most part, though, the sequence data suggests that "neutral evolution, rather than adaptive selection, can explain the rare mutations across SARS-CoV-2 genomes," authors note, hinting that "potential vaccine candidates should cover all circulating variants."

A University of Illinois at Urbana-Champaign-led team presents a portable approach for identifying SARS-CoV-2 from nasopharyngeal swab samples using a combination of reverse transcription loop-mediated isothermal amplification (RT-LAMP), specified viral transport medium, and a point-of-care microfluidic chip cartridge-based device. After testing the reliability and sensitivity of the RT-LAMP assay with synthetic coronavirus-containing nasal swab samples, the researchers applied a point-of-care and smartphone reader version of the approach to clinical samples, where it picked up authentic COVID-19 cases within around half an hour. The authors conclude that the "promising results of the present study could likely be extended for use with saliva samples for non-invasive, portable, rapid, and scalable testing for COVID-19."

Investigators in Indonesia, the US, Germany, and Australia identify a population of highland wild dogs in New Guinea that appear to be ancestral to New Guinea singing dogs — a group of canids named for their vocalizations. Using genome sequence data for three dogs sampled at high-altitude sites in New Guinea's highlands in 2018, along with available sequence data for nearly 1,400 domestic dogs, New Guinea singing dogs, and wild canids, the team saw highland wild dog sequences and vocalization behaviors that resembled those found in New Guinea singing dogs kept in captivity. "We provide DNA-based evidence for an ancestral relationship between highland wild dogs and captive [New Guinea singing dogs] suggesting that the founding population of the [New Guinea singing dogs] is not, in fact, extinct and that [highland wild dogs] should be resourced for conservation efforts to rebuild this unique canid population."