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PLOS Papers on Extraction-Free SARS-CoV-2 Detection, Kaposi's Sarcoma, Leishmania Genetics

Investigators with Sidra Medicine and Weill Cornell Medical College-Qatar describe a strategy for detecting SARS-CoV-2 directly from nasopharyngeal samples for a paper in PLOS One. Using an RT-qPCR-based approach and samples tested in Doha, the team came up with a viral RNA extraction-free protocol to directly test nasopharyngeal flocked swab samples for RNA originating from SARS-CoV-2 or other coronaviruses. In a set of more than 100 samples compared with standard RNA extraction-based strategies, the authors report that the RT-qPCR-based method could detect SARS-CoV-2 with 95 percent sensitivity, 99 percent specificity, and an accuracy of more than 98 percent. Based on these and other results, the authors suggest that a direct RT-qPCR-based testing approach may "be useful for resource-limited countries to expand their capacity for RT-qPCR testing" by curbing the cost and reagents required.

A team from the US, Tanzania, and Zambia takes a look at gene expression patterns in Kaposi's sarcoma cases in sub-Saharan Africa stemming from endemic Kaposi's sarcoma-associated herpesvirus infections or from epidemic cases related to treated or untreated HIV infections. As they report in PLOS Pathogens, the researchers did RNA sequencing on matched normal and skin lesion samples from 24 male or female Kaposi's sarcoma patients in Tanzania and Zambia, including half a dozen individuals with endemic forms of the disease. When they compared the samples to one another and to samples from a handful of healthy donors, the authors saw similar gene expression features regardless of the broader KS co-infection context, treatment, or biological sex, though the endemic cases tended to have slightly more gene regulation shifts. "[T]he trend toward higher magnitude of gene dysregulation in [endemic KS] coupled with the absence of HIV-1 transcripts in [epidemic KS] may suggest an indirect or systemic effect of HIV-1 to promote KS tumorigenesis," they write.

For a paper in PLOS Neglected Tropical Diseases, Italian researchers share findings from a population genetic study on Leishmania strains collected in Sicily from 2012 to 2014 — work done to get a better understanding of the relatively high rates of leishmaniasis in some parts of Italy. Starting with a set of 78 L. infantum isolates from Sicily, along with half a dozen L. infantum reference samples, the team relied on polymorphic gene profiling, genotyping, and microsatellite typing to explore genetic diversity in the Sicilian samples, uncovering clusters that corresponded to isolates from humans and dogs. "Our results demonstrate that genetic tools are able to discriminate Leishmania strains and to give useful insights into the epidemiology of leishmaniasis," they report, "raising questions on the role of dogs as main reservoirs for human leishmaniasis in the Sicily region."