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This Week in PLOS: Mar 11, 2019

In PLOS Genetics, investigators at the National Cancer Institute and elsewhere explore population genetic, gene flow, and selection patterns in parts of sub-Saharan Africa with high rates of endemic Burkitt lymphoma, a pediatric cancer that is more common in regions with high rates of Plasmodium falciparum malaria. With genotypes for more than 1,700 individuals from communities in Ghana and Northern Uganda, the authors found evidence for "diverse ancestral origins of the Ugandan, Kenyan, and Tanzanian Great Lakes African populations, reflecting a confluence of Nilotic, Cushitic, and Bantu migrations in the last 3,000 years." For example, the team saw West African and Central African ancestry in dozens of tribes from Ghana, along with gene flow from Gambia and East Africa. The Ugandan populations showed varying ancestry by region, meanwhile, with Northern Ugandan showing signs of malaria-related selection affecting an erythrocyte calcium transport gene ATP2B4.

For a paper appearing in PLOS Neglected Tropical Diseases, a team from Brazil, the UK, and US present findings from a genomic, phylogenetic, and epidemiological analysis of Chikungunya virus (CHIKV) strains from an outbreak in Brazil's Roraima state. Using Oxford Nanopore Technologies MinION nanopore portable sequencing, the researchers did genome sequencing on 20 CHIKV isolates from an East-Central-South America (ECSA) CHIKV genotype in the Brazilian Amazon. Based on a subsequent phylogenetic analysis, they saw signs that the CHIKV-ECSA lineage made its way into Roraima's Boa vista municipality from northeastern Brazil, outpacing infections by an Asian CHIKV genotype introduced to the area earlier. "Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region," the authors report.

A gene expression meta-analysis in PLOS One points to shared expression signatures and pathways contributing to tuberculosis and rheumatoid arthritis. Researchers from the University of Freiburg relied on computational biology and half a dozen publicly available, array-based gene expression datasets representing whole blood or blood cell samples from 41 individuals with active tuberculosis, 33 individuals with rheumatoid arthritis, and 67 healthy, unaffected individuals. The approach revealed 172 genes with significantly altered expression or regulation in both conditions, including components of immune-related pathways such as the T cell receptor signaling pathway, Toll-like receptor signaling pathway, and virus defense pathway.