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PLOS Papers on Human Herpesvirus Integrations, Expression Prediction, APOBEC3 Viral Impacts

In PLOS Genetics, a team led by investigators in Japan searches for human herpesvirus 6 (HHV-6) sequence patterns in whole-genome sequences from nearly 7,500 BioBank Japan participants. Following from prior data suggesting the virus is prone to integrating in telomere regions of the genome, with potential ties to variants in the PIWI-interacting RNA (piRNA)-related chromosome 22 sub-telomere gene MOV10L1, the researchers explain, they used genome screening to clarify these associations, uncovering evidence of HHV-6 co-evolution with human sequences as well as signs that some individuals carry viral excision sequences that may lead to HHV-6 reactivation. "[W]e leverage human genome sequencing to address both new and long-standing clinically-relevant questions about chromosomal integration of HHV-6," they write, noting that the findings so far "raise new hypotheses about these viruses' co-evolution with humans."

Researchers from the University of California, San Francisco, the University of Colorado Anschutz Medical Campus, and elsewhere explore gene expression prediction across populations for another PLOS Genetics paper. Using RNA sequencing and genotyping profiles from more than three dozen African-American individuals from the "Study of African Americans, Asthma, Genes, and Environment" pediatric cohort study, the team looked at the performance of predictive gene expression models trained with data from other populations, along with related expression quantitative loci (eQTL) impacts. "Our investigations into the architecture of gene expression indicate that the power to detect associations is primarily determined by the degree of shared eQTLs across populations," the authors write, concluding that "clinical and biomedical research communities must push for more diverse genotype-expression resources to ensure that the fruits of genomic studies benefit all populations."

For a paper in PLOS Pathogens, a Belgian team takes a look at the impact that human APOBEC3 innate immune effector enzymes exert on the viruses that are at home in humans. The researchers relied on an APOBEC3 motif-focused analysis focused on genome sequences from some 33,400 human viruses, uncovering signs of APOBEC3-based selective pressure on more than one in five known human viral species spanning several human viral families. While endemic members of the coronavirus family appeared prone to APOBEC3 evolutionary "footprints," for example, the authors note that "no such footprint has been detected on the zoonotic MERS-CoV, SARS-Cov-1, and SARS-CoV-2 coronaviruses.