Herpes simplex virus genomes from an under-sampled population in Namibia reveal novel genetic diversity

Abstract Herpes simplex virus (HSV) is an endemic pathogen, infecting most adults world-wide. HSV infection can cause a wide spectrum of disease outcomes, ranging from asymptomatic infection or mild lesions to rare cases of infectious keratitis, encephalitis, and death. HSV genome sequences have been shown to differ between individual patients, as well as within individuals. To date, the vast majority of publicly available HSV genomic data has come from Europe and North America. Our current understanding of these patterns are missing data from under-sampled populations, particularly in South America, Africa, and Asia. Also missing have been HSV samples from non-industrial (e.g., agricultural, pastoral) populations, for which the natural environment plays a large role in health and disease dynamics. In this study, we capitalized on Whatman FTA card stabilization of DNA to develop a procedure for capturing oral and genital swabs from a geographically isolated pastoralist population in a desert region of northern Namibia. These are the first data to document HSV diversity in this type of remote setting. These are also the first HSV genomes from Namibia. These approaches may prove useful in broadening the accessibility of viral detection for these chronic pathogens, help improve diagnostics, and raise public health awareness about the burden of these pathogens in under-served populations.