RT Journal Article SR Electronic T1 Genotypic and phenotypic diversity within the neonatal HSV-2 population JF bioRxiv FD Cold Spring Harbor Laboratory SP 262055 DO 10.1101/262055 A1 Lisa N. Akhtar A1 Christopher D. Bowen A1 Daniel W. Renner A1 Utsav Pandey A1 Ashley N. Della Fera A1 David W. Kimberlin A1 Mark N. Prichard A1 Richard J. Whitley A1 Matthew D. Weitzman A1 Moriah L. Szpara YR 2018 UL http://biorxiv.org/content/early/2018/02/08/262055.abstract AB Neonates infected with herpes simplex virus (HSV) at the time of birth can have different courses of clinical disease. Approximately half of those infected display manifestations limited to the skin, eyes, or mouth (SEM disease, 45%). However, others develop invasive infections that spread systemically (disseminated, 25%) or to the central nervous system (CNS, 30%); both of which are associated with significant morbidity and mortality. The viral and/or host factors that predispose a neonate to these invasive forms of HSV infection are not known. To define the level of viral diversity within the neonatal population we evaluated ten HSV-2 isolates cultured from neonates with a range of clinical presentations. To assess viral fitness independent of host immune factors, we measured viral growth characteristics of each isolate in cultured cells. We found that HSV-2 isolates displayed diverse in vitro phenotypes. Isolates from neonates with CNS disease were associated with larger average plaque size and enhanced spread through culture, with isolates derived directly from the cerebrospinal fluid (CSF) exhibiting the most robust growth characteristics. We then sequenced the complete viral genomes of all ten neonatal HSV-2 isolates, providing the first insights into HSV genomic diversity in this clinical setting. We found extensive inter-host variation between isolates distributed throughout the HSV-2 genome. Furthermore, we assessed intra-host variation and found that each HSV-2 isolate contained minority variants, with two viral isolates containing ten-fold higher levels of allelic variation than other neonatal isolates or comparable adult isolates. HSV-2 glycoprotein G (gG, US4), gI (US7), gK (UL53), and viral proteins UL8, UL20, UL24, and US2 contained variants that were found only in neonatal isolates associated with CNS disease. Many of these genes encode viral proteins known to contribute to cell-to-cell spread and/or neurovirulence in mouse models of CNS disease. This study represents the first-ever application of comparative pathogen genomics to neonatal HSV disease.