The Mucosal Barrier and Anti-Viral Immune Responses can Eliminate Portions of the Viral Population during Transmission and Early Viral Growth

• DOI: 10.20944/preprints202105.0206.v1
• Publication Date: 2021-05-11T08:22:03Z
• Authors: Athena E. Golfinos; Dane D. Gellerup; Hannah Schweigert; Jaffna Mathiaparanam; Alexis J. Balgeman; Andrea M. Weiler; Thomas C. Friedrich; Brandon F. Keele; Miles P. Davenport; Vanessa Venturi; Shelby L. O'Connor
• Keywords: Simian immunodeficiency virus

Little is known about how individual virus lineages replicating during acute Human Immunodeficiency Virus or Simian (HIV/SIV) infection persist into chronic infection. In this study, we use molecularly barcoded SIV (SIVmac239M) to track distinct viral for 12 weeks after intravenous and intrarectal challenge in macaques. Two Mafa-A1*063+ cynomolgus macaques (Macaca fascicularis) were challenged intravenously (IV), two Mamu-A1*001+ rhesus mulatta) intrarectally (IR) with 200,000 Infectious Units (IU) of SIVmac239M. We deep sequenced the molecular barcode from all animals over characterize diversity persistence lineages, as well sequences T cell epitopes During first three post-infection, found ~175-950 times more unique circulating than those intrarectally, suggesting that route primary driver restricting transmission lineages. Additionally, emergence escape variants can occur on multiple templates simultaneously, but elimination some likely a consequence additional host factors. These data imply present be eliminated population even initial selection.