Simian immunodeficiency virus Genome sequencing and assembly

These sequences refer to those described in our manuscript, "Vaccination with Live Attenuated Simian Immunodeficiency Virus (SIV) Protects from Mucosal, but not Necessarily Intravenous, Challenge with a Minimally Heterologous SIV". Here, there were three animals who had been immunized with a live attenuated SIV and then challenged with a pathogenic SIV containing different sequences. These three animals developed high viremia after this challenge. We sequenced the replicating virus to determine if it was a recombinant of the live attenuated SIV and the challenge virus.