Immune clearance of highly pathogenic SIV infection

Established infections with the human and simian immunodeficiency viruses (HIV and SIV, respectively) are thought to be permanent with even the most effective immune responses and antiretroviral therapies only able to control, but not clear, these infections 1–4 .W hether the residual virus that maintains these infections is vulnerable to clearance is a question of central importance to the future management of millions of HIV-infected individuals. We recently reported that approximately 50% of rhesus macaques (RM; Macaca mulatta) vaccinated with SIV protein-expressing rhesus cytomegalovirus (RhCMV/ SIV) vectors manifest durable, aviraemic control of infection with the highly pathogenic strain SIVmac239 (ref. 5). Here we show that regardless of the route of challenge, RhCMV/SIV vector-elicited immune responses control SIVmac239 after demonstrable lymphatic and haematogenous viral dissemination, and that replicationcompetent SIV persists in several sites for weeks to months. Over time, however, protected RM lost signs of SIV infection, showing a consistent lack of measurable plasma- or tissue-associated virus using ultrasensitive assays, and a loss of T-cell reactivity to SIV determinants not in the vaccine. Extensive ultrasensitive quantitative PCR and quantitative PCR with reverse transcription analyses of tissues from RhCMV/SIV vector-protected RM necropsied 69–172 weeks after challenge did not detect SIV RNA or DNA sequences above background levels, and replication-competent SIV was not detected in these RM by extensive co-culture analysis of tissues or by adoptive transfer of 60 million haematolymphoid cells to naive RM. These data provide compelling evidence for progressive clearance of a pathogenic lentiviral infection, and suggest that some lentiviral reservoirs may be susceptible to the continuous effector memory T-cell-mediated immune surveillance elicited and maintained by cytomegalovirus vectors. Clinical and experimental observations have suggested that HIV and SIV infections might be vulnerable to immune control or pharmacological clearance in the first few hours to days of infection, before both the viral amplification needed for efficient mutational escape and the establishment of the highly resilient viral reservoir that sustains the infection 4,6–8 . Cytomegalovirus (CMV) vectors were designed to exploit this putative window of vulnerability, based on their ability to elicit and indefinitely maintain high frequency, effector-differentiated, and broadly targeted virus-specific T cells in potential sites of early viral replication 5,9,10 . Indeed, the pattern of protection observed in approximately 50% of RhCMV/SIV vector-vaccinated RM after intrarectal SIVmac239 challenge was consistent with early immunological interception of the nascent SIV infection at the portal of viral entry and immune control before irreversible systemic spread 5 . Protected RM manifested a very transient viraemia at the onset of infection, followed by control of plasma SIV levels to below the threshold levels of quantification, except for occasional plasma viral ‘blips’ that waned over time, and after one year, demonstrated only trace levels of tissue-associated SIV RNA and DNA at necropsy using ultrasensitive assays. The occurrence of plasma viral blips and the recurrence of ‘breakthrough’ progressive SIV infection in 1 of the 13 RhCMV/ SIV vector-protected RM at day 77 after infection indicated that SIV was not immediately cleared from these protected RM, but the failure to find more than trace levels of SIV nucleic acid in systemic lymphoid tissues was consistent with the productive infection being largely contained at the portal of entry with the possibility of eventual clearance. Given the crucial importance of understanding the degree to which a highly pathogenic lentivirus can be contained or even cleared by adaptive immunity, we sought to define more precisely the spread and dynamics of SIV infection in RM that controlled the infection as a consequence of RhCMV/ SIV vector vaccination, and in particular, the extent to which residual SIV was eventually cleared from these animals. To establish the extent of SIV spread early after the onset of RhCMV/ SIV vector-mediated control, we studied a group of five RM vaccinated with RhCMV vectors containing SIV Gag, Rev/Tat/Nef, Env and Pol (but not Vif) inserts that were taken to necropsy within 24 days of controlling plasma viraemia after intrarectal inoculation with SIVmac239. All of these RM had measureable SIV RNA in plasma for one or two weekly time points after challenge, followed by at least three consecutive weekly samples with plasma SIV RNA below 30 copy equivalents (equiv.) per