This research investigated the ethical and legal issues that impact on the urgent implementation of Nurse Initiated and Managed Anti-Retroviral Treatment (NIMART) in South Africa, which is part of the task-shifting strategy recommended by the World Health Organization (WHO) to deal with the human resource shortage that has negatively impacted access to Anti-Retroviral Treatment (ART) in developing countries (WHO;2006). The objectives were to review and analyse the existing legal framework and provisions for NIMART in South Africa; and to identify ethical issues and implications of NIMART within the current legal framework. It analysed the legal issues that impact on the implementation of NIMART within the public health service in South Africa, as well as the ethical basis and implications of NIMART on the practice of nurses in the scale-up of Anti-Retroviral Treatment in Primary Health Care (PHC). A comparative analysis was done with case studies of task-shifting in other developing countries and evidence-based recommendations for an enabling and long-term sustainable ethico-legal approach to task-shifting were established. The research concluded that despite the existing legal framework for NIMART in South Africa being firmly founded in the Constitution and further enabled by health policy, challenges exist in implementation of certain critical aspects of the enabling legislation relating to nurse training and accreditation required for full authorization to practice NIMART and that these technical challenges if not attended to could threaten the long-term sustainability of NIMART.

A dissertation submitted to Faculty of Health Sciences, University of the Witwatersrand, in fulfillment of the requirements for the degree of Master of Science in Medicine Johannesburg, June 2016 / Human Leukocyte Antigen (HLA) class I (HLA-I)-restricted CD8+ cytotoxic T lymphocyte (CTL) responses are major drivers of human immunodeficiency virus type 1 (HIV-1) evolution, resulting in the selection of CTL escape mutants. This is particularly well described for HIV-1 proteins such as Gag, Pol and Nef. For the accessory proteins Vif, Vpr and Vpu though, it is still not clear to what extent HLA-I-mediated responses influence their evolution. Moreover, preliminary data from our laboratory showed that Vpu was the most targeted of the accessory proteins with regards to CD8+ CTL and natural killer (NK) cell responses in a long term non progressor/elite controller cohort. Thus, the overall aims of the study were to describe immune escape in Vif, Vpr and Vpu epitopes from HIV-1 infected patients in South Africa, and to clone, express and purify recombinant Vpu for the ultimate detection of anti-Vpu antibodies in South African patient sera. Longitudinal plasma samples were available for 25 patients from two cohorts (18 from Lung and seven from M002). Viral RNA was extracted and the vif, vpr and vpu regions were RT-PCR (Reverse transcription polymerase chain reaction) amplified and sequenced. HLA-A, B and C data for Lung cohort individuals were available, thus the HLA-A, B and C alleles were typed and assigned for the M002 cohort individuals. The Vif, Vpr and Vpu amino acid sequences were subsequently extensively analysed for HLA-driven CTL escape mutations. Lastly, three vpu sequences, Cons. C, 05ZAFV05 and 05ZAFV15 were selected for codon-optimization (humanized), each cloned into the pcDNA3.1/V5-His mammalian expression vector, and used to optimize expression of recombinant Vpu proteins in HEK 293T cells. The HEK 293T cells were harvested and the Vpu was purified using standard nickel affinity chromatography procedures. Protein expression and purification was monitored by SDS-PAGE, Western blot and dot blot analyses. Overall, longitudinal sequences were obtained from Vif, Vpr and Vpu from eight of the 18 patients in the Lung cohort and all seven patients in the M002 cohort. Of these, HLA-driven immune escape mutations were detected in four patients from the Lung cohort and six from the M002 cohort. Interestingly, for the M002 cohort, some reversions to the baseline sequences were noted over time. None of the identified escape mutations are amongst the best described and most optimal HIV-1 CD8+ CTL epitopes of HIV-1 accessory proteins in the HIV-1 databases. Eight and eleven HLA alleles contributed to immune escape in the Lung and M002 cohort Vif, Vpr and/or Vpu sequences, respectively. Overall, HLA-driven immune pressure in the Vif, Vpr and/or Vpu motifs described here may have contributed to the changes in viral loads seen in these patients over time, and likely impacted iii on disease progression, albeit in combination with escape mutations in the more highly targeted HIV-1 proteins, such as Gag, Pol and Nef. Future work looking at longitudinal sequence analysis of the entire HIV-1 proteome in these patients will likely reveal the contributing factors leading to immune escape and ultimately impact disease progression to AIDS. Expression of all three recombinant Vpu proteins in HEK 293T cells was successfully optimized however, as evidenced by SDS-PAGE, Western blot and dot blot analyses, the expression and purification protocol used in this study did not provide sufficient protein yields, nor an optimally purified protein for use in the downstream assays required. Future work will focus on optimization of Vpu expression and purification protocols to aid in the detailed elucidation of the role of Vpu and anti-Vpu immune responses in control of HIV-1 infection. / MT2016

Thesis (Ph.D. (Virology))--University of the Witwatersrand, Faculty of Health Sciences, 2012 / The majority of HIV-1 infections around the world occur via sexual intercourse and women, especially in developing countries, are disproportionately affected. Recently a number of strategies have been proposed to control the spread of HIV, among these the use of microbicides to prevent the sexual transmission of the virus. A clinical trial of 1% tenofovir gel that conferred up to 39% protection provided a proof-of-concept that an anti-HIV microbicide is feasible. Various other compounds, acting at different stages of HIV-1 life cycle, are also being investigated as potential microbicides. These include the lectins Griffithsin (GRFT), cyanovirin-N (CV-N) and scytovirin (SVN). GRFT was isolated from the red algae griffithsia sp. while CV-N and SVN were isolated from the blue green alga Nostoc ellipsosporum and the cyanobacterium Scytonema varium, respectively. These lectins bind mannose-rich glycans found on the surface of HIV-1 envelope and act as entry inhibitors. Although HIV-1 subtype C is the main cause of infections around the world, almost all studies conducted with GRFT, CV-N and SVN are based on subtype B viruses. The Chapter Two sought to establish the neutralization sensitivity of HIV-1 subtype C viruses to the three lectins, using both a cell line and primary cells, and compared this sensitivity to subtype B. This Chapter also examined mannose-rich glycans on HIV-1 that are involved in GRFT, CV-N and SVN binding. The conclusion from this study was that the neutralization of subtype C viruses by these lectins is similar to subtype B and that the 234 and 295 mannose-rich glycans were involved in their interaction with the virus. In general these data supported further studies on the use of GRFT, CV-N and SVN for prevention of HIV-1 subtype C sexual transmission. In Chapter Three, the ability of GRFT to expose the CD4 binding site (CD4bs) on HIV-1 gp120 is explored. I found that this exposure resulted in the enhancement of HIV-1 binding to plates coated with anti-CD4bs antibodies b12 and b6 or the CD4 receptor mimetic CD4-IgG2. This lectin also synergized with b12 and HIVpositive plasma containing antibodies to the CD4bs to neutralize the virus. Furthermore, the glycan at position 386, which shields the CD4bs, was shown to be involved in both GRFT enhancement of HIV-1 binding to b12 and b6 and in the synergistic interaction between the lectin and these antibodies. The importance of this study is that it investigated in details the effect of GRFT binding on HIV-1 envelope and also suggests this lectin can be used in combination with anti-HIV-1 antibodies to synergistically enhance the anti-viral activity. In Chapter Four I investigated GRFT, CV-N and SVN inhibition of the virus binding to the DC-SIGN receptor and their inhibition of the DCSIGN transfer of HIV-1 to target cells. These lectins only moderately inhibited the virus binding to the receptor while they potently inhibited its transfer to target cells. However, the inhibition of transfer was stronger when the virus bound the lectins after binding the DC-SIGN receptor compared to when it bound the lectins prior to binding the receptor. These three lectins can, therefore, inhibit the sexual transmission of HIV-1 since the DCSIGN- mediated transfer of the virus to susceptible cells is pivotal to this mode of transmission. Chapter Five is an investigation of the ability of HIV-1 subtype C to escape GRFT, CV-N and SVN, which involved growing the virus under escalating concentrations of these compounds. This was to know how this virus behaves under conditions of continuous exposure to the lectins. I found that HIV-1 subtype C became increasingly resistant to the lectins and viral envelope sequence analysis showed that this was associated with the deletion of mannose-rich glycans on gp120. Furthermore, of the 11 potential mannose-rich glycosylation sites on gp120 seven (230, 234, 241, 289, 339, 392 and 448) were involved in GRFT, CV-N and SVN resistance. Thus, the conclusion was that although these three lectins are potent inhibitors of HIV-1 infection, the virus is also able to escape their neutralization by deleting mannose-rich glycans on its envelope. However, the fact that escape to these lectins involved multiple deglycosylation and was only partial suggests that HIV-1 subtype C escape from GRFT, CV-N and SVN in a microbicide formulation may not be an easy process. We discuss the implications of these findings in Chapter Six and suggest future studies that could complement data presented in this thesis. Overall our data show that GRFT, CV-N and SVN can prevent the sexual transmission of both free and DC-SIGN associated HIV-1 particles and supports further development of these lectins as microbicides against HIV-1.

HIV-1 infections can be treated but not cured by the current antiretroviral therapy regimens. One of the major barriers to HIV-1 eradication is the persistence of the virus in treated HIV+ individuals under the form of reservoirs. A continuum of molecular mechanisms, at the epigenetic, transcriptional and post-transcriptional levels maintains HIV-1 gene expression silent in its reservoirs. A better understanding of HIV-1 molecular mechanisms of persistence thus allows to devise novel therapeutic approaches to eradicate the virus. In this context, our thesis aimed at characterizing the molecular mechanisms of HIV-1 persistence in its T-lymphoid and myeloid reservoirs. More specifically, we have studied the epigenetic and transcriptional mechanisms of HIV-1 persistence at three different levels. First, we have investigated the DNA methylation-mediated mechanisms underlying the heterogeneity of the DNA methylation inhibitor 5-aza-2’-deoxycytidine potency in the reactivation of HIV-1 gene expression from latently-infected CD4+ T cells. Second, we have studied the contribution of the intragenic binding sites for the cellular PU.1 transcription factor in the specific regulation of HIV-1 gene expression in myeloid lineages. Finally, in a third study, we have designed a new tool to study the transcriptional landscape of HIV-1 in LTRs-suppressed proviruses. Collectively, our work has offered individual insights into the molecular mechanisms underlying the heterogeneity of HIV-1 T-lymphoid and myeloid reservoirs, with the ultimate goal of developing new HIV-1 curative strategies and improving the quality of life of HIV+ individuals. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

L'autophagie est une voie majeure de dégradation et de recyclage des constituants cytoplasmiques. C'est également un mécanisme de l'immunité innée et adaptative. Au cours de l'infection par le VIH-1, l'autophagie est déclenchée dans les lymphocytes T CD4 non infectés après contact avec les glycoprotéines d'enveloppe virale (Env). Cette autophagie participe alors à l'induction de l'apoptose dans ces cellules, mécanisme connu pour être responsable de la disparition des lymphocytes T CD4 au cours de l'infection, et donc de l'évolution vers la phase SIDA. Nos travaux ont permis de montrer que l'activité fusogénique de gp41 est responsable de l'induction d'autophagie et de la mort des lymphocytes T CD4 non infectés après leur contact avec Env. De façon tout à fait surprenante, il apparaît que l'autophagie est bloquée dans les lymphocytes T CD4 productivement infectés par le VIH-1 (souches X4 ou R5). Par contre, les macrophages, autre population cellulaire ciblée par ce virus, ne présentent aucun signe d'autophagie en réponse à la fixation de Env (souches X4 ou R5), alors qu'elle est induite dans les macrophages infectés par ces mêmes virus. Enfin, les derniers résultats nous ont permis de mettre en évidence une phase d'autophagie plus précoce, intervenant dans les deux heures suivant le contact avec Env. L'étude des acteurs impliqués dans l'induction de cette première phase a montré qu'elle était indépendante de la fusion membranaire induite par gp41, ainsi que de la liaison de Env aux récepteurs CD4 et CXCR4. Cette première phase d'autophagie est également présente dans les premières étapes d'infection des lymphocytes T CD4 par du virus libre, et est nécessaire à la réplication du VIH-1. Le VIH-1 adopte donc une stratégie d'exploitation du mécanisme autophagique afin d'optimiser sa réplication, mais également la propagation de l'infection. / Autophagy is a major catabolic pathway involved in the degradation and recycling of cytoplasmic components. It is also a mechanism of adaptive and innate immunity. During HIV-1 infection, autophagy is induced in uninfected CD4 T lymphocytes after contact with cells expressing HIV-1 envelope glycoproteins (Env, gp120/gp41). This process is a pre-requisite to their apoptosis. Thus, autophagy is implicated in the depletion of CD4 T lymphocytes during HIV-1 infection, mechanism leading to AIDS. The results obtained during my PhD have shown that the fusogenic function of gp41 is responsible for the induction of autophagy in the uninfected CD4 T lymphocytes. Surprisingly, this process is blocked in productively HIV-1-infected CD4 T lymphocytes (X4 or R5 strains). In contrast, uninfected macrophages, a preserved cell population during HIV-1 infection, do not undergo X4 or R5 Env-mediated autophagy. However, autophagosomes are present in infected macrophages. Our last results demonstrated that an early autophagic phase is triggered in target CD4 T cells 2h after the contact with Env-expressing cells. Neither the fusogenic function of gp41, nor gp120 binding to CD4 and CXCR4 is implicated in the induction of this early autophagic phase. Interestingly, this process seems necessary to establish an efficient HIV-1 replication. Our results suggest that HIV-1 adopts a strategy to use the autophagic pathway to its own profit and pointes this process as a key for the HIV-1-associated physiopathology.

Made available in DSpace on 2014-07-29T15:26:23Z (GMT). No. of bitstreams: 1 Tese Alexsander A da Silveira.pdf: 1353788 bytes, checksum: cc5086322eeed096d004e0a95e5ae244 (MD5) Previous issue date: 2011-03-15 / Introdução: Estudos locais sobre prevalência de mutações de resistência transmitida, secundária e diversidade genética do HIV-1 em diferentes populações, especialmente em um país continental como o Brasil que oferece tratamento gratuito com os antirretrovirais (ARVs), pode contribuir para uma melhor prevenção contra a infecção pelo HIV-1. Objetivos: Investigar as mutações de resistência transmitida e secundária associadas aos ARVs e a diversidade genética do HIV-1 no Centro Oeste Brasileiro. Métodos: Pacientes sem tratamento ARV foram recrutados em Campo Grande/MS em 2008 e 2010 (n=49) e 27 presidiários infectados com HIV-1 em terapia ARV foram envolvidos no estudo de Campo Grande/MS e Goiânia/Goiás recrutados nos anos de 2008/2009. Fragmentos dos genes da protease (PR), transcripatase reversa (TR) e env gp41 foram retrotranscritos a partir do RNA HIV-1 do plasma, sequenciados e genotipados após a reação de cadeia da polimerase (PCR). As mutações de resistência transmitida e secundária foram identificadas empregando a ferramenta de Calibração de Resistência Populacional (CPR) disponibilizada no site da Universidade de Stanford e pelo banco de dados do IAS-USA (The International AIDS Society). Os subtipos do vírus HIV-1 foram determinados e identificados empregando análises no banco de dados do REGA, pelo software jpHMM-HIV e por inferência filogenética. Resultados: As análises filogenéticas dos fragmentos da PR e TR apresentaram que dois homens que fazem sexo com homens (4,1%; 2/49) apresentaram isolado do HIV-1 com a mutação de resistência V75M, um paciente apresentou um isolado com a mutação de reversão T215S e 4 apresentaram a mutação V179D/E. A maioria dos isolados de HIV-1 (65.3%, 32/49) foram identificados como subtipo BPRBRT, 10.2% subtipo CPRCRT e 8.2% subtipo F1PRF1RT. A recombinação intersubtipo foi de 16.3%. Sequências de isolados de HIV-1 na região env gp41 de 32/49 pacientes indicaram resistência transmitida para o T-20 em 3 pacientes: mutação L44M (n=2), mutação V38A (n=1). A prevalência do HIV-1 B foi de 84%, F1 foi de 12.5% (4/32) e do subtipo C foi de 3%. As mutações de resistência secundárias tiveram uma prevalência de 37% (10/27) entre os pacientes prisioneiros: 5/10 apresentaram mutações para os ITRNs+ITRNNs, 3/10 tinham mutações para os ITRNs, 2/10 eram multiresistentes aos ARVs. A prevalência do HIV-1 foi de 48% para o subtipo B e 11% de subtipo C. Padrões de recombinação complexos foram observados em 41% dos pacientes. Análises filogenéticas utilizando sequências locais indicaram isolados com altos valores sugestivos de transmissão intra-presídio no MS: duas mulheres usuárias de drogas injetáveis com subtipo C, 2 grupos de homens que fazem sexo com homens presidiários: um representado pelo subtipo B do HIV-1, outro pelo recombinante BF1. Conclusão: Este estudo apresentou uma baixa prevalência de resistência transmitida associada com a mutação V75M para os ITRNs e uma moderada prevalência (9%) de resistência transmitida associada ao T-20. Investigações do monitoramento das taxas de transmissão de resistência transmitida nos genes pol são necessárias no Centro Oeste e estudos subseqüentes podem indicar o impacto das mutações para o T-20 no risco da falha terapêutica. A alta prevalência de resistência secundária associada aos ARVs (37%) nos pacientes presidiários dos estados do MS e GO, as complexas formas recombinantes do HIV-1 e a possível transmissão intra-presídio observadas sugerem uma falta de boa adesão ao tratamento com os ARVs e acentuam a necessidade de estratégias de aconselhamento, prevenção e tratamento para a população presidiária por parte das instituições de saúde pública.

Abstract There are approximately 5.5 Million individuals in South Africa infected with HIV-1, predominantly subtype C (HIV-1C). The emergence of drug resistance to the current Antiretroviral (ARV) regimes is of great concern, thus development of novel, effective drugs/vaccines is vital. Certain conserved and thus vulnerable epitopes within the viral envelope (Env) involved in coreceptor binding are usually protected from the immune system in peripheral blood by the variable loops. However, in immune-privileged sites the Env of CD4-independent viruses may exist in a pre-triggered state where these coreceptor binding epitopes are exposed. Targeting the conserved sites could effectively neutralize HIV-1. This study aimed to adapt an HIV-1C primary isolate towards CD4- independence in the Cf2Th cell line through serial in vitro passage. Primary viruses from 20 drug-naïve HIV-1 AIDS patients were isolated and genotypically and phenotypically characterized. The highest percentage (30%) of CXCR4-usage amongst primary isolates from HIV-1C (and CD recombinant) infected AIDS patients worldwide was detected. These data may illustrate the increasing frequency of HIV-1C CXCR4- utilizing (X4) viruses with time and may support the theory that env is capable of evolving. The emergence/evolution of HIV-1C X4 viruses may have profound implications for viral pathogenesis, disease progression and future use of CCR5 antagonists as ARVs. Longitudinal follow-up studies on larger cohorts may confirm this finding. The CXCR4-utilizing isolate 05ZAFV03 was successfully adapted and serially passaged 12 times through Cf2Th cells, whilst gradually decreasing amounts of CD4 expressing cells numbers over time. Viral growth was detected with 10% CD4 expressing cells however, 100% CD4-independence was not reached. Proviral DNA from each stage of the adaptation process was sequenced and analyzed for mutations acquired within env. The only amino acid change noted was an E152K mutation within the V1 region at passage 4. Overall, the extent of env diversity appears to be a complex relationship between isolate-specific and cell-type specific factors. Future attempts to obtain and characterize an HIV-1C CD4-independent isolate will provide potential sites for therapeutic intervention by compounds such as small molecule inhibitors and/or neutralizing antibodies against the most globally prevalent HIV-1 subtype.

Productive HIV-1 transcription yields a single ∼­9.2kb RNA. From this ∼9.2kb genomic RNA, greater than 40 different subgenomic mRNAs can be produced through alternative splicing using four 5' splice sites (ss) and seven 3'ss. Splice site utilization is governed by the inherent strength of the splice sites and by several identified cis acting elements. The HIV-1 Vif protein, required to overcome the cellular antiviral factor APOBEC3G, is encoded by a singly-spliced mRNA coupling 5'ss D1 to 3'ss A1. Alternatively, mRNAs spliced at A1 can utilize a downstream 5'ss, D2, resulting in inclusion of non-coding exon 2 in a small percentage of mRNAs. Expression of vif mRNA within infected cells is required but maintained at low levels. The purpose of studies described in this thesis was to identify and characterize elements within the HIV-1 genome regulating vif mRNA splicing. We identified an exonic splicing enhancer (ESE) within the 18nt downstream of HIV-1 3'ss A1, ESEVif. Mutation of ESEVif within the HIV-1 proviral clone pNL4-3 resulted in a dramatic decrease in vif mRNA, Vif protein, and undetectable levels of non-coding exon 2 inclusion. The cellular splicing factor SRp75 was found to selectively bind ESEVif in vitro. ESEVif mutant virus replicated in APOBEC3G-deficient T-cell lines as efficiently as wild-type virus. In APOBEC3G-producing T-cell lines, ESEVif mutant virus replicated to lower levels than wild-type virus. Other studies have identified additional mRNA splicing elements regulating splicing at A1: the downstream 5'ss D2 can promote or repress splicing, a G4 motif downstream of D2 represses splicing, and two ASF/SF2 dependent splicing enhancers, ESEM1 and ESEM2, promote splicing. Mutational analysis described in this thesis determined that loss of both ESEVif and the G4 motif resulted in wild-type levels of splicing at A1. Mutations of each identified ESE influenced vif mRNA splicing in the order ESEVif>ESEM2>ESEM1. The data presented in this thesis support a model of vif mRNA splicing regulation in which exon 2 ESE act to overcome the negative G4 motif insuring sufficient levels of Vif production for efficient replication in the presence of APOBEC3G.

Doctor of Philosophy (PhD) / This thesis describes synthetic studies towards the HIV-1 integrase inhibitory natural products lithospermic acid and integramycin, resulting in a formal total synthesis of the former. A modular, flexible and convergent synthetic strategy to lithospermic acid was devised. In this approach, a Sonogashira coupling was used to unite the C1–C7 and C20–C27 fragments that were subsequently manipulated to then participate in the key step of the synthesis, a palladium-mediated carbonylative annulation. Reduction of the benzofuran nucleus with magnesium in methanol then provided the desired dihydrobenzofuran core of lithospermic acid. Various protecting group strategies were investigated to complete this sequence in an efficient manner. Further synthetic manipulations afforded the complete C1–C9/C19–C27 fragment, which was united with the C10–C18 fragment to deliver the entire carbon skeleton of lithospermic acid. A two step deprotection sequence was undertaken, however, complications with the final deprotective step prevented definitive proof that the total synthesis of lithospermic acid had been achieved. An alternate protecting group strategy was sought, and a formal total synthesis of lithospermic acid was achieved by intercepting an advanced intermediate from a previous total synthesis. Several strategies for the enantioselective synthesis of the dihydrobenzofuran core of lithospermic acid were evaluated, however, none proved successful. A synthetic route towards the tetramic acid subunit of integramycin was also investigated. 3- Methoxymaleimide was constructed using known chemistry, and the regioselective reduction of this ring system was developed. Attempts to further functionalise this ring system were thwarted by difficulties associated with handling. The scope of the regioselective reduction was investigated on an array of N- substituted methoxymaleimides with the procedure found to be generally high yielding and highly regioselective.

Replication of HIV-1 is inhibited by azidothymidine (AZT), which leads to chain termination and inhibition of DNA synthesis. Resistance to AZT is frequently the result of mutations that increase the ability of RT to remove the chain-terminating nucleotides after they have been incorporated. It has been proposed that RNase H cleavage of the RNA template can occur when RT is stalled near the site of chain termination and contributes to the inhibition by causing the dissociation of the primer-template before the chain terminator can be excised. Mutations in the connection and RNase H domains of RT have been shown to increase excision. It has long been known that resistance to thymidine analogs is conferred by the mutations M41L, D67N, K70R, L210W, T215F/Y and T219Q/E in RT and that this resistance is suppressed by the additional presence of the M184V mutation. Changes in excision activity on DNA templates have been observed with these mutant RTs, but effects on RNase H cleavage resulting in indirect effects on excision activity is also possible with RNA templates. We used a 5'-labeled -3'-chain-terminated DNA primer annealed to either a DNA or RNA template to evaluate primer rescue activities, a 5'-labeled RNA template to evaluate RNA cleavage activity and a biotin-tagged chain-terminated oligodeoxynucleotide to monitor primer-template dissociation. We first investigated differences between RNA and DNA templates when the primers were chain terminated and observed a correlation between RNase H activities and template/primer (T/P) dissociation. An inverse correlation was observed between excision rescue rates and RNase H cleavages leading to T/P dissociation. We observed that the chain terminator (i.e. AZTMP or ddAMP) affected RNase H cleavages and excision rates with RNA template and dNTPs. When we investigated mutations in the N-terminal domain of RT associated with nucleoside reverse transcriptase inhibitor (NRTI) resistance we found that primer rescue was decreased when M184V was present in combination with thymidine analog mutations (TAMs) and the template was RNA with either ATP or PPi as excision substrate. RNase H cleavage at secondary cleavage sites (-7, -8) was substantially reduced with M41L/T215Y RT in comparison with wild type RT, and primer-template dissociation was decreased. In contrast, when M184V was present, RNase H cleavage at the secondary cleavage sites and dissociation of the primer-template occurred at higher levels and excision rescue was decreased. The ability of RT to rescue an AZT terminated primer in the presence of the 184V mutation was restored when the RNase H activity was inactivated by the RNase H negative mutation E478Q. Electromobility shift assay (EMSA) analysis of AZT-resistant mutant RT with M184V showed an increased Kd for formation of the ternary complex. These results suggest that RNase H-mediated RNA-DNA template-primer dissociation is influenced by mutations associated with thymidine analog resistance, and that suppression of resistance to nucleoside RT inhibitors by M184V may be partly explained by effects on RNase H cleavage that decrease the time available for excision to occur. This is the first time that mutations in the polymerase domain are shown to affect excision rescue through an RNase H-dependent mechanism.