Leucemia/linfoma de células T do adulto associado a infecção pelo HTLV-1 em adolescente brasileiro

We present the case of a 15-year-old patient infected with HTLV-1 who developed a cutaneous T-cell lymphoma, confirmed by histopathological and immunohistochemical examination, as well as clinically and hematologically confirmed leukemia. The patient died 3 months after initial presentation of the disease. The rarity of the disease in this age group justifies the present report.Apresentamos o caso de um adolescente de 15 anos de idade com infecção pelo HTLV-1 que desenvolveu linfoma cutâneo de células T, confirmado por exame histopatológico e imunohistoquímico, assim como leucemia, diagnosticada por exame clínico e avaliação de sangue periférico. O paciente morreu 3 meses após o início da doença. A raridade da doença nesta faixa etária justifica o relato de caso

Some aspects of HTLV-1 infection in Natal, South Africa.

Doctoral Degree. University of KwaZulu-Natal, Durban.Abstract available in PDF.Publications listed on page v-vi

Persistent immune activation in HIV-1 infected individuals|btrigering mechanisms = Hiperactivación inmune en pacientes infectados por VIH-1 : origen multifactorial

Texto en inglés, y discusión y resumen en inglés y españolLa implantación de tratamiento antirretroviral de alta eficacia (TARGA) en pacientes infectados por el virus de la inmunodeficiencia humana tipo 1 (VIH-1) controla la replicación viral y contribuye a la recuperación inmunológica del individuo, disminuyendo considerablemente la morbilidad y mortalidad de estos pacientes. No obstante, los niveles de inflamación y activación inmunológica en pacientes bajo tratamiento permanecen significativamente elevados, relacionándose con un mayor riesgo de padecer enfermedades cardiovasculares y cáncer, entre otras. Los mecanismos responsables de la activación inmune en individuos infectados por VIH-1 continúa siendo tema de controversia. Algunos estudios señalan continuos ciclos de replicación viral como posible factor desencadenante de una activación crónica generalizada. Y otros, en cambio, proponen la translocación bacteriana como un proceso desencadenante de inflamación local y activación inmune mediante la secreción de citoquinas proinflamatorias. Estos fenómenos se agravarían en presencia de coinfecciones, frecuentemente producidas en individuos infectados por VIH-1, entre las que destaca el virus de la hepatitis C (VHC). La finalidad de este estudio es contribuir a clarificar los efectos que pueden tener varios factores biológicos en la activación inmune persistente asociada a la infección por VIH-1, en particular, la translocación bacteriana y la influencia de algunas coinfecciones frecuentes en este tipo de pacientes, ya sea parasitaria, como la infección por Leishmania., o víricas como la infección por VHC y el virus linfotrópico de células T humanas (HTLV). Los individuos VIH-1-positivos analizados, con revisiones médicas periódicas en el Hospital Ramón y Cajal, en Madrid, tenían carga viral indetectable (< 50 copias ARN/ ml) durante un periodo largo de tiempo bajo tratamiento antirretroviral. Los individuos que se someten a intensificación de tratamiento muestran una reducción en la activación inmune, sin embargo los niveles de translocación se mantienen estables o incluso aumentan durante el periodo de intensificación, sin correlación entre los niveles de translocación bacteriana y la activación inmune en individuos con relativamente buena recuperación inmunológica bajo con intensificación de tratamiento antirretroviral. Los individuos coinfectados por Leishmania muestran niveles de activación inmune, inflamación, translocación bacteriana y senescencia celular superiores a los individuos inmunológicamente discordantes a tratamiento. Por otro lado, la coinfección por HIV-1/HTLV-2 muestra menores niveles de carga viral por VIH-1 previo inicio de tratamiento, además de mayores niveles de células T CD8+ en comparación con individuos negativos para HTLV-2. En individuos coinfectados por HIV-1/HCV, la infección por HTLV-2 muestra menores niveles de activación celular, alanina transaminasa y fibrosis hepáticas que aquellos individuos no infectados por HTLV-2. En conclusión, este estudio demuestra que los niveles de translocación bacteriana se asocian con la inflamación y activación inmune en individuos infectados por VIH-1. Sin embargo, esta asociación no se evidencia en individuos virológicamente suprimidos en tratamiento bajo un largo periodo de tiempo. La coinfección por Leishmania acelera el nivel de inmunosupresión asociado a infección por VIH-1, con características inmunológicas, como los niveles de translocación bacteriana, inflamación y activación inmune peores que los detectados en individuos inmunológicamente discordantes a tratamiento. Se corrobora además la función protectora de HTLV-2 en individuos coinfectados, y se evidencia el papel protector de HTLV-2 en individuos coinfectados por VIH-1 y HCV, reduciendo niveles de activación inmune y, además, ralentizando el desarrollo de enfermedades hepáticas

Recent Advances in HTLV Research 2015

The human T-cell leukemia virus types 1 and 2 (HTLV-1 and HTLV-2) were both discovered over three decades ago and infect millions people worldwide. HTLV-1 is associated with the adult T-cell leukemia/lymphoma (ATLL) in about 2% of individuals infected, and another 2 to 3% of individuals develop a neurologic disorder called HTLV-associated myelopathy (HAM). HTLV-2 causes HAM in approximately 1 to 2% of infected individuals, but does not cause ATLL. HTLV-1 and HTLV-2 have served as excellent models for the study of the epidemiology and pathogenesis of virus-associated cancers as well as autoimmune conditions such as multiple sclerosis. Recently, two new members—HTLV-3 and HTLV-4—have been discovered in bushmeat hunters from central Africa, which emphasizes the urgent need for continual surveillance for new human retroviruses and their capacity to cause disease. Important public health issues remain open issues to be addressed in spite of the basic epidemiology of HTLV-1 and HTLV-2 being reasonably well defined. Clinical research is needed in developing potential HTLV-1 and HTLV-2 vaccines, as well as development of treatment options for ATLL and HAM. This ‘Recent Advances Issue’ contains both reviews and updates on research that encompasses these areas

Persistent immune activation in HIV-1 infected individuals|btrigering mechanisms = Hiperactivación inmune en pacientes infectados por VIH-1 : origen multifactorial

Texto en inglés, y discusión y resumen en inglés y españolLa implantación de tratamiento antirretroviral de alta eficacia (TARGA) en pacientes infectados por el virus de la inmunodeficiencia humana tipo 1 (VIH-1) controla la replicación viral y contribuye a la recuperación inmunológica del individuo, disminuyendo considerablemente la morbilidad y mortalidad de estos pacientes. No obstante, los niveles de inflamación y activación inmunológica en pacientes bajo tratamiento permanecen significativamente elevados, relacionándose con un mayor riesgo de padecer enfermedades cardiovasculares y cáncer, entre otras. Los mecanismos responsables de la activación inmune en individuos infectados por VIH-1 continúa siendo tema de controversia. Algunos estudios señalan continuos ciclos de replicación viral como posible factor desencadenante de una activación crónica generalizada. Y otros, en cambio, proponen la translocación bacteriana como un proceso desencadenante de inflamación local y activación inmune mediante la secreción de citoquinas proinflamatorias. Estos fenómenos se agravarían en presencia de coinfecciones, frecuentemente producidas en individuos infectados por VIH-1, entre las que destaca el virus de la hepatitis C (VHC). La finalidad de este estudio es contribuir a clarificar los efectos que pueden tener varios factores biológicos en la activación inmune persistente asociada a la infección por VIH-1, en particular, la translocación bacteriana y la influencia de algunas coinfecciones frecuentes en este tipo de pacientes, ya sea parasitaria, como la infección por Leishmania., o víricas como la infección por VHC y el virus linfotrópico de células T humanas (HTLV). Los individuos VIH-1-positivos analizados, con revisiones médicas periódicas en el Hospital Ramón y Cajal, en Madrid, tenían carga viral indetectable (< 50 copias ARN/ ml) durante un periodo largo de tiempo bajo tratamiento antirretroviral. Los individuos que se someten a intensificación de tratamiento muestran una reducción en la activación inmune, sin embargo los niveles de translocación se mantienen estables o incluso aumentan durante el periodo de intensificación, sin correlación entre los niveles de translocación bacteriana y la activación inmune en individuos con relativamente buena recuperación inmunológica bajo con intensificación de tratamiento antirretroviral. Los individuos coinfectados por Leishmania muestran niveles de activación inmune, inflamación, translocación bacteriana y senescencia celular superiores a los individuos inmunológicamente discordantes a tratamiento. Por otro lado, la coinfección por HIV-1/HTLV-2 muestra menores niveles de carga viral por VIH-1 previo inicio de tratamiento, además de mayores niveles de células T CD8+ en comparación con individuos negativos para HTLV-2. En individuos coinfectados por HIV-1/HCV, la infección por HTLV-2 muestra menores niveles de activación celular, alanina transaminasa y fibrosis hepáticas que aquellos individuos no infectados por HTLV-2. En conclusión, este estudio demuestra que los niveles de translocación bacteriana se asocian con la inflamación y activación inmune en individuos infectados por VIH-1. Sin embargo, esta asociación no se evidencia en individuos virológicamente suprimidos en tratamiento bajo un largo periodo de tiempo. La coinfección por Leishmania acelera el nivel de inmunosupresión asociado a infección por VIH-1, con características inmunológicas, como los niveles de translocación bacteriana, inflamación y activación inmune peores que los detectados en individuos inmunológicamente discordantes a tratamiento. Se corrobora además la función protectora de HTLV-2 en individuos coinfectados, y se evidencia el papel protector de HTLV-2 en individuos coinfectados por VIH-1 y HCV, reduciendo niveles de activación inmune y, además, ralentizando el desarrollo de enfermedades hepáticas

Epidemiology of emerging human-infective RNA viruses: discovery, geographical extent, and disappearance

Previous investigations into human infectious diseases have revealed RNA viruses as major etiological agents. Given the recent rate of newly detected human-infective RNA viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Middle East respiratory syndrome coronavirus, and Bundibugyo ebolavirus, targeting virus discovery in high-risk regions, characterizing viruses with the greatest likelihood of spreading and establishing sustained infection in humans would benefit better preparedness for future outbreaks. There is a lack of evidence on determinants of spatio-temporal patterns in the discovery of human-infective RNA viruses, though previous studies have attempted to identify hotspots of emerging infectious diseases caused by various pathogens. There are also no quantitative studies exploring predictors of geographical extent and the disappearance for all currently known human-infective RNA viruses. This thesis aimed to address the following gaps. 1. Identifying predictors discriminating between areas with and without discovery of human-infective RNA viruses and predicting discovery hotspots, at both global and regional scales. Predictors identified include socio-economic, climatic, land use, and biodiversity variables. 2. Prediction of the geographical extent and the disappearance of human-infective RNA viruses, using features such as taxonomy, virus structure, transmission mode, host range, origin, and clinical presentation. 3. Taking SARS-CoV-2 as an example, investigating how predictors related to demographics, socioeconomics, travel, healthcare, co-morbidities, readiness, geography, COVID-19 testing, and interventions have affected the epidemic of the disease it caused—coronavirus disease 2019 (COVID-19)—between countries in the WHO African Region. In order to address the gaps outlined above, I firstly geocoded the first reports of 223 human-infective RNA viruses at the global scale. Using a Poisson boosted regression tree (BRT) model, I identified GDP growth, GDP, and urbanization as top predictors of virus discovery, and predicted discovery hotspots including both historical hotspots—eastern North America, Europe, central Africa, eastern Australia, and north-eastern South America, and new hotspots—East and Southeast Asia, India, and Central America. Stratified analyses suggested discovery of vector-borne viruses and strictly zoonotic viruses was more correlated with climatic variables and biodiversity, whereas the discovery of non-vector-borne viruses and human-transmissible viruses was more strongly correlated with GDP and urbanization. Next, I focused on comparisons of the specific predictors of RNA virus discovery in three different regions with different GDP—United States, China, and Africa. A similar methodology as the global analysis was used on each region separately, the results showed that predictors such as GDP and land use continued to be top predictors in three regions, but climate and biodiversity variables were consistently less important predictors than at a global scale. To identify predictors of the geographical extent and the disappearance (no record of infection in the literature for the past ten years or more), I collated information for 223 human-infective RNA viruses on their geographical extents and persistence in causing human infections from peer-reviewed literature. By fitting Bernoulli BRT models, I observed that viral features that predicted wide geographic extent included transmissibility between humans, a +ssRNA genome, narrow host range [i.e. infecting humans only or humans and other non-human primates (NHP) only], and having a reservoir host in a NHP. Viruses were more likely to disappear if they were incapable of transmission between humans, have had a localised geographic extent, a dsRNA genome, were non-pathogenic and non-fatal, were firstly discovered through active discovery programmes rather than passive investigation of the aetiology, and were transmitted by vectors and direct contact. Results for both geographical extent and virus disappearance did not change after factoring out reporting effort. I concluded that multiple characteristics determined the geographical extent and disappearance of human-infective RNA viruses; however, transmission mode and structure were consistently the most important predictors of the geographical extent and disappearance of human-infective RNA viruses. Host range was an important predictor of geographical extent, though less important for disappearance. Geographical extent, clinical presentation and discovery process all contributed to the probability of a virus disappearing. To understand the differences between epidemics of COVID-19 between countries of the WHO African Region, I selected the timing of the first case and the mortality rate in the first and second waves as the three outcomes. By applying a series of statistical models including Cox proportional hazards regression models, generalized linear mixed models and multinomial logistic regression models, I found that COVID-19 in Africa arrived earlier and caused greater mortality in countries with more pre-pandemic international connectivity and a more urban population. Mortality was exacerbated by high HIV prevalence. The stringency and timing of government restrictions on behaviour were not associated with a lower per capita mortality rate. A more urban population and a higher infectious disease resilience score were associated with more stringent restrictions and/or a higher per capita mortality rate. The predictor set for the first and second waves were similar, and first wave per capita mortality was a significant predictor of second wave per capita mortality. In summary, studies in this thesis showed that there were variations in predictors of discovery both between virus types and geographical regions, and identified high-risk regions for virus discovery beyond their historical extent. The studies also provided proof-of-principle for the prediction of attributes such as mortality, geographical extent, and disappearance for new human-infective RNA viruses. These results help identify priority regions for investment in surveillance systems for new human-infective viruses, and to make risk assessments once they have emerged

Male genital tract versus blood HIV-1 compartmentalization and selection: the first step of the transmission bottleneck?

Introduction Sexual transmission of HIV-1 accounts for more than 80% of all the transmissions globally. After transmission, approximately 80% of the newly disseminated infections can be traced to a single variant, which comes from the minor HIV-1 population within the transmitting donor. This has led to the widely accepted idea of an HIV-1 transmission bottleneck. The nature of this bottleneck is not fully understood. Many studies working on understanding the nature of the transmitted virus have reported discordant traits of transmitted/founder viruses compared to viral isolates from chronically infected individuals. Such studies therefore lacked analysis of the intermediate step between these two populations: HIV-1 from the genital tract of the donors: where viruses are on their way to transmission to a new recipient. Importantly, numerous prior studies have shown that there is compartmentalization of HIV-1 populations between the general circulation and the genital tract, raising the possibility that the genital tract is an important selective environment. Collectively, prior studies of genital tract compartmentalization in males detected compartmentalization in about half of the donors studied, although by using techniques with limited depth of sampling than that employed in our study. The virus that establishes disseminated infection in a new recipient is selected. However, the extent to which this selection occurs before, during or after crossing the mucosal surfaces of the recipient is less clear – the period during which transmission selection could extend far back to the donor, and the donor’s genital tract. In other words, it is not clear as to what extent the transmission bottleneck occurs during compartmentalization of viral populations in the genital tract tissues. The design of an effective vaccine and other intervention strategies will rely upon the understanding the nature of the transmitted virus as this is the virus that must be targeted. This thesis Compartmentalization of minor variants cannot be tracked by techniques previously used to describe compartmentalization between the genital tract and the blood circulation. We therefore used deep sequencing-based techniques to further understand compartmentalization of viral populations between blood and the male genital tract. In addition, we tested the sensitivity of variants to a range of entry and other inhibitors in order to explore possible changes in function that may arise when viral variants grow in the shifted selective milieu of the genital tract. We further hypothesized that this change of selective milieu as HIV-1 moves from blood into the genital tract may lead to viral variants in semen that are sensitive to autologous neutralization because such sensitive variants may be able to grow in the genital tract, which is presumably partially or completely shielded from antibodies. Because the viral populations in semen comes from a site that may be relatively protected from antibodies, they may be permitted to evolve differently in the relative absence of antibody pressure. It is possible that evolution of the virus within the genital tract is a significant part of the change the virus undergoes on its way to establishment of a new disseminated infection in the new recipient. We considered this possibility because even some small molecules like those of some antiretroviral drugs do not penetrate the genital tract effectively under some circumstances, raising the possibility that antibodies might not always penetrate in all areas of the genital tract. This thesis had three objectives: 1. To evaluate HIV-1 compartmentalization in blood and the male genital tract using next generation sequencing to understand the nature of viral populations in these anatomical sites in greater detail. 2. To identify the differences in sensitivity of blood and semen variants to entry inhibitors to obtain information about differences in function between HIV-1 populations in blood vs the male genital tract. 3. To compare neutralization sensitivities of viral variants compartmentalized in blood and semen by testing their sensitivity to neutralization by autologous antibodies. As a control, we measured sensitivity to a pool of clade-matched heterologous sera to determine if any observed difference was due to global changes in neutralization sensitivity. Methods Study participants Forty-four HIV-1 seropositive men were recruited and then requested to donate blood and semen samples at ANOVA Health’s Ivan Toms clinics at Woodstock and Green Point or through their mobile clinic in Khayelitsha, all in Cape Town, South Africa. Viral loads from blood and semen and CD4+ T cell counts from blood were measured. HIV-1 was enriched from semen using a Nycodenz gradient, and then concentrated using ultracentrifugation. Chapter 2: HIV-1 Compartmentalization in blood and semen Next generation sequencing on Illumina paired-end Miseq platform was performed. To our knowledge there is no published study that has used this technique to study male genital tract HIV-1 variants in chronically infected male donors, although there is one that does so for acutely infected donors. We argue here that this is a superior method of sampling populations in blood and the male genital tract. In particular, it allowed us to more accurately track minor populations within each compartment. Additionally, the use of PrimerID approach allowed us to more clearly identify clonal amplification events in the HIV-1 populations. Sequencing was performed on either the V3 or C3-V5 region of the HIV-1 envelope gene from paired blood and semen samples from 11 donors. To evaluate compartmentalization, populations from blood and semen were compared using three standard techniques, Slatkin Maddison Test (SMT), Wrights measure of population subdivision (FST) and nearest neighbour statistic (Snn). Clonal amplification and results of modelling a lower depth of sampling are also presented. Chapter 3: Sensitivity of blood and semen variants to entry inhibitors and changes in function From three subjects who exhibited the highest extent of compartmentalization, full-length envelope clones derived from semen and blood RNA were made using limiting dilution PCR (single genome amplification), which provided the advantage of minimizing PCR-based artificial recombination. A high fidelity Taq polymerase was also used to minimize base-substitution errors. An average of 10 clones were isolated per compartment. Pseudoviruses were then constructed from the full-length envelope clones from blood and semen. The sensitivities of these pseudoviruses were tested against HIV-1 entry inhibitors; Maraviroc, PSCRANTES, enfurvirtide (T-20) and JM2987. Maraviroc and PSC-RANTES are CCR5 inhibitors while JM2987 is a CXCR4 inhibitor. Enfurvirtide (T-20) is a fusion inhibitor blocking the virus from entering cells. The full-length clones used to make the pseudoviruses were also sequenced and genomic variations in variable loop characteristics (length and number of potential glycosylation sites) between blood and semen compared. Chapter 4: Sensitivity of blood and semen variants to autologous and heterologous antibodies To study the differences in sensitivity of blood and semen variants to antibodies, pseudoviruses cloned from semen RNA and blood RNA (above) were tested for their sensitivities to donor antibodies collected at the same time the samples were collected or to a pool of HIV-1 subtype C sera. Results Objective 1: Viral compartmentalization via next generation sequencing HIV-1 populations were compartmentalized in all the 11 donors studied but to varying extents. Donor SVB043 had the most compartmentalized viral populations between blood and the male genital compartment using all the three measures of compartmentalization. Further analysis of the phylogenetic trees revealed that some clusters contained either purely blood or semen sequences, even in trees generated from analysis of donors with weakest compartmentalization. This might explain the viral compartmentalization signal in these weakly compartmentalized donors. To mimic reduced sampling depth, subsampling of the Illumina Miseq data with a small number of sequences was done. This analysis revealed that viral compartmentalization between blood and male genital tract would likely (>50% estimated likelihood) have been detected in only 5/11 (45%) of the donors, a proportion which is very similar to the aggregate proportion from previous studies that had used single genome amplification (SGA) analysis. This means that the difference in detecting HIV-1 compartmentalization in this thesis vs previous studies can be explained by the depth of sequencing achieved here and that there is no evidence that the dynamics of the viral populations studied in this thesis were different from those previously studied. In addition, the most recent common ancestor of semen variants was mostly located in blood, indicating the male genital tract was seeded by incoming variants from blood. Clonal amplification was also observed in all the 11 study participants and it was a characteristic of variants from blood and the male genital tract and its frequency did not obviously correlate with the severity of compartmentalization. In sum, blood and male genital tract HIV-1 compartmentalization and clonal amplification is present in most or all HIV-1 infected males but was not detected in all individuals in previous studies when using techniques with lower depth of sampling. Objective 2: Sensitivities of blood and semen variants to entry inhibitors and variable loop characteristics Viral variants from the most compartmentalized donors had variations in sensitivities to entry inhibitors; although the direction of the difference was inconsistent. Donor SVB043 who had the most severely compartmentalized viral populations between blood and semen, had semen viruses that were 1.67 (95%CI 1.08 – 2.56) times more resistant to maraviroc (p=0.024) while SVB008 which was the second most compartmentalized donor, had semen isolates that were 4.8 (95%CI 2.76 – 8.28) times more sensitive to inhibition by maraviroc (p < 0.0001). The meaning of this discrepancy is not entirely clear. It could mean that trait(s) that are selected for in genital tract variants over blood circulation variants are linked to the CCR5 binding region, and that the linked CCR5 genotype was carried along with the selected trait(s). There were no differences in sensitivity to maraviroc between blood and semen clones for donor SVB049 (p=0.847); although this donor on further investigation was found to have functional levels of efavirenz in his blood (3µg/ml, which were within the therapeutic range of 1-4µg/ml) indicating that he was likely on antiretroviral therapy (ART). This was not known to the clinic staff at the clinic at which he was known to receive care and was recruited to this study. The direction of sensitivities to PSC_RANTES (another CCR5 inhibitor) was concordant to that observed for maraviroc for donors SVB008 and SVB049 but not for donor SVB043 where semen variants were 1.67 (95%CI 1.08 – 2.56) times less sensitive than blood variants to maraviroc, with no detected difference in sensitivity to PSC_RANTES (p = 0.783). This discrepancy for donor SVB043 probably reflects the difference in mode of action between Maraviroc and PSC_RANTES. The change in envelope conformation over movement from blood into the genital tract presumably affected the maraviroc binding site and not PSC_RANTES. All the clones from blood and semen for the three most viral compartmentalized donors were resistant to CXCR4 inhibitor suggesting that they were all R5 tropic viruses. There were no differences in sensitivities of blood and semen viruses to fusion inhibitor T-20. The findings here suggest a changed viral envelope conformation/structure for the viruses in the male genital tract. The discordance suggests that the selected trait over movement of virus from blood into genital tract is linked or close to CCR5 binding site but itself does not involve binding to CCR5 coreceptor. Differences in length and number of glycosylation sites were found between variants from blood and those from the genital tract but the direction of the difference was also inconsistent. Donor SVB043 who had the most compartmentalized blood and seminal variants had semen variants that had longer and more glycosylated envelopes. Donor SVB008 who had the second most compartmentalized blood and semen variants had no difference in variable loop length, but semen variants were less glycosylated. This therefore shows that selection for some of the previous reported traits of acute viral isolates may have started in the genital tract in a subset of the donors. Objective 3: Sensitivities of blood and semen variants to autologous and heterologous antibodies Viral populations compartmentalized in blood and the male genital compartment displayed a range of sensitivities to autologous and heterologous neutralization. Donor SVB043 who had the most compartmentalized viral populations between blood and the genital tract; had semen clones that were 1.75 (95%CI 1.11-2.78) times more sensitive to autologous neutralization compared to blood clones (p = 0.018). In contrast, donors SVB008 and SVB049 who exhibited substantial compartmentalization, but to a lesser extent than that found in donor SVB043, showed no differences in sensitivities of blood and semen variants to autologous serum. Neutralization sensitivity to a pool of heterologous subtypematched sera revealed no differences in sensitivities between clones from blood and semen for donors SVB043 and SVB008. Interpretation of results from donor SVB049 are clouded by the donor’s ART use. Overall, these results suggest that, in some individuals, a shift in selective milieu of the genital tract virus occurs. This is presumably due to partial or complete shielding of the genital tract tissue from circulating antibodies, and this shielding shape the populations of HIV-1 variants available for transmission from some but not all individuals. Overall conclusions Our data add to the existing knowledge of existence of distinct viral populations between blood and the male genital tract of chronically HIV-1 infected donors. Importantly, and for the first time, we present evidence that HIV-1 compartmentalization between blood and the male genital tract is present in most or all donors, and that some clones are severely compartmentalized even in donors who exhibit very mild compartmentalization. It appears that viral compartmentalization and clonal amplification in these anatomical sites may be present in most individuals but remained undetected in some individuals in previous studies due to the lower depth of sampling applied. We observed a discordance in entry inhibitor sensitivities and variable loop characteristics between blood vs semen variants among different donors. This may suggest a changed envelope conformation over importation of virus from blood into the genital tract. This change seems to be near or linked to the co-receptor binding site but does not appear to directly involve the co-receptor binding tested in this thesis. This interpretation also may explain the discordance in viral characteristics for the virus establishing infection reported in other studies. This thesis also shows that some of these traits of the transmitted/founder virus relating to neutralization sensitivity, sensitivity to entry inhibitors and variable loop characteristics may originate in and/or be enhanced by transition through the genital tract on the way to becoming a founder virus. These results are important in understanding how the populations in the genital compartment are selected, giving rise to the population of HIV-1 that is available for transmission to a new individual. An understanding of the dynamics of HIV-1 populations prior to and during transmission is important for vaccine design and other intervention strategies

The involvement of retroviruses in human T cell leukaemias and lymphomas

Human T lymphotropic virus type 1 (HTLV-I) causes adult T cell leukaemia/lymphoma (ATL), a neoplasm of CD4+ T cells. The related virus HTLV-I I has been isolated from cases of CD8+ T cell variant hairy cell leukaemia but has not been definitively associated with neoplasia. Bovine leukaemia virus (BLV), which causes B cell leukaemia and lymphoma in cattle, belongs to the same group of retroviruses. The hypothesis tested in this study was that HTLV-I, HTLV-II or related viruses are associated with T cell leukaemias and lymphomas in the United Kingdom, particularly mycosis fungoides (MF) and Sezary syndrome (SS). A combination of cell and molecular biology techniques was used in an attempt to identify retroviruses in patients with these neoplasms. Lymphocytes were cultivated from blood, skin and lymph nodes of patients with cutaneous lymphoid infiltrates to establish continuous T cell lines that might propagate HTLV-I, HTLV-II or related retroviruses. Techniques for the establishment of cultures included stimulation with mitogens, cytokines, conditioned medium and cocultivation. Cultured cells were examined for evidence of retroviruses by electron microscopy (EM), reverse transcriptase (RT) assay and the polymerase chain reaction (PCR). No retroviruses were isolated from 158 cultures initiated from 18 patients with cutaneous T cell lymphomas (predominantly MF and SS) and three patients with cutaneous B cell lymphomas (CBCLs). Four interleukin 2-dependent CD8