<p>Reverse transcriptase (RT) is a crucial enzyme for retrovirus replication, and its presence in the virion is indispensable for infectivity. This thesis illustrates the use of RT activity assays as tools for quantitation and characterization of different retroviruses, particularly HIV. </p><p>A non radioactive assay, using microtiter plates, for the RT of Moloney murine leukemia virus (MMuLV) was developed. Assay conditions for MMuLV and HIV-1 RT, together with isozyme specific RT activity blocking antibodies, were shown useful for discrimination between RTs from different retrovirus genera. RT activity assay for HIV-1 was found to quantitate different subtypes more equally efficient than p24 antigen assays did.</p><p>Viral load (VL), the amount of HIV particles in the blood, is an important marker of the clinical status of an infected person. A method for VL determination based on RT activity (ExaVir Load) was developed. After plasma pretreatment, to inactivate cellular DNA polymerases, virions in patient plasma were immobilized on a gel, which was washed to remove disturbing factors. The virions were lysed with a detergent containing buffer and the lysate eluted. Finally, the RT activity in the lysate was determined and found to correlate strongly to VL by RNA according to a PCR based standard method (Roche Amplicor 1.5). The second version of the method was able to measure VL down to approximately 400 HIV-1 RNA copies/ml. The usefulness of RT from the VL procedure for determination of susceptibility towards anti-HIV drugs was demonstrated, and the results were in agreement with genotypic data. </p><p>Due to its technical simplicity, and ability to detect a broad range of HIV-1 subtypes, ExaVir Load and the drug susceptibility application are interesting for clinical use, particularly but not only in resource limited settings. The concept is also potentially useful for research purposes, e.g. in combination with specific RT assay conditions.</p>

<p>Antiretroviral regimens have side effects that can threaten adherence by patients resulting in evolution of viral resistance due to suboptimal drug levels. Studies have shown that drug adherence of at least 80% can result in viral load suppression. There is no literature on the association between the level of adherence to antiretroviral therapy and the degree of virological suppression in Namibia. The aim of the present study was to determine the therapeutic and virological outcomes in HIV/AIDS patients at 6 and 12 months after initiation of highly-active antiretroviral therapy (HAART) in an urban population in Namibia. The distribution of viral load results showed a low uptake (35%) of virological monitoring at 6 month time point and even lower (12%) at 12 months. A conservative viral load threshold for virological response is required in the Namibian setting. The current adherence level of &gt / 80% encourage increased ARV therapy rollout. Poor virological outcome was associated with self-reported adherence.</p>

Oncogenic human papillomaviruses (HPVs) are implicated in 99.7 % of cervical cancer cases but require the co-operation of other factors. To investigate potential genetic risk factors we have typed the HLA class II DRB1 and DQB1 loci in 478 women diagnosed with cervical carcinoma in situ and in 608 age-matched controls. Quantitative measurements of HPV 16, HPV 18/45 and HPV 31 were obtained. The DRB1*1501 and DQB1*0602 alleles were found to increase the risk of HPV 16 infection. Carriers of DRB1*1501 and DQB1*0602 were also shown to have an increased risk of a higher viral load compared to non-carriers. The DRB1*1301 and DQB1*0603 alleles were found to protect from HPV 18/45 and 31 infections as well as resulting in a lower viral load in carriers compared to non-carriers. Women with a high HPV 16, 18/45 or 31 viral load were more prone to long-term infections and women with a low HPV 16 viral load were more prone to short-term infections. Carriers of DRB1*1501 and DQB1*0602 alleles were also shown to have an increased risk of long-term infections compared to short-term infections. We also tested if an HPV susceptibility locus found for epidermodysplasia verruciformis (EV) was also linked to HPV susceptibility in cervical cancer. We did not find any linkage to this locus in a set of 77 families, each with at least three cases diagnosed with cervical carcinoma in situ. Other potential risk factors tested were HPV 16 E6 variants together with a p53 codon 72 polymorphism and HLA class II alleles. We found an association between the E6 L83V variant and the HLA DR4-DQ3 haplotype, as well as an increased frequency of Arg homozygosity of p53 in women infected with the L83V variant. These results show that alleles at HLA class II loci represents risk factors for persistent HPV infection and thereby also contribute to the risk of development of cervical carcinoma in situ.

Reverse transcriptase (RT) is a crucial enzyme for retrovirus replication, and its presence in the virion is indispensable for infectivity. This thesis illustrates the use of RT activity assays as tools for quantitation and characterization of different retroviruses, particularly HIV. A non radioactive assay, using microtiter plates, for the RT of Moloney murine leukemia virus (MMuLV) was developed. Assay conditions for MMuLV and HIV-1 RT, together with isozyme specific RT activity blocking antibodies, were shown useful for discrimination between RTs from different retrovirus genera. RT activity assay for HIV-1 was found to quantitate different subtypes more equally efficient than p24 antigen assays did. Viral load (VL), the amount of HIV particles in the blood, is an important marker of the clinical status of an infected person. A method for VL determination based on RT activity (ExaVir Load) was developed. After plasma pretreatment, to inactivate cellular DNA polymerases, virions in patient plasma were immobilized on a gel, which was washed to remove disturbing factors. The virions were lysed with a detergent containing buffer and the lysate eluted. Finally, the RT activity in the lysate was determined and found to correlate strongly to VL by RNA according to a PCR based standard method (Roche Amplicor 1.5). The second version of the method was able to measure VL down to approximately 400 HIV-1 RNA copies/ml. The usefulness of RT from the VL procedure for determination of susceptibility towards anti-HIV drugs was demonstrated, and the results were in agreement with genotypic data. Due to its technical simplicity, and ability to detect a broad range of HIV-1 subtypes, ExaVir Load and the drug susceptibility application are interesting for clinical use, particularly but not only in resource limited settings. The concept is also potentially useful for research purposes, e.g. in combination with specific RT assay conditions.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2010.

L’histoire naturelle de l’infection anale par le virus du papillome de type 16 (VPH-16) est mal définie pour les hommes ayant des relations sexuelles avec d’autres hommes (HARSAHs) VIH-séropositifs. Le but de cette étude était d’évaluer l’association entre la charge épisomale et intégrée du VPH-16 et la progression de la néoplasie intraépithéliale anale (AIN). Les charges épisomales et intégrées du VPH-16 furent mesurées par PCR quantitatif en temps réel sur 665 spécimens anaux obtenus de 135 hommes VPH-16-positifs participant à l’étude prospective HIPVIRG (Human Immunodeficiency and Papilloma VIrus Research Group). Le grade de l’AIN fut déterminé sur des biopsies obtenues lors des anuscopies à haute résolution périodiques. L’intégration du VPH-16 fut confirmée par DIPS-PCR pour démontrer la présence de jonctions virales-cellulaires. La charge épisomale du VPH-16 [ratio de cote (OR) 1.5, intervalle de confiance (IC) à 95%=1.1–2.1], le nombre de types de VPH [OR 1.4 (IC 95%=1.1–1.8)] et le tabagisme actuel [OR 4.8 (IC 95%=1.3–18.6)], mais non la charge intégrée, furent associés aux lésions de haut-grade (AIN-2,3) après ajustement pour l’âge et le décompte des lymphocytes CD4. La charge épisomale du VPH-16 était le seul facteur prédictif de progression de l’AIN de bas-grade (AIN-1) vers l’AIN-2,3 [OR 8.0 (IC 95%=1.2–55.4)]. Les spécimens avec une charge épisomale du VPH-16 élevée étaient moins susceptibles de contenir de l’intégration [OR 0.5 (IC 95%=0.3–0.8)]. L’intégration du VPH-16 fut détectée en absence d’AIN, dans l’AIN-1 et dans l’AIN-2,3. L’analyse des jonctions virales-cellulaires ne permit pas d’identifier un site d’intégration spécifique. / The natural history of human papillomavirus type 16 (HPV-16) anal infection is undefined among HIV-seropositive men having sex with men (MSM). The aim of this study was to assess the association between HPV-16 episomal and integrated viral loads and the progression of anal intraepithelial neoplasia (AIN). HPV-16 episomal and integrated loads were measured on 665 specimens from 135 HPV-16-positive men participating in the prospective HIPVIRG (Human Immunodeficiency and Papilloma VIrus Research Group) study. AIN grade was evaluated on biopsies obtained during periodical high-resolution anoscopies. HPV-16 integration was confirmed by DIPS-PCR to demonstrate the presence of viral-cellular junctions. HPV-16 episomal loads [odds ratio (OR) 1.5, 95% confidence interval (CI)=1.1–2.1], burden of HPV infection [OR 1.4 (95% CI=1.1–1.8)] and current smoking [4.8 (95% CI=1.3–18.6)], but not integrated loads, were associated with high-grade lesions (AIN-2,3) after age and CD4 counts adjustment. A high HPV-16 episomal load was the only predictive factor of progression from low-grade AIN to high-grade AIN [OR 8.0 (95% CI=1.2–55.4)]. Specimens with higher HPV-16 episomal loads were less likely to contain integration [OR 0.5 (95% CI=0.3–0.8)]. HPV-16 integration was detected in the absence of AIN, in AIN-1 and in AIN-2,3. The analysis of the viral-cellular junctions did not allow identifying a specific site of integration.

Le VPH-16 de même que certains VPH, dont le VPH-18, causent le cancer du col utérin. Son intégration dans le génome humain pourrait être un marqueur de progression de l’infection. Les charges virales totale et intégrée sont présentement mesurées en quantifiant par PCR en temps réel les gènes E6 (RT-E6) et E2 (RT-E2-1) du VPH-16. Nous avons évalué l’impact du polymorphisme du gène E2 sur la quantification de l’ADN du VPH-16 dans des spécimens cliniques. Dans un premier temps, le gène E2 de 135 isolats de VPH-16 (123 appartenaient au clade Européen et 12 à des clades non- Européens) fut séquencé. Ensuite, un test de PCR en temps réel ciblant les séquences conservées dans E2 (RT-E2-2) fut développé et optimisé. Cent trente-neuf spécimens (lavages cervicaux et vaginaux) provenant de 74 participantes (58 séropositives pour le VIH, 16 séronégatives pour le VIH) ont été étudiés avec les trois tests E2 (RT-E2-2), E6 (RT-E6) et E2 (RT-E2-1). Les ratios de la quantité d’ADN de VPH-16 mesuré avec RT-E2-2 et RT-E2-1 dans les isolats Européens (médiane, 1.02; intervalle, 0.64-1.80) et Africains 1 (médiane, 0.80; intervalle, 0.53-1.09) sont similaires (P=0.08). Par contre, les ratios mesurés avec les isolats Africains 2 (médiane, 3.23; intervalle, 1.92-3.49) ou Asiatique- Américains (médiane, 3.78; intervalle, 1.47-37) sont nettement supérieurs à ceux obtenus avec les isolats Européens (P<0.02 pour chaque comparaison). Les distributions des quantités de E2 contenues dans les 139 échantillons mesurées avec RT-E2-2 (médiane, 6150) et RT-E2-1 (médiane, 8960) étaient statistiquement différentes (P<0.0001). Nous avons observé que les charges virales totale (odds ratio (OR) OR, 2.16 95% intervalle de confiance (IC) 1.11-4.19), et épisomale du VPH-16 (OR, 2.14 95% IC 1.09-4.19), mais pas la présence de formes intégrées (OR, 3.72 95% IC 1.03-13.4), sont associées aux néoplasies intraepitheliales cervicales de haut grade (CIN-2,3), et ce, en contrôlant pour des facteurs confondants tels que l’âge, le taux de CD4 sanguin, l’infection au VIH, et le polymorphisme de VPH-16. La proportion des échantillons ayant un ratio E6/E2 > 2 pour les femmes sans lésion intraépithéliale (7 de 35) est similaire à celle des femmes avec CIN-2,3 (5 de 11, p=0.24) ou avec CIN- 1 (4 de14, P=0.65). Le polymorphisme du gène E2 est un facteur qui influence la quantification des charges intégrées de VPH-16. / Episomal and integrated HPV-16 loads are currently estimated by quantitation with real-time PCR of HPV-16 E6 (RT-E6) and E2 (RT-E2-1) DNA. We assessed the impact of HPV-16 E2 polymorphism on quantitation of integrated HPV-16 DNA in clinical specimens. First, HPV-16 E2 was sequenced from 135 isolates (123 from European and 12 from non-European lineages). A novel assay targeting conserved HPV-16 E2 sequences (RT-E2-2) was optimized and applied with RT-E6 and RTE2- 1 on 139 HPV-16-positive cervicovaginal lavages collected from 74 women (58 HIV-seropositive, 16 HIV-seronegative). Ratios of HPV-16 DNA copies measured with RT-E2-2 and RT-E2-1 with European (median, 1.02; range, 0.64-1.80) and African 1 (median, 0.80; range, 0.53-1.09) isolates were similar (P=0.08). Ratios obtained with African 2 (median, 3.23; range, 1.92-3.49) or Asian-American (median, 3.78; range, 1.47-37) isolates were greater than those with European isolates (P<0.02 for each comparison). Distributions of HPV-16 E2 copies measured in 139 samples with RT-E2-2 (median, 6150) and RT-E2-1 (median, 8960) were different (P<0.0001). HPV-16 total (odds ratio (OR) OR, 2.16 95% confidence interval (CI) 1.11-4.19), episomal (OR, 2.14 95% CI 1.09-4.19) but not integrated (OR, 3.72 95% CI 1.03-13.4) load, were associated with high-grade cervical intraepithelial neoplasia (CIN-2,3) after controlling for age, CD4 count and HIV, and HPV-16 polymorphism. The proportion of samples with an E6/E2 ratio >2 in women without SIL (7 of 35) was similar to that of women with CIN-2,3 (5 of 11, P=0.24) or CIN-1 (4 of 14, P=0.65). E2 polymorphism was a factor that influenced measures of HPV-16 integrated load.

<p>Antiretroviral regimens have side effects that can threaten adherence by patients resulting in evolution of viral resistance due to suboptimal drug levels. Studies have shown that drug adherence of at least 80% can result in viral load suppression. There is no literature on the association between the level of adherence to antiretroviral therapy and the degree of virological suppression in Namibia. The aim of the present study was to determine the therapeutic and virological outcomes in HIV/AIDS patients at 6 and 12 months after initiation of highly-active antiretroviral therapy (HAART) in an urban population in Namibia. The distribution of viral load results showed a low uptake (35%) of virological monitoring at 6 month time point and even lower (12%) at 12 months. A conservative viral load threshold for virological response is required in the Namibian setting. The current adherence level of &gt / 80% encourage increased ARV therapy rollout. Poor virological outcome was associated with self-reported adherence.</p>

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Virginia, 2007. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.