Browsing by Author "De Oliveira, Tulio De Paiva Nazareth Andrade."

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Dolutegravir for first-line antiretroviral therapy in low-income and middle-income countries: uncertainties and opportunities for implementation and research.
(Elsevier., 2018) Dorward, Jienchi.; Lessells, Richard John.; Drain, Paul K.; Naidoo, Kogieleum.; De Oliveira, Tulio De Paiva Nazareth Andrade.; Pillay, Yogan.; Abdool Karim, Salim Safurdeen.; Garrett, Nigel Joel.
Abstract available in pdf.
The epidemiology and impact of pretreatment HIV drug resistance in adults in South Africa.
(2018) Chimukangara, Benjamin.; De Oliveira, Tulio De Paiva Nazareth Andrade.; Naidoo, Kogieleum.; Samuel, Reshmi.
HIV drug resistance (HIVDR) present prior to initiating or re-initiating antiretroviral therapy (ART), is known as pretreatment drug resistance (PDR). Conventionally, PDR is detected by Sanger sequencing. Drug resistant minority variants (DRMVs) that are not reliably detected by Sanger sequencing can be detected by next generation sequencing. The aims of this research were to assess levels of PDR in HIV hyper-endemic areas (with high HIV incidence and prevalence) in KwaZulu-Natal (KZN) province, trends of PDR in South Africa, and the impact of DRMVs on ART. To assess PDR in adults from KZN hyper-endemic areas, 1845 sequences were analyzed from two population-based HIV surveillance studies; a longitudinal HIV surveillance programme in northern KZN (2013-2014), and the HIV Incidence Provincial Surveillance System (HIPSS) in central KZN (2014-2015). Overall, 182/1845 (10.0%) had NNRTI-PDR mutations, and when analyzed by study year, NNRTI-PDR was 10.2% (CI:7.5-12.9) for the HIPSS study in 2014. To assess PDR trends in South Africa, 6880 HIV-1 sequences were collated from 38 datasets of ART-naïve adults (2000-2016). Increasing levels of PDR were observed, most marked from 2010. Crude pooled prevalence of NNRTI-PDR reached 10% in 2014, with a 1.18-fold (CI:1.13- 1.23) annual increase (p<0.001), consistent with findings from the HIPSS data. This provided the first evidence of high-level NNRTI-PDR in KZN and South Africa, supporting the transition to dolutegravir in standard first-line ART, as recommended by the World Health Organization when NNRTI-PDR reaches ≥10%. A case-control (2:1) study in HIV/TB co-infected adult patients was done to assess the impact of DRMVs at different thresholds. Cases were patients that initiated ART and had viral loads ≥1000 copies/mL after ≥6 months on ART, and controls were those that initiated ART and achieved virologic suppression through 24 months. Pre-ART NNRTI-resistance was associated with ART failure. NGS improved detection of HIVDR at lower thresholds, but reduced the specificity of identifying patients at risk of virologic failure, with the specificity reducing from 97% (CI:92-99) at 20% threshold, to 79% (CI:71-86) at 2% threshold. In all, the findings presented in this thesis provide a broad message about the need to improve quality in HIV prevention and treatment services.
Extraction, sequencing and bioinformatics analysis of DNA from dried blood spots.
(2016) Mjoli, Phiwokuhle Bulelwa.; Sommer, Paula.; De Oliveira, Tulio De Paiva Nazareth Andrade.
The Africa Centre for Health and Population Studies has a demographic surveillance site 200km north of Durban at the Umkhanyakude district. In this setting, blood samples are routinely collected and used for the diagnosis of HIV infection. In this setting and in many settings in Africa, samples are normally collected and stored on filter paper as dried blood spots (DBS) as those are easy to transport and store. DNA can be isolated/extracted from DBS and used for viral and/or host genomic analysis. The aim of this work was to extract DNA from DBS of sufficient quality and yield that could be used for subsequent analysis. Specifically, we aimed to perform host HLA genotyping from DBS as HLA type has an impact on HIV-1 replication levels. Dried blood spots were prepared from anonymous samples that are commonly used for the validation of new laboratory methods at the Africa Centre Virology Laboratory in Durban. The QIAamp DNA Mini Kit method was optimised to isolate DNA from DBS. DNA levels were quantified using the Qubit 2.0 Fluorometer (Qubit Assay). Polymerase chain reactions (PCR) were used to amplify the HLA Class 1A, 1B and 1C loci and the PCR products were purified using the Pure Link Purification Kit (Invitrogen Life Technologies). Sanger sequencing techniques were used to genotype the HLA‟s PCR products. AssignTM ATF Softwere v1.5 was used to detect HLA allele variations in the consensus sequences produced through Sanger sequencing. The DNA yield that could be extracted from the DBS was low. This was most probably due to the low quantity of blood that can be stored in one DBS. Despite the relatively low DNA yields sequencing of the target gene (HLA Class 1A, 1B and 1C) was successful using Sanger Sequencing and variations in the majority of the HLA alleles were detected. This MSc study shows that it is possible to sequence HLA loci directly from DBS.
HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis.
(Elsevier., 2018) Gupta, Ravindra K.; Gregson, John.; Parkin, Neil.; Haile-Selassie, Hiwot.; Tanuri, Amilcar.; Andrade Forero, Liliana.; Kaleebu, Pontiano.; Watera, Christine.; Aghokeng, Avelin.; Mutenda, Nicholus.; Dzangare, Janet.; Hone, San.; Hang, Zaw Zaw.; Garcia, Judith.; Garcia, Judith.; Garcia, Zully.; Marchorro, Paola.; Beteta, Enrique.; Giron, Amalia.; Hamers, Raph.; Inzaule, Seth.; Frenkel, Lisa M.; Chung, Michael H.; De Oliveira, Tulio De Paiva Nazareth Andrade.; Pillay, Deenan.; Naidoo, Kogieleum.; Kharsany, Ayesha Bibi Mahomed.; Kugathasan, Ruthiran.; Cutino, Teresa.; Hunt, Gillian.; Avila Rios, Santiago.; Doherty, Meg.; Jordan, Michael R.; Bertagnolio, Silvia.
Abstract available in pdf.
The influence of HIV-1 genomic target region selection and sequence length on the accuracy of inferred phylogenies and clustering outcomes.
(2017) Sibisi, Zandile.; De Oliveira, Tulio De Paiva Nazareth Andrade.
To improve the methodology of HIV-1 cluster analysis, we addressed how analysis of HIV-1 clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering, tree certainty, subtype diversity ratio (SDR), subtype diversity variance (SDV) and Shimodaira-Hasegawa (SH)-like support values were compared between 2881 HIV-1 full genome sequences and sub-genomic regions of which 2567 were retrieved from the LANL HIV Database and 314 were sequenced from blood samples from a cohort in KwaZulu-Natal. Sliding window analysis was based on 99 windows of 1000 bp, 45 windows of 2000 bp and 27 windows of 3000 bp. Clusters were enumerated for each window sequence length, and the optimal sequence length for cluster identification was probed. Potential associations between the extent of HIV clustering and sequence length were also evaluated. The phylogeny based on the full-genome sequences showed the best tree accuracy; it ranked highest with regards to both tree certainty and SH-like support. Product 4, a region associated with env, had the best tree accuracy among the sub-genomic regions. Among the HIV-1 structural genes, env had the best tree certainty, SH-like support, SDR score and the best SDV score overall. The hierarchy of cluster phylotype enumeration mirrored the tree accuracy analysis, with the full genome phylogeny showing the highest extent of clustering, and the product 4 region being second best. Among the structural genes, the highest number of phylotypes was enumerated from the pol phylogeny, followed by env. The extent of HIV-1 clustering was slightly higher for sliding windows of 3 000 bp than 2000 bp and 1000 bp, thus 3000 bp was found to be the optimal length for phylogenetic cluster analysis. We found a moderate association between the length of sequences used and proportion of HIV sequences in clusters; the influence of viral sequence length may have been diminished by the substantial number of taxa. Full-genome sequences could provide the most informative HIV cluster analysis. Selected sub-genomic regions with the best combination of high extent of HIV clustering and high tree accuracy, such as env, could also be considered as a second choice.
An investigation of multi-label classification techniques for predicting HIV drug resistance in resource-limited settings.
(2014) Brandt, Pascal.; Moodley, Deshendran.; Pillay, Anban Woolaganathan.; Seebregts, Christopher.; De Oliveira, Tulio De Paiva Nazareth Andrade.
South Africa has one of the highest HIV infection rates in the world with more than 5.6 million infected people and consequently has the largest antiretroviral treatment program with more than 1.5 million people on treatment. The development of drug resistance is a major factor impeding the efficacy of antiretroviral treatment. While genotype resistance testing (GRT) is the standard method to determine resistance, access to these tests is limited in resource-limited settings. This research investigates the efficacy of multi-label machine learning techniques at predicting HIV drug resistance from routine treatment and laboratory data. Six techniques, namely, binary relevance, HOMER, MLkNN, predictive clustering trees (PCT), RAkEL and ensemble of classifier chains (ECC) have been tested and evaluated on data from medical records of patients enrolled in an HIV treatment failure clinic in rural KwaZulu-Natal in South Africa. The performance is measured using five scalar evaluation measures and receiver operating characteristic (ROC) curves. The techniques were found to provide useful predictive information in most cases. The PCT and ECC techniques perform best and have true positive prediction rates of 97% and 98% respectively for specific drugs. The ECC method also achieved an AUC value of 0:83, which is comparable to the current state of the art. All models have been validated using 10 fold cross validation and show increased performance when additional data is added. In order to make use of these techniques in the field, a tool is presented that may, with small modifications, be integrated into public HIV treatment programs in South Africa and could assist clinicians to identify patients with a high probability of drug resistance.
Moderate-to-high levels of pretreatment HIV drug resistance in KwaZulu-Natal Province, South Africa.
(Mary Ann Liebert., 2019) Chimukangara, Benjamin.; Naidoo, Kogieleum.; Rhee, Soo-Yon.; Manasa, Justen.; Gräf, Tiago.; Lewis, Lara.; Cawood, Cherie.; Khanyile, David.; Diallo, Karidia.; Ayalew, Kassahun A.; Shafer, Robert W.; Hunt, Gillian.; Pillay, Deenan.; De Oliveira, Tulio De Paiva Nazareth Andrade.; Abdool Karim, Salim Safurdeen.; Lessells, Richard John.; Kharsany, Ayesha Bibi Mahomed.
Abstract available in PDF.
Molecular epidemiology of HIV-2 infection in KwaZulu-Natal Provnce, South Africa.
(2013) Singh, Lavanya.; De Oliveira, Tulio De Paiva Nazareth Andrade.
Infection with HIV-2 has important implications for the diagnosis, treatment and management of the infection. The objective of this study was to describe the seroprevalence and molecular epidemiology of HIV-2 in KwaZulu-Natal – the province with the highest HIV prevalence in South Africa, which in turn is the country with the highest HIV prevalence in the world. HIV-1 positive samples were screened using a rapid test for HIV-2. Samples showing antibody positivity were subject to molecular confirmation by PCR and / or serological confirmation by Western blot. There was a large difference in results (10.6% by Western blotting versus 0% by PCR). This discrepancy between molecular and serological confirmation by Western blot. There was a large difference in results (10.6% by Western blotting versus 0% by PCR). This discrepancy between molecular and serological confirmation was attributed to cross-reacting antibodies. The use of rapid tests and Western blots for HIV-2 diagnosis in South Africa, should, therefore, be interpreted with caution. Based on the results of this study, HIV-2 is most probably not present in KwaZulu-Natal.
Prevalence of minority HIV-1 drug resistant quasi-species in children patients at virologic failure in a rural KwaZulu-Natal cohort.
(2016) Mthiyane, Hloniphile Ruth.; Danaviah, Sivapragashini.; De Oliveira, Tulio De Paiva Nazareth Andrade.
Abstract available in PDF file.
Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa : a community-wide phylogenetic study.
(Elsevier., 2017) De Oliveira, Tulio De Paiva Nazareth Andrade.; Kharsany, Ayesha Bibi Mahomed.; Gräf, Tiago.; Cawood, Cherie.; Khanyile, David.; Grobler, Anna Christina.; Puren, Adrian.; Madurai, Savathree.; Baxter, Cheryl.; Abdool Karim, Quarraisha.; Abdool Karim, Salim Safurdeen.
Abstract available in pdf.