Pediatric hiv-1 drug resistance in Botswana
| dc.contributor.advisor | Van Zyl, Gert U. | en_ZA |
| dc.contributor.advisor | Moyo, Sikhulile | en_ZA |
| dc.contributor.advisor | Gaseitsiwe, Simani | en_ZA |
| dc.contributor.author | Moraka, Natasha Onalenna | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology. | en_ZA |
| dc.date.accessioned | 2021-05-26T07:44:30Z | en_ZA |
| dc.date.accessioned | 2022-02-22T10:15:25Z | en_ZA |
| dc.date.available | 2022-02-23T03:00:08Z | en_ZA |
| dc.date.issued | 2021-12 | en_ZA |
| dc.description | Thesis (MSc)--Stellenbosch University, 2022. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: Antiretroviral therapy (ART) treatment in pregnant women and new-borns for prevention of mother-to-child transmission (PMTCT) can result in Human Immunodeficiency Virus drug resistance (HIVDR) in paediatrics; either transmitted or arising de novo after transmission. To our knowledge, there is paucity of data describing patterns of HIVDR in infants in Botswana. The aims of this dissertation were to describe HIVDR patterns in newly diagnosed infants in Botswana and determine the prevalence and role of HIVDR mutations in HIV-1 cell associated DNA (HIV-1 CAD) of early treated <18-month-old infants. Seventy-eight residual dried blood spots (DBS) from <18-month-old HIV positive children from the Botswana HIV early infant diagnosis (EID) program (2016 - 2019) were available for HIVDR surveillance. Protease and reverse transcriptase regions were amplified and sequenced using ATCC HIV-1 Drug Resistance Genotyping kits and big dye chemistry. Surveillance drug-resistance mutations (SDRMs) were assessed using the Calculated Population Resistance program. We analysed 257 proviral near full-length sequences (nFLS) obtained from peripheral blood mononuclear cells (PBMCs) of 27 infants in the Botswana early infant treatment (EIT) Study. Sanger sequencing of HIV pol was also performed for 22 maternal samples at delivery and at clinical failure in children. All nFLS and HIV pol sequences were analysed for the presence of HIVDR mutations using the Stanford HIV Drug Resistance database. Of the 78 DBS samples, 32 (41%) were successfully amplified and sequenced. The median age was 2 months (IQR: 2-4). Three (9.7%) newly diagnosed infants had detectable SDRMs. Among these infants, one (33%) had a non-nucleoside reverse transcriptase inhibitor (NNRTI) HIV SDRM (K103N) detected and two (67%) had a detectable protease inhibitor (PI) SDRMs (M46L and L23I). A total of 27 (56.2%) EIT infants had nFLS within one month of life. The median age at enrolment for infants was 2 days [Range: 2-3], with a median digital droplet PCR (ddPCR) HIV-1 CAD load value of 492 units [IQR: 78-1246]. Cell-associated HIVDR mutations were detected in 3/27 (11.1%) infants with intact HIV-1 CAD. A total of 106 (41.3%) intact sequences had at least 1 DRM; 29.2% had NNRTI, 7.5% NRTI, 0.9% PI and none with INSTI associated mutations. A total of 151 (58.7%) defective sequences had at least 1 DRM; 31.8% NNRTI, 15.2% NRTI, 5.3% PI and 15.5% INSTI associated mutations. Higher frequency of DRM was detected in defective HIV-1 CAD compared to intact infant HIV-1 CAD, although not statistically significant (p=0.14). Three infants had the same HIVDR mutations detected in their intact HIV-1 CAD and corresponding maternal plasma at delivery. Archived HIV-1 CAD HIVDR mutations were detectable at later clinical rebound on only one occasion. In conclusion, we report relatively high rates of HIVDR mutations among newly diagnosed and early treated infants with known and unknown PMTCT exposure in Botswana. Our results suggest that exclusion of sequences with defects when interpreting HIVDR mutations from HIV-1 CAD is crucial as these may overestimate true mutations which may impact future clinical outcomes in children. | en_ZA |
| dc.description.abstract | AFRIKAANS OPSOMMING: Antiretrovirale behandeling (ART) in swanger vrouens en pasgebore babas wat moeder-tot-kind oordrag van menslike immuniteitsgebreksvirus (MIV) voorkom, kan lei tot middelweerstandige MIV in babas wat of oorgedra word of de novo kan ontstaan. Tans is daar min data beskikbaar wat patrone van MIV middelweerstandigheid (MIVMW) in babas van Botswana beskryf. Die doelwitte van hierdie tesis was om MIVMW patrone te beskryf in pas gediagnoseerde babas in Botswana en om die voorkoms en rol van MIVMW-mutasies in MIV-1-sel-geassosieerde deoksiribonukleïensuur (DNS) (MIV-1 SGD) van vroegbehandelde babasjonger as 18 maande te bepaal. Agt-en-sewentig residuele gedroogde bloedvlekke (GBV) van MIV-gediagnoseerde kinders jonger as 18 maande oud wat by die Botswana program vir vroeë baba-diagnose (VBD) (2016-2019) gewerf was, was beskikbaar vir MIVMW bestudering. Protease- en tru-transkriptase gene is geamplifiseer en volgorde bepaling is gedoen met behulp van ATCC MIV-1MW genotiperings kits en BigDye™ chemie. Middelweerstandige mutasies monitering(SDRMs) is geondersoek deur die Berekende Bevolkingsweerstandsprogram. Twee honderd sewe-en-vyftig provirale naby-vollengte volgordes (nFLS) van perifere mononukleêre selle van 27 babas, van die studie vir vroeë babas in Botswana, is geanaliseer. Sanger-volgordebepaling van MIV pol is ook uitgevoer vir 22 monsters van moeders met geboorte en wanneer kinders klinies faal. Alle nFLS- en HIV-pol volgordes is geanaliseer vir die teenwoordigheid van MIVMW-mutasies deur gebruik te maak van die Stanford HIV Drug Resistance databasis. Twee-en-dertig (41%) van die 78 GBV-monsters is suksesvol geamplifiseer en die volgorde is bepaal. Die mediaan-ouderdom was 2 maande (IQR: 2-4). Drie (9,7%) pas gediagnoseerde babas het opspoorbare SDRMs gehad. Van hierdie babas het een (33%) 'n nie-nukleosied tru-transkriptase-inhibitor (NNRTI) MIV SDRM (K103N) gehad en twee (67%) het protease-inhibitor (PI) SDRMs (M46L en L23I). Sewe-en-twintig (56,2%) EIT-babas het binne een maand van hul lewe nFLS gehad. Die mediaan ouderdom by die inskrywing vir babas was 2 dae [Reeks: 2-3], met 'n mediaan digitale druppel PCR (ddPCR) MIV-1 SGD-laadwaarde van 492 eenhede [IQR: 78-1246]. Sel-geassosieerde MIVMW-mutasies is opgespoor in 3/27 (11,1%) babas met ongeskonde MIV-1 SGD. Honderd en ses (41,3%) ongeskonde volgorde bepalings het ten minste eenmiddelweerstandige mutasie gehad; van die 29,2% was NNRTI, 7,5% NRTI, 0,9% PI en geen het INSTI geassosieerde mutasies gehad nie. Altesaam 151 (58,7%) defektiewe volgordes het ten minste een middelweerstamdige mutasie gehad; 31,8% was NNRTI, 15,2% NRTI, 5,3% PI en 15,5% INSTI was geassosieerde mutasies. 'n Hoër frekwensie van middelweerstandige mutasies is opgespoor in defektiewe MIV-1 SGD in vergelyking met ongeskonde MIV-1 SGD, alhoewel nie statisties beduidend nie (p = 0.14). Dieselfde MIVMW-mutasies is opgespoor in ongeskonde MIV-1 SGD en ook in die ooreenstemmende moeder plasma tydens die geboorte in drie van die babas. Geargiveerde MIV-1 SGD MIVMW-mutasies was optelbaar tydens ‘n kliniese terugslag slegs een keer. Ter afsluiting, ons rapporteer relatief hoë koerse van MIVMW-mutasies onder pas gediagnoseerde en vroegbehandelde babas met bekende en onbekende blootstelling aan PMTCT in Botswana. Daarom is die uitsluiting van volgordes met defekte is noodsaaklik tydens die interpretasie van MIVMW-mutasies van MIV-1 SGD, aangesien dit ware mutasies kan oorskat wat die toekomstige kliniese uitkomste by kinders kan beïnvloed. | af_ZA |
| dc.description.version | MSc | en_ZA |
| dc.description.version | Masters | en_ZA |
| dc.embargo.terms | 2022-01-03 | en_ZA |
| dc.format.extent | xix, 86 pages : illustrations | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/124191 | en_ZA |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | HIV (Viruses) -- Prevention and control | en_ZA |
| dc.subject | Drug resistance | en_ZA |
| dc.subject | HIV-positive women | en_ZA |
| dc.subject | HIV (Viruses) -- Transmission | en_ZA |
| dc.subject | Mother and infant -- Health aspects | en_ZA |
| dc.subject | Breastfeeding -- Immunological aspects | en_ZA |
| dc.subject | UCTD | en_ZA |
| dc.title | Pediatric hiv-1 drug resistance in Botswana | en_ZA |
| dc.type | Thesis | en_ZA |