Thesis (MScMedSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Background: The conventional sequence analysis is the most common method used for the detection of drug-resistant mutants. Due to its sensitivity limitations, it is unable to detect these mutants when comprising less than 20% (minor populations) of the total virus population in a sample. However, real-time PCR-based assays offer a rapid, sensitive, specific and easy detection and quantification of such mutants. The HIV-1 variants harbouring the K103N mutation are associated with resistance to nevirapine (NVP) and efavirenz (EFV). The persisting drug-resistant mutants decay slowly to low levels, and therefore they are called minor drug-resistant mutants. Consequently, they affect subsequent treatment with the drugs of the relevant class. Objectives: The objective of this study was to design two TaqMan real-time PCR-based assays called selective-polymerase chain reaction (SPCR), namely the total viral copy SPCR assay and the K103N-SPCR assay. The former detects HIV-1 of subtype C reverse transcriptase sequences, whereas the latter detects K103N drug-resistant variants in these sequences. Design and Methods: In developing the SPCR assays, sets of appropriate primers and probes for the HIV-1 subtype C reverse transcriptase (RT) were developed to use in the K103N-specific reaction and the total copy reaction. Twelve DNA plasmid standards with sequence diversity were constructed for the assay from two HIV-1subtype C samples known to harbour the K103N mutation (AAC or AAT) in our Department‟s Resistance Databank. Their RT regions were amplified, cloned and verified with sequencing. Site-directed mutagenesis was used to induce mutations at 103 amino acid position in some of these clones to generate more standards with either one of the three codons (AAA, AAC and AAT). The two assays were optimized and validated, and a standard curve was generated for each assay using 10-fold serial dilution (5x107-5x100 DNA copy/μL) of a K103N-mutant plasmid standard. The optimized and validated SPCR assays were used to screen 40 nested PCR products of previously genotyped patient samples for minor K103N variants. Results: Two sensitive and reproducible selective real-time PCR (SPCR) assays, with cut-offs of 8.23 and 10.33 and a detection limit of 0.01% for the K103N resistance variants, were successfully developed. The assays detected a prevalence of 25.64-46.15% for the K103N resistance mutation in 39 patient samples. The genotyping (population sequencing) missed 40-53.85% of these variants. Conclusion: In conclusion, sensitive and reliable selective real-time PCR assays to detect and quantify minor K103N variants of HIV-1 in nested PCR products were successfully developed. The assay had a lower detection limit of 0.01%. / AFRIKAANSE OPSOMMING: Agtergrond: Konvensionele volgorde bepaling analise is die mees algemeenste metode wat gebruik word vir die opsporing van middel-weerstandige mutasies, maar weens beperkte sensitiwiteit is dit nie moontlik om hierdie mutante op te spoor wanneer dit minder as 20% (minderheids populasie) van die totale viruspopulasie in `n monster uitmaak nie. Nietemin, kwalitatiewe PKR-gebaseerd toetse bied vinnige, sensitiewe, spesifieke en makliker opsporings en kwantifisering van sulke mutante aan. MIV-1 variante wat die K103N mutasie bevat word geassosieer met weerstand teen nevirapine (NVP) and efavirenz (EFV). Volhoudende middel-weerstandige mutasies vergaan stadig na laer vlakke en word daarom na minderheids middel weerstandige mutasies verwys. Gevolglik affekteer dit opvolgende behandeling met die middel van die relevante klas. Doelwitte: Die doel van die studie was om twee TaqMan kwantifiserende PKR gebaseerde selektiewe polymerase ketting reaksies (SPKR), naamlik totale virale kopie SPKR en K103N-SPKR te ontwikkel. Die voormalige toets het die MIV-1 subtipe C omgekeerde transkriptase volgorde bepaal, waar K103N die middel-weerstand variante in hierdie volgorde opspoor. Ontwerp en Metodes: `n Geskikte stel inleiers en peiler was ontwikkel vir die MIV-1 subtipe C omgekeerde transkriptase (OT) vir gebruik in die K103N-spesifieke en die totaal kopie reaksie. Twaalf DNS plasmied standaarde met volgorde diversiteit was saamgestel vir die toets vanaf twee MIV-1 subtipe C monsters wat volgens ons Departement se weerstand databasis geklassifeer is vir die besit van die K103N mutasie (AAC of AAT). Die OT streke was geamplifiseer, gekloneer en geverifieer deur volgorde bepaling. Punt-gerigte mutagenese is gebruik om `n mutasie by die amino suur posisie 103 van sekere klone te induseer om meer standaarde te genereer wat een van die drie kodons (AAA, AAC en AAT) bevat. Die twee toetse is geoptimiseer en gevalideer en `n standard kurwe is genereer vir elk van die toetse deur die gebruik van tienvoud serie verdunnings (107-1 DNS kopie/μL) van `n algemene K103N-mutante plasmied standard. Die geoptimiseerde en gevalideerde SPKR toets was gebruik om vir die minderheids K103N variante in 40 “nested” PKR produkte van voorheen gegenotipeerde pasiënt te soek. Resultate: Twee sensitiewe en herproduseerbare selektiewe kwantitiewe PKR toetse met `n ΔCt afsnypunt van 8.23 en `n deteksie limiet van 0.006% was ontwikkel vir die K103N weerstand variant. Die toets het `n voorkomsyfer van 25.6 % vir die K103N weerstand mutasie in 40 pasiënt monsters bepaal, waar genotipering (populasie volgorde ) 40% van hierdie variante nie opgespoor het nie. Gevolgtrekking: `n Sensitiewe en betroubare selektiewe kwantitatiewe PKR toets vir die opspoor en kwantifisering van die minderheids K103N variante van MIV-1 in PKR produkte was ontwikkel. Hierdie toets het `n laer opsporings limiet van 0.01%. / Poliomyelitis Research Foundation (PRF) / National Research Fund (NRF) / National Health Laboratory Service Research Trust (NHLS RT)

Thesis (MScMedSc (Pathology. Medical Virology))--University of Stellenbosch, 2010. / Bibliography / ENGLISH ABSTRACT: Throughout history disease entities have been described which match the description of diseases now known to be caused by hantaviruses; however these viruses were first identified as the aetiologic agent in 1976, the first species named Hantaan virus after the river near which its natural host, the rodent species Apodemus agrarius, was captured. Since then numerous species in the Hantavirus genus, family Bunyaviridae, have been found, with today more than 30 species worldwide being known. Hantaviruses are hosted by rodents from the Muridae and Cricetidae families and by shrews (insectivores) in the Soricidae family. There are two types of hantavirus disease, Haemorrhagic fever with renal syndrome (HFRS) in the Old World and Hantavirus cardiopulmonary syndrome (HCPS) in the New World. The first two African hantaviruses were identified in 2006 in Guinea, West Africa; Sangassou virus (SANGV) in a rodent, the African wood mouse (Hylomyscus simus), and Tanganya virus (TGNV) in Therese’s shrew (Crocidura theresae). In this study, rodents and shrews were trapped at localities in the Western Cape and Northern Cape provinces of South Africa, and in the southern regions of Namibia. RNA was extracted from their lungs and screened for hantavirus sequences by RTPCR, using degenerate primers designed to detect all members of the Hantavirus genus. In addition, an in-house IgG ELISA assay was set up, based on recombinant N antigen from Dobrava virus, DOB-rN, and Puumala virus, PUU-rN. The assay was used to screen patient sera collected in an anonymous convenience serological survey using residual serum samples left over from routine testing at NHLS laboratories in the Western Cape for hantavirus-specific antibodies. RNA from 576 animal specimens was screened by RT-PCR; no hantavirus genome was detected in any of the specimens. Sera from 161 patients were screened for hantavirus antibodies; 11.18% of the sera were reactive to DOB-rN, 4.97% against PUU-rN and 2.48% against both antigens. v Though no virus was detected in the animals screened, this does not necessarily mean that there are no hantaviruses present in Southern Africa. A previous seroepidemiological survey conducted in South Africa reported on the presence of hantavirus specific antibodies by IFA in two species of rodents trapped in the Western Cape and Northern Cape Aethomys namquensis and Tatera leucogaster. Our was the second known study in South Africa conducted that determined and proved the presence of hantavirus specific antibodies in humans. / AFRIKAANSE OPSOMMING: Dwarsdeur die geskiedenis was daar beskrywings van siektes wat ooreenstem met die beskrywing van hantavirus simptome, maar die eerste etiologiese oorsaak van die siekte is eers in 1976 geïdentifiseer en Hantaan virus genoem, vernoem na die rivier waar naby die gasheer, Apodemus agrarius, gevang is. Van daar af het die soektog na nuwe hantavirusse intensief gevorder en vandag is daar meer as 30 spesies wêreldwyd wat aan die Hantavirus genus, ’n lid van die Bunyaviridae familie, behoort. Knaagdiere van die Muridae en Cricetidae families, sowel as spitsmuise (insekvreters) in die Soricidae familie is gasheer vir hantavirusse. Twee tipes hantavirus siekte is bekend, hemorragische koors met nier sindroom (HFRS) in die Ou Wêreld en hantavirus kardiopulmonale sindroom in die Nuwe Wêreld. Die eerste twee Afrika hantavirusse is in 2006 in Guinee Wes-Afrika geïdentifiseer; Sangassou virus (SANGV) in ’n knaagdier, die Afrika hout muis (Hylomyscus simus) en Tanganya virus (TGNV) in Therese se spitsmuis (Crocidura theresae). In hierdie studie is knaagdiere en spitsmuise op verskeie plekke in die Wes- en Noord-Kaap provinsies, asook die Suide van Namibië, gevang. RNS is onttrek vanuit die longe en hantavirus volgordes is gesoek deur middel RT-PKR deur gebruik te maak van Pan-Hanta primers wat ontwerp is om alle lede van die Hantavirus genus op te spoor. ’n Self-ontwerpde IgG ELISA, gebasseer op rekombinante N antigeen van Dobrava virus, DOB-rN en Puumala virus, PUU rN, is opgestel en gebruik om pasiënt serum, verkry in ’n anonieme serologiese opname, te toets; oorblywende serum, na toetse uitgevoer is deur NHLS laboratoriums in die Wes-Kaap, is verkry en getoets vir hantavirus spesifieke teenliggaampies. RNS van 576 dier monsters is getoets deur middel van RT-PKR en geen hantavirus is in enige van die monsters geïdentifiseer nie. Serum van 161 pasiënte is getoets vir hantavirus teenliggaampies; 11.18% van die serum was reaktief teen DOB-rN, 4.97% teen PUU-rN en 2.48% teen albei antigene. Alhoewel geen virus in die diere geïdentifiseer is nie, beteken dit nie noodwendig dat geen hantavirusse in Suidelike-Afrika voorkom nie. ‘n Vorige sero-epidemiologiese opname wat in Suid-Afrika gedoen is het die teenwoordigheid van hantavirus spesifieke teenliggaampies in twee knaagdier spesies, Aethomys namquensis en Tatera leucogaster gevang in die Wes-en Noord-Kaap, gevind. Ons studie is die tweede studie bekend in Suid-Afrika uitgevoer, wat die teenwoordigheid van hantavirus spesifieke teenliggaampies bevind en bewys het.

Thesis (MScMedSc)--Stellenbosch University, 2013. / Bibliography / The efficiency in which HIV-1 can infect, spread and evade the attack of therapeutic agents can be attributed to a high mutation rate and frequent recombination events. These factors have collectively contributed to the diversity observed in HIV-1 and resulted in a multitude of subtypes, sub-subtypes, circulating recombinant forms (CRF’s) and unique recombinant forms (URF’s). The aim of this study was to investigate HIV-1 diversity in Cape Town using a small cohort of treatment naive patients being investigated for HIV Associated Neurocognitive Disorders (HAND). Four different genomic domains: gag, pol, accessory and gp41 genes were sequenced to subtype the virus. HIV-1 tat was further investigated because the dicysteine motif has been reported to play a role in HAND. Viral RNA and proviral DNA was extracted from 64 patients and used for the amplification and sequencing of the genes. Rega and jpHMM online tools were used to identify HIV-1 subtypes and recombinants while Neighbor-joining phylogenetic trees were constructed for phylogenetic analysis. The pol gene was further investigated using SCUEAL to detect possible intra-subtype recombination and was also screened for the presence of transmitted drug resistance. In addition tat sequence datasets retrieved from the Los Alamos sequence database were investigated and compared with the newly generated sequences for the detection of point mutations and amino acid signature patterns. Sequencing identified most of the samples as subtype C; however six inter-subtype recombinants (AE, A1G, A1CU and two BC) and 9 intra-subtype C recombinants were identified. In addition 13% of pol sequences were identified with resistance mutations. Signature pattern analysis identified a high level of variability in the tat sequences: 68% were identified with C30S31; 29% with the C30C31 mutation and a single sequence with a novel mutation C30A31. Functional analysis of these mutations indicated that all mutations investigated were capable of inducing apoptosis in cell culture. The C30C31 mutation generated the highest level of apoptosis, closely followed by the C30A31 mutation. However no statistical significance could be detected between tat mutations and the observed levels of apoptosis.