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Doctoral Degrees (Virology)

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Browsing Doctoral Degrees (Virology) by SDG "SDG3"

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    Coevolution of mutations in HIV-1 ENV and GAG-PR genes: implications for the development of protease inhibitors resistance.
    (2023) Maphumulo, Ntombikhona Fortunate.; Gordon, Michelle Lucille.
    Cross-resistance in PIs-exposure has been reported to be driven by Gag, however recent studies suggest Env also contributes to PIs resistance. Although studies have reported gp41 mutations in PI failures, the impact of the full-length Env on PI resistance remains unclear. We investigate the prevalence of subtype C Env mutations in patients failing PIs, the coevolution of Env mutations with Gag-PR mutations and determine whether mutations in gp120 as a result of PI resistance, affect coreceptor usage. Lastly, determine the structural changes in the Env during PI failure. The study used generated sequences from subtype C infected patients failing LPV/r inclusive treatment and HIV-1 subtype C drug-naïve sequences downloaded from the Los Alamos HIV database to compare the frequency of Env mutations in patients failing LPV/r. Bayesian network probability was applied to determine the relationship between mutations occurring within the Env and Gag-PR regions and LPV/r treatment. Furthermore, Los Alamos sequence database tools, Geno2Pheno[coreceptor], and Molecular dynamics simulations were used to demonstrate structural changes and to understand how gp120 mutations affect co-receptor usage. Lastly, Molecular dynamics simulation followed by Ring server was used to determine the structural changes caused by mutations in gp41, and gag mutations, and to look for interaction (hydrogen bond contact and VDW) between mutations and the nearby residues. Thirty-five mutations in the Env region had significantly higher frequencies in LPV/r treated patients. Env mutations were shown to coevolve with Gag-PR and they form a potential pathway to LPV/r resistance. Gp120 sequences from the PIs treated patients showed to modulate viral entry by protecting the virus from antibody recognition through the increased length in V1/V2 and V5 variable loops and the number of N-glycosylation sites observed in VI/V2. Results further showed that gp120 mutations could modulate viral entry through coreceptor switching induced by a higher charge in the V3 region, mutations in coreceptor-specific sites, and those that interact with the coreceptor binding site. Three mutations in gp41 (D632E-HR2, I688-TM, and P724Q/S-CT) were shown to influence folding by stabilizing the β-turns in their respective regions. Env coevolution with Gag-PR (mainly MA and CA) was shown through the pathway to LPV/r resistance. The gp120 mutations were also shown to contribute to viral entry through coreceptor usage and immune escape, while gp41 and Gag mutations played a role in stabilizing the α-helices which might influence the fusion of the virus. Further investigations using site-directed mutagenesis are needed to determine the effect of mutations on replication capacity. Iqoqa. Isingeniso Ukungezweli okuthelelanayo ekuvezekeni kwama-PIs kwabikwa ukuthi kuphushwa yi-Gag, kodwa ucwaningo olusanda kwenziwa luphakamisa ukuthi i-Env inomthelela ekungazweleni kwama-PIs. Nakuba ucwaningo lubike izinhlobo ze-gp41 ekwehlulekeni kwe-PI, umthelela wobude obuphelele be-Env ekungezwelini kwe-PI kuhlezi kungacacile. Siphenya ukwanda kwezinhlobo eziyisubtype C envelope nezinhlobo ze-Gag-PR nokuhlonza ukuthi izinhlobo kwi-gp120 njengomphumela wokungezweli kwe-PI, okunomthelela wokusetshenziswa kwesisizisemukeli. Okokugcina, ukuhlonza ushintsho lwesakhiwo emvilophini ngesikhathi sokwehluleka kwe-PI. Izindlelakwenza zocwaningo Ucwaningo lwasebenzisa ukulandelana okwenziwe lususelwa ezigulini ezitheleleke ngesubtype C okwehluleka kokwelapha okufaka konke kwe-LPV/r kanye ne-HIV-1 subtype C nokulandelana okungezwani nemithi yokwelapha okudawunilodwe kwisizindalwazi seLos Alamos HIV ukuqhathanisa nezikhawu zezinhlobo ze-Env ezigulini ze-LPV/r eyehlulekayo. Ukuba khona kobuxhakaxhaka beBayesian basetshenziswa ukuhlonza ubudlelwane phakathi kwezinhlobo ezenzeka kwi-Env nezindawo ze-gag-PR nemithi yokwelapha i-LPV/r. Ngaphezu kwalokho, izisetshenziswa zesizindalwazi zokulandela zeLos Alamos, i-Geno2Pheno[coreceptor], nezinhlobo zamadayinamikhi amamolekhyuli asetshenziswa ukuveza ushintsho lomumo nokuqonda ukuthi izinhlobo zama-gp120 nokunomthelela ekusetshenzisweni kwesisizisemukeli. Okokugcina, uhlobo lokwehluka kwamamolekhyuli lulandelwa yi-Ring server yasetshenziswa ukuhlonza ushintsho lomumo oludalwe yizinhlobo zakwi- gp41, nezinhlobo ze-gag, nokubheka ukuxhumana (ukuthintana nokuxhumana nehayidrojini ne-VDW) phakathi kwezinhlobo nezinsalela eziseduze. Imiphumela Izinhlobo ezingamashumi amathathu nanhlanu esifundeni se-Env yaba nezivuvabakwenzeka eziphezulu ezigulini ezelashelwa i-LPV/r. Izinhlobokuxetshulwa ze-Env zakhonjiswa njengeziguquke ne-Gag-PR nokwakha indlela engaba khona ukumelana ne-LPV/r. Ukulandelana kwe-Gp120 ezigulini ezelashelwa ama-PIs kwakhombisa ukuguqulela ukungena kwegciwane ngokuvikela igciwane ekubonakaleni emasosheni omzimba ngobude obunwetshiwe kumavariyebhuli e- V1/V2 ne-V5 kanye nenombolo yezindawo ze-N-glycosylation ezibhekwe kwi-VI/V2. Imiphumela iphinde yakhombisa ukuthi izinhlobo ze-gp120 engaguqula ukungena kwegciwane ngokuguqula okudalwa yisisizisemukeli equbuka kakhulu endaweni eyi-V3, izinhlobo zezindawo yezisizizemukeli eziqondile, nalezo ezisebenzisana nendawo efaka nesisizisemukeli. Izinhlobo ezintathu kwi-gp41 (D632E-HR2, I688-TM, ne-P724Q/S-CT) zakhombisa ukuba nomthelela ngokusimamisa ama-β-turns ezindaweni zawo. Isiphetho Lolu cwaningo luphakamisa ukuthi i-gp120 iqhube ngendlela engaqondile ukusebenza ngokungezweli kwe-PI ngokuthola izinhlobo eziphakamisa ubude be-V1/V2, njengomphumela yenyusa inani jikelele lezindawo ze-N-glycosylation, kanjalo nokwenyuka nokushaja okuphelele kwi-V3. Ngale ndlela, lezi zinhlobo zenza ukungena kwegciwane ngokuputshuka kwamasosha, nokuhambisa uguquko emagciwaneni e-CXCR4 okungaphucula ukuziphindaphinda kwegciwane. Ngaphezu kwalokho, izinhlobo ze-gp41 ezibikwe kulolu cwaningo zithinta ukuziguquguqukela kwephrotheyni. Ekugcineni, izinhlobo ze-Env zifaka isandla ekungezwelini komuthi we-PI ngokuguquka nezinhlobo kwi-Gag ezaziwa ngokufaka isandla ekwehlulekeni kwe-PI nokuchibiyela ukulahlekelwa amandla kwegciwane, okuveza ukuthi kunokusebenzisana phakathi kwamasosha nokuphakama kokungezweli komuthi.
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    Defining HIV persistence and host immune responses in lymph nodes of combined antiretroviral therapy (cART) suppressed individuals and the determination of the impact of HIV infection on SARS-COV-2 specific t cell responses in South Africa = Ukuchazwa kokuphikelela kwe-HIV kanye nokulwisana nayo kwamasosha okwelashwa ngemishanguzo exubile eyaziwa nge-cART okubonakala ezimbilaphweni kubantu abangakhombisi ukuthi banegciwane le-HIV, kanye nokuvela kwemithelela yokutheleleka ngegciwane le-HIV ekulweni kwamaseli awuhlobo lwe-T kwi-SARS-CoV-2 eNingizimu Afrikha.
    (2023) Chasara, Caroline.; Ndhlovu, Zaza Mtine.
    Abstract 1 People living with HIV (PLWH) who have unsuppressed HIV are at a greater risk of acquiring infectious diseases such as Coronavirus disease of 2019 (COVID-19). More recent data has shown that unsuppressed HIV is associated with severe COVID-19 symptoms, but the mechanisms underpinning this susceptibility are still unclear. In our study we used flow cytometry and culture T lymphocyte expansion to assess the impact of HIV infection on the quality and epitope specificity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) T cell responses in the first wave and second wave of the COVID-19 epidemic in South Africa. We observed that HIV-seronegative individuals had significantly greater CD4+ T cell responses against the Spike protein compared to the viremic individuals living with HIV. In addition, there was diminished T cell cross-recognition between the two waves, which was more pronounced in individuals with unsuppressed HIV infection. Importantly, we identified four mutations in the Beta variant that resulted in the abrogation of T cell recognition. These findings partly explain the increased susceptibility of PLWH to diseases such as COVID-19 and highlight their vulnerability to emerging SARS-CoV-2 variants of concern. Abstract 2 The major keys to developing an HIV cure is through understanding HIV reservoir dynamics. The role of tissue macrophages in HIV reservoirs is complex and not yet fully understood. However, their ability to support viral replication, longevity, localization in immune sanctuaries, and potential for viral latency all contribute to the persistence and resilience of HIV reservoirs in various tissues throughout the body. Understanding and targeting these reservoirs is a critical area of research in the quest for an HIV cure. To gain insight into the macrophage reservoir, we used a combination of flow cytometry and immunofluorescence microscopy to characterize and investigate HIV persistence in lymph node (LN) macrophages. We detected pro-inflammatory (CD68+ ) macrophages harboring HIV Gag p24 and HIV1 RNA in the germinal centers of HIV positive early and late treated individuals suggesting their potential role as an HIV reservoir. In contrast, anti-inflammatory (CD206+ ) macrophages were localized along lymphatic vessels and outside the germinal centers. Importantly, we show the presence of longlived CD4+ TIM-4+ macrophages in LNs. The data reported in this thesis will go a long way in furthering our understanding of macrophage HIV reservoirs in lymph node macrophages. Iqoqa 1. Abantu abaphila ne-HIV (PLWH) abakhombisayo ukuthi bane-HIV basengozini enkulu yokuthola izifo ezithathelwanayo njenge-Coronavirus ka-2019 (COVID-19). Imininingo yakamuva ibonise ukuthi i-HIV ebonakalayo ihlotshaniswa nezimpawu ezinzima ze-COVID-19, kodwa izindlela ezisekela lokhu kuba sengozini azikacaci. Ocwaningweni lwethu siqale sasebenzisa i-flow cytometry kanye nokwandiswa kokuhlolwa kwamaseli egazini angamasosha okulwisana nezifo ukuze kubonakale umthelela wokuchaphazeleka nge-HIV kwikhwalithi nokucaciswa kokuvela kwezimpawu zezinkinga zokuphefumula kanzima ze-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kanye nendlela amaseli ayi-T cell alwa ngayo ekugaseleni kuqala kanye nokwesibili kobhubhane lwe-COVID-19 eNingizimu Afrika. Siqaphele ukuthi abantu abangenalo igciwane le-HIV, amaseli abo ayi- CD4+ T ayelwa ngendlela enamandla amakhulu ngokumelene ne-Spike protein uma kuqhathaniswa nabantu abanegciwane egazini abaphila ne-HIV. Ukwengeza, kube nokuncipha kokuqashelwa kwe-T cell phakathi kwalezi ziwombe zokugasela ezimbili, okwakubonakala kakhulu kubantu abane-HIV engacashile. Okubalulekile, sihlonze izinguquko ezine kwi-DNA yo hlobo lwe-Beta okuholele ekucindezelekeni kokusebenza kweseli ye-T. Imiphumela ichazile nakuba kungaphelele ukuhlaseleka kwe-PLWH ezifweni ezinjenge-COVID-19 kanti futhi kugqamisa nokuba sengozini kwabo kwezinye izinhlobo ze-SARS-CoV-2 ezisaqubuka ngendlela eyethusayo. Iqoqa 2. Izindlela ezinqala zokuthuthukisa ikhambi lokwelapha i-HIV zisekuqondeni iziguquguquli zesidlekemagciwane se-HIV. Iqhaza lamaseli ayi-macrophage ezicutshini zesidlekemagciwane se-HIV liyinkimbinkimbi futhi alikaqondakali ngokugcwele. Kodwa-ke, amandla awo okusekela ukuphindaphindeka kwegciwane, ukuphila isikhathi eside, ukutholakala kwawo ezindaweni ezivikela amasosha omzimba, kanye nokukwazi ukungazivezi njengegciwane, konke kunomthelela ekuphikeleleni nasekuqineni kwesidlekemagciwane se-HIV ezicutshini ezihlukahlukene emzimbeni wonke. Ukuqonda kanye nokuhlasela lezi zidlekemagciwane kuyingxenye ebaluleke kakhulu kulolu cwaningo emizamweni yokuthola ikhambi lokwelapha i-HIV. Ukuthola ukuqonda ngesidlekemagciwane se-macrophage sisebenzise inhlanganisela yeqhinga elaziwa nge-flow cytometry kanye ne-immunofluorescence microscopy ukuze kutholakale futhi kuphenywe ukuphikelela kwe-HIV kuma-macrophage asezimbilaphweni. Sithole ama-macrophage avunana nokuvuvukala i-(CD68+) okucashe kuwo i-HIV-Gag p24 kanye ne-HIV-1 RNA ezindaweni la kumila khona igciwane le-HIV kubantu abane-HIV abasaqala ukwelashwa nalabo asebenesikhathi eside belashwa, okukhombisa indima angayidlala njengesidlekemagciwane se-HIV. Ngokuphambene nalokho, ama-macrophage alwa nokuvuvukala i-(CD206+) atholakala emithanjeni yezimbilapho kanye nangaphandle kwezindawo okumila kuzo igciwane. Okubalulekile ukuthi sibonisa ukuba khona kwama-macrophage CD4+TIM-4+ asemadala ezimbilaphweni. Imininingo ebikwe kulo mqingo izohamba ibanga elide ekuqhubekiseleni phambili ukuqonda kwethu izidlekemagciwane zama-macrophage e-HIV kuma-macrophage atholakala ezimbilaphweni.