Research
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RESEARCH
SARS-CoV-2 GENOMICS
Project | Spatial and Genomic monitoring of COVID-19 and SARS-CoV-2 in South Africa |
Principal Investigator(s) | Tulio de Oliveira & Richard Lessells (KRISP, UKZN) |
Collaborators | Nokukhanya Msomi (NHLS, UKZN), Koleka Mlisana (NHLS), Susan Engelbrecht ( NHLS, Stellenbosch University), Jinal Bhiman (NHLS, NICD), Dominique Goedhals (NHLS, UFS), Marvin Hsiao, Diana Hardie ( NHLS, UCT), Carolyn Williamson ( UCT)
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Objectives | To increase access to genomic methods in to sequence SARS-CoV-2 close to the source of outbreaks in South Africa. To support the production and analysis of SARS-CoV-2 genomic data in South Africa in near real-time. To trace SARS-CoV-2 introductions, identify community transmissions and use this information to characterize and control local outbreaks.
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Project | The implementation of SARS-CoV-2 genomic surveillance: The South African experience |
Principal Investigator(s) | Nokukhanya Msomi, Kerusha Govender |
Objective | Description of COVID genomic surveillance network |
Project | Genomic and Geographic distribution of SARS-CoV-2 in KZN |
Supervisor | Nokukhanya Msomi |
Student | Cherise Naicker (MMed Project)
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Collaborators | Lilisha Gounder |
Objective | To describe the clade and geographic distribution of SARS-CoV-2 in KwaZulu-Natal from May 2020 to March 2021. |
Project | Incidence of SARS-CoV-2 infection among healthcare workers: Does re-infection occur? |
Principal Investigator | Quarraisha Abdool Karim (CAPRISA, UKZN ) |
Collaborators | Nokukhanya Msomi, Lilishia Gounder (NHLS, UKZN), Koleka Mlisana (NHLS) |
Objective | To compare incidence rates of SARS-CoV-2 infection in health care workers and high-risk populations during different waves of infections, including those previously infected. |
Project | Prevalence of COVID-19 infection in patients with preterm labour – A South African Experience |
Student | Kaashifa Akbar Ismail (MMed Project) |
Supervisor | Prof Motshedisi Sebitloane (Department of Obstetrics & Gynaecology, UKZN) |
Co-Supervisor | Dr Kerri-Lee Francois (NHLS, UKZN) |
Objective | To determine prevalence of Covid-19 infection in all patients presenting with PTL or PPROM as compared to presenting in labour at term To determine the presence of COVID-19 infection in the lower genital tract of women with Covid-19 infection using placental swabs |
Project | Seroprevalence of SARS-CoV-2 IgG in KwaZulu-Natal |
Principal Investigator | Kerri-Lee Francois (NHLS, UKZN) |
Collaborators | Nokukhanya Msomi, Lilishia Gounder, Pravi Moodley, Kerusha Govender, (NHLS, UKZN), Raveen Parboosing (NHLS, UKZN/WITS) |
Objective | To determine the prevalence of SARS-CoV-2 IgG in residual clinical specimens referred for non-COVID-19 related diagnostic testing in HIV-infected versus uninfected specimens. |
HIV GENOMICS
Project | Monitoring and analysis of HIV-1 drug resistance in Kwa-Zulu Natal, South Africa
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Principal Investigator | Lilisha Gounder (PhD Project)
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Supervisor | Ben Chimukangara (UKZN, CAPRISA, NIH)
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Co-Supervisor | Raveen Parboosing (NHLS, UKZN/WITS)
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Collaborators | Kogielum Naidoo, Sandrini Moodley (CAPRISA) Sontaga Manyane, Melen Pillay (NHLS, UKZN)
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Objective | To develop a database and GIS tools for monitoring HIV-1 drug resistance in Kwa-Zulu Natal
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Project | A Randomized Controlled Clinical Trial to Estimate the Efficacy and Cost-Effectiveness of Resistance Testing to Improve Management of Virologic Failure in sub-Saharan Africa (REVAMP) |
Principal Investigator | Mark J. Siedner (Massachusetts General Hospital, Boston) |
Collaborators | M Paul, R Gandhi, K Ard ( Massachusetts General Hospital, Boston); MB Bwana, I Aturinda, W Muyindike (Mbarara University of Science and Technology, Uganda); Y Moosa, H Sunpath, S Pillay, J Brijkumar, T Rautenberg, G George (UKZN); B Johnson (University of Rochester, NY); V Marconi ( Emory University, Atlanta), Pravi Moodley (NHLS, UKZN) |
Objective | Determining whether addition of routine resistance testing at the time of first-line virologic failure improves clinical outcomes and how it impacts cost of care for patients with HIV infection in sub-Saharan Africa. |
Project | HIV-1 RNA Genotypic Resistance Tests |
Principal Investigator | Suzanne McCluskey (Harvard Medical School) |
Collaborators | REVAMP Study Group, Pravi Moodley (NHLS, UKZN) |
Objective | Investigation of baseline HIV-1 RNA Genotyping in a sub-population from the REVAMP Study |
Project | Novel virologic and pharmacologic assays to predict clinical outcomes after first-line ART failure in sub-Saharan Africa |
Principal Investigator | Jonathan Li (Harvard Medical School) & Pravi Moodley (PI SA) |
Collaborators | Vincent Marconi (Emory University), Mark Siedner (Harvard Medical School, Boston), Castillo-Mancilla (University of Colorado), Heather Ribaudo and Yu Zheng (Center for Biostatistics in AIDS Research, Harvard School of Public Health), Davey Smith ( University of California), Ben Chimukangara (UKZN, CAPRISA, NIH) |
Student | Melen Pillay (PhD Project) |
Supervisor | Raveen Parboosing (NHLS, UKZN/WITS)
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Objective | Investigation of novel Next Generation Sequencing techniques for First line ART Failure in sub-Saharan Africa |
Project | Monitoring of HIV Drug Resistance in South Africa and innovative approaches to HIV Drug Resistance testing |
Principal Investigator | Ben Chimukangara (UKZN, CAPRISA, NIH) |
Collaborators | Kogie Naidoo (CAPRISA, UKZN), Pravi Moodley (UKZN), Lili Gounder (UKZN), Sontaga Manyana (UKZN) |
Objective | Design innovative HIV Drug Resistance diagnostic tools and monitor levels of acquired HIV Drug Resistance in South Africa |
Project | Innovative and affordable HIV-1 Drug Resistance testing for resource limited settings |
Principal Investigator | Sontaga Manyana (UKZN) |
Collaborators | Ben Chimukangara (UKZN, CAPRISA, NIH), Lili Gounder (UKZN), Kogie Naidoo (CAPRISA, UKZN) |
Objective | Design an affordable and cost-effective HIV Drug Resistance assay for detecting HIV Drug Resistance mutations in all relevant genes |
Project | Investigate pan-resistant HIV-1 among highly treatment experienced patients |
Student | Tendai Washaya (University of Zimbabwe) |
Supervisor
| Ben Chimukangara (UKZN, CAPRISA, NIH) |
Collaborators | Justen Manasa, Nyasha Chin’ombe (University of Zimbabwe), Cleophas Chimbetete (Newlands Clinic) |
Objective | Investigate pan-resistant HIV-1 and develop a simple HIV-1 drug resistance point mutation assays |
Project | HIV drug resistance on Dried Bloods Spots
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Student | Tshepiso Mosito (MMed Project)
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Supervisor | Kerusha Govender (NHLS, UKZN)
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Objective | To investigate patterns of HIV drug resistance on Dried Bloods Spots in children |
HBV GENOMICS
Project | Hepatitis B Virus variants in HBV mono-infected and HIV/HBV co-infected patients in a high dual infection setting |
Principal Investigator | Nokukhanya Msomi (PhD Project) |
Supervisor | Raveen Parboosing (NHLS, UKZN/WITS) |
Collaborators | Koleka Mlisana (NHLS), Eduan Wilkinson, Tulio de Oliviera, Jennifer Giandhari (KRISP, UKZN) |
Objective | To determine the evolution of HBV variants in patients with Chronic
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Project | Correlation of HBV Core gene mutations with serological profiles of patients co-infected with HIV-1 in KwaZulu-Natal, South Africa |
Student | Peter Matsapola (MMedSci Project ) |
Supervisor | Nokukhanya Msomi (NHLS, UKZN)
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Objective | To investigate correlation of HBV core gene mutations in patients co-infected with HIV-1 in KwaZulu-Natal, South Africa
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HPV GENOMICS
Project | The role of human papillomavirus (HPV) in head and neck squamous cell carcinomas in KwaZulu-Natal, South Africa |
Principal Investigator | Aabida Khan (PhD Project) |
Supervisors | Nokukhanya Msomi (NHLS, UKZN), Raveen Parboosing (NHLS, UKZN/WITS) |
Collaborators | Melen Pillay, Pravi Moodley (NHLS, UKZN), Andile Lindokuhle, Sibiya Rishan Bipath (Department of Otorhinolaryngology, DOH, UKZN), Mpumelelo Msimang, Gamalenkosi Nhlonzi (Department of Anatomical Pathology, NHLS, UKZN), James Zachary Porterfield ( NIH Fogarty International Center, Global Health Equity Fellow, University of Kentucky, UKZN) |
Objective | Assess the prevalence, genotype and anatomical site distribution of HPV in head and neck squamous cell carcinoma tissue specimens using PCR and sequencing. Genomic characterization of HPV positive head and neck squamous cell carcinomas using next generation sequencing. Compare HPV positive versus HPV negative head and neck squamous cell carcinomas with clinical features and outcomes, including HIV infection |
CMV GENOMICS
Project | Assessing compartmentalization of human cytomegalovirus in the respiratory system using a whole-genome sequencing approach |
Principal Investigator
| Kerusha Govender (PhD Project) |
Supervisor | Raveen Parboosing (NHLS, UKZN/WITS) |
Objective | To describe CMV pneumonitis in infants in high HIV prevalence settings, and the difficulty in diagnosing it. To generate whole CMV genome sequences from KwaZulu-Natal, and the molecular signature of CMV which predicts progression to CMV pneumonitis in infants. To describe the differences in strains between lung and blood compartments |
Project | Validation of Dried Blood Spot for CMV Viral Load in HIV infected infants
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Supervisor | Kerusha Govender (NHLS, UKZN) |
Student | Joedene Chetty (MMed Project ) |
Objective | To validate Dried Blood Spot for CMV Viral Load and to describe prevalence of CMV in HIV infected infants
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NANOTECHNOLOGY
Project | Aptamer-functionalized carbosilane dendrimers to reactivate HIV-1 latency |
Supervisor | Raveen Parboosing (NHLS, UKZN/WITS) |
Student | William Serumula ( PhD Project) |
Collaborator | Aptus Biotech (Spain) |
Objective | To investigate reactivation of HIV-1 latency by Aptamer-functionalized carbosilane dendrimers |
Project | Optimisation of a novel method to screen for molecules that inhibit viral packaging |
Supervisor | Raveen Parboosing (NHLS, UKZN/WITS) |
Student | Cassandra Soobramoney (PhD Project) |
Objective | To identify sequences that inhibit viral packaging |
Project | Eco-friendly synthesis of silver nanoparticles using plant extracts as a biocompatible novel antioxidant and immunomodulatory agent for the treatment of HIV-1 |
Principal Investigator
| Raveen Parboosing (NHLS, UKZN/WITS) |
Objective | To investigate the antioxidant and immunomodulatory effects of silver nanoparticles |
Project | Combination siRNAs targeting HIV-1 |
Principal Investigator | Raveen Parboosing (NHLS, UKZN/WITS) |
Objective | To investigate the effect of Combination siRNAs on HIV replication |
Project | Targeted delivery of siRNA into T-Lymphocytes using PEI-AuNP-Antibody complexes |
Supervisor | Raveen Parboosing (NHLS, UKZN/WITS) |
Student | Nomfundo Ncobeni ( MMedSci Project) |
Objective | In vitro experiments for Delivery of RNA to lymphocytes using polyethyleneimine capped gold nano particles and anti CD4 antibodies. |
HIV TRANSLATIONAL SCIENCE
Project | Development of a point of care urine tenofovir immunoassay to distinguish adherence versus resistance-based HIV treatment failure |
Principal Investigator
| Suzanne McCluskey (Harvard Medical School) |
Collaborators | Mark Siedner & Bethany Hedt-Gauthier ( Harvard Medical School), Mwebesa Bwana (Mbarara University of Science and Technology, Uganda), John Adamson ( Africa Health Research Institute), Alere ( San Francisco, CA), Monica Gandhi (University of California), Pravi Moodley, Melen Pillay (NHLS,UKZN) |
Objective | Investigation of performance characteristics of a point of care urine tenofovir immunoassay |
Project | An adaptive randomised evaluation of nurse-led HIV treatment retention interventions for women living with HIV |
Principal Investigators | Harry Hausler (TB/HIV Care, SA) & Stefan Baral (John Hopkins University) |
Collaborators | Katherine Young (TB/HIV Care, SA), Sheree Schwartz, Jason Farley, David Dowdy, Chris Beyrer, Carly Comins (Johns Hopkins University), Elvin Geng (University of California), Sharmistha Mishra (University of Toronto), Pravi Moodley, Kerusha Govender, Melen Pillay ( NHLS, UKZN), Rene Phetlhu (University of Western Cape), |
Objective | To compare the effective and durability of mobile decentralized treatment programme (DTP) model vs. a peer-led individual case management (ICM) program to achieve HIV viral suppression. |
Project | Point-of-care viral load testing to enable task shifting for chronic HIV care- The “POC Viral Load Study” |
Principal Investigators | Paul Drain (University of Washington) & Nigel Garrett (CAPRISA, UKZN) |
Collaborators | Natasha Samsunder, Kogie Naidoo, Salim Abdool Karim (CAPRISA,UKZN), Hope Ngobese (eThekwini Municipality, KZN),Connie Celum, Ruanne Barnabas, Deborah Donnell (University of Washington), Wendy Stevens (WITS,NHLS), Pravi Moodley (NHLS,UKZN) |
Objective | Using Point-of-care viral load testing to improve retention of patients in care |
Project | PrEP uptake/adherence to reduce periconception HIV risk for South African women (“ZINK”) |
Principal Investigator
| Lynn Matthews (University of Alabama Medical School) |
Collaborators | Jennifer Smit, Yolandie Kriel (WITS University/Match), Manjeetha Jaggernath (MATCH), Jennifer Norman (UCT), Pravi Moodley, Melen Pillay (NHLS, UKZN) |
Objective | Investigation of ART PrEP uptake and adherence to reduce periconception HIV risk for South African women |
Project | The association between the HIV status and clinical outcomes of infants admitted with viral pneumonia, to Greys Paediatric Intensive Care Unit between January 2016 and December 2018. |
Student | Fortunate Nonhlanhla Langa/Bhengu (MMed Project) |
Supervisor | Sbekezelo Thembelihle Hlophe (Department of Paediatrics, Greys Hospital) |
Co-Supervisor | Kerri-Lee Francois (NHLS, UKZN) |
Objective | To determine the difference in the of morbidity and mortality in infants who are HIV-infected, HIV-exposed and uninfected and HIV-unexposed and uninfected |
Project | Patterns and Prevalence of Congenital Viral Infections in Kwa-Zulu Natal, South Africa
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Student | Nelisiwe Ngcaba (MMed Project)
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Supervisor | Nokukhanya Msomi (NHLS, UKZN)
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Collaborator | Lilisha Gounder (NHLS, UKZN)
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Objective | To describe the patterns and prevalence of Congenital Viral Infections in Kwa-Zulu Natal, South Africa
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Project | Lower Respiratory Tract Infections Risk Factors and Seasonal Association in children one month to five years admitted at King Edward VIII Hospital Kwa-Zulu Natal, South Africa
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Student | Neziswa Marafungana (MMed Project)
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Supervisors | Prof Refiloe Masekela & Dr Kimesh Naidoo (Department of Paediatrics, UKZN)
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Collaborator | Lilisha Gounder (NHLS, UKZN/WITS)
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Objective | To assess the Seasonality of Viruses causing LRTI in children To identify the common causative organisms and risk factors associated with admission in children <5 years
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