Discipline of Virology

Research

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)

 

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.

 

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)

 

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

 

Principal Investigator

Lilisha Gounder (PhD Project)

 

Supervisor

Ben Chimukangara (UKZN, CAPRISA, NIH)

 

Co-Supervisor

Raveen Parboosing (NHLS, UKZN/WITS)

 

Collaborators

Kogielum Naidoo, Sandrini Moodley (CAPRISA) Sontaga Manyane, Melen Pillay (NHLS, UKZN)

 

Objective

To develop a database and GIS tools for monitoring HIV-1 drug resistance in Kwa-Zulu Natal

 

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)

 

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

 

Student

Tshepiso Mosito (MMed Project)

 

Supervisor

Kerusha Govender (NHLS, UKZN)

 

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

 

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)

 

Objective

To investigate correlation of HBV core gene mutations in patients co-infected with HIV-1 in KwaZulu-Natal, South Africa

 

 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

 

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

 

 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

 

Student

Nelisiwe Ngcaba (MMed Project)

 

Supervisor

Nokukhanya Msomi (NHLS, UKZN)

 

Collaborator

Lilisha Gounder (NHLS, UKZN)

 

Objective

To describe the patterns and prevalence of Congenital Viral Infections in Kwa-Zulu Natal, South Africa

 

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

 

Student

Neziswa Marafungana (MMed Project)

 

Supervisors

Prof Refiloe Masekela & Dr Kimesh Naidoo (Department of Paediatrics, UKZN)

 

Collaborator

Lilisha Gounder (NHLS, UKZN/WITS)

 

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