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08 June 2021 | Story André Damons | Photo Charl Devenish
African solidarity through medical research
Left: Prof Martin Nyaga, an Associate Professor: Next Generation Sequencing (UFS-NGS) and Director of the WHO Collaborating Centre (WHO CC), says there is a need to invest heavily in medical research, especially in next-generation sequencing facilities. Right: Dr Peter Mwangi is a Postdoctoral Research Fellow: NGS and Research Scientist in the WHO Collaborating Centre (WHO CC) at the University of the Free State (UFS).
South Africa is at the forefront of SARS-CoV-2 genomics surveillance in Africa, and the University of the Free State (UFS) Next Generation Sequencing (UFS-NGS) Unit is playing a major role in responding rapidly to public health threats in South Africa and other African countries.

Prof Martin Nyaga, Associate Professor in the UFS-NGS Unit and Director of the World Health Organization Collaborating Centre (WHO CC), and Dr Peter Mwangi, a Postdoctoral Research Fellow in the UFS-NGS Unit, say medical research in Africa is seriously deficient when benchmarked against other developed continents in terms of the capacity to perform SARS-CoV-2 genomics. According to them, an article published in a nature science journal provided evidence that African nations were largely uninvolved in clinical trials for the development of a COVID-19 vaccine.

“If African leaders are to learn one thing from the current pandemic, it is the need to provide adequate resources and funding for medical research, especially in next-generation sequencing facilities. Anyone keen on real-time data and information on the COVID-19 pandemic understands how fundamental sequencing the SARS-CoV-2 genome is. Rapid sequencing of the SARS-CoV-2 genome has played a key role in accelerating the development of emergency vaccines against this devastating disease,” say the two researchers.

Genome sequencing projects are collaborative efforts
Prof Nyaga is heading the WHO CC after the UFS was designated as a collaborating centre for vaccine-preventable diseases (VPD) surveillance and pathogen genomics last year. The centre is located in the Division of Virology in the Faculty of Health Sciences. It is also part of the Network for Genomic Surveillance in South Africa (NGS-SA), a genomics network/consortium established to respond rapidly to public health threats in South Africa.

Genome sequencing projects are usually collaborative efforts involving different stakeholders, including the national government through the Ministry of Health, scientists, and clinicians. The UFS-NGS Unit is actively involved in sequencing SARS-CoV-2 samples in the Free State channelled through the National Health Laboratory Services (NHLS-FS).

The sequenced data generated by the unit is continuously deposited in the Global Initiative on Sharing Avian Influenza Data (GISAID) database through the code name UFS-VIRO-NGS. The UFS-NGS Unit is currently performing whole-genome sequencing runs of approximately 100 SARS-CoV-2 samples per month.

“Through continuous processing of SARS-CoV-2 samples, the UFS-NGS Unit has optimised several techniques for COVID-19 genomics, from wet-lab to dry-lab analysis, captured in the internal protocols of the unit. The unit is continuously generating quality SARS-CoV-2 sequence data for the national consortium that is important for vaccine immunogenicity research projects geared towards regional vaccine development,” says Prof Nyaga.

Analysis of genome sequence data plays significant role in vaccine development
According to Prof Nyaga and Dr Mwangi, the sequence data generated in the UFS-NGS Unit has been key to establishing the SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC). The VOI and VOC require one or more appropriate public health actions, including enhanced sequence surveillance, enhanced laboratory characterisation, or epidemiological investigations to assess how easily the virus spreads, the severity of disease, the risk of infection, and whether currently authorised vaccines offer protection.

“An example of a VOC strain is the 20H/501.V2 in lineage B.1.351 that was first discovered in South Africa after analysis of whole-genome sequence data, highlighting the importance of whole-genome SARS-CoV-2 surveillance. Consequently, analysis of the whole genome sequence data plays a significant role not only in vaccine development efforts, but also in advising policy to global and African governments on protection measures to be undertaken to curtail COVID-19 transmission,” explain the researchers.

The UFS-NGS Unit has been working collaboratively with other African scientists and actively training African students from different cultural backgrounds, not only on SARS-CoV-2 genomics, but also on different research clusters. The diversity of ideas through engagement with African researchers to share knowledge and push scientific innovation exemplifies the value of working together in the spirit of Ubuntu to develop solutions to our African problems. As we commemorate Africa Month 2021, let us be inspired by our hardworking UFS researchers, who are promoting African solidarity by working collaboratively in medical research to strive for a safe, healthy, and prosperous Africa.

• The key members of NGS-SA working on SARS-CoV-2 genomics samples from the Free State, are Prof Dominique Goedhals (Head: Division of Virology), Prof Martin Nyaga, Mr Phillip Bester (Medical Scientist: Division of Virology), Dr Peter Mwangi, Mr Milton Mogotsi (Research Assistant: UFS-NGS Unit), and Mr Ayodeji Ogunbayo (Research Assistant: UFS-NGS Unit).

News Archive

The state of HIV/AIDS at the UFS
2010-05-11

“The University of the Free State (UFS) remains concerned about the threat of HIV/AIDS and will not become complacent in its efforts to combat HIV/AIDS by preventing new infections”, states Ms Estelle Heideman, Manager of the Kovsies HIV/AIDS Centre at the UFS.

She was responding to the results of a study that was done at Higher Education Institutions (HEIs) in 2008. The survey was initiated by Higher Education AIDS (HEAIDS) to establish the knowledge, attitudes, behaviours and practices (KABP) related to HIV and AIDS and to measure the HIV prevalence levels among staff and students. The primary aim of this research was to develop estimates for the sector.

The study populations consisted of students and employees from 21 HEIs in South Africa where contact teaching occurs. For the purpose of the cross-sectional study an ‘anonymous HIV survey with informed consent’ was used. The study comprised an HIV prevalence study, KABP survey, a qualitative study, and a risk assessment.

Each HEI was stratified by campus and faculty, whereupon clusters of students and staff were randomly selected. Self-administered questionnaires were used to obtain demographic, socio-economic and behavioural data. The HIV status of participants was determined by laboratory testing of dry blood spots obtained by finger pricks. The qualitative study consisted of focus group discussions and key informant interviews at each HEI.

Ethical approval was provided by the UFS Ethics Committee. Participation in all research was voluntary and written informed consent was obtained from all participants. Fieldwork for the study was conducted between September 2008 and February 2009.

A total of 1 004 people participated at the UFS, including the Main and the Qwaqwa campuses, comprising 659 students, 85 academic staff and 256 administration/service staff. The overall response rate was 75,6%.

The main findings of the study were:

HIV prevalence among students was 3,5%, 0% among academics, 1,3% among administrative staff, and 12,4% among service staff. “This might not be a true reflection of the actual prevalence of HIV at the UFS, as the sample was relatively small,” said Heideman. However, she went on to say that if we really want to show our commitment towards fighting this disease at our institution a number of problem areas should be addressed:

  • Around half of all students under the age of 20 have had sex before and this increased to almost three-quarters of students older than 20.

     
  • The majority of staff and a third of students had ever been tested for HIV.

     
  • More than 50% of students drink more than once per week and 44% of students reported being drunk in the past month. Qualitative data suggests that binge drinking over weekends and at campus ‘bashes’ is an area of concern.

Recommendations of the study:

  • Emphasis should be on increased knowledge of sexual risk behaviours, in particular those involving a high turnover of sexual partners and multiple sexual partnerships. Among students, emphasis should further be placed on staying HIV negative throughout university study.

     
  • The distribution of condoms on all campuses should be expanded, systematised and monitored. If resistance is encountered, attempts should be made to engage and educate dissenting institutional members about the importance of condom use in HIV prevention.

     
  • The relationship between alcohol misuse and pregnancy, sexually transmitted infections (STIs), HIV and AIDS needs to be made known, and there should be a drive to curb high levels of student drinking, promote non-alcohol oriented forms of recreation, and improve regulation of alcohol consumption at university-sponsored “bashes”.

     
  • There is need to reach out to students and staff who have undergone HIV testing and who know their HIV status, but do not access or benefit from support services. Because many HIV-positive students and staff are not receiving any kind of support, resources should be directed towards the development of HIV care services, including support groups.

Says Heideman, “If we really want to prove that we are serious about an HIV/AIDS-free campus, these results are a good starting point. It definitely provides us with a strong basis from which to work.” Since the study was done in 2008 the UFS has committed itself to a more comprehensive response to HIV/AIDS. The current proposed ‘HIV/AIDS Institutional response and strategic plan’, builds and expands on work that has been done before, the lessons learned from previous interventions, and a thorough study of good practices at other universities.

Media Release
Issued by: Mangaliso Radebe
Assistant Director: Media Liaison
Tel: 051 401 2828
Cell: 078 460 3320
E-mail: radebemt@ufs.ac.za  
10 May 2010

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