Page 12 - AnnualReport2022-23

ACHIEVEMENTS AND HIGHLIGHTS

Pandemic and Vaccine within the consortium with bulk reagent deals and
Preparedness this helped the network exceed their sequencing
targets.
Since the start of the COVID-19 pandemic in South
Africa in March 2020, the SAMRC has, together with The network has been a pillar of the South African
key partners such as the National Department of COVID-19 pandemic response, generating data
Science and Innovation (DSI), driven the research to uncover new COVID-19 variants, informing
and innovation response, with more than R500 pandemic control measures, and gaining
million raised and/or reallocated to support more international recognition for South Africa’s role in
than 50 projects. While a portfolio of these projects the global pandemic response through a plethora of
is still being managed, in the 2022/23 financial year high impact publications in journals such as Nature
the SAMRC has focused its pandemic preparedness and the Lancet. Furthermore, the success of the
and response on surveillance and the vaccine consortium was magnified by the pivotal role they
response through continued support of the Network played in capacity development and the roll out
for Genomic Surveillance in South Africa (NGS- of pathogen genomic sequencing in other African
SA) and the Wastewater Surveillance and Research countries to assist in their pandemic response.
Programme; the execution of various COVID-19 The NGS-SA Programme model was leveraged to
vaccine studies; participation in the mRNA develop the Pathogen Genomics Initiative (PGI) for
Technology Transfer Hub; and initiation of the Chan Pandemic Preparedness through the Africa Centres
Soon-Shiong Family Foundation-SAMRC Capacity for Disease Control. PGI has managed to enable
Development Programme. capacity for pathogen genomics sequencing across
the African continent, helping some countries
The NGS-SA Genomics Surveillance Programme, localize omics technologies and data capacities.
led by Prof Tulio de Oliveira from the Centre for
Epidemic Response and Innovation (CERI), is a The SAMRC has continued to drive several
shining example of collaboration and harnessing the COVID-19 vaccine studies to ensure that globally
skills set within our borders to enable a rapid and developed vaccines are tested in our populations
coordinated response to the COVID-19 pandemic. and to inform policy around vaccination and
The network, initiated with funds from the SAMRC boosting. The Sisonke and Sisonke Homologous
and DSI at the Kwa-Zulu Natal Research Innovation Boost studies delivered the Johnson and Johnson
and Sequencing Platform (KRISP), aimed to rapidly Ad26.COV2.S vaccine and boost to 496,424 and
sequence as many outbreak samples as possible 230,488 participants, respectively, during 2021.
and to log the data on the global GISAID database, Follow up and data analysis on these studies have
which is used to track the global COVID-19 continued during 2022/23 with a total follow up time
pandemic. It took a major team effort using next- of 2 years included in the protocol. Results from the
generation sequencing technologies and a cutting- study will be published during 2023/24. The Sisonke
edge bioinformatics pipeline to enable real-time studies were funded by an allocation from National
analysis and reporting of the data and contribution Treasury through the National Department of Health
to the global database, enabling rapid release of and grant funding from the Michael and Susan Dell
information on the magnitude and characteristics Foundation, the ELMA Vaccines and Immunisation
of the South African pandemic. The network was Foundation, the Solidarity Fund, the Bill and
also enabled by the already robust workflow in Melinda Gates Foundation and Janssen Vaccines
place at the National Institute for Communicable & Prevention B.V. The SAMRC initiated the Sisonke
Diseases (NICD), leveraging off the National Heterologous mRNA-1273 boost after prime with
Health Laboratory Services laboratory network for Ad26.COV2.S (SHERPA) study in May 2022 to examine
a streamlined workflow from access to samples to the real-world effectiveness of a heterologous boost
sequencing to data generation and analysis. We with the Moderna mRNA-1273 vaccine in those
saw technology suppliers also playing their role who received either a single or double dose of

10 SAMRC ANNUAL REPOR T 2022-23