During the second week of December 2021, Africa reported more than 196,000 COVID-19 cases, marking the biggest surge in the continent for the year . Adding to the concern around such an increase in cases were the associated projections related to vaccine rollout efforts across African countries. This round of data signaled Africa’s increased vulnerability to the spread of disease due to low immunization rates. According to the World Health Organization, as the end of the year approached, only two African countries had reached the 70% vaccine coverage target for controlling the spread of disease, and the majority had yet to vaccinate even 10% of their populations .
A continued focus on vaccine rollout is essential, but barriers such as lack of funding, limited equipment for transport and storage, insufficient numbers of healthcare workers, cold chain capacity restrictions, and vaccine hesitancy are proving difficult to overcome . As public health organizations across the continent work to improve overall vaccination rates, accessible testing and comprehensive surveillance will be key tools in gaining control of the pandemic.
At the African Society of Laboratory Medicine (ASLM) meeting in November 2021, past and present pandemic control measures across the continent remained an important topic of conversation. Highlights included talks on Africa’s essential COVID-19 testing tactics and surveillance initiatives.
Infrastructure investments to manage increasing COVID-19 testing demands
During the ASLM event, Dr. Alex Alexandre, head of the CSIR Diagnostic Laboratory & Acting Research Group for Array Tech, gave an overview of how Africa’s Council for Scientific and Industrial Research (CSIR) is built and staffed two biosafety level 3 (BSL-3) labs from the ground up to meet increasing COVID-19 testing demand. These facilities were designed with special protective measures and system controls to manage airflow and maintain negative pressure, reducing exposure risk for those handling SARS-CoV-2 positive samples.
In addition to expanded space and more personnel, CSIR also needed to invest in laboratory equipment and consumables to process samples and ensure reliable results, such as the KingFisher Sample Purification Systems from Thermo Fisher Scientific. The labs have now run over 50,000 tests and are pivotal in helping keep employees working and the economy up and running during COVID-19 surges, like the one Africa is currently experiencing.
In addition to COVID-19 testing, CSIR is now offering expanded testing services, such as a TaqPath multiplex test to screen sick patients for multiple respiratory infections with greater ease and efficiency. Looking ahead past the pandemic, they plan to use their new facilities and trained staff to extend testing to DNA processing and analysis for newborn screening and forensic applications.
Surveillance efforts to identify and track SARS-CoV-2 variants
Identifying known and novel variants is important to pandemic control measures, as these variants have the potential to evade prior immunity and transmit more easily. South Africa’s surveillance efforts were recently commended when they expeditiously identified the latest SARS-CoV-2 variant of concern, Omicron, allowing the rest of the world to act quickly in response . During the ASLM meeting, Kathleen Subramoney, a medical scientist at NHLS Charlotte Maxeke Johannesburg Academic Hospital, offered insight into some of these surveillance strategies by highlighting regional variant test data from Johannesburg, South Africa over the period from June to September 2021.
During this time, when South Africa was experiencing a third wave of infections, the team in Johannesburg tracked variant activity across multiple regions by randomly selecting positive samples for testing with the TaqMan SARS-CoV-2 Mutation Panel, a genotyping assay designed to identify mutations associated with variants of concern. Not surprisingly, the Delta variant dominated in all regions tested during South Africa’s third wave. The recent introduction of Omicron – which is believed to be more contagious than Delta – and future variant activity will continue to drive positive cases and shift these findings over time, making ongoing active regional surveillance of SARS-CoV-2 critically important .
For information on Africa’s COVID-19 testing and surveillance efforts, please download the ASLM talks on demand.
To learn more about Thermo Fisher Scientific’s COVID-19 Testing Solutions, visit https://www.thermofisher.com/covid19.