The COVID -19 pandemic has rapidly become the deadliest coronavirus outbreak in history, surpassing the combined death toll of Severe Acute Respiratory Syndrome (SARS) and Middle-East Respiratory Syndrome (MERS). Currently affecting 155 countries, with over 180 000 cases and 7000 deaths recorded globally, the fight against COVID-19 requires urgent evidence-informed public health action locally and globally
At present, Africa only has < 1000 recorded cases. This may seem small within the global context, but this is exactly why an urgent, proactive intervention and response strategy is needed to limit spread across the continent
This rapid and proactive response is also critical because a large percentage of the African population are in the most vulnerable position due to the already strained healthcare systems available, the poor socio-economic living conditions and the existing disease burdens and health deficiencies that these communities face.
As part of our activities, we are:
1) Setting up qPCR diagnostics in our laboratory to support local public health interventions and critical research in Africa
We have ordered and are certifying the Thermo Fisher Scientific and the Beijing Genomics Institute (BGI) qPCR testing. Our aim is to have in stock at least 5,000 qPCR tests at a given time so we can support public health response. We are concerned that the use of only national reference laboratories may not be enough to face the pandemic in Africa. The USA recently decided to allow academic and private laboratories to do further testing as the US CDC did not have the capacity to test and characterize all of the samples. Africa's capacity to deal with COVID-19 is also very limited.
2) Training front line health care personnel in KwaZulu-Natal, South Africa
In the last three weeks, we have made our senior infectious diseases specialist available full time for this activity, which is led by the UKZN Coronavirus war room. We have participated in the training of different cadres of health care workers and medical students and will continue to be part of the front line response in collaboration with local infectious diseases specialists, clinical virologists and public health specialists.
3) Importing and distributing personal protective equipment (PPE) for health care workers and laboratory staff
We have ordered 1,000 PPE units from China which will be used by laboratory personnel, but we will distribute them free to charge to clinical staff at UKZN.
4) Setting up SARS-CoV-2 whole genome sequencing (WGS) in South Africa and providing it to other African countries
We have imported primers and reagents for WGS sequencing. We are setting up both Oxford Nanopore technologies, with support from ARTIC Network and the Brazilian FioCruz foundation, who flew someone to South Africa and brought all of the primers and reagents. WGS of the COVID-19 virus is crucial to understand local transmission and to guide public health responses. All genomes will be deposited in public databases (i.e. GISAID for consensus genome and SRA for short reads) as soon they are produced.
5) Making available a software application to characterize coronavirus genomes and mutations
In response to this crisis, we released the first version of our new Genome Detective Coronavirus Typing Tool on 21 January 2020 and our paper on 17 February. This tool has been used 1000s of times and it is freely available. Genome Detective Coronavirus Typing Tool paper and software openly accessible here.
6) Analysing epidemiological and genomic data in real-time to guide public health interventions
We have already participated in the Belgian and Brazilian response and now are focusing on the African response. We will be releasing daily COVID-19 reports on epidemiology and genomics analysis.
To date, all of our activities have been done pro-bono and have used much of our existing financial reserves. Our personnel has also worked for free and taken time out of their daily jobs. We would like to appeal to funders and the public to help us to continue providing these valuable scientific resources to fight this pandemic, by donating to our activities here.
News date: 2020-03-17
KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).