key: cord-309509-ftwpys3y authors: Ondoa, Pascale; Kebede, Yenew; Loembe, Marguerite Massinga; Bhiman, Jinal N; Tessema, Sofonias Kifle; Sow, Abdourahmane; Sall, Amadou Alpha; Nkengasong, John title: COVID-19 testing in Africa: lessons learnt date: 2020-07-03 journal: Lancet Microbe DOI: 10.1016/s2666-5247(20)30068-9 sha: doc_id: 309509 cord_uid: ftwpys3y nan www.thelancet.com/microbe Vol 1 July 2020 e103 Laboratory testing is a pillar of the COVID-19 outbreak response. Unlike the 2014 Ebola epidemic, Africa has reacted early and collectively to the COVID-19 pandemic, ramping up severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic capacity from two to 43 countries between February and April, 2020. The Africa Centres for Disease Control and Prevention (Africa CDC)-led African Task Force for Coronavirus Preparedness and Response (AFTCOR)-a coalition between the African Union (AU), AU member states, the WHO Regional Office for Africa, and other stakeholdershas been instrumental in this impressive achievement, promoting coordination and alignment for evidencebased public health action. AFTCOR has led COVID-19 testing capacity scale-up as one of the key objectives under the Africa joint continental strategy for COVID-19 outbreak. 1 AFTCOR collaborated with the South African National Institute for Infectious Diseases, the Senegalese Institute Pasteur of Dakar, and the West African Health Organization to train expert staff from reference laboratories for molecular detection of SARS-CoV-2. To date, 1ยท6 million tests donated by the Jack Ma Foundation (Hangzou, China), and more than 1 million tests procured by Africa CDC have been distributed across the 55 AU member states. By May 21, 2020, Africa had reported more than 95 000 confirmed cases of COVID-19. 2 The Africa CDC Pathogen Genomics Intelligence Institute, which is also part of the joint continental COVID-19 strategy, provides training and resources to 16 AU member states to generate up to 2500 SARS-CoV-2 whole-genome sequences and will enable the submission of these sequences to the Global Initiative on Sharing all Influenza Data platform. 3, 4 With Africa currently contributing only 1% of all sequences submitted globally, this boost will support the design of locally relevant assays, therapeutics, and vaccines. To limit further spread of COVID-19, AU member states must expand diagnostic capacity at the subnational level. Africa CDC aims to increase the number of tests from 1300 to 16 000 per million population, while supporting countries to use every positive result for case isolation, contact tracing and quarantine, and supportive care. PCR testing platforms' footprint within national disease control programmes, and the private and animal laboratory sectors offer an opportunity to make use of free testing capacity and sample referral routes for COVID-19 diagnostics. Access to this capacity could potentially yield up to 55 million molecular tests annually. On May 16, 2020, the Nigeria Centre for Disease Control activated 26 COVID-19 testing sites, using high-throughput HIV molecular testing and tuberculosis GeneXpert instruments. Similarly, Ethiopia increased its capacity to 7600 tests per day after Abbott agreed to reconfigure its closed platform to accommodate COVID-19 testing, and after academic and animal health laboratories were engaged. Repurposing laboratory facilities for COVID-19 testing is daunting for many governments. It is complex to ensure quality-assured testing; uninterrupted supply chains; workforce supervision; and prevention of the scale back of essential diagnostic services for HIV, tuberculosis, and malaria. Pressure from the public or manufacturers has prompted some countries to decentralise COVID-19 testing, using serology assays. Whereas antibodydetecting and antigen-detecting serology tests could alleviate the pressure on PCR laboratories and support large-scale testing for diagnostic, surveillance, or epidemiology studies, WHO does not currently recommend their use in the absence of performance data. Results of independent assay evaluations by FIND 5 are awaited to inform the design of serology-based strategies for public health and to fast-track emergency use authorisations. Africa's dependency on external suppliers considerably limits the expansion of COVID-19 testing. Africa has to compete with higher income nations to access COVID-19 in vitro diagnostics and, despite the pooled procurement of tests facilitated by WHO global access to COVID-19 tools, 6 the continent remains underserved. To address these challenges, Africa CDC launched the Partnership to Accelerate COVID-19 Testing on request from AU heads of states, with the following key strategic areas: (1) organising all AU member states as one large customer and coordinating the continuous supply of test kits and commodities at a negotiated price and based on accurate forecast of needs; (2) decentralising COVID-19 testing through strategic planning that can guarantee laboratory quality, biosafety, and the establishment of robust sample referral systems; e104 www.thelancet.com/microbe Vol 1 July 2020 (3) increasing the throughput of molecular testing by supporting automated PCR methods, validated protocols for pooled testing, and optimised laboratory workflows; and (4) increasing the number and capacity of the laboratory workforce, including skill development to design and troubleshoot manual PCR testing protocols, and to understand validation and verification processes for new technologies. These various areas underscore persisting weaknesses in laboratory systems and networks. While maintaining its robust mobilisation against COVID-19, it is imperative that Africa develops a vision that reaches beyond an immediate reaction. The quick wins and low-hanging fruit strategies need to give way to deep-rooted approaches towards sustainable and resilient laboratory systems. First, countries need to institutionalise knowledge and resources, to routinely collect and analyse information on the capacity and functionality of national laboratory networks. This will fast-track the selection of facilities most amenable to repurposing or upgrading testing services; calculation of fastest routes for transporting sample or supplies; and reduction of geographical areas with unmet demand for health services. The LabMap project of the African Society of Laboratory Medicine and Africa CDC, collecting GIS information on laboratory network capacity, 7 and software such as LabEquip 8 and Supply Chain Guru from Llamasoft 9 are examples of resources that can support the quick, evidence-based remodelling, and optimisation of laboratory networks to respond to health emergencies. Second, countries must implement national laboratory quality management policies to ensure routine provision of quality-assured results at all tiers of the national laboratory network, beyond the sole accreditation of central-level laboratories. Finally, Africa must reduce its dependency on external expertise for diagnostics. Such a reduction requires options to reconfigure closed testing platforms to be made available, and expansion of Africa's domestic capacity for the production of high-quality diagnostics. Africa Centres for Disease Control and Prevention. Africa joint continental strategy for COVID-19 outbreak Africa Centres for Disease Control and Prevention. COVID-19 daily update Global Initiative on Sharing all Influenza Data Genomic epidemiology of novel coronavirus-Africa-focused subsampling FIND evaluation update: SARS-CoV-2 immunoassays Access to COVID-19 tools (act) accelerator ForLab laboratory quantification tool and LabEQIP software tool We declare no competing interests.