key: cord-0843327-6o3hydg6
authors: Odeyemi, Festus Ayotunde; Adekunle, Ibrahim Ayoade; Ogunbanjo, Olakitan Wahab; Folorunso, Jamiu Bello; Akinbolaji, Thompson; Olawoye, Idowu Bolade
title: Gauging the laboratory responses to coronavirus disease (COVID‐19) in Africa
date: 2020-08-27
journal: J Public Aff
DOI: 10.1002/pa.2280
sha: b824f1567bdd28d6716dd4bd1be182787281cbc4
doc_id: 843327
cord_uid: 6o3hydg6

The rampaging effect of coronavirus disease (COVID‐19) in Africa is huge and have impacted almost every area of life. Across African states, there exist variations in the laboratory measures adopted, and these heterogeneous approaches, in turn, determines the successes or otherwise recorded. In this study, we assessed the various forms of laboratory responses to the containment, risk analyses, structures and features of COVID‐19 in high incidence African countries (Nigeria, South Africa, Egypt, Ghana, Algeria, Morocco, etc.) to aid better and efficient laboratory responses to the highly infectious diseases.

The critical roles of laboratory testing cannot be overemphasised in the prevention and management of infectious diseases outbreak (Bedford et al., 2020) . Laboratory professionals play essential roles in diagnosis, epidemiologic surveillance and monitoring of patients with suspected and established cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is the virus strain that causes coronavirus disease (COVID-19; Lippi & Plebani, 2020) . The effort of the laboratory professionals and the country strategies in the containment, risk analysis, structures and features of the novel coronavirus deserves understudying for some reasons. For a disease condition that has been categorised as transmitting from human-tohuman, there is a greater need for quick detection and subsequent isolation in order to flatten the curve and reduce the strain on the medical facilities that are largely dilapidated in Africa. In other climes, clustering analysis is an essential pre-requisite to epidemic management and care surveillance aimed at the efficacy of treatment procedures. By identifying the cluster or group of society that are most vulnerable and susceptible to viral loads induced by contagion with pathogens from the virus, further care and treatment procedure can be established. In recent findings, O, rhesus D positive (+) individuals are reported to have more excellent antibodies to resist infestation of coronavirus. By assessing the laboratory response to Africa, this study aims to establish the depth of COVID-19 growth and subsequent policy recommendations, particularly as it relates to easing lockdown directives in place in most Africa countries. It informs the government and stakeholders restrictive measures and the desire to return to a healthy life.

COVID-19 is an infectious disease of the novel coronavirus. The COVID-19 pandemic is the third eventful zoonotic coronavirus disease outbreak in 20 years (Mackenzie & Smith, 2020) . (Poon & Peiris, 2020) . The current pandemic emerged in Wuhan, China and has spread rapidly around the world (Adnan, Khan, Kazmi, Bashir, & Siddique, 2020) with an estimated over 3 million cases globally with 259,474 deaths, above 1.6 million cases in Europe with around 152,179 deaths, over 634,000 cases in Asia with around 21,501 deaths (WHO, 2020a). 1 We observed heterogeneous approaches in the laboratory responses across nations in Africa. These variations in the laboratory responses of the containment of COVID-19 were primarily to aid early detection of the virus for prompt isolation, management of the infected individuals, and prevention of community transmission or sporadic cases of the virus (Loeffelholz & Tang, 2020) .

The laboratory response of this novel virus comprises of a collection of appropriate samples from patients who meet up with suspect case definitions (as contained in the WHO guidelines) and selection of accurate laboratory methods (WHO, 2020b). The SARS-CoV-2 has been detected from a multifarious of upper and lower respiratory sources, including throat, nasopharyngeal, sputum, and so on (WHO, 2020c) . A number of laboratory methods have been adopted in Africa for COVID-19 testing, and they include the Molecular test method of Nucleic Acid Amplification Tests (NAAT), Serological testing, and Viral Genome Sequencing (Abdullahi et al., 2020; Loeffelholz & Tang, 2020) . Amid these global health challenges which have caused panorama of problems in global medical supply chains, African countries have no options than to result to indigenous (herbal solutions) ways of combatting the pandemic, although in line with international practices. In this study, an attempt is made to unravel the underlying testing procedures adopted by high incidence African nations (Nigeria, South Africa, Egypt, Ghana, Morocco, Algeria) with attendant efficacy relative to their population density.

Policy measures, particularly alternative approaches that could induce greater efficiency in the laboratory reactions to the growth curve of COVID-19, are discussed in the study. In Figures 1 and 2 testing, which contained the laboratory techniques which are currently in use and the future ones they hope to adopt to increase access to testing (MLSCN, 2020) . Molecular method of reverse transcription polymerase chain reaction (RT-PCR) has been adopted as the gold standard for accurate testing of the pandemic in Nigeria with minimum sensitivity and specificity of 99% each (MLSCN, 2020) .

In the RT-PCR method, a reverse transcriptase approach was employed to convert the RNA template into a complementary DNA (cDNA) with subsequent use of the cDNA as a template for exponential amplification using PCR (Abdullahi et al., 2020; Udugama et al., 2020) . In the RT-PCR procedure, we confirm the existence of SARS-CoV-2 in a patient when the assay is positive. It should be noted that a laboratory outcome showing negative findings does not entirely rule out the presence of coronavirus in a patient (MLSCN, 2020) . By intuition, a negative laboratory finding premediated on a suspected patient implies that the viral density was well below the detection point. In other climes, an RT-PCR assay laboratory finding could show adverse outcomes if the infection has run its cause leading to viral clearance (MLSCN, 2020).

NCDC also developed a framework for incorporation of up to high throughput HIV molecular testing laboratories, which are capable of raising national capacity to a minimum of 5,000 tests per day (NCDC, 2020a) . 41 GeneXpert machines have also been slated for incorporation into the laboratory network with a capacity of further increasing national capacity to 7,000 tests per day (NCDC, 2020b). Serology testing helps to investigate the current pandemic and retrospective assessment of the extent of the outbreak. Nigeria's NCDC plan to look into the relevance of this antigen and antibody tests in the future to understand the rate of infectivity of the virus in the country. However, this method is subject to validation by the Medical Laboratory Science Council of Nigeria (MLSCN) before it can be deployed for routine testing in Nigeria (NCDC, 2020). MLSCN specifies that the sensitivity and specificity of this method of the assay must not be less than 95% with RT-PCR as a standard before approval can be given for its complimentary usage with other molecular methods (MLSCN, 2020). Nigeria's Laboratory capacity for COVID-19 testing is being worked on to carry out 2 million tests in the next 3 months by the utilisation of the maximum capacity of various laboratories within its network to improve the nation's undesirable testing coverage among countries with over 1,000 cases across Africa (NCDC, 2020a).

Confirmed cases of COVID-19 in South Africa stand at 8,895 with 178 mortalities as the time of writing (8th May 2020). A total of 307,752 tests has been done in all provinces of the country, but less than 1% of the South African population, which is over 57 million (Statistics South Africa, 2020), has been covered in COVID-19 testing (National Department of Health, 2020). Testing coordination for the novel coronavirus in South Africa is led by the National Health Laboratory Service (NHLS), which is the biggest diagnostic pathology service provider with roles of assisting the national and provincial health authorities in healthcare deliv- NHLS has 11 laboratories in nine provinces across South Africa designated for Coronavirus testing (NHLS, 2020). NHLS procured 67 mobile sampling and testing units which were deployed F I G U R E 1 African countries COVID-19 cases nationwide to join 180 testing sites and 320 testing units already in place across the country. NHLS is currently using the molecular method of RT-PCR for COVID testing across its network of regional laboratories and mobile testing sites. South Africa planned to deploy the mobile laboratories for rapid serological kits for population surveillance when they are available in the country (UN, 2020c) . National Institute of Communicable Diseases (NICD) partnered with the South African National Bioinformatics Institute at the University of Western Cape to publish a complete genome sequence of SARS-CoV-2 isolated from a South African patient with coronavirus disease 2019 who had returned to South Africa after travelling to Italy (Allam et al., 2020) . With this, South Africa is on the verge of increasing her current 5,000 tests for COVID-19 daily by six-folds (National Department of Health, 2020).

Egypt has recorded 8,478 COVID-19 laboratory-confirmed cases and (Hassany et al., 2020) . Egypt's laboratory network includes 17 laboratories with the plan to augment with another four and University hospital laboratories, which can increase national capacity to 200,000 in a total testing frame (WHO, 2020d).

Algeria has recorded 5,182 confirmed cases of COVID 19 cases with 483 deaths as of 8th May 2020 (WHO, 2020a) having conducted tests on 6,500 samples, which constitute 0.01% of the total population of over 42 million (UN, 2020a) . Laboratory response to COVID-19 management in Algeria is anchored by the Institut Pasteur Algeria (IPA). The Institut Pasteur Algeria (IPA) based out of capital Algiers was testing samples from across the country (WHO, 2020e). The Institut Pasteur Algeria (IPA) also invited hospital laboratories with the equipment to get involved in screening for the virus to meet the demand for more tests (Kezzal, 2020) . RT-PCR is the method of choice for testing for the SARS COV 2 virus in Institut Pasteur Algeria (IPA) Laboratory Network (Kezzal, 2020) . IPA laboratory network is being expanded to accommodate other annexes in Oran, Constantine and Ouargla, which is capable of increasing the testing capacity to 400 tests per day. testing with procurements of tens of thousands of Reverse transcription-polymerase chain reaction (RT-PCR) kits (Amuedo, 2020) .

Also, Moroccan health authorities are planning to diversify its laboratory expertise by adopting a more straightforward diagnostic techniques for more comprehensive national coverage and expansion of the COVID-19 laboratory network without the inclusion of private laboratories for the time being (Kasraoui, 2020) . Reverse transcriptionpolymerase chain reaction (RT-PCR) is the only method of analysis currently in use for COVID-19 testing in the country. Morocco is currently deploying all machinery to achieve 10,000 tests daily capacity to curb the spread of the virus in the Arab peninsula (Amuedo, 2020 Ghana has also adopted the pooled testing algorithm for the RT- Services, 2020). An effort is also in place to add 100 Regional and District Tuberculosis Gene Expert Laboratories, which will make each region have at least one testing centre for COVID-19 screening (Ghana News Agency, 2020).

Despite the rampaging nature of coronavirus disease across the world, laboratory responses in Africa's high incidence In Figure 3 , we reported the laboratory testing conducted in the six high incidence countries in Africa based on indices in Table 1 following.

The pictorial representation and the tabular information apparently reveals that in all high incidence countries in Africa, less than 1% of the total population has been tested. The implications of this are many, and the consequences are immense (Adekunle, Onanuga,

Akinola & Olakitan, 2020). A large number of the populace who could have been in contact with an infected person has not been detected.

Thus, scaling up the risk of community transmission that could eventually strain already dilapidated and inadequate health facilities in Africa. It remains to be seen what the dimension of COVID-19 spread could take in Africa in the coming days and months. We reported test per population in all African countries in Table 2 .

The authors give thanks to Almighty. 

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The authors declare no potential conflict of interest.

Festus Ayotunde Odeyemi: Conceived and designed the template for the study, wrote the paper. Ibrahim A. Adekunle: Proofread and reworked the draft manuscript and vet the final paper, wrote the paper. Olakitan Wahab Ogunbanjo: Provided the spatial density distribution, interpretations, wrote the paper. Jamiu Bello Folorunso, Thompson Akinbolaji and Idowu B. Olawoye: Contributed materials, data, analysis tools, wrote the paper.

The dataset(s) supporting the conclusions of this article is available in the