COVID-19: Are Africa’s diagnostic challenges blunting response effectiveness?

Since its emergence in Wuhan, China in December 2019, novel Coronavirus disease - 2019 (COVID-19) has rapidly spread worldwide, achieving pandemic status on 11 th March, 2020. As of 1 st April 2020, COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had infected over 800,000 people and caused over 40,000 deaths in 205 countries and territories. COVID-19 has had its heaviest toll on Europe, United States and China. As of 1 st of April 2020, the number of confirmed COVID-19 cases in Africa was relatively low, with the highest number registered by South Africa, which had reported 1,380 confirmed cases. On the same date (also the date of this review), Africa had reported 5,999 confirmed cases, of which 3,838 (almost 65%) occurred in South Africa, Algeria, Egypt, Morocco and Tunisia, with the remaining 2,071 cases distributed unevenly across the other African countries. We speculate that while African nations are currently experiencing much lower rates of COVID-19 relative to other continents, their significantly lower testing rates may grossly underestimate incidence rates. Failure to grasp the true picture may mean crucial windows of opportunity shut unutilized, while limited resources are not deployed to maximum effect. In the absence of extensive testing data, an overestimation of spread may lead to disproportionate measures being taken, causing avoidable strain on livelihoods and economies. Here, based on the African situation, we discuss COVID-19 diagnostic challenges and how they may blunt responses.


Emergence and global spread of SARS-CoV2
In December 2019, a spate of pneumonia cases of unknown cause was observed in Wuhan, Hubei province, China (He et al., 2020). Soon after, the causative agent for the novel illness was found to be a novel Coronavirus (2019-nCoV) (Lu et al., 2020;Zhou et al., 2020;Zhu et al., 2020). Coronaviruses (CoVs), are a large group of viruses that frequently cause mild respiratory disease in humans, including common cold (Saif, 2004;NIAID, 2020). Hundreds of coronaviruses exist in wild and domestic animals. In the last 20 years, 3 highly infectious CoVs have crossed from animals into humans through spillover events and spread globally, causing severe respiratory illnesses ( COVID-19 then rapidly spread within China, where it infected over 82,000 people and caused more than 3,000 fatalities, mainly in Hubei province (WHO, 2020b). The disease's spread accelerated globally, prompting the WHO to declare it a global pandemic on 11 th March 2020 (Bedford et al., 2020). As of 1 st April 2020, over 800,000 COVID-19 cases and more than 40,000 COVID-19-associated deaths had been confirmed in 205 countries and territories. Europe and North America are currently the continents most affected by COVID-19. So far, Africa has reported the lowest number of confirmed COVID-19 cases (WHO, 2020b). As of writing, 5,999 COVID-19 cases have been reported in Africa with South Africa reporting the highest number. 5 countries (South Africa, Tunisia, Morocco, Egypt, and Algeria) account for close to 65% (3,838 cases) of the confirmed cases, with the remainder being unevenly distributed in the rest of the continent. Within the East African community, there have been a total of 222 confirmed cases (African Arguments, 2020; WHO, 2020b).

SARS-CoV-2 transmission and pathogenesis
SARS-CoV2, is an enveloped single stranded positive sense RNA virus belonging to the family Coronaviridae and genus Betacoronavirus (Lai et al., 2020). The SARS-CoV-2 virion ranges between 50-200nm in diameter and houses a 29,881 bp genome (Chen et al., 2020a; Chen et al., 2020b). Among other genes, the SARS-CoV-2 genome encodes 4 structural proteins named spike (S), envelope (E), membrane (M) and nucleocapsid (N). The N protein holds the viral genome while S, M and E construct the viral envelope, where S mediates viral entry into the host cell (Wu et al., 2020). SARS-CoV-2 is easily transmissible. According to the WHO, the main mode of COVID-19 transmission is direct/indirect human-human contact, where the virus is transmitted in respiratory droplets or via contact routes. Droplet transmissions happen when one gets into close proximity, (typically within a meter) with an individual exhibiting respiratory symptoms, such as sneezing or coughing. Indirect transmission may occur when one touches objects handled by an infected individual and then touches their mouth, nose or eyes. Transmission has also been reported to occur via airborne droplet transmission. In such cases, the virus is contained in droplet nuclei, which are typically <5µm in diameter and can remain airborne for extended periods. Airborne transmission can occur over distances beyond 1 meter but such nuclei are typically generated by processes that generate aerosols, usually patient care procedures (WHO, 2020d). As such, social distancing, rigorous hand washing, and avoiding touching the face have been recommended as means of minimizing transmission risk (WHO, 2020a). Once SARS-CoV-2 has gained access to the host's respiratory mucosa, it enters the host cells through an interaction between its S protein and the host cell's ACE2 (angiotensin-converting enzyme 2) receptors (Hoffmann et al., 2020). Unlike other coronaviruses that cause upper respiratory tract disease only, SARS-CoV-2 is capable of colonizing the lower respiratory tract as well (Heymann & Shindo, 2020). After infection, the virus incubates for a median period of about 5 days before the onset of symptoms and almost all infections become symptomatic by day 11 (Lauer et al., 2020; Rothan & Byrareddy, 2020). Symptoms include fever, fatigue, headache, dry cough, diarrhea and lymphopenia. While most patients experience mild symptoms that they overcome without need for hospital care, some experience serious complications including severe pneumonia, acute respiratory distress syndrome (ARDS), acute cardiac injury and acute ground glass opacity (GGO) that may necessitate life support (Heymann & Shindo, 2020; Rothan & Byrareddy, 2020).

COVID-19 diagnostic testing
COVID-19 diagnostic testing is recommended for individuals that satisfy the suspect case definition (Leitmeyer et al., 2020). According to the WHO organization, the decision to test should be based on clinical signs, epidemiological factors and the possibility of infection (Leitmeyer et al., 2020), such as contact with an infected individual. The WHO (WHO, 2020c) defines a suspect case as one that: a) Shows symptoms of acute respiratory illness i.e. fever and at least one respiratory disease symptom e.g. coughing and shortness of breath, and has travelled or resided in an area with community COVID-19 transmission in the 14 days prior to symptoms onset; or, b) Shows acute symptoms of any respiratory illness and has been in contact with a confirmed or suspected case in the 14 days prior to the onset of symptoms; or, c) Shows symptoms of acute respiratory illness i.e. fever and at least one respiratory disease symptom e.g. coughing and shortness of breath and requires hospitalization in the absence of alternative diagnosis that fully accounts for the symptoms.
Suspected cases should then be validated by laboratory tests. This is routinely done by carrying out nucleic acid amplification tests (NAAT). Currently, RT-PCR detection of unique sequences of the viral genome is the gold standard for COVID-19 testing where the N, E, S and RdRP (RNA-dependent RNA polymerase) genes are targeted. Sample handling should be carried out in a BSL-2 biosafety cabinet under strict adherence to personal protective equipment (PPE) guidelines. However, RT-PCR is labor intensive, severely constraining the capacity for quick turnaround times from sample collection to results transmission. In many contexts, getting results takes days (NPR, 2020). As a consequence, laboratory testing of suspect cases is characterized by long wait periods and an exponential increase in demand for tests. To address this bottleneck, rapid diagnostic tests with turnaround times ranging between 10 and 30 minutes have been developed, even though most of these are currently undergoing clinical validation and therefore not in routine use (ECDC, 2020).

COVID-19 testing for surveillance and pandemic control
In addition to suspect case diagnosis, widespread COVID-19 testing is critical for disease monitoring and surveillance. Such testing is recommended so as to meet the following objectives (WHO, 2020c):  (Day, 2020). Mass testing has been suggested as a means to quickly stop the COVID-19 epidemic in the UK (Peto, 2020) and delayed roll out of large-scale testing is considered to have blinded the US to its worsening COVID-19 situation (Cohen, 2020; New York Times, 2020). In Germany, large-scale testing has been credited for limiting disease spread and the low fatality rate reported by Germany relative to its neighbors (Financial Times, 2020a). While many countries are ramping up surveillance testing, there are no guidelines for large-scale testing and decisions are based on individual countries' assessments.

Surmounting COVID-19 diagnostic challenges
COVID-19 diagnostic challenges are not unique to African countries and LMICs. Consequently, numerous private and public institutions have developed rapid diagnostic tests (RDTs) aimed at speeding and expanding testing, crucial factors in the struggle to slow COVID-19 spread. RDTs, which are largely based on immunoassays, may be direct, through detection of SARS-CoV-2 antigens or indirect, through detection of anti-SARS-CoV-2 antibodies (ECDC, 2020). Advantages of RDTs include ease of use as they do not require special equipment or highly trained personnel and stability at room temperature, removing the need for constant refrigeration/freezing. RDTs are therefore highly suited for point of care diagnosis (POCD) and are highly amenable to deployment in low resource settings, removing the need for sample transportation. Several COVID-19 RDTs, capable of giving results in 10-30 minutes are now commercially available or in development (ECDC, 2020). In many African contexts, RDTs would reduce the time needed to get test results from days to minutes. Therefore, RDTs offer a means to aggressively deploy mass testing across Africa. However, the cost of RDTs for mass testing may still be prohibitively high, calling for homegrown solutions.
The COVID-19 diagnostic challenges faced by African nations highlight long-running diagnostic challenges for a wide range of diseases. Part of our group's research has been the development of RDTs and POCDs for various diseases, including placental malaria and bacterial infections. We contend that an effective means of achieving mass testing at the required scale, is to fund the development COVID-19 RDTs locally, to meet local demand -bearing in mind that the knowledge and relevant local and international collaborations are already in place. Such solutions should then be aggressively deployed for points of care and home use, particularly in rural settings. In fact, this strategy is being used by Senegal, which together with UK collaborators, is developing an affordable COVID-19 RDT (expected to cost $1 per test) for home use in African countries (Financial Times, 2020b). Similar approaches by other African countries would provide local solutions to the continent's test needs while supporting Africa's research and innovation.

COVID-19 point of care testing strategies
Evidently, COVID-19 testing by RT-PCR is not applicable in most parts of Africa considering that vast populations live in rural settings with poor transport and communication infrastructure. RT-PCR requires expensive equipment, skilled personnel, reagents and reliable power supplies. Additionally, the long turnaround time of 4-24 hours (and days in some contexts) (NPR, 2020), may discourage many from seeking tests. Different strategies exist for point of care testing, all with inherent merits and demerits: 1) Use of antibody testing. As the body mounts an immune response, antibodies against SARS-CoV-2 antigens are generated. These antibodies may serve as indicators of infection. However, since detectable antibodies may lag behind the appearance of clinical symptoms, most infections will be missed, causing a high rate of false negatives. Conversely, persistence of antibodies after virus elimination from the body may result in a high rate of false positives. Moreover, a high cross reactivity of SARS-CoV-2 and SARS-CoV S protein against plasma samples from 15 patients has been observed, which may impact test interpretation (Lv et al., 2020). However, in spite of these drawbacks, antibody tests will still be useful in community surveillance of exposed populations and this information will be useful in determining the extent of 'herd' immunity and guide tailored public health interventions. Other near point of care tests include radiological imaging with Chest CT-scan. This approach has been shown to be highly sensitive (at 97%) but poorly specific (at 48%) in a Chinese study (Ai et al., 2020). CT-Scan, unlike RT-PCR enables shorter result times especially when coupled with artificial intelligence (AI) enabled image analysis and interpretation. But this technology is highly limited to higher level hospitals in most African countries, with very low numbers of radiologists and poor adoption of AI. This technology may not be sufficient in addressing the COVID-19 diagnosis challenges in Africa.
Given these considerations, it is clear that the current gold standard tools, RT-PCR and radiological imaging, cannot adequately meet Africa's COVID-19 diagnosis challenges in the low resource settings that characterize most hospitals in sub-Saharan Africa. Indeed, as the pandemic situation evolves with control goals focusing on both containment and mitigation (Parodi & Liu, 2020; WHO, 2020f), capacity for large-scale diagnosis at most if not all levels of health care systems will be vital for sustainable control. Crucially, as treatment solutions for the disease become available, prompt diagnosis will be essential in ensuring prompt treatment and determining isolation/quarantine decisions.

Conclusion
COVID-19 has severely tested the adequacy of global diagnostic preparedness and ability to rapidly develop point of care tests for emerging infections. The prompt release of SARS-Cov-2 whole genomic sequence data by Chinese scientists helped with development of RT-PCR protocols that have been used worldwide. However, as the pandemic evolves, it is increasingly important to develop point of care tests that will facilitate proper last mile epidemiology, inform treatment and public health interventions. These POC tests will leverage available molecular platforms such as CRISPR, or be based on antigen or antibody detection. Critically, it should be understood that these strategies have inherent merits and demerits and synergy will only be achieved where all are used appropriately. Additionally, the COVID-19 pandemic has highlighted the need for development and growth of in-continent POC diagnostics development capacity ranging from assay development, device fabrication, prototyping, validation, implementation research and entrepreneurial ecosystems including venture capitalization and regulation.

Data availability
Underlying data No data are associated with this article.