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COVID-19: Test me if you can

OpenNiqash
May 4 · 10 min read

Authors: Dr. Jaber Belkhiria , Dr. Zied Bouslama, Dr. Amine Ghrabi, and Dr. Oussama Zekri

About OpenNiqash

(Version française )

unisia’s response to its COVID-19 epidemic is continuously adjusted to the contextual epidemiological changes. More recently, the virus progressed within the larger Tunisian population and became autochthonous. It is now harder to detect the disease, particularly among silent spreaders, as they showcase little to no symptoms. In consequence, testing became the only available window to acquire clarity on the epidemic dynamics.

As of 1st May 2020, Tunisia has conducted a total of 23,526 tests (1,991 tests per million), more than any other country in North Africa. The government is planning a future scale-up of its testing capabilities while contemplating the use of rapid testing methods for a broader identification of cases.

To this end, Tunisian health policymakers are faced with the daunting task of tailoring the country’s testing strategy to the current and future needs. Various options are being eyed to detect infective individuals; each has advantages and shortcomings. This is exactly why extensive knowledge about testing methods becomes crucial in designing and implementing the strategy that suits the Tunisian epidemiological context best.

Ultimately, would scaling-up rapid testing effectively help ease the current restrictive measures?

Current testing strategy in Tunisia

Once a suspect case is identified, a swab sample is taken from the patient’s nostrils. This nasopharyngeal swab is placed in a tube and sent to a reference laboratory. Sample collection and shipment has been managed in coordination between the Health Emergency Medical Service (SAMU), hospitals, and healthcare authorities.

The World Health Organization (WHO) recommends a COVID-19 diagnosis that detects the SARS-CoV-2’s genetic information (RNA). The real-time RT-PCR (RT-qPCR) test is considered a gold standard. However, this test is complex and requires multiple reagents, a specific laboratory (BSL-2 security level), and highly skilled technologists; not necessarily available in low-resource settings.

The process starts by inactivating the virus and releasing its RNA molecule. Once the RNA is purified, the proper Polymerase Chain Reaction (PCR) begins. Laboratory technicians carefully mix specific chemicals with each sample and run those combinations in a laboratory machine (thermal cycler). The subsequent analysis determines if the sample is positive or negative. As of now, It takes 24 to 48 hours from sampling to issuing a final RT-qPCR test result. This timespan depends on the number of queued samples, shipping, and testing durations, as well as the laboratory’s infrastructure and human resources capacities.

At the early stages of the epidemic, the microbiology laboratory at Charles Nicolle University Hospital in Tunis served as the national reference laboratory for COVID-19 diagnosis. However, the rapid increase in suspects and their contacts led to a higher need for testing. Consequently, four additional laboratories started to conduct the same procedure in Tunis (Institut Pasteur de Tunis), Sousse (Farhat Hached University Hospital), Monastir (Fattouma Bourguiba University Hospital), and Sfax (Habib Bourguiba University Hospital). Additionally, the Military Hospital of Instruction of Tunis has been mainly involved in the testing of the armed forces’ personnel and their dependents. On 15 April 2020, a military mobile laboratory started to be deployed for temporary missions to serve the country’s southern region.


Two critical factors challenge the use of RT-qPCR test:

RT-qPCR is slow: it takes at least one day to get a result. Having more laboratories across the country, with more advanced material, such as “rapid real-time automated PCR”, would significantly accelerate the process while reducing human errors.

RT-qPCR requires strict laboratory criteria, supplies, and equipment: Some reagents can be produced locally; however, most need to be imported. Additionally, specimen handling for molecular testing needs to be performed in BSL-2 facilities.

The high cost associated with the ad-hoc training of personnel and the purchase of high-end equipment, along with the time required to confirm results hinder the government’s reliance on RT-qPCRs. This is why Tunisian decision-makers are looking at cheaper and faster rapid testing methods as a potential alternative.


Rapid testing as a complementary diagnosis tool

Rapid testing for SARS-CoV-2 would theoretically provide the advantage of a faster result delivery compared to RT-qPCR. In fact, antigen and antibody rapid tests do not require extensive laboratory expertise and can offer results in a maximum of 20 minutes.

Antigen rapid test: directly detects the presence of SARS-CoV-2. The needed nasopharyngeal swabs, for instance, might contain a live virus. For this reason, antigen rapid tests must be performed in a BSL-2 laboratory with proper Personal Protective Equipment (PPE) in place.

Antibody rapid test: detects an immune response specific to SARS-CoV-2 (i.e., IgM and/or IgG antibodies). Early studies suggest that the production of IgM and IgG in COVID-19 patients typically occurs between 7 and 11 days after the onset of symptoms, with IgM antibodies appearing first followed by IgGs. The test requires a blood sample collection following a strict sampling protocol. However, this test can safely be performed at a point of care and does not require a BSL-2 laboratory.

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Figure 1: Different COVID-19 clinical courses and trajectories of adaptive immune response and viral shedding. (Adapted from Matricardi et al., 2020)

Both tests serve different roles and could be used in different scenarios. The rapid antigen can be used to test suspect cases, whereas rapid antibody is used to screen for previous viral exposure within target populations such as healthcare workers. One could think that the combination of these two rapid testing methods is an efficient alternative to RT-qPCR. However, there are variances in the ability of these rapid tests to provide an accurate result. Two critical parameters can assess test accuracy:

Sensitivity: measures the proportion of actual positives that are correctly identified as such (true positive rate). For example, if we have 100 infectives (that tested positive to RT-qPCR) and test them with a 90% sensitivity rapid test, only 90 of them will test positive. Those are “True-Positives”. The remaining 10 infectives will wrongly test negative.

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Figure 2: Results from testing 10 COVID-19 sick (PCR positive) individuals by a 90% sensitivity rapid test — by Nadhir Bouslama

Specificity: measures the proportion of actual negatives that are correctly identified as such (true negative rate). For example, if we have 100 non-infectives (that tested negative to RT-qPCR) and test them with a 90% specificity rapid test, only 90 of them will test negative. Those are called “true negatives.” The remaining 10 non-infectives will wrongly test positive.

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Figure 3: Results from testing 10 healthy (PCR negative) individuals by a 90% specificity rapid test — by Nadhir Bouslama

Minimizing test errors is key to efficiently control the epidemic by avoiding the release of still-infective individuals or prolonging restrictive measures for non-infective populations. Below are four mitigation plans to reduce false-positives and/or false-negatives:

  • Choosing a highly sensitive and highly specific test: ideally, a test would be 100% sensitive and 100% specific. Unfortunately, there is no such test and both sensitivity and specificity should be considered carefully. It is essential to acknowledge that manufacturers’ assessments are based on small size samples, not considering demographic and geographic diversity. These estimations do not provide a full picture of test performances.
  • Using the appropriate test for each epidemiological scenario: the prevalence of the disease can influence a test’s predictive values. This implies that if we test in a high prevalence setting (i.e., high-risk groups), it is more likely that individuals who test positive, genuinely have the disease, compared to when the test is applied to a low prevalence setting (i.e. general population).
  • Cross-checking test results with complementary methods: confirming a diagnosis might require more than one test in some specific circumstances. For instance, given the low sensitivity of antigen rapid tests, all negative results must be confirmed by the gold standard method.
  • Collecting and shipping samples properly: sampling at the right time is important given variabilities in viral shedding and production of antibodies. Besides, it is essential to respect shipping requirements to avoid altering the sample.

Future testing steps in Tunisia

On 28 March 2020, the Central Pharmacy of Tunisia (PCT) opened a tender for the purchase of 400,000 COVID-19 rapid tests with immediate delivery, aiming to increase the country’s testing capacity. This total number was evenly distributed between antigen and antibody rapid tests.

At this point, rapid tests’ performances must be accounted for when evaluating proposals to state clients. Knowledge about these tests, however, is scarce and information provided by manufacturers is not foolproof because of their novelty. Several state clients ended up with non-operational kits due to a poor triaging of bidders’ proposals. Even when assuming test selection is optimal, public health authorities need to ensure proper protocols are established and adequate training of personnel is conducted. These are safeguards against manipulation errors.

The current Tunisian testing strategy outlined how to combine both standard and rapid testing methods when responding to the epidemic. Rapid tests are not meant to replace RT-qPCR. Antigen rapid tests will serve as a first-intention diagnosis among COVID-19 suspect cases or for populations at risk in order to identify clusters. Yet, all negative samples from antigen rapid tests must be coupled with an RT-qPCR for confirmation, given their low sensitivity. Antibody rapid tests, on the other hand, will be used in epidemiological investigations to help better understand the spread of the disease in a given population. Pilots have already been implemented in four districts Hrairia (Tunis), Dar Fadhal (Ariana), Hammam-Lif (Ben Arous), and Manouba Ville (Manouba) to estimate the prevalence of the disease in the Greater Tunis area.

The strategy also stated general guidelines about laboratory biosafety requirements where antigen rapid tests, as well as PCR tests (real-time automated and rapid real-time automated), are all restricted to laboratories that meet BSL-2 criteria. However, it is not clear how these biosafety requirements will be implemented and monitored.

Given the ambiguity around the biosafety accreditation process, private laboratory lobbyists pushed for the inclusion of private testing facilities in the current national strategy. If testing is expanded to private laboratories, questions related to biosafety, access, and cost should be raised. Equitable access to testing when needed should be paramount. Eventually, positive cases confirmed in the private sector need to be included in the existing patient referral pathways.

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Health officials have been vocal about using rapid testing methods as the quick-fix to enhance the country’s testing capacity. This is realistic if appropriately implemented.

The diagnostic has to be reliable so as to raise confidence levels about test accuracy. At the moment, the available rapid tests come with varying performances that require relying on different test combinations. Besides, taking into account the current limited resources, testing is approved only when a specific definition of a suspect case is met, then performed at a designated laboratory. A strict application of case definitions and appropriate indications for each testing method is crucial to ensure COVID-19 quality diagnosis. Nevertheless, the definition of a suspect case must remain on par with the latest available information about the distribution of COVID-19 cases in the general population and advances in testing technologies. Results should still be interpreted with caution. Using rapid testing will potentially lead to more dependence on PCRs to confirm some results. Thus, Tunisia’s testing capacity threshold can be overwhelmed, which in turn raises concern about the ability to access testing services.

In fact, Tunisian laboratories have finite capacities. Even when available, public BSL-2 laboratories are unevenly distributed geographically, which defeats the time-benefit sought from the use of some rapid testing methods that also depend on such institutions (i.e., antigen rapid test). As authorities expand testing capacities, national accreditation agencies should enforce biosafety guidelines on all potential institutions that might be able to join the current national testing efforts. Finally, equitable access to quality testing must be ensured regardless of their ability to pay.

It is important to mention that the global scarcity of supplies, indispensable to sustain laboratory testing, is pushing nations to compete. Tunisia is no exception, and the active involvement of Tunisia’s economic diplomacy in the future short term is required. In the near-future, ad hoc training of personnel will also be key to sustainability; to prepare the human resources needed to fight the current wave and beyond. In the long run, the state budget allocated to research activities and hiring for highly specialized laboratory positions should be revised.

Proper testing remains the cornerstone of transition plans from the current lockdown arrangements. The Tunisian response to COVID-19 has been elaborated by a scientific committee mainly composed of medical doctors. Scientifically sound instructions on sampling, testing, contact tracing, and treatment have been provided over several scattered guidance documents. However, the response heavily relies on the population’s full compliance to succeed. In order to gain the trust needed to comply, the government response framework should be inclusive of communities and guided by a participatory approach. To date, this has not been the case, as the population still lags behind the government decisions to control the epidemic. In other words, the adopted approach is exclusively biomedical, dismissing ecological and social factors that influence the behavior of individuals. Experts in social science and socio-ecological determinants of health might help the current scientific committee to efficiently implement more contextually relevant interventions.

So far, failure to meet rapid testing targets and mediatization of test manipulation errors have been the source of much public frustration and confusion. Gradually easing down the lockdown will require a collective effort. This means a certain loss of personal liberties for the greater public benefit. It is thus essential that health officials demonstrate trustworthiness and give a reason for people to further cooperate.

On 4 May 2020, the country gradually reopened. Future decisions to relax or further enforce current restrictive measures imposed on the population should recognize the country’s ability to test proactively. Efforts to control the spread of the virus through testing services need to be sustained. It will also require reliance on surveillance through the use of data collection and reporting technologies to inform future decisions.

Policymaking in uncertain times is difficult. For this reason, lifting the current veil of ignorance must be pursued using the best available scientific tools. A real-time and comprehensive collection of data can provide clarity in times of crisis to inform and shape policies. Furthermore, the scientific basis on which the official testing strategy is built should be subject to challenge. It needs to be open to analysis, evaluation, and critique.

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