South Africa's coronavirus testing strategy is broken and not fit for purpose: It's time for a change.

Abstract

429 June 2020, Vol. 110, No. 6 The COVID-19 epidemic in South Africa (SA) is now in its exponential phase,[1] and the focus needs to be on mitigation of severe illness and death rather than aspiring to containment. Cases are increasing rapidly in many areas, most apparent in Western Cape Province, where the testing rate per capita exceeds all the other provinces, and testing is more targeted and focused on suspected ‘hotspot’ communities. The doubling time of mortality in the Cape Town metro is now 8 9 days,[2] and although the health system is better prepared as a result of the initial lockdown, major cracks are starting to show, causing a deterioration in clinical service that will threaten the country’s response to the epidemic if not stemmed. The Western Cape is only the forerunner, and urgent action needs to be taken now, to re-focus the testing platform. Diagnosis of COVID-19 relies on a reverse transcriptasepolymerase chain reaction (RT-PCR) test that is simple but laborious. The turnaround time (TAT) of the test, i.e. the time from the sample being taken to communication of the result, is influenced by the speed at which the sample reaches the laboratory, the laboratory’s capacity to run the test (access to reagents and test kits, number of analysis machines, availability of staff, errors leading to need for retesting), and the communication process for results. Although early reports by the National Health Laboratory Service (NHLS) CEO indicated that the NHLS would be able to test 36 000 per day by the end of April 2020,[3,4] this has not materialised. Reasons for this failure include factors internal to NHLS planning, as well as the realities that SA is dependent on foreign companies for testing materials and kits, for which there is a high demand globally, leading to serious shortages. Currently, the number of tests received exceeds all capacity of the centralised NHLS laboratories earmarked to do testing, and results are not being made available within 12 24 hours of sampling. In many parts of the country, including in the Western Cape, TAT has increased from <24 hours to 5 14 days[5] as a result of a number of failures in the pathway of tests getting to laboratories and overwhelming of the laboratory capacity. For instance, at Greenpoint Laboratory in Cape Town, which has capacity for 1 000 tests per day and is working 24/7, 10 000 untested samples from the community and hospitals were waiting to be tested as of 7 May (Dr M Hsiao, personal communication). Laboratory TAT is critical in determining success of both the community screening and testing (CST) programme and hospital management of cases. SA’s ambitious CST programme relies on identifying infected persons, isolating them, tracing their contacts, and isolating or quarantining them. This has the potential to slow the rate of transmission of the virus, especially if implemented effectively at an early stage of the outbreak. The house-to-housebased visiting strategy is unsustainable, however, and has limited potential to interrupt community transmission on multiple fronts. Foremost, a single household visit, while identifying or excluding the presence of a symptomatic case at a point in time, has limited value if such visits are not undertaken regularly (probably every 3 4 days), which is not realistic even in the short term. This is manifest in the fact that, despite up to 28 000 field workers having been mobilised to undertake screening at households, each field worker will on average need to take on the responsibility of screening >500 of the 14.5 million households in SA. In practical terms, each field worker is likely only to be able to undertake screening of ~30 households per day, so, repeat household visits will at best take place 6 weeks (rather than 3 4 days) later. Also, sustaining this sort of approach over what is expected to be at least 2 3 waves of outbreaks over the next 2 3 years is not feasible. The situation is compounded by 50 80% of individuals infected with SARS-CoV-2 being asymptomatic,[6] so they would not even be identified as needing testing. Nevertheless, identification of even only a quarter of infectious cases, coupled with adequate tracing of their contacts and ensuring isolation (of cases) and quarantine (for up to 14 days) of testnegative contacts, could assist in slowing the rate of (not preventing) community transmission of the virus and mitigate to some extent the anticipated surge in severe COVID-19 cases occurring over a very short period of time. By doing so, healthcare facilities may be somewhat better equipped to deal with the anticipated surge of COVID-19 cases in the current wave of the SARS-CoV-2 epidemic over the next 2 3 months in SA. However, for this CST strategy to be effective requires a clear line of sight in terms of efficiency of testing, isolation of cases as quickly as possible (within 12 24 hours of being tested), and effective and immediate tracing of their close contacts. An average person may have ~20 close contacts (defined as someone who spends more than 15 30 minutes within 1.5 m of the person) per day. Assuming that isolation occurs on day 3 after symptom onset, and close contacts occurred from at least 2 3 days before the onset of symptoms, for each case there would be ~120 close contacts to be followed up. For this strategy to assist with slowing the rate of spread of the virus, tracing (and physical contact for screening for symptoms) of ~80% of contacts is required.[7] Although possibly achievable in the initial phase of the epidemic during the attempt to contain community transmission, it becomes an unrealistic goal to aspire to when identifying 400 ‘new cases’ each day, as that would require tracking and physical tracing of ~80% of the 5 200 contacts. As the inevitable occurs and community transmission continues, even if at a lower rate, aspiring to achieve what was not attainable prior to the lockdown when cases were few and only ~20% of contacts were actually traced, would be setting up for failure in the context of addressing this goal of testing. This is exacerbated when there is a delay of 5 14 days in the TAT for delivery of results. In essence, identified cases are being placed into isolation (if based on when the test result becomes available) at a time point when they are no longer infectious.[8-10] Rather, considering the delay in TAT, the current ‘new’ cases reported in SA reflect cases that were probably sampled about a week ago. Although, if there is uniformity in rates of testing across different settings, this could be informative in geospatial mapping of the epidemic, the same could be achieved, and would be subject to less biases between settings, using rapid and less costly serology assays that have now been licensed in SA. However, this accepts that the strategy of actively searching for infectious cases is now likely to yield little value, and that there is acceptance that transmission will be ongoing (and will not be reversed by going back into a harsher lockdown). The focus should rather be getting public buy-in to adopting the non-pharmaceutical interventions of maintaining physical distancing, avoiding ‘mass gatherings’, meticulous performance of This open-access article is distributed under Creative Commons licence CC-BY-NC 4.0.