Implementation of Antibody Rapid Diagnostic Testing versus Real-Time Reverse Transcription-PCR Sample Pooling in the Screening of COVID-19: a Case of Different Testing Strategies in Africa

Improving testing capacity for COVID-19: experiences and lessons from Senegal, Uganda, Nigeria, and the Democratic Republic of Congo

Background

African countries leveraged testing capacities to enhance public health action in response to the COVID-19 pandemic. This paper describes experiences and lessons learned during the improvement of testing capacity throughout the COVID-19 response in Senegal, Uganda, Nigeria, and the Democratic Republic of the Congo (DRC).

Methods

The four countries' testing strategies were studied using a mixed-methods approach. Desk research on COVID-19 testing strategies was conducted and complemented by interviewing key informants. The findings were synthesized to demonstrate learning outcomes across the four countries.

Results

The four countries demonstrated severely limited testing capacities at the onset of the pandemic. These countries decentralized COVID-19 testing services by leveraging preexisting laboratory systems such as PCR and GeneXpert used for the diagnosis of tuberculosis (TB) to address this gap and the related inequities, engaging the private sector, establishing new laboratories, and using rapid diagnostic tests (RDTs) to expand testing capacity and reduce the turnaround time (TAT). The use of digital platforms improved the TAT. Testing supplies were sourced through partners, although access to global markets was challenging. Case detection remains suboptimal due to high costs, restrictive testing strategies, testing access challenges, and misinformation, which hinder the demand for testing. The TAT for PCR remained a challenge, while RDT use was underreported, although Senegal manufactured RDTs locally. Key findings indicate that regionally coordinated procurement and manufacturing mechanisms are required, that testing modalities must be simplified for improved access, and that the risk-based testing strategy limits comprehensive understanding of the disease burden.

Conclusion

Although testing capacities improved significantly during the pandemic, case detection and access to testing remained suboptimal. The four countries could benefit from further simplification of testing modalities and cost reduction. Local manufacturing and pooled procurement mechanisms for diagnostics are needed for optimal pandemic preparedness and response.

SARS-CoV-2 Testing Strategies in the Diagnosis and Management of COVID-19 Patients in Low-Income Countries: A Scoping Review

The accuracy of diagnostic laboratory tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can impact downstream clinical procedures in managing and controlling the outbreak of coronavirus disease 2019 (COVID-19). To assess the effectiveness of laboratory tools for managing COVID-19 patients in low-income countries (LICs), we systematically searched the PubMed, Embase, Scopus and CINHAL databases for reports published between January 2020 and June 2022. We found that 22 of 1303 articles reported the performance of various SARS-CoV-2 detection tools across 10 LICs. These tools were (1) real-time reverse transcriptase polymerase chain reaction (RT-PCR); (2) reverse transcription loop-mediated isothermal amplification (RT-LAMP); (3) rapid diagnostic tests (RDTs); (4) enzyme-linked immunosorbent assay (ELISA); and (5) dot-blot immunoassay. The detection of COVID-19 is largely divided into two main streams-direct virus (antigen) detection and serology (immunoglobulin)-based detection. Point-of-care testing using antigen-based RDTs is preferred in LICs because of cost effectiveness and simplicity in the test procedures. The nucleic acid amplification technology (RT-PCR and RT-LAMP) has the highest diagnostic performance among the available tests, but it is not broadly used in this context due to costs and shortage of facilities/trained staff. The serology-based test method is affected by antibody interferences and varying amounts of SARS-CoV-2 immunoglobulins expressed at different stages of disease onset. We further discuss the effectiveness and shortcomings of each of these tools in the diagnosis and management of COVID-19. Using the LICs as the study model, our findings highlight ways to improve the quality and turnaround time of COVID-19 testing in resource-constrained settings, notably through local/international collaborative efforts to refine the molecular-based or immunoassay-based testing technologies.

A systematic review of strategies adopted to scale up COVID-19 testing in low-, middle- and high-income countries

OBJECTIVE

We undertook a systematic review of strategies adopted to scale up COVID-19 testing in countries across income levels to identify successful approaches and facilitate learning.

METHODS

Scholarly articles in English from PubMed, Google scholar and Google search engine describing strategies used to increase COVID-19 testing in countries were reviewed. Deductive analysis to allocate relevant text from the reviewed publications/reports to the a priori themes was done.

MAIN RESULTS

The review covered 32 countries, including 11 high-income, 2 upper-middle-income, 13 lower-middle-income and 6 low-income countries. Most low- and middle-income countries (LMICs) increased the number of laboratories available for testing and deployed sample collection and shipment to the available laboratories. The high-income countries (HICs) that is, South Korea, Germany, Singapore and USA developed molecular diagnostics with accompanying regulatory and legislative framework adjustments to ensure the rapid development and use of the tests. HICs like South Korea leveraged existing manufacturing systems to develop tests, while the LMICs leveraged existing national disease control programmes (HIV, tuberculosis, malaria) to increase testing. Continent-wide, African Centres for Disease Control and Prevention-led collaborations increased testing across most African countries through building capacity by providing testing kits and training.

CONCLUSION

Strategies taken appear to reflect the existing systems or economies of scale that a particular country could leverage. LMICs, for example, drew on the infectious disease control programmes already in place to harness expertise and laboratory capacity for COVID-19 testing. There however might have been strategies adopted by other countries but were never published and thus did not appear anywhere in the searched databases.

The deuce-ace of Lassa Fever, Ebola virus disease and COVID-19 simultaneous infections and epidemics in West Africa: clinical and public health implications

Globally, the prevailing COVID-19 pandemic has caused unprecedented clinical and public health concerns with increasing morbidity and mortality. Unfortunately, the burden of COVID-19 in Africa has been further exacerbated by the simultaneous epidemics of Ebola virus disease (EVD) and Lassa Fever (LF) which has created a huge burden on African healthcare systems. As Africa struggles to contain the spread of the second (and third) waves of the COVID-19 pandemic, the number of reported cases of LF is also increasing, and recently, new outbreaks of EVD. Before the pandemic, many of Africa's frail healthcare systems were already overburdened due to resource limitations in staffing and infrastructure, and also, multiple endemic tropical diseases. However, the shared epidemiological and pathophysiological features of COVID-19, EVD and LF as well their simultaneous occurrence in Africa may result in misdiagnosis at the onset of infection, an increased possibility of co-infection, and rapid and silent community spread of the virus(es). Other challenges include high population mobility across porous borders, risk of human-to-animal transmission and reverse zoonotic spread, and other public health concerns. This review highlights some major clinical and public health challenges toward responses to the COVID-19 pandemic amidst the deuce-ace of recurrent LF and EVD epidemics in Africa. Applying the One Health approach in infectious disease surveillance and preparedness is essential in mitigating emerging and re-emerging (co-)epidemics in Africa and beyond.

Does the data tell the true story? A modelling assessment of early COVID-19 pandemic suppression and mitigation strategies in Ghana

This paper uses publicly available data and various statistical models to estimate the basic reproduction number (R0) and other disease parameters for Ghana's early COVID-19 pandemic outbreak. We also test the effectiveness of government imposition of public health measures to reduce the risk of transmission and impact of the pandemic, especially in the early phase. R0 is estimated from the statistical model as 3.21 using a 0.147 estimated growth rate [95% C.I.: 0.137-0.157] and a 15-day time to recovery after COVID-19 infection. This estimate of the initial R0 is consistent with others reported in the literature from other parts of Africa, China and Europe. Our results also indicate that COVID-19 transmission reduced consistently in Ghana after the imposition of public health interventions-such as border restrictions, intra-city movement, quarantine and isolation-during the first phase of the pandemic from March to May 2020. However, the time-dependent reproduction number (Rt) beyond mid-May 2020 does not represent the true situation, given that there was not a consistent testing regime in place. This is also confirmed by our Jack-knife bootstrap estimates which show that the positivity rate over-estimates the true incidence rate from mid-May 2020. Given concerns about virus mutations, delays in vaccination and a possible new wave of the pandemic, there is a need for systematic testing of a representative sample of the population to monitor the reproduction number. There is also an urgent need to increase the availability of testing for the general population to enable early detection, isolation and treatment of infected individuals to reduce progression to severe disease and mortality.

Supporting scale-up of COVID-19 RT-PCR testing processes with discrete event simulation

Testing is critical to mitigating the COVID-19 pandemic, but testing capacity has fallen short of the need in the United States and elsewhere, and long wait times have impeded rapid isolation of cases. Operational challenges such as supply problems and personnel shortages have led to these bottlenecks and inhibited the scale-up of testing to needed levels. This paper uses operational simulations to facilitate rapid scale-up of testing capacity during this public health emergency. Specifically, discrete event simulation models were developed to represent the RT-PCR testing process in a large University of Maryland testing center, which retrofitted high-throughput molecular testing capacity to meet pandemic demands in a partnership with the State of Maryland. The simulation models support analyses that identify process steps which create bottlenecks, and evaluate “what-if” scenarios for process changes that could expand testing capacity. This enables virtual experimentation to understand the trade-offs associated with different interventions that increase testing capacity, allowing the identification of solutions that have high leverage at a feasible and acceptable cost. For example, using a virucidal collection medium which enables safe discarding of swabs at the point of collection removed a time-consuming “deswabbing” step (a primary bottleneck in this laboratory) and nearly doubled the testing capacity. The models are also used to estimate the impact of demand variability on laboratory performance and the minimum equipment and personnel required to meet various target capacities, assisting in scale-up for any laboratories following the same process steps. In sum, the results demonstrate that by using simulation modeling of the operations of SARS-CoV-2 RT-PCR testing, preparedness planners are able to identify high-leverage process changes to increase testing capacity.

Humanitarian Surgical Missions in Times of COVID-19: Recommendations to Safely Return to a Sub-Saharan Africa Low-Resource Setting

Background

Since the declaration of the pandemic, humanitarian medicine has been discontinued. Until now, there have been no general recommendations on how humanitarian surgical missions should be organized.

Methods

Based on our experience in the field of humanitarian surgical missions to Sub-Saharan Africa, a panel of recommendations in times of COVID-19 was developed. The fields under study were as follows: (1) Planning of a multidisciplinary project; (2) Organization of the infrastructure; (3) Screening, management and treatment of SARS-COV-2; (4) Diagnostic tests for SARS-COV-2; (5) Surgical priorization and (6) Context of patients during health-care assistance. We applied a risk bias measurement to obtain a consensus among humanitarian health-care providers with experience in this field.

Results

A total of 94.36% of agreement were reached for the approval of the recommendations. Emergency surgery must be a priority, and elective surgery adapted. For emergency surgery, we established a priority level 1a (< 24 h) and 1b (< 72 h). For an elective procedure, according our American College of Surgeon adaptation score, process with more than 60 points should be reconsidered. Due to the low life expectancy in many African countries, we consider 45–50 years as age of risk. In case of SARS-COV-2 active infection or high clinical suspicion, the screening, management and treatment should be following the international guidelines adapted to duration of the stay, available infrastructure, size of the cooperation team and medical resources.

Conclusions

Humanitarian surgical mission in times of COVID-19 is a challenge that must extrapolate the established recommendations to the local cooperation environment.

Supplementary Information

The online version contains supplementary material available at (10.1007/s00268-021-06001-x).

Considerations for Group Testing: A Practical Approach for the Clinical Laboratory

Group testing, also known as pooled sample testing, was first proposed by Robert Dorfman in 1943. While sample pooling has been widely practiced in blood-banking, it is traditionally seen as anathema for clinical laboratories. However, the ongoing COVID-19 pandemic has re-ignited interest for group testing among clinical laboratories to mitigate supply shortages. We propose five criteria to assess the suitability of an analyte for pooled sample testing in general and outline a practical approach that a clinical laboratory may use to implement pooled testing for SARS-CoV-2 PCR testing. The five criteria we propose are: (1) the analyte concentrations in the diseased persons should be at least one order of magnitude (10 times) higher than in healthy persons; (2) sample dilution should not overly reduce clinical sensitivity; (3) the current prevalence must be sufficiently low for the number of samples pooled for the specific protocol; (4) there is no requirement for a fast turnaround time; and (5) there is an imperative need for resource rationing to maximise public health outcomes. The five key steps we suggest for a successful implementation are: (1) determination of when pooling takes place (pre-pre analytical, pre-analytical, analytical); (2) validation of the pooling protocol; (3) ensuring an adequate infrastructure and archival system; (4) configuration of the laboratory information system; and (5) staff training. While pool testing is not a panacea to overcome reagent shortage, it may allow broader access to testing but at the cost of reduction in sensitivity and increased turnaround time.