Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Strategies for Increasing the Throughput of Genetic Screening: Lessons Learned from the COVID-19 Pandemic within a University Community

Amidst the COVID-19 pandemic, the Polytechnic University of Setúbal (IPS) used its expertise in molecular genetics to establish a COVID-19 laboratory, addressing the demand for community-wide testing. Following standard protocols, the IPS COVID Lab received national accreditation in October 2020 and was registered in February 2021. With the emergence of new SARS-CoV-2 variants and safety concerns for students and staff, the lab was further challenged to develop rapid and sensitive diagnostic technologies. Methodologies such as sample-pooling extraction and multiplex protocols were developed to enhance testing efficiency without compromising accuracy. Through Real-Time Reverse Transcription Polymerase Chain Reaction (RT-qPCR) analysis, the effectiveness of sample pooling was validated, proving to be a clear success in COVID-19 screening. Regarding multiplex analysis, the IPS COVID Lab developed an in-house protocol, achieving a sensitivity comparable to that of standard methods while reducing operational time and reagent consumption. This approach, requiring only two wells of a PCR plate (instead of three for samples), presents a more efficient alternative for future testing scenarios, increasing its throughput and testing capacity while upholding accuracy standards. The lessons learned during the SARS-CoV-2 pandemic provide added value for future pandemic situations.

ADSP: An adaptive sample pooling strategy for diagnostic testing

BACKGROUND

We often must conduct diagnostic tests on a massive volume of samples within a limited time during outbreaks of infectious diseases (e.g., COVID-19,screening) or repeat many times routinely (e.g., regular and massive screening for plant virus infections in farms). These tests aim to obtain the diagnostic result of all samples within a limited time. In such scenarios, the limitation of testing resources and human labor drives the need to pool individual samples and test them together to improve testing efficiency. When a pool is positive, further testing is required to identify the affected individuals; whereas when a pool is negative, we conclude all individuals in the pool are negative. How one splits the samples into pools is a critical factor affecting testing efficiency.

OBJECTIVE

We aim to find the optimal strategy that adaptively guides users on optimally splitting the sample cohort into test-pools.

METHODS

We developed an algorithm that minimizes the expected number of tests needed to obtain the diagnostic results of all samples. Our algorithm dynamically updates the critical information according to the result of the most recent test and calculates the optimal pool size for the next test. We implemented our novel adaptive sample pooling strategy into a web-based application, ADSP (https://ADSP.uvic.ca). ADSP interactively guides users on how many samples to be pooled for the current test, asks users to report the test result back and uses it to update the best strategy on how many samples to be pooled for the next test.

RESULTS

We compared ADSP with other popular pooling methods in simulation studies, and found that ADSP requires fewer tests to diagnose a cohort and is more robust to the inaccurate initial estimate of the test cohort's disease prevalence.

CONCLUSION

Our web-based application can help researchers decide how to pool their samples for grouped diagnostic tests. It improves test efficiency when grouped tests are conducted.

Epidemiological analysis of coronavirus disease (COVID-19) patients on ships arriving at Busan port in Korea, 2020

Quarantine played an important role in preventing the spread of infectious diseases between countries in the early stages of the COVID-19 outbreak. In particular, in ports, infection during transit can cause a large number of patients on board ships and can flow into the community. In this study investigated cause of the cause of transmission in ships and suggested the way of preventing secondary transmission by analyzing clinical and epidemiological characteristics of COVID-19 patients identified at Busan Port (South Korea) in 2020. During the study period, out of 19,396 ships that arrived at Busan Port, 50 ships had COVID-19 confirmed cases. Among the 50 ships, type of deep-sea fishing vessels (24 ships, 48.0%), ships weighing less than 5,000 tons (31 ships, 62.0%), and ships from Russia (41 ships, 82.0%) had the highest positivity rates. Total 283 of the 25,450 arrivals tested positive for COVID-19 (a positivity rate of 1.1%), and 270 (95.4%) were asymptomatic. Moreover, the number of COVID-19 patients increased with the duration of the waiting period between arrival and sample collection (12.7% to 37.4%), and the positivity rate was significantly higher for those working as stewards (64.3%). These results indicate secondary transmission was active on board ships and that infection among stewards importantly contributed to group outbreaks. In addition, onboard residence time after arrival significantly elevated to COVID-19 positivity rates, indicating that rapid isolation, as determined using various screening techniques, might be effective at preventing onboard transmission and subsequent community outbreaks.

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.

Optimizing SARS-CoV-2 Pooled Testing Strategies Through Differentiated Pooling for Distinct Groups

Pooled testing has been successfully used to expand SARS-CoV-2 testing, especially in settings requiring high volumes of screening of lower-risk individuals, but efficiency of pooling declines as prevalence rises. We propose a differentiated pooling strategy that independently optimizes pool sizes for distinct groups with different probabilities of infection to further improve the efficiency of pooled testing. We compared the efficiency (results obtained per test kit used) of the differentiated strategy with a traditional pooling strategy in which all samples are processed using uniform pool sizes under a range of scenarios. For most scenarios, differentiated pooling is more efficient than traditional pooling. In scenarios examined here, an improvement in efficiency of up to 3.94 results per test kit could be obtained through differentiated versus traditional pooling, with more likely scenarios resulting in 0.12 to 0.61 additional results per kit. Under circumstances similar to those observed in a university setting, implementation of our strategy could result in an improvement in efficiency between 0.03 to 3.21 results per test kit. Our results can help identify settings, such as universities and workplaces, where differentiated pooling can conserve critical testing resources.

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

Background

Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic.

Methods

Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis.

Results

During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity.

Conclusions

Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission.

Funding

This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.

Maintaining laboratory quality assurance and safety in a pandemic: Experiences from the KEMRI-Wellcome Trust Research Programme laboratory’s COVID-19 response

Laboratory diagnosis plays a critical role in the containment of a pandemic. Strong laboratory quality management systems (QMS) are essential for laboratory diagnostic services. However, low laboratory capacities in resource-limited countries has made the maintenance of laboratory quality assurance, especially during a pandemic, a daunting task. In this paper, we describe our experience of how we went about providing diagnostic testing services for SARS-CoV-2 through laboratory reorganization, redefining of the laboratory workflow, and training and development of COVID-19 documented procedures, all while maintaining the quality assurance processes during the COVID-19 pandemic at the Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme (KWTRP) laboratory. The KWTRP laboratory managed to respond to the COVID-19 outbreak in Kenya by providing diagnostic testing for the coastal region of the country, while maintaining its research standard quality assurance processes. A COVID-19 team comprising of seven sub-teams with assigned specific responsibilities and an organizational chart with established reporting lines were developed. Additionally, a total of four training sessions were conducted for county Rapid Response Teams (RRTs) and laboratory personnel. A total of 11 documented procedures were developed to support the COVID-19 testing processes, with three for the pre-analytical phases, seven for the analytical phase, and one for the post-analytical phase. With the workflow re-organization, the development of appropriate standard operating procedures, and training, research laboratories can effectively respond to pandemic outbreaks while maintaining research standard QMS procedures.

Assessment of performance and implementation characteristics of rapid point of care SARS-CoV-2 antigen testing

Background: The COVID-19 pandemic has resulted in a need for rapid identification of infectious cases. Testing barriers have prohibited adequate screening for SARS-CoV-2, resulting in significant delays in commencement of treatment and outbreak control measures. This study aimed to generate evidence on the performance and implementation characteristics of the BD Veritor™ Plus System rapid antigen test as compared to reverse transcription polymerase chain reaction (RT-PCR) for diagnosis of SARS-CoV-2 in Kenya. Methods: This was a field test performance evaluation in adults undergoing testing for SARS-CoV-2. Recruited participants were classified as SARS-CoV-2-positive based on RT-PCR carried out on nasopharyngeal swabs. Antigen tests were performed with simultaneous RT-PCR on 272 participants, allowing estimation of sensitivity, specificity, positive and negative predictive values for the rapid antigen test. Implementation characteristics were assessed. Results: We enrolled 97 PCR negative symptomatic and 128 PCR negative asymptomatic, and 28 PCR positive symptomatic and 19 PCR positive asymptomatic participants. Compared to RT-PCR, the sensitivity of the rapid antigen test was 94% (95% confidence interval [CI] 86.6 to 100.0) while the specificity was 98% (95% CI 96 to 100). There was no association between sensitivity and symptom status, or between the cycle threshold value and sensitivity of the BD Veritor. The rapid test had a quick turnaround time, required minimal resources, and laboratory personnel conducting testing found it easier to use than RT-PCR. The relatively high sensitivity of BD Veritor may be partially attributed to shortages of RT-PCR testing materials, resulting in specimen analysis delays and potential degradation of viral genetic material. Therefore, in resource-constrained settings, rapid antigen tests may perform better than the reference RT-PCR, resulting in prompt institution of isolation and treatment measures.  Conclusion: The BD Veritor rapid antigen test’s high sensitivity should be interpreted with consideration to the challenges occasioned by RT-PCR testing in resource-constrained settings.

Maintaining laboratory quality assurance and safety in a pandemic: Experiences from the KEMRI-Wellcome Trust Research Programme laboratory’s COVID-19 response

Laboratory diagnosis plays a critical role in the containment of a pandemic. Strong laboratory quality management systems (QMS) are essential for laboratory diagnostic services. However, low laboratory capacities in resource-limited countries has made the maintenance of laboratory quality assurance, especially during a pandemic, a daunting task. In this paper, we describe our experience of how we went about providing diagnostic testing services for SARS-CoV-2 through laboratory reorganization, redefining of the laboratory workflow, and training and development of COVID-19 documented procedures, all while maintaining the quality assurance processes during the COVID-19 pandemic at the Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme (KWTRP) laboratory. The KWTRP laboratory managed to respond to the COVID-19 outbreak in Kenya by providing diagnostic testing for the coastal region of the country, while maintaining its research standard quality assurance processes. A COVID-19 team comprising of seven sub-teams with assigned specific responsibilities and an organizational chart with established reporting lines were developed. Additionally, a total of four training sessions were conducted for county Rapid Response Teams (RRTs) and laboratory personnel. A total of 11 documented procedures were developed to support the COVID-19 testing processes, with three for the pre-analytical phases, seven for the analytical phase, and one for the post-analytical phase. With the workflow re-organization, the development of appropriate standard operating procedures, and training, research laboratories can effectively respond to pandemic outbreaks while maintaining research standard QMS procedures.

Evaluation of pooling of samples for testing SARS-CoV- 2 for mass screening of COVID-19

BACKGROUND

The current pandemic of the SARS-CoV-2 virus, widely known as COVID-19, has affected millions of people around the world. The World Health Organization (WHO) has recommended vigorous testing to differentiate SARS-CoV-2 from other respiratory infections to aid in guiding appropriate care and management. Situations like this have demanded robust testing strategies and pooled testing of samples for SARS-CoV-2 virus has provided the solution to mass screening of people for COVID-19. A pooled testing strategy can be very effective in testing when resources are limited, yet it comes with its own limitations. These benefits and limitations need critical consideration when it comes to testing highly infectious diseases like COVID-19.

METHODS

This study evaluated the pooled testing of nasopharyngeal swabs for SARS-COV-2 by comparing the sensitivity of individual sample testing with 4-and 8-pool sample testing. Median cycle threshold (Ct) values were compared, and the precision of pooled testing was assessed through an inter- and intra-assay of pooled samples. Coefficient of variance was calculated for inter- and intra-assay variability.

RESULTS

The sensitivity becomes considerably lower when the samples are pooled. There is a high percentage of false negative reports with larger sample pool size and when the patient viral load is low or weak positive samples. High variability was seen in the intra- and inter-assay, especially among weak positive samples and when more number of samples are pooled together.

CONCLUSION

As COVID - 19 infection numbers and need for testing remain high, we must meticulously evaluate the testing strategy for each country depending on its testing capacity, infrastructure, economic strength, and need to determine the optimal balance on the cost-effective strategy of resource saving and risk/ cost of missing positive patients.

Gichuki B, Njuguna S, Riako D, Mutua S, Gitonga JN, Sein Y, Bartilol B, Mwangi SJ, O. Omuoyo D, M. Morobe J, de Laurent ZR, Bejon P, Ochola-Oyier LI, Tsofa B. Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.

Gichuki B, Njuguna S, Riako D, Mutua S, Gitonga JN, Sein Y, Bartilol B, Mwangi SJ, O. Omuoyo D, M. Morobe J, de Laurent ZR, Bejon P, Ochola-Oyier LI, Tsofa B. Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.