Group Testing for SARS-CoV-2: Forward to the Past?

Pouwels, Koen B; Roope, Laurence; Barnett, Adrian; Hunter, David J.; Nolan, Terry; Clarke, Philip

doi:10.1007/s41669-020-00217-8

Cited by 18 publications

(20 citation statements)

References 13 publications

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“…The results must be interpreted taking into account the testing strategy for SARS-CoV-2 virus in Romania, which implies a prioritization of the subjects according to the medical context, epidemiological investigations, and also the available resources. Even in the most developed countries, the rRT-PCR testing is applied in selected cases, due to the low availability of key supplies [ 35 ]. The situation in Romania is also comparable to that of many European countries, which have a similar testing strategy, based on WHO recommendations [ 36 ].…”

Section: Discussionmentioning

confidence: 99%

An Epidemiological Study on the Prevalence of the Clinical Features of SARS-CoV-2 Infection in Romanian People

Ciucurel

Iconaru

2020

IJERPH

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The aim of this study was to investigate the prevalence of the clinical features of the SARS-CoV-2 infection in Romanian population through a novel online survey. The survey included categorical socio-demographic and health-related variables. A total of 1830 participants were selected for statistical data processing (a response rate of 90.9%). We determined reasonable reliability of the survey section for clinical features of SARS-CoV-2 infection (Cronbach’s Alpha 0.671). Two meaningful dimensions were identified through CATPCA (Categorical Principal Component Analysis) for the survey’s items. We separated two significant clusters of items, each measuring a distinct factor: the sociodemographic characteristics linked to social distancing and the relevant clinical features of SARS-CoV-2 infection. Next, a two-step cluster analysis helped to classify the sample group taking into consideration the similarity of subjects. The clustering revealed a three-cluster solution, with significant differences between clusters and allowed the cluster detection of a group of individuals, possibly more affected by the infection with the SARS-CoV-2 virus. Through binomial logistic regression analysis, we identified a statistically significant prediction model for the presumptive diagnostic of some relevant clinical features of SARS-CoV-2 infection. Our study validated a cost-effective model for rapid assessment of the health status of subjects, adapted to the context of SARS-CoV-2 pandemic.

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Section: Discussionmentioning

confidence: 99%

An Epidemiological Study on the Prevalence of the Clinical Features of SARS-CoV-2 Infection in Romanian People

Ciucurel

Iconaru

2020

IJERPH

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“…Yet COVID-19 surveillance is limited in practice by available testing capacity and health-economic resources, particularly for institutions in low-and middle-income settings [31,32]. In light of testing shortages, group testing (sample pooling, combining clinical specimens from multiple individuals into a single biological sample for a single RT-PCR test) has garnered attention as a diagnostically sensitive and resource-efficient alternative to individualbased testing [33][34][35][36][37][38].…”

Section: Introductionmentioning

confidence: 99%

Optimizing COVID-19 surveillance in long-term care facilities: a modelling study

Duval

Pouwels

et al. 2020

BMC Med

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Background Long-term care facilities (LTCFs) are vulnerable to outbreaks of coronavirus disease 2019 (COVID-19). Timely epidemiological surveillance is essential for outbreak response, but is complicated by a high proportion of silent (non-symptomatic) infections and limited testing resources. Methods We used a stochastic, individual-based model to simulate transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) along detailed inter-individual contact networks describing patient-staff interactions in a real LTCF setting. We simulated distribution of nasopharyngeal swabs and reverse transcriptase polymerase chain reaction (RT-PCR) tests using clinical and demographic indications and evaluated the efficacy and resource-efficiency of a range of surveillance strategies, including group testing (sample pooling) and testing cascades, which couple (i) testing for multiple indications (symptoms, admission) with (ii) random daily testing. Results In the baseline scenario, randomly introducing a silent SARS-CoV-2 infection into a 170-bed LTCF led to large outbreaks, with a cumulative 86 (95% uncertainty interval 6–224) infections after 3 weeks of unmitigated transmission. Efficacy of symptom-based screening was limited by lags to symptom onset and silent asymptomatic and pre-symptomatic transmission. Across scenarios, testing upon admission detected just 34–66% of patients infected upon LTCF entry, and also missed potential introductions from staff. Random daily testing was more effective when targeting patients than staff, but was overall an inefficient use of limited resources. At high testing capacity (> 10 tests/100 beds/day), cascades were most effective, with a 19–36% probability of detecting outbreaks prior to any nosocomial transmission, and 26–46% prior to first onset of COVID-19 symptoms. Conversely, at low capacity (< 2 tests/100 beds/day), group testing strategies detected outbreaks earliest. Pooling randomly selected patients in a daily group test was most likely to detect outbreaks prior to first symptom onset (16–27%), while pooling patients and staff expressing any COVID-like symptoms was the most efficient means to improve surveillance given resource limitations, compared to the reference requiring only 6–9 additional tests and 11–28 additional swabs to detect outbreaks 1–6 days earlier, prior to an additional 11–22 infections. Conclusions COVID-19 surveillance is challenged by delayed or absent clinical symptoms and imperfect diagnostic sensitivity of standard RT-PCR tests. In our analysis, group testing was the most effective and efficient COVID-19 surveillance strategy for resource-limited LTCFs. Testing cascades were even more effective given ample testing resources. Increasing testing capacity and updating surveillance protocols accordingly could facilitate earlier detection of emerging outbreaks, informing a need for urgent intervention in settings with ongoing nosocomial transmission.

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“…For an optimal pooled testing protocol, there are three key considerations 16 : (i) the diagnostic protocol limit of detection (LoD) to ensure adequate sample volume is included in the pools, (ii) the diagnostic test sensitivity and specificity and (iii) the prevalence of the infection to guide the optimal pool size (e.g. if infection prevalence reaches 30%, then pooling in groups of 3 would lead to most pools being positive and the need for individual testing, hence no gain in efficiency).…”

Section: Methodsmentioning

confidence: 99%

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

Agoti¹,

Mutunga²,

Lambisia³

et al. 2020

Wellcome Open Res

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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.

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Group Testing for SARS-CoV-2: Forward to the Past?

Cited by 18 publications

References 13 publications

An Epidemiological Study on the Prevalence of the Clinical Features of SARS-CoV-2 Infection in Romanian People

An Epidemiological Study on the Prevalence of the Clinical Features of SARS-CoV-2 Infection in Romanian People

Optimizing COVID-19 surveillance in long-term care facilities: a modelling study

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

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