Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance

Brault, Vincent; Mallein, Bastien; Rupprecht, Jean-François

doi:10.1371/journal.pcbi.1008726

Cited by 32 publications

(30 citation statements)

References 69 publications

(125 reference statements)

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“…23,24 Lastly, an epidemic curve can be used to visually track the natural progression, as well as the effect of control measures on an epidemic. 25 Regarding COVID-19 specifically, this can be carried out with various degrees of precision, from simply monitoring the incidence of cases measured by virus detection methods, 26,27 through inferences via combining data from virus detection methods with seroprevalence studies 28 to more granular attempts to forecast trends via viral load distributions. 29…”

Section: Epidemiologymentioning

confidence: 99%

COVID-19: a review of current knowledge regarding exposure, quarantine, isolation and other preventive measures

Rosolanka

Henao-Martínez

Pisney

et al. 2021

Therapeutic Advances in Infection

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Deeper understanding of the spread, morbidity, fatality, and development of immune response associated with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, is necessary in order to establish an appropriate epidemiological and clinical response. Exposure control represents a key part of the combat against COVID-19, as the effectiveness of current therapeutic options remains partial. Since the preventive measures have not been sufficiently able to slow down this pandemic, in this article we explore some of the pertinent knowledge gaps, while overall looking to effective vaccination strategies as a way out. Early on, such strategies may need to rely on counting the convalescents as protected in order to speed up the immunization of the whole population.

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Section: Epidemiologymentioning

confidence: 99%

COVID-19: a review of current knowledge regarding exposure, quarantine, isolation and other preventive measures

Rosolanka

Henao-Martínez

Pisney

et al. 2021

Therapeutic Advances in Infection

View full text Add to dashboard Cite

show abstract

“…For example, with the French population size, this would translate to 871,000 daily tests. Pooled sample testing strategies could be a solution to reduce the number of testing kits needed, and is a particularly reasonable option when the positive testing rate is very low (Brault et al, 2021), i.e., when the prevalence of infected individuals in a community is close to zero.…”

Section: Discussionmentioning

confidence: 99%

“…We find that for a cluster size to be below 30 infected individuals (on average), each day around 0.13% of a total population would need to be randomly selected for testing, i.e., independently of the individual’s infection status. Pooled sample testing strategies could be a solution to reduce the number of testing kits needed, and is a particularly reasonable option when the prevalence of infected individuals in a community is close to zero [33].…”

Section: Discussionmentioning

confidence: 99%

The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection

Czuppon

Schertzer

Blanquart

et al. 2020

Preprint

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The identification of a first case (e.g. by a disease-related death or hospitalization event) raises the question of the actual size of a local outbreak. Quick estimates of the outbreak size are required to assess the necessary testing, contact tracing and potential containment effort. Using general branching processes and assuming that epidemic parameters (including the basic reproductive number) are constant over time, we characterize the distribution of the first hospitalization time and of the epidemic size at this random time. We find that previous estimates either overestimate or largely underestimate the actual epidemic size. In addition, we provide upper and lower bounds for the number of infectious individuals of the local outbreak over time. The upper bound is the cumulative epidemic size, and the lower bound is a constant fraction of it. Lastly, we compute the number of detectable cases if one were to test the whole local outbreak at a single point in time. In a growing epidemic, most individuals have been infected recently, which can strongly limit the detection of infected individuals when there is a delay between an infection and its potential detection. Overall, our analysis provides new analytical estimates about the epidemic size at identification of a first disease-related case. This piece of information is important to inform policy makers during the early stages of an epidemic outbreak.

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“…Nevertheless, individual screening of large asymptomatic cohorts by RNA extraction and RT-qPCR can be expensive and wasteful when pathogens are present in the population at low carriage rates. As recommended by the FDA ( and accessed on 15 May 2021), sample pooling could be an important public health tool to increase testing capacity because it allows for more individuals to be analyzed rapidly at once, using fewer testing resources [ 13 , 14 , 15 , 16 ]. Moreover, this may be even more relevant if the screening involves a community, such as a school or a faculty returning to work or class, in order to promptly implement preventive measures if needed.…”

Section: Introductionmentioning

confidence: 99%

Sample-Pooling Strategy for SARS-CoV-2 Detection among Students and Staff of the University of Sannio

et al. 2021

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Since the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, it has been clear that testing large groups of the population was the key to stem infection and prevent the effects of the coronavirus disease of 2019, mostly among sensitive patients. On the other hand, time and cost-sustainability of virus detection by molecular analysis such as reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) may be a major issue if testing is extended to large communities, mainly asymptomatic large communities. In this context, sample-pooling and test grouping could offer an effective solution. Here we report the screening on 1195 oral-nasopharyngeal swabs collected from students and staff of the Università degli Studi del Sannio (University of Sannio, Benevento, Campania, Italy) and analyzed by an in-house developed multiplex RT-qPCR for SARS-CoV-2 detection through a simple monodimensional sample pooling strategy. Overall, 400 distinct pools were generated and, within 24 h after swab collection, five positive samples were identified. Out of them, four were confirmed by using a commercially available kit suitable for in vitro diagnostic use (IVD). High accuracy, sensitivity and specificity were also determined by comparing our results with a reference IVD assay for all deconvoluted samples. Overall, we conducted 463 analyses instead of 1195, reducing testing resources by more than 60% without lengthening diagnosis time and without significant losses in sensitivity, suggesting that our strategy was successful in recognizing positive cases in a community of asymptomatic individuals with minor requirements of reagents and time when compared to normal testing procedures.

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Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance

Cited by 32 publications

References 69 publications

COVID-19: a review of current knowledge regarding exposure, quarantine, isolation and other preventive measures

COVID-19: a review of current knowledge regarding exposure, quarantine, isolation and other preventive measures

The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection

Sample-Pooling Strategy for SARS-CoV-2 Detection among Students and Staff of the University of Sannio

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