Pooling of nasopharyngeal swab specimens for SARS‐CoV‐2 detection by RT‐PCR

Torres, Ignacio; Albert, Eliseo; Navarro, David

doi:10.1002/jmv.25971

Cited by 86 publications

(107 citation statements)

References 9 publications

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“…As previous studies [8,9,18], our results using pools showed an increase of 3-5 cycles in the Cq value between pooled tests and individual positive samples. It has not carried out loss of sensitivity in pools for samples with Cq value within the rst three quartiles observed in our population.…”

Section: Discussionsupporting

confidence: 89%

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Pooling for SARS-CoV-2 Control in Care Institutions

Cabrera-Alvargonzález

Cao

Castro

et al. 2020

Preprint

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Background Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources.The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people.Methods 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were tested using RT-PCR. Prevalence and distribution of positive detection in Care Homes was calculated. Pools of 19 negative samples and one positive sample were tested using RT-PCR as well. Prevalence and distribution of positive detection in Care Homes was calculated. Results Distribution of SARS-CoV-2 infection at Care Houses was uneven. As the virus circulation global rate was low in our area, the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on quantification cycle (Cq) values. Conclusions A new surveillance system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Houses, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.

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Section: Discussionsupporting

confidence: 89%

“…Pooling strategies have proven to preserve SARS-CoV-2 testing resources and time with an increase in testing capability of the 69% for an incidence rate of SARS-CoV-2 infection of 10% or less [4,5,6,7], but it could be associated with a decrease in detection [8,9].…”

Section: Introductionmentioning

confidence: 99%

Pooling for SARS-CoV-2 Control in Care Institutions

Cabrera-Alvargonzález

Cao

Castro

et al. 2020

Preprint

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“…The pooling method was validated for nCov tests by many laboratories [2][3][4][5][6][7][8][9][10][11][12][13][14][15]. However, the following questions remained open, which we address in this paper.…”

Section: Introductionmentioning

confidence: 99%

Pooling of coronavirus tests under unknown prevalence

Pikovski

2020

Epidemiol. Infect.

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Diagnostic testing for the novel coronavirus is an important tool to fight the coronavirus disease (Covid-19) pandemic. However, testing capacities are limited. A modified testing protocol, whereby a number of probes are ‘pooled’ (i.e. grouped), is known to increase the capacity for testing. Here, we model pooled testing with a double-average model, which we think to be close to reality for Covid-19 testing. The optimal pool size and the effect of test errors are considered. The results show that the best pool size is three to five, under reasonable assumptions. Pool testing even reduces the number of false positives in the absence of dilution effects.

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“…To overcome some of these limitations, laboratories have adapted and developed innovative methods for testing, such as the pooling of two or more samples either prior to, or after, nucleic acid extraction, [32][33][34][35] which has been done previously for the mass screening of samples for influenza virus. 36 If SARS-CoV-2 RNA is subsequently detected, repeat testing of the individual samples from the original pool is performed 37 However, the advantages of pooling are negated when the prevalence of COVID-19 in the population tested is high, as more pooled samples will require individual testing.…”

Section: Sars-cov-2 Nucleic Acid Testingmentioning

confidence: 99%

Laboratory diagnosis of severe acute respiratory syndrome coronavirus 2

et al. 2020

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The first laboratory confirmed case of Coronavirus disease 2019 (COVID-19) in Australia was in Victoria on 25 January 2020 in a man returning from Wuhan city, Hubei province, the People's Republic of China. This was followed by three cases in New South Wales the following day. The Australian Government activated the Australian Health Sector Emergency Response Plan for Novel Coronavirus on 27 February 2020 in anticipation of a pandemic. Subsequently, the World Health Organization declared COVID-19 to be a Public Health Emergency of International Concern followed by a pandemic on 30 January 2020 and 11 March 2020, respectively. Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is key in identifying infected persons to guide timely public health actions of contact tracing and patient isolation to limit transmission of infection. This article aims to provide a comprehensive overview of current laboratory diagnostic methods for SARS-CoV-2, including nucleic acid testing, serology, rapid antigen detection and antibody tests, virus isolation and whole genome sequencing. The relative advantages and disadvantages of the different diagnostic tests are presented, as well as their value in different clinical, infection control and public health contexts. We also describe the challenges in the provision of SARS-CoV-2 diagnostics in Australia, a country with a relatively low COVID-19 incidence in the first pandemic wave but in which prevalence could rapidly change.

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Pooling of nasopharyngeal swab specimens for SARS‐CoV‐2 detection by RT‐PCR

Cited by 86 publications

References 9 publications

Pooling for SARS-CoV-2 Control in Care Institutions

Pooling for SARS-CoV-2 Control in Care Institutions

Pooling of coronavirus tests under unknown prevalence

Laboratory diagnosis of severe acute respiratory syndrome coronavirus 2

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