Pooled nasopharyngeal swab collection in a single vial for the diagnosis of SARS CoV-2 infection: An effective cost saving method

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Abstract

Background

Pool testing is one of the strategy to expedite testing capacities while simultaneously conserving various diagnostic kits, reagents and consumables and time. In the present study, we investigated potential role of combined specimen collection technique for the diagnosis of SARS-CoV-2 virus infection where five nasopharyngeal swabs were collected from different individuals and pooled together in a single viral transport medium (VTM).

Material and methods

This pilot study was conducted on different cohorts of Delhi state. Two nasopharyngeal swabs were collected from each enrolled individual. One swab was put into VTM vial to be further used for individual swab testing (ID). The other swab was put into a fresh VTM for pool swab collection. Each pool comprised five swabs collected from five different patients in one VTM vial. Both IDs and pools were tested in parallel for the detection of SARS-CoV-2 using real time PCR.

Results

A total of 46 pools were collected from 230 enrolled individuals.Among 230 ID tested, 60 were found to be positive for both E and RdRp gene. Among 46 pools, 25 pools included all negatives samples and remaining 21 pools included one or more positives. Comparing ID with pool results, overall concordance was seen in 42 pools (91.3%). Four pools showed false positive results as all included samples on ID testing were found to be negative. Considering ID results as reference, swab pool showed 100% sensitivity, 84% specificity, 84% positive predictive value and 100% negative predictive value.

Conclusion

The pooling of swab strategy could be beneficial only among asymptomatic in low prevalence areas.

Related collections

Most cited references 22

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Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Victor M Corman, Olfert Landt, Marco Kaiser … (2020)

Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

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Laboratory Diagnosis of COVID-19: Current Issues and Challenges

Yi-Wei Tang, Jonathan E. Schmitz, David Persing … (2020)

The COVID-19 outbreak has had a major impact on clinical microbiology laboratories in the past several months. This commentary covers current issues and challenges for the laboratory diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the preanalytical stage, collecting the proper respiratory tract specimen at the right time from the right anatomic site is essential for a prompt and accurate molecular diagnosis of COVID-19. Appropriate measures are required to keep laboratory staff safe while producing reliable test results.

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Evaluation of COVID-19 RT-qPCR test in multi-sample pools

Idan Yelin, Noga Aharony, Einat Shaer Tamar … (2020)

Abstract Background The recent emergence of SARS-CoV-2 lead to a current pandemic of unprecedented scale. Though diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare systems are already experiencing shortages of reagents associated with this test, calling for a lean immediately-applicable protocol. Methods RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using RT-qPCR, alone or in pools of different sizes (2-, 4-, 8- ,16-, 32- and 64-sample pools) with negative samples. Transport media of additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8. Results A single positive sample can be detected in pools of up to 32 samples, using the standard kits and protocols, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles. Single positive samples can be detected when pooling either after or prior to RNA extraction. Conclusions As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close organic groups, such as hospital departments, army units, or factory shifts.

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Author and article information

Journal

Journal ID (nlm-ta): Indian J Med Microbiol

Journal ID (iso-abbrev): Indian J Med Microbiol

Title: Indian Journal of Medical Microbiology

Publisher: Indian Association of Medical Microbiologists. Published by Elsevier B.V.

ISSN (Print): 0255-0857

ISSN (Electronic): 1998-3646

Publication date PMC-release: 27 January 2021

Publication date (Electronic): 27 January 2021

Affiliations

[a ]Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India

[b ]Department of Hospital Operations, Institute of Liver and Biliary Sciences, New Delhi, India

[c ]Department of Research, Institute of Liver and Biliary Sciences, New Delhi, India

[d ]Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India

Author notes

[∗ ]Corresponding author. Department of Clinical Virology, Institute of Liver and Biliary Sciences (ILBS), New Delhi, India.

Article

Publisher Item ID: S0255-0857(20)31828-4

DOI: 10.1016/j.ijmmb.2020.11.002

PMC ID: 7839627

PubMed ID: 33515633

SO-VID: 06f60c4d-95c9-46d6-a5e6-cef05993c7e3

License:

Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

Pooled nasopharyngeal swab collection in a single vial for the diagnosis of SARS CoV-2 infection: An effective cost saving method

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Novel Coronavirus Disease COVID-19

Most cited references 22

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Laboratory Diagnosis of COVID-19: Current Issues and Challenges

Evaluation of COVID-19 RT-qPCR test in multi-sample pools

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