Evaluation of sample pooling for screening of SARS CoV-2

The coronavirus disease 2019 (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability, an efficient method is urgently needed. To establish an efficient, time and resource...

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Published in:	PloS one Vol. 16; no. 2; p. e0247767
Main Authors:	Mulu, Andargachew, Alemayehu, Dawit Hailu, Alemu, Fekadu, Tefera, Dessalegn Abeje, Wolde, Sinknesh, Aseffa, Gebeyehu, Seyoum, Tamrayehu, Habtamu, Meseret, Abdissa, Alemseged, Bayih, Abebe Genetu, Beyene, Getachew Tesfaye
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 26-02-2021 Public Library of Science (PLoS)
Subjects:	Acids Algorithms Biology and Life Sciences Community Coronaviridae Coronaviruses COVID-19 COVID-19 - diagnosis COVID-19 - virology COVID-19 Nucleic Acid Testing - economics COVID-19 Nucleic Acid Testing - methods Diagnostic systems Diagnostic tests Disease transmission Editing Evaluation Health surveillance Humans Laboratories Mass Screening - economics Mass Screening - methods Medical screening Medicine and Health Sciences Methodology Methods Pandemics Public health Research and analysis methods Respiratory diseases RNA, Viral - genetics RNA, Viral - isolation & purification SARS-CoV-2 - genetics SARS-CoV-2 - isolation & purification Sensitivity and Specificity Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Specimen Handling - economics Specimen Handling - methods Supervision Surveillance Transport media Viral diseases Workflow Ethiopia China Addis Ababa Ethiopia
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Summary:	The coronavirus disease 2019 (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability, an efficient method is urgently needed. To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2. We evaluated pooling approach on both direct clinical and NA samples. The standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 was employed targeting the nucleocapsid (N) and open reading frame (ORF1ab) genomic region of the virus. The experimental pools were created using SARS CoV-2 positive clinical samples and extracted RNA spiked with up to 9 negative samples. For the direct clinical samples viral NA was extracted from each pool to a final extraction volume of 200μL, and subsequently both samples tested using the SARS CoV-2 RT-PCR assay. We found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the cycle threshold (Ct) value of the original sample, corresponding to high, and low SARS CoV-2 viral copies per reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend pooling of 4/5 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 5 in 1 was expected to retain accuracy of the test irrespective of the Ct value samples spiked, and result in a 137% increase in testing efficiency. The approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community. We recommend clinical sample pooling of 4 or 5 in 1. However, we don't advise pooling of clinical samples when disease prevalence is greater than 7%; particularly when sample size is large.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Competing Interests: The authors have declared that no competing interests exist.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0247767