Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study
Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the...
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| creator | Singh, Anirudh K Nema, Ram Kumar Joshi, Ankur Shankar, Prem Nema, Shashwati Raghuwanshi, Arun Patankar, Chitra Mathew, Bijina J Shrivas, Arti Pandey, Ritu Tripathi, Ranu Biswas, Debasis Singh, Sarman |
| description | Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. |
| doi_str_mv | 10.1371/journal.pone.0239492 |
| format | Article |
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Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0239492</identifier><identifier>PMID: 32960929</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Asymptomatic ; Betacoronavirus ; Biology and Life Sciences ; Clinical Laboratory Techniques - economics ; Clinical Laboratory Techniques - methods ; Clinical Laboratory Techniques - standards ; Containment ; Control ; Coronavirus Infections - diagnosis ; Coronavirus Infections - economics ; Coronaviruses ; Councils ; COVID-19 ; COVID-19 diagnostic tests ; COVID-19 Testing ; Diagnosis ; Diagnostic Errors - statistics & numerical data ; Diagnostic systems ; Disease Outbreaks - prevention & control ; Disease transmission ; Epidemics ; Evaluation ; Health aspects ; Humans ; India ; Infections ; Management ; Mass Screening - economics ; Mass Screening - methods ; Medical diagnosis ; Medical research ; Medicine and Health Sciences ; Outbreaks ; Pandemics ; Pilot Projects ; Pneumonia, Viral - diagnosis ; Polymerase chain reaction ; Pools ; Reverse Transcriptase Polymerase Chain Reaction ; RNA-directed DNA polymerase ; Sampling (Statistics) ; SARS-CoV-2 ; Severe acute respiratory syndrome coronavirus 2 ; Singh, Ram ; Software ; Specimen Handling - methods ; Strategy ; Testing laboratories ; Time Factors ; Values ; Viral diseases ; Virology ; Waivers</subject><ispartof>PloS one, 2020-09, Vol.15 (9), p.e0239492-e0239492</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Singh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Singh, Anirudh K</au><au>Nema, Ram Kumar</au><au>Joshi, Ankur</au><au>Shankar, Prem</au><au>Nema, Shashwati</au><au>Raghuwanshi, Arun</au><au>Patankar, Chitra</au><au>Mathew, Bijina J</au><au>Shrivas, Arti</au><au>Pandey, Ritu</au><au>Tripathi, Ranu</au><au>Biswas, Debasis</au><au>Singh, Sarman</au><au>Roques, Pierre</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-09-22</date><risdate>2020</risdate><volume>15</volume><issue>9</issue><spage>e0239492</spage><epage>e0239492</epage><pages>e0239492-e0239492</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32960929</pmid><doi>10.1371/journal.pone.0239492</doi><tpages>e0239492</tpages><orcidid>https://orcid.org/0000-0003-3087-0413</orcidid><orcidid>https://orcid.org/0000-0002-7557-3693</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2020-09, Vol.15 (9), p.e0239492-e0239492 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2444863716 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS) Journals Open Access; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Asymptomatic Betacoronavirus Biology and Life Sciences Clinical Laboratory Techniques - economics Clinical Laboratory Techniques - methods Clinical Laboratory Techniques - standards Containment Control Coronavirus Infections - diagnosis Coronavirus Infections - economics Coronaviruses Councils COVID-19 COVID-19 diagnostic tests COVID-19 Testing Diagnosis Diagnostic Errors - statistics & numerical data Diagnostic systems Disease Outbreaks - prevention & control Disease transmission Epidemics Evaluation Health aspects Humans India Infections Management Mass Screening - economics Mass Screening - methods Medical diagnosis Medical research Medicine and Health Sciences Outbreaks Pandemics Pilot Projects Pneumonia, Viral - diagnosis Polymerase chain reaction Pools Reverse Transcriptase Polymerase Chain Reaction RNA-directed DNA polymerase Sampling (Statistics) SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Singh, Ram Software Specimen Handling - methods Strategy Testing laboratories Time Factors Values Viral diseases Virology Waivers |
| title | Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study |
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