SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: A screening strategy of choice for active surveillance
The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propag...
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| Veröffentlicht in: | PloS one 2022-04, Vol.17 (4), p.e0266408-e0266408 |
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| creator | Castellaro, Andrés Marcos Velez, Pablo Giaj Merlera, Guillermo Rondan Dueñas, Juan Condat, Felix Gallardo, Jesica Makhoul, Aylen Cinalli, Camila Rosales Cavaglieri, Lorenzo Di Cola, Guadalupe Sicilia, Paola López, Laura Bocco, José Luis Barbás, María Gabriela Cardozo, Diego Hernán Pisano, María Belén Ré, Viviana Belaus, Andrea Castro, Gonzalo |
| description | The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation.
Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed.
From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%.
This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic. |
| doi_str_mv | 10.1371/journal.pone.0266408 |
| format | Article |
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Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed.
From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%.
This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0266408</identifier><identifier>PMID: 35363805</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Argentina ; Biology and Life Sciences ; Comparative analysis ; Control ; Coronaviruses ; COVID-19 ; COVID-19 - diagnosis ; COVID-19 - epidemiology ; Cycle protein ; Diagnostic systems ; Dilution ; Disease ; Engineering and Technology ; Epidemics ; Feasibility studies ; Health surveillance ; Humans ; Medicine and Health Sciences ; Methods ; N gene ; Nucleic acids ; Overloading ; Pandemics ; Pools ; RNA, Viral - genetics ; SARS-CoV-2 - genetics ; Sensitivity and Specificity ; Sentinel health events ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Signs and symptoms ; Specimen Handling - methods ; Supervision ; Surveillance ; Viral diseases ; Viruses ; Watchful Waiting</subject><ispartof>PloS one, 2022-04, Vol.17 (4), p.e0266408-e0266408</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Castellaro 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Castellaro et al 2022 Castellaro et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-ae7e4c95b40b2ca716833050487fd6ee593dc7dd91e14f9cdb4ad1a1535157b33</citedby><cites>FETCH-LOGICAL-c692t-ae7e4c95b40b2ca716833050487fd6ee593dc7dd91e14f9cdb4ad1a1535157b33</cites><orcidid>0000-0003-3707-0670 ; 0000-0003-2360-0175 ; 0000-0002-0984-3835</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8975135/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8975135/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35363805$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Castellaro, Andrés Marcos</creatorcontrib><creatorcontrib>Velez, Pablo</creatorcontrib><creatorcontrib>Giaj Merlera, Guillermo</creatorcontrib><creatorcontrib>Rondan Dueñas, Juan</creatorcontrib><creatorcontrib>Condat, Felix</creatorcontrib><creatorcontrib>Gallardo, Jesica</creatorcontrib><creatorcontrib>Makhoul, Aylen</creatorcontrib><creatorcontrib>Cinalli, Camila</creatorcontrib><creatorcontrib>Rosales Cavaglieri, Lorenzo</creatorcontrib><creatorcontrib>Di Cola, Guadalupe</creatorcontrib><creatorcontrib>Sicilia, Paola</creatorcontrib><creatorcontrib>López, Laura</creatorcontrib><creatorcontrib>Bocco, José Luis</creatorcontrib><creatorcontrib>Barbás, María Gabriela</creatorcontrib><creatorcontrib>Cardozo, Diego Hernán</creatorcontrib><creatorcontrib>Pisano, María Belén</creatorcontrib><creatorcontrib>Ré, Viviana</creatorcontrib><creatorcontrib>Belaus, Andrea</creatorcontrib><creatorcontrib>Castro, Gonzalo</creatorcontrib><creatorcontrib>Facultad de Ciencias Químicas UNC Group</creatorcontrib><title>SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: A screening strategy of choice for active surveillance</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation.
Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed.
From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%.
This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.</description><subject>Argentina</subject><subject>Biology and Life Sciences</subject><subject>Comparative analysis</subject><subject>Control</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>COVID-19 - diagnosis</subject><subject>COVID-19 - epidemiology</subject><subject>Cycle protein</subject><subject>Diagnostic systems</subject><subject>Dilution</subject><subject>Disease</subject><subject>Engineering and Technology</subject><subject>Epidemics</subject><subject>Feasibility studies</subject><subject>Health surveillance</subject><subject>Humans</subject><subject>Medicine and Health Sciences</subject><subject>Methods</subject><subject>N gene</subject><subject>Nucleic 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Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Castellaro, Andrés Marcos</au><au>Velez, Pablo</au><au>Giaj Merlera, Guillermo</au><au>Rondan Dueñas, Juan</au><au>Condat, Felix</au><au>Gallardo, Jesica</au><au>Makhoul, Aylen</au><au>Cinalli, Camila</au><au>Rosales Cavaglieri, Lorenzo</au><au>Di Cola, Guadalupe</au><au>Sicilia, Paola</au><au>López, Laura</au><au>Bocco, José Luis</au><au>Barbás, María Gabriela</au><au>Cardozo, Diego Hernán</au><au>Pisano, María Belén</au><au>Ré, Viviana</au><au>Belaus, Andrea</au><au>Castro, Gonzalo</au><aucorp>Facultad de Ciencias Químicas UNC Group</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: A screening strategy of choice for active surveillance</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2022-04-01</date><risdate>2022</risdate><volume>17</volume><issue>4</issue><spage>e0266408</spage><epage>e0266408</epage><pages>e0266408-e0266408</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation.
Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed.
From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%.
This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35363805</pmid><doi>10.1371/journal.pone.0266408</doi><tpages>e0266408</tpages><orcidid>https://orcid.org/0000-0003-3707-0670</orcidid><orcidid>https://orcid.org/0000-0003-2360-0175</orcidid><orcidid>https://orcid.org/0000-0002-0984-3835</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2022-04, Vol.17 (4), p.e0266408-e0266408 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2646133991 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Argentina Biology and Life Sciences Comparative analysis Control Coronaviruses COVID-19 COVID-19 - diagnosis COVID-19 - epidemiology Cycle protein Diagnostic systems Dilution Disease Engineering and Technology Epidemics Feasibility studies Health surveillance Humans Medicine and Health Sciences Methods N gene Nucleic acids Overloading Pandemics Pools RNA, Viral - genetics SARS-CoV-2 - genetics Sensitivity and Specificity Sentinel health events Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Signs and symptoms Specimen Handling - methods Supervision Surveillance Viral diseases Viruses Watchful Waiting |
| title | SARS-CoV-2 detection in multi-sample pools in a real pandemic scenario: A screening strategy of choice for active surveillance |
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