Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR
IntroductionThe declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2024-01-01
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| Series: | Frontiers in Public Health |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpubh.2023.1340420/full |
| _version_ | 1797353359376646144 |
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| author | Antonella Pacini Antonella Pacini Franco Paredes Franco Paredes Sofia Heckel Sofia Heckel Sofia Heckel Guadalupe Ibarra Guadalupe Ibarra Maria Victoria Petreli Maria Victoria Petreli Marilina Perez Yanina Agnella Yanina Agnella Laura Piskulic Maria Belen Allasia Luis Caprile Alejandro Colaneri Juliana Sesma Juliana Sesma Juliana Sesma |
| author_facet | Antonella Pacini Antonella Pacini Franco Paredes Franco Paredes Sofia Heckel Sofia Heckel Sofia Heckel Guadalupe Ibarra Guadalupe Ibarra Maria Victoria Petreli Maria Victoria Petreli Marilina Perez Yanina Agnella Yanina Agnella Laura Piskulic Maria Belen Allasia Luis Caprile Alejandro Colaneri Juliana Sesma Juliana Sesma Juliana Sesma |
| author_sort | Antonella Pacini |
| collection | DOAJ |
| description | IntroductionThe declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the emergence of new variants but also to understand their spread. We present a cost-effective digital PCR-based pooled sample testing methodology tailored for early variant surveillance.MethodsUsing 1200 retrospective SARS-CoV-2 positive samples, either negative or positive for Delta or Omicron, we assessed the sensitivity and specificity of our detection strategy employing commercial TaqMan variant probes in a 1:9 ratio of variant-positive to variant-negative samples.ResultsThe study achieved 100% sensitivity and 99% specificity in 10-sample pools, with an Area Under the Curve (AUC) exceeding 0.998 in ROC curves, using distinct commercial TaqMan variant probes.DiscussionThe employment of two separate TaqMan probes for both Delta and Omicron establishes dual validation routes, emphasizing the method’s robustness. Although we used known samples to model realistic emergence scenarios of the Delta and Omicron variants, our main objective is to demonstrate the versatility of this strategy to identify future variant appearances. The utilization of two divergent variants and distinct probes for each confirms the method’s independence from specific variants and probes. This flexibility ensures it can be tailored to recognize any subsequent variant emergence, given the availability of its sequence and a specific probe. Consequently, our approach stands as a robust tool for tracking and managing any new variant outbreak, reinforcing our global readiness against possible future SARS-CoV-2 waves. |
| first_indexed | 2024-03-08T13:29:00Z |
| format | Article |
| id | doaj.art-f75699876f8d48099b4e0d04d0215cd2 |
| institution | Directory Open Access Journal |
| issn | 2296-2565 |
| language | English |
| last_indexed | 2024-03-08T13:29:00Z |
| publishDate | 2024-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj.art-f75699876f8d48099b4e0d04d0215cd22024-01-17T11:27:51ZengFrontiers Media S.A.Frontiers in Public Health2296-25652024-01-011110.3389/fpubh.2023.13404201340420Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCRAntonella Pacini0Antonella Pacini1Franco Paredes2Franco Paredes3Sofia Heckel4Sofia Heckel5Sofia Heckel6Guadalupe Ibarra7Guadalupe Ibarra8Maria Victoria Petreli9Maria Victoria Petreli10Marilina Perez11Yanina Agnella12Yanina Agnella13Laura Piskulic14Maria Belen Allasia15Luis Caprile16Alejandro Colaneri17Juliana Sesma18Juliana Sesma19Juliana Sesma20Molecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaInstituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaFacultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaInstituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, ArgentinaFacultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaFacultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaFacultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaFacultad de Ciencias Veterinarias, Universidad Nacional de Rosario, Casilda, ArgentinaÁrea Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, ArgentinaÁrea Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaConsejo Nacional de Investigaciones Científicas y Técnicas, Rosario, ArgentinaMolecular Biology Department, Hospital Provincial de Rosario, Rosario, ArgentinaInstituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, ArgentinaFacultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, ArgentinaIntroductionThe declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the emergence of new variants but also to understand their spread. We present a cost-effective digital PCR-based pooled sample testing methodology tailored for early variant surveillance.MethodsUsing 1200 retrospective SARS-CoV-2 positive samples, either negative or positive for Delta or Omicron, we assessed the sensitivity and specificity of our detection strategy employing commercial TaqMan variant probes in a 1:9 ratio of variant-positive to variant-negative samples.ResultsThe study achieved 100% sensitivity and 99% specificity in 10-sample pools, with an Area Under the Curve (AUC) exceeding 0.998 in ROC curves, using distinct commercial TaqMan variant probes.DiscussionThe employment of two separate TaqMan probes for both Delta and Omicron establishes dual validation routes, emphasizing the method’s robustness. Although we used known samples to model realistic emergence scenarios of the Delta and Omicron variants, our main objective is to demonstrate the versatility of this strategy to identify future variant appearances. The utilization of two divergent variants and distinct probes for each confirms the method’s independence from specific variants and probes. This flexibility ensures it can be tailored to recognize any subsequent variant emergence, given the availability of its sequence and a specific probe. Consequently, our approach stands as a robust tool for tracking and managing any new variant outbreak, reinforcing our global readiness against possible future SARS-CoV-2 waves.https://www.frontiersin.org/articles/10.3389/fpubh.2023.1340420/fullPool testingdroplet digital PCRCOVID-19 pandemicnew variant outbreakSARS-CoV-2 wave surveillanceDelta/Omicron tracking |
| spellingShingle | Antonella Pacini Antonella Pacini Franco Paredes Franco Paredes Sofia Heckel Sofia Heckel Sofia Heckel Guadalupe Ibarra Guadalupe Ibarra Maria Victoria Petreli Maria Victoria Petreli Marilina Perez Yanina Agnella Yanina Agnella Laura Piskulic Maria Belen Allasia Luis Caprile Alejandro Colaneri Juliana Sesma Juliana Sesma Juliana Sesma Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR Frontiers in Public Health Pool testing droplet digital PCR COVID-19 pandemic new variant outbreak SARS-CoV-2 wave surveillance Delta/Omicron tracking |
| title | Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR |
| title_full | Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR |
| title_fullStr | Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR |
| title_full_unstemmed | Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR |
| title_short | Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR |
| title_sort | ready for new waves optimizing sars cov 2 variants monitoring in pooled samples with droplet digital pcr |
| topic | Pool testing droplet digital PCR COVID-19 pandemic new variant outbreak SARS-CoV-2 wave surveillance Delta/Omicron tracking |
| url | https://www.frontiersin.org/articles/10.3389/fpubh.2023.1340420/full |
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