Cargando…
Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test
BACKGROUND: Sensitive and high throughput molecular detection assays are essential during the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The vast majority of the SARS-CoV-2 molecular assays use nasopharyngeal swab (NPS) o...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901781/ https://www.ncbi.nlm.nih.gov/pubmed/33621263 http://dx.doi.org/10.1371/journal.pone.0243183 |
_version_ | 1783654429620174848 |
---|---|
author | Sun, Qing Li, Jonathan Ren, Hui Pastor, Larry Loginova, Yulia Madej, Roberta Taylor, Kristopher Wong, Joseph K. Zhang, Zhao Zhang, Aiguo Lu, Chuanyi M. Sha, Michael Y. |
author_facet | Sun, Qing Li, Jonathan Ren, Hui Pastor, Larry Loginova, Yulia Madej, Roberta Taylor, Kristopher Wong, Joseph K. Zhang, Zhao Zhang, Aiguo Lu, Chuanyi M. Sha, Michael Y. |
author_sort | Sun, Qing |
collection | PubMed |
description | BACKGROUND: Sensitive and high throughput molecular detection assays are essential during the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The vast majority of the SARS-CoV-2 molecular assays use nasopharyngeal swab (NPS) or oropharyngeal swab (OPS) specimens collected from suspected individuals. However, using NPS or OPS as specimens has apparent drawbacks, e.g. the collection procedures for NPS or OPS specimens can be uncomfortable to some people and may cause sneezing and coughing which in turn generate droplets and/or aerosol particles that are of risk to healthcare workers, requiring heavy use of personal protective equipment. There have been recent studies indicating that self-collected saliva specimens can be used for molecular detection of SARS-CoV-2 and provides more comfort and ease of use for the patients. Here we report the performance of QuantiVirus(™) SARS-CoV-2 test using saliva as the testing specimens with or without pooling. METHODS: Development and validation studies were conducted following FDA-EUA and molecular assay validation guidelines. Using SeraCare Accuplex SARS-CoV-2 reference panel, the limit of detection (LOD) and clinical performance studies were performed with the QuantiVirus(™) SARS-CoV-2 test. For clinical evaluation, 85 known positive and 90 known negative clinical NPS samples were tested. Additionally, twenty paired NPS and saliva samples collected from recovering COVID-19 patients were tested and the results were further compared to that of the Abbott m2000 SARS-CoV-2 PCR assay. Results of community collected 389 saliva samples for COVID-19 screening by QuantiVirus(™) SARS-CoV-2 test were also obtained and analyzed. Additionally, testing of pooled saliva samples was evaluated. RESULTS: The LOD for the QuantiVirus(™) SARS-CoV-2 test was confirmed to be 100–200 copies/mL. The clinical performance studies using contrived saliva samples indicated that the positive percentage agreement (PPA) of the QuantiVirus(™) SARS-CoV-2 test is 100% at 1xLOD, 1.5xLOD and 2.5xLOD. No cross-reactivity was observed for the QuantiVirus(™) SARS-CoV-2 test with common respiratory pathogens. Testing of clinical samples showed a positive percentage agreement (PPA) of 100% (95% CI: 94.6% to 100%) and a negative percentage agreement (NPA) of 98.9% (95% CI: 93.1% to 99.9%). QuantiVirus(™) SARS CoV-2 test had 80% concordance rate and no significant difference (p = 0.13) between paired saliva and NPS specimens by Wilcoxon matched pairs signed rank test. Positive test rate was 1.79% for 389 saliva specimens collected from local communities for COVID-19 screening. Preliminary data showed that saliva sample pooling up to 6 samples (1:6 pooling) for SARS-CoV-2 detection is feasible (sensitivity 94.8% and specificity 100%). CONCLUSION: The studies demonstrated that the QuantiVirus(™) SARS-CoV-2 test has a LOD of 200 copies/mL in contrived saliva samples. The clinical performance of saliva-based testing is comparable to that of NPS-based testing. Pooling of saliva specimens for SARS-CoV-2 detection is feasible. Saliva based and high-throughput QuantiVirus(™) SARS-CoV-2 test offers a highly desirable testing platform during the ongoing COVID-19 pandemic. |
format | Online Article Text |
id | pubmed-7901781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-79017812021-03-02 Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test Sun, Qing Li, Jonathan Ren, Hui Pastor, Larry Loginova, Yulia Madej, Roberta Taylor, Kristopher Wong, Joseph K. Zhang, Zhao Zhang, Aiguo Lu, Chuanyi M. Sha, Michael Y. PLoS One Research Article BACKGROUND: Sensitive and high throughput molecular detection assays are essential during the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The vast majority of the SARS-CoV-2 molecular assays use nasopharyngeal swab (NPS) or oropharyngeal swab (OPS) specimens collected from suspected individuals. However, using NPS or OPS as specimens has apparent drawbacks, e.g. the collection procedures for NPS or OPS specimens can be uncomfortable to some people and may cause sneezing and coughing which in turn generate droplets and/or aerosol particles that are of risk to healthcare workers, requiring heavy use of personal protective equipment. There have been recent studies indicating that self-collected saliva specimens can be used for molecular detection of SARS-CoV-2 and provides more comfort and ease of use for the patients. Here we report the performance of QuantiVirus(™) SARS-CoV-2 test using saliva as the testing specimens with or without pooling. METHODS: Development and validation studies were conducted following FDA-EUA and molecular assay validation guidelines. Using SeraCare Accuplex SARS-CoV-2 reference panel, the limit of detection (LOD) and clinical performance studies were performed with the QuantiVirus(™) SARS-CoV-2 test. For clinical evaluation, 85 known positive and 90 known negative clinical NPS samples were tested. Additionally, twenty paired NPS and saliva samples collected from recovering COVID-19 patients were tested and the results were further compared to that of the Abbott m2000 SARS-CoV-2 PCR assay. Results of community collected 389 saliva samples for COVID-19 screening by QuantiVirus(™) SARS-CoV-2 test were also obtained and analyzed. Additionally, testing of pooled saliva samples was evaluated. RESULTS: The LOD for the QuantiVirus(™) SARS-CoV-2 test was confirmed to be 100–200 copies/mL. The clinical performance studies using contrived saliva samples indicated that the positive percentage agreement (PPA) of the QuantiVirus(™) SARS-CoV-2 test is 100% at 1xLOD, 1.5xLOD and 2.5xLOD. No cross-reactivity was observed for the QuantiVirus(™) SARS-CoV-2 test with common respiratory pathogens. Testing of clinical samples showed a positive percentage agreement (PPA) of 100% (95% CI: 94.6% to 100%) and a negative percentage agreement (NPA) of 98.9% (95% CI: 93.1% to 99.9%). QuantiVirus(™) SARS CoV-2 test had 80% concordance rate and no significant difference (p = 0.13) between paired saliva and NPS specimens by Wilcoxon matched pairs signed rank test. Positive test rate was 1.79% for 389 saliva specimens collected from local communities for COVID-19 screening. Preliminary data showed that saliva sample pooling up to 6 samples (1:6 pooling) for SARS-CoV-2 detection is feasible (sensitivity 94.8% and specificity 100%). CONCLUSION: The studies demonstrated that the QuantiVirus(™) SARS-CoV-2 test has a LOD of 200 copies/mL in contrived saliva samples. The clinical performance of saliva-based testing is comparable to that of NPS-based testing. Pooling of saliva specimens for SARS-CoV-2 detection is feasible. Saliva based and high-throughput QuantiVirus(™) SARS-CoV-2 test offers a highly desirable testing platform during the ongoing COVID-19 pandemic. Public Library of Science 2021-02-23 /pmc/articles/PMC7901781/ /pubmed/33621263 http://dx.doi.org/10.1371/journal.pone.0243183 Text en © 2021 Sun et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Sun, Qing Li, Jonathan Ren, Hui Pastor, Larry Loginova, Yulia Madej, Roberta Taylor, Kristopher Wong, Joseph K. Zhang, Zhao Zhang, Aiguo Lu, Chuanyi M. Sha, Michael Y. Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test |
title | Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test |
title_full | Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test |
title_fullStr | Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test |
title_full_unstemmed | Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test |
title_short | Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test |
title_sort | saliva as a testing specimen with or without pooling for sars-cov-2 detection by multiplex rt-pcr test |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901781/ https://www.ncbi.nlm.nih.gov/pubmed/33621263 http://dx.doi.org/10.1371/journal.pone.0243183 |
work_keys_str_mv | AT sunqing salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT lijonathan salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT renhui salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT pastorlarry salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT loginovayulia salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT madejroberta salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT taylorkristopher salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT wongjosephk salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT zhangzhao salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT zhangaiguo salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT luchuanyim salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest AT shamichaely salivaasatestingspecimenwithorwithoutpoolingforsarscov2detectionbymultiplexrtpcrtest |