Evaluations of modes of pooling specimens for COVID-19 screened by quantitative PCR and droplet digital PCR.
Pooled specimens
SARS-CoV-2
Sampling swab
Sensitivity
Swab pooling
Virus preservation solution
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
13 05 2024
13 05 2024
Historique:
received:
11
08
2023
accepted:
08
05
2024
medline:
14
5
2024
pubmed:
14
5
2024
entrez:
13
5
2024
Statut:
epublish
Résumé
Though pooling samples for SARS-CoV-2 detection has effectively met the need for rapid diagnostic and screening tests, many factors can influence the sensitivity of a pooled test. In this study, we conducted a simulation experiment to evaluate modes of pooling specimens and aimed at formulating an optimal pooling strategy. We focussed on the type of swab, their solvent adsorption ability, pool size, pooling volume, and different factors affecting the quality of preserving RNA by different virus solutions. Both quantitative PCR and digital PCR were used to evaluate the sampling performance. In addition, we determined the detection limit by sampling which is simulated from the virus of different titers and evaluated the effect of sample-storage conditions by determining the viral load after storage. We found that flocked swabs were better than fibre swabs. The RNA-preserving ability of the non-inactivating virus solution was slightly better than that of the inactivating virus solution. The optimal pooling strategy was a pool size of 10 samples in a total volume of 9 mL. Storing the collected samples at 4 °C or 25 °C for up to 48 h had little effect on the detection sensitivity. Further, we observed that our optimal pooling strategy performed equally well as the single-tube test did. In clinical applications, we recommend adopting this pooling strategy for low-risk populations to improve screening efficiency and shape future strategies for detecting and managing other respiratory pathogens, thus contributing to preparedness for future public health challenges.
Identifiants
pubmed: 38740976
doi: 10.1038/s41598-024-61631-0
pii: 10.1038/s41598-024-61631-0
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
10923Subventions
Organisme : National Natural Science Foundation of China
ID : 82041027
Organisme : The Capital Health Development and Research of Special
ID : 2022-1G-3014
Organisme : National Key R&D Program of China
ID : 2021ZD0114100
Organisme : National Key R&D Program of China
ID : 2021ZD0114103
Organisme : Beijing Science and Technology Planning Project of Beijing Science and Technology Commission
ID : Z211100002521015
Organisme : Beijing Science and Technology Planning Project of Beijing Science and Technology Commission
ID : Z211100002521019
Organisme : the Cultivation Fund of Beijing Center for Disease Prevention and Control
ID : 2020-BJYJ-22
Organisme : Horizontal scientific research cooperation project
ID : 2022-jk-cd-021
Organisme : High-level public health technical talent construction project
ID : Key member-02-11
Informations de copyright
© 2024. The Author(s).
Références
Zou, L. et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N. Engl. J. Med. 382, 1177–1179 (2020).
doi: 10.1056/NEJMc2001737
pubmed: 32074444
pmcid: 7121626
Umakanthan, S. et al. Origin, transmission, diagnosis and management of coronavirus disease 2019 (COVID-19). Postgrad. Med. J. 96, 753–758. https://doi.org/10.1136/postgradmedj-2020-138234 (2020).
doi: 10.1136/postgradmedj-2020-138234
pubmed: 32563999
Majumder, J. & Minko, T. Recent developments on therapeutic and diagnostic approaches for COVID-19. AAPS J. 23, 14. https://doi.org/10.1208/s12248-020-00532-2 (2021).
doi: 10.1208/s12248-020-00532-2
pubmed: 33400058
Langford, B. J. et al. Bacterial co-infection and secondary infection in patients with COVID-19: A living rapid review and meta-analysis. Clin. Microbiol. Infect. 26, 1622–1629. https://doi.org/10.1016/j.cmi.2020.07.016 (2020).
doi: 10.1016/j.cmi.2020.07.016
pubmed: 32711058
pmcid: 7832079
Li, L. et al. Effect of convalescent plasma therapy on time to clinical improvement in patients with severe and life-threatening COVID-19: A randomized clinical trial. JAMA 324, 460–470. https://doi.org/10.1001/jama.2020.10044 (2020).
doi: 10.1001/jama.2020.10044
pubmed: 32492084
Zhou, Y. et al. Sensitivity evaluation of 2019 novel coronavirus (SARS-CoV-2) RT-PCR detection kits and strategy to reduce false negative. PLoS One 15, e0241469. https://doi.org/10.1371/journal.pone.0241469 (2020).
doi: 10.1371/journal.pone.0241469
pubmed: 33206690
pmcid: 7673793
Smith, E. et al. Analytical and clinical comparison of three nucleic acid amplification tests for SARS-CoV-2 detection. J. Clin. Microbiol. 58, e01134-01120 (2020).
doi: 10.1128/JCM.01134-20
Sharfstein, J. M., Becker, S. J. & Mello, M. M. Diagnostic testing for the novel coronavirus. JAMA 323, 1437–1438. https://doi.org/10.1001/jama.2020.3864 (2020).
doi: 10.1001/jama.2020.3864
pubmed: 32150622
Corman, V. M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045 (2020).
doi: 10.2807/1560-7917.ES.2020.25.3.2000045
pubmed: 33243353
pmcid: 7693167
Chaimayo, C. et al. Rapid SARS-CoV-2 antigen detection assay in comparison with real-time RT-PCR assay for laboratory diagnosis of COVID-19 in Thailand. Virol. J. 17, 177. https://doi.org/10.1186/s12985-020-01452-5 (2020).
doi: 10.1186/s12985-020-01452-5
pubmed: 33187528
pmcid: 7665091
Lohse, S. et al. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. Lancet Infect. Dis. 20, 1231–1232. https://doi.org/10.1016/s1473-3099(20)30362-5 (2020).
doi: 10.1016/s1473-3099(20)30362-5
pubmed: 32530425
pmcid: 7194818
Yu, J., Huang, Y. & Shen, Z. J. Optimizing and evaluating PCR-based pooled screening during COVID-19 pandemics. Sci. Rep. 11, 21460. https://doi.org/10.1038/s41598-021-01065-0 (2021).
doi: 10.1038/s41598-021-01065-0
pubmed: 34728759
pmcid: 8564549
Mercer, T. R. & Salit, M. Testing at scale during the COVID-19 pandemic. Nat. Rev. Genet. 22, 415–426. https://doi.org/10.1038/s41576-021-00360-w (2021).
doi: 10.1038/s41576-021-00360-w
pubmed: 33948037
pmcid: 8094986
Lagopati, N. et al. Sample pooling strategies for SARS-CoV-2 detection. J. Virol. Methods 289, 114044. https://doi.org/10.1016/j.jviromet.2020.114044 (2021).
doi: 10.1016/j.jviromet.2020.114044
pubmed: 33316285
de Salazar, A. et al. Sample pooling for SARS-CoV-2 RT-PCR screening. Clin. Microbiol. Infect. 26, 1687 e1681-1687 e1685. https://doi.org/10.1016/j.cmi.2020.09.008 (2020).
doi: 10.1016/j.cmi.2020.09.008
Abdalhamid, B. et al. Assessment of specimen pooling to conserve SARS CoV-2 testing resources. Am. J. Clin. Pathol. 153, 715–718. https://doi.org/10.1093/ajcp/aqaa064 (2020).
doi: 10.1093/ajcp/aqaa064
pubmed: 32304208
pmcid: 7188150
Abid, S. et al. Assessment of sample pooling for SARS-CoV-2 molecular testing for screening of asymptomatic persons in Tunisia. Diagn. Microbiol. Infect. Dis. 98, 115125. https://doi.org/10.1016/j.diagmicrobio.2020.115125 (2020).
doi: 10.1016/j.diagmicrobio.2020.115125
pubmed: 32768876
pmcid: 7335417
Hogan, C. A., Sahoo, M. K. & Pinsky, B. A. Sample pooling as a strategy to detect community transmission of SARS-CoV-2. JAMA 323, 1967–1969. https://doi.org/10.1001/jama.2020.5445 (2020).
doi: 10.1001/jama.2020.5445
pubmed: 32250394
pmcid: 7136853
Lohse, S. et al. Challenges and issues of SARS-CoV-2 pool testing—Authors’ reply. Lancet Infect. Dis. 20, 1234–1235. https://doi.org/10.1016/s1473-3099(20)30455-2 (2020).
doi: 10.1016/s1473-3099(20)30455-2
pubmed: 32679086
pmcid: 7836822
Watkins, A. E. et al. Pooling saliva to increase SARS-CoV-2 testing capacity. medRxiv https://doi.org/10.1101/2020.09.02.20183830 (2020).
doi: 10.1101/2020.09.02.20183830
pubmed: 32909003
pmcid: 7480055
Chen, F. et al. Comparing two sample pooling strategies for SARS-CoV-2 RNA detection for efficient screening of COVID-19. J. Med. Virol. 93, 2805–2809. https://doi.org/10.1002/jmv.26632 (2021).
doi: 10.1002/jmv.26632
pubmed: 33107614
Christoff, A. P. et al. Swab pooling: A new method for large-scale RT-qPCR screening of SARS-CoV-2 avoiding sample dilution. PLoS One 16, e0246544. https://doi.org/10.1371/journal.pone.0246544 (2021).
doi: 10.1371/journal.pone.0246544
pubmed: 33539474
pmcid: 7861376
Centers For Disease Control And Prevention, Interim Guidance for Use of Pooling Procedures in SARS-CoV-2 Diagnostic and Screening Testing. https://www.cdc.gov/coronavirus/2019-ncov/lab/pooling-procedures.html (2021).
Ambrosi, C. et al. SARS-CoV-2: Comparative analysis of different RNA extraction methods. J. Virol. Methods https://doi.org/10.1016/j.jviromet.2020.114008 (2021).
doi: 10.1016/j.jviromet.2020.114008
pubmed: 33160015
Dang, Y. et al. Comparison of qualitative and quantitative analyses of COVID-19 clinical samples. Clin. Chim. Acta 510, 613–616. https://doi.org/10.1016/j.cca.2020.08.033 (2020).
doi: 10.1016/j.cca.2020.08.033
pubmed: 32858058
pmcid: 7446654
Li, H. et al. Application of droplet digital PCR to detect the pathogens of infectious diseases. Biosci. Rep. https://doi.org/10.1042/bsr20181170 (2018).
Garg, J. et al. Evaluation of sample pooling for diagnosis of COVID-19 by real time-PCR: A resource-saving combat strategy. J. Med. Virol. 93, 1526–1531. https://doi.org/10.1002/jmv.26475 (2020).
doi: 10.1002/jmv.26475
pubmed: 32869865
Tan, C. et al. Applications of digital PCR in COVID‐19 pandemic. View https://doi.org/10.1002/viw.20200082 (2021).
doi: 10.1002/viw.20200082
pubmed: 34766158
Wagner, K. et al. A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva. Sci. Rep. https://doi.org/10.1038/s41598-023-29858-5 (2023).
doi: 10.1038/s41598-023-29858-5
pubmed: 38114575
pmcid: 10730523
Mahmoud, S. A. et al. Evaluation of pooling of samples for testing SARS-CoV-2 for mass screening of COVID-19. BMC Infect. Dis. https://doi.org/10.1186/s12879-021-06061-3 (2021).
doi: 10.1186/s12879-021-06061-3
pubmed: 34284735
pmcid: 8293485
Vasudevan, H. N. et al. Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification. Sci. Rep. https://doi.org/10.1038/s41598-020-80715-1 (2021).
doi: 10.1038/s41598-020-80715-1
pubmed: 34599198
pmcid: 8486835
Weng, Y., Zhou, J. & Shi, Y. A virus preservation solution that inactivates the virus while maintaining the virus particle intact. Ann. Transl. Med. 10, 1064–1064. https://doi.org/10.21037/atm-22-4295 (2022).
doi: 10.21037/atm-22-4295
pubmed: 36330392
pmcid: 9622497
Lian, J.-S. et al. Comparison of epidemiological and clinical characteristics of COVID-19 patients with and without Wuhan exposure. J. Zhejiang Univ. Sci. B 21, 369–377. https://doi.org/10.1631/jzus.B2000112 (2020).
doi: 10.1631/jzus.B2000112
pubmed: 32425002
pmcid: 7210103
Wu, H.-X. et al. Clinical evaluation of bacterial DNA using an improved droplet digital PCR for spontaneous bacterial peritonitis diagnosis. Front. Cell. Infect. Microbiol. https://doi.org/10.3389/fcimb.2022.876495 (2022).
doi: 10.3389/fcimb.2022.876495
pubmed: 36846550
pmcid: 9813413
Perez-Zabaleta, M. et al. Long-term SARS-CoV-2 surveillance in the wastewater of Stockholm: What lessons can be learned from the Swedish perspective?. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2022.160023 (2023).
doi: 10.1016/j.scitotenv.2022.160023
pubmed: 37120021