Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples

被引:9
作者
Baccini, Michela [1 ,2 ]
Rocco, Emilia [1 ,2 ]
Paganini, Irene [3 ]
Mattei, Alessandra [1 ,2 ]
Sani, Cristina [3 ]
Vannucci, Giulia [1 ,2 ]
Bisanzi, Simonetta [3 ]
Burroni, Elena [3 ]
Peluso, Marco [3 ]
Munnia, Armelle [3 ]
Cellai, Filippo [3 ]
Pompeo, Giampaolo [3 ]
Micio, Laura [3 ]
Viti, Jessica [3 ]
Mealli, Fabrizia [1 ,2 ]
Carozzi, Francesca Maria [3 ]
机构
[1] Univ Florence, Dept Stat, Comp Sci, Applicat, Florence, Italy
[2] Univ Florence, Florence Ctr Data Sci, Florence, Italy
[3] Inst Prevent Res & Oncol Network ISPRO, Reg Lab Canc Prevent, Florence, Italy
来源
PLOS ONE | 2021年 / 16卷 / 05期
关键词
LARGE-SCALE; COVID-19;
D O I
10.1371/journal.pone.0251589
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the first emergency phase of the epidemic, RT-qPCR on nasopharyngeal (NP) swabs, which is the most reliable technique to detect ongoing infections, exhibited limitations due to availability of reagents and budget constraints. This stressed the need to develop screening procedures that require fewer resources and are suitable to be extended to larger portions of the population. RT-qPCR on pooled samples from individual NP swabs seems to be a promising technique to improve surveillance. We performed preliminary experimental analyses aimed to investigate the performance of pool testing on samples with low viral load and we evaluated through Monte Carlo (MC) simulations alternative screening protocols based on sample pooling, tailored to contexts characterized by different infection prevalence. We focused on the role of pool size and the opportunity to develop strategies that take advantage of natural clustering structures in the population, e.g. families, school classes, hospital rooms. Despite the use of a limited number of specimens, our results suggest that, while high viral load samples seem to be detectable even in a pool with 29 negative samples, positive specimens with low viral load may be masked by the negative samples, unless smaller pools are used. The results of MC simulations confirm that pool testing is useful in contexts where the infection prevalence is low. The gain of pool testing in saving resources can be very high, and can be optimized by selecting appropriate group sizes. Exploiting natural groups makes the definition of larger pools convenient and potentially overcomes the issue of low viral load samples by increasing the probability of identifying more than one positive in the same pool.
引用
收藏
页数:15
相关论文
共 36 条
  • [1] Abdalhamid B, 2020, AM J CLIN PATHOL, V153, P715, DOI [10.1093/AJCP/AQAA064, 10.1093/ajcp/aqaa064, 10.1101/2020.04.03.20050195]
  • [2] Optimization of group size in pool testing strategy for SARS-CoV-2: A simple mathematical model
    Aragon-Caqueo, Diego
    Fernandez-Salinas, Javier
    Laroze, David
    [J]. JOURNAL OF MEDICAL VIROLOGY, 2020, 92 (10) : 1988 - 1994
  • [3] Assessing the dilution effect of specimen pooling on the sensitivity of SARS-CoV-2 PCR tests
    Bateman, Allen C.
    Mueller, Shanna
    Guenther, Kyley
    Shult, Peter
    [J]. JOURNAL OF MEDICAL VIROLOGY, 2021, 93 (03) : 1568 - 1572
  • [4] A robust pooled testing approach to expand COVID-19 screening capacity
    Bish, Douglas R.
    Bish, Ebru K.
    El-Hajj, Hussein
    Aprahamian, Hrayer
    [J]. PLOS ONE, 2021, 16 (02):
  • [5] Centers for Disease Control and Prevention, 2020, INT GUID COLL HANDL
  • [6] Centers for Disease Control and Prevention, CDC 2019-novel coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel
  • [7] Evaluation of pool-based testing approaches to enable population-wide screening for COVID-19
    de Wolff, Timo
    Pfluger, Dirk
    Rehme, Michael
    Heuer, Janin
    Bittner, Martin-Immanuel
    [J]. PLOS ONE, 2020, 15 (12):
  • [8] COVID-19-New Insights on a Rapidly Changing Epidemic
    del Rio, Carlos
    Malani, Preeti N.
    [J]. JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION, 2020, 323 (14): : 1339 - 1340
  • [9] Eberhardt JN, 2020, J CLIN VIROL, V128, DOI 10.1016/j.jcv.2020.104382
  • [10] Farfan Mauricio J., 2020, Rev. chil. infectol., V37, P276