ReportCORONAVIRUS

Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests

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Science Translational Medicine  14 Apr 2021:
Vol. 13, Issue 589, eabf2823
DOI: 10.1126/scitranslmed.abf2823
  • Fig. 1 Overall statistics of pool sizes of eight and five.

    (A) Weekly average of eight-sample (blue) and five-sample (red) pools counts, together with the weekly average of the prevalence rate among pooled samples (black). (B and C) Pool results for eight-sample (B) and five-sample (C) pools, respectively. (D and E) Counts of positive pools aggregated by the number of positive samples identified within the pool, for eight-sample (D) and five-sample (E) pools.

  • Fig. 2 Comparisons of pool Ct and sample Ct.

    (A) Comparison of sample viral Ct (x axis) and pool viral Ct (y axis) for all 935 amplified eight-sample pools with a single positive sample. Linear regression with a predetermined slope of 1 is marked in yellow, and y = x is marked in gray. (B) As in (A), including also pools with 241 two amplified samples (light blue) and 82 three or more positive samples (gray). (C) Distributions of viral Ct values of positive samples in positive pools divided into two groups: samples with the minimal Ct in their pool (blue) and samples with the nonminimal Ct in their pool (gray).

  • Table 1 Statistics and efficiency of pool sizes of eight and five.

    NA, not applicable.

    Pools of eightPools of fiveAll together
    Total number of pools14,697324817,945
    Number of positive
    pools
    13677172084
    Total number of
    samples
    117,57616,240133,816
    Number of positive
    samples
    19939362929
    Total number of PCR
    reactions
    25,633683332,466
    Prevalence rate1.7%5.8%2.19%
    Optimal (predicted)
    Dorfman efficiency
    3.95532.1891NA
    Our empirical
    efficiency
    4.5872.3774.122
    P value of empirical
    Dorfman efficiency
    <10−50.00584NA

Supplementary Materials

  • stm.sciencemag.org/cgi/content/full/scitranslmed.abf2823/DC1

    Fig. S1. Dorfman efficiency and infection prevalence over time.

    Fig. S2. Weekly average of percentage of positive samples observed over time, for pooled and unpooled samples.

    Table S1. Primers and probes used in multiplex RT-PCR.

    Movie S1. Pooling pipeline protocol.

    Data file S1. Raw data of all viral and human Ct values in the studied samples and pools.

  • The PDF file includes:

    • Materials and methods
    • Fig. S1. Dorfman efficiency and infection prevalence over time.
    • Fig. S2. Weekly average of percentage of positive samples observed over time, for pooled and unpooled samples.
    • Table S1. Primers and probes used in multiplex RT-PCR.

    [Download PDF]

    Other Supplementary Material for this manuscript includes the following:

    • Movie S1. Pooling pipeline protocol. (mp4)
    • Data file S1. Raw data of all viral and human Ct values in the studied samples and pools. (csv)

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