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Pooled testing for COVID-19 diagnosis by real-time RT-PCR: A multi-site comparative evaluation of 5- & 10-sample pooling.

Authors :
Praharaj I
Jain A
Singh M
Balakrishnan A
Dhodapkar R
Borkakoty B
Ashok M
Das P
Biswas D
Kalawat U
Turuk J
Sugunan AP
Prakash S
Singh AK
Barathidasan R
Subhadra S
Sabat J
Manjunath MJ
Kanta P
Mudhigeti N
Hazarika R
Mishra H
Abhishek K
Santhalembi C
Dikhit MR
Vijay N
Narayan J
Kaur H
Giri S
Gupta N
Source :
The Indian journal of medical research [Indian J Med Res] 2020 Jul & Aug; Vol. 152 (1 & 2), pp. 88-94.
Publication Year :
2020

Abstract

Background & Objectives: Public health and diagnostic laboratories are facing huge sample loads for COVID-19 diagnosis by real-time reverse transcription-polymerase chain reaction (RT-PCR). High sensitivity of optimized real-time RT-PCR assays makes pooled testing a potentially efficient strategy for resource utilization when positivity rates for particular regions or groups of individuals are low. We report here a comparative analysis of pooled testing for 5- and 10-sample pools by real-time RT-PCR across 10 COVID-19 testing laboratories in India.<br />Methods: Ten virus research and diagnostic laboratories (VRDLs) testing for COVID-19 by real-time RT-PCR participated in this evaluation. At each laboratory, 100 nasopharyngeal swab samples including 10 positive samples were used to create 5- and 10-sample pools with one positive sample in each pool. RNA extraction and real-time RT-PCR for SARS-CoV-2-specific E gene target were performed for individual positive samples as well as pooled samples. Concordance between individual sample testing and testing in the 5- or 10-sample pools was calculated, and the variation across sites and by sample cycle threshold (C <subscript>t</subscript> ) values was analyzed.<br />Results: A total of 110 each of 5- and 10-sample pools were evaluated. Concordance between the 5-sample pool and individual sample testing was 100 per cent in the C <subscript>t</subscript> value ≤30 cycles and 95.5 per cent for C <subscript>t</subscript> values ≤33 cycles. Overall concordance between the 5-sample pooled and individual sample testing was 88 per cent while that between 10-sample pool and individual sample testing was 66 per cent. Although the concordance rates for both the 5- and 10-sample pooled testing varied across laboratories, yet for samples with C <subscript>t</subscript> values ≤33 cycles, the concordance was ≥90 per cent across all laboratories for the 5-sample pools.<br />Interpretation & Conclusions: Results from this multi-site assessment suggest that pooling five samples for SARS-CoV-2 detection by real-time RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools, there may be considerably higher numbers of false negatives. However, testing laboratories should perform validations with the specific RNA extraction and RT-PCR kits in use at their centres before initiating pooled testing.<br />Competing Interests: None

Details

Language :
English
ISSN :
0971-5916
Volume :
152
Issue :
1 & 2
Database :
MEDLINE
Journal :
The Indian journal of medical research
Publication Type :
Academic Journal
Accession number :
32893844
Full Text :
https://doi.org/10.4103/ijmr.IJMR_2304_20