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

Praharaj, Ira; Jain, Amita; Singh, Mini; Balakrishnan, Anukumar; Dhodapkar, Rahul; Borkakoty, Biswajyoti; Ashok, Munivenkatappa; Das, Pradeep; Biswas, Debasis; Kalawat, Usha; Turuk, Jyotirmayee; Sugunan, A.P.; Prakash, Shantanu; Singh, Anirudh K.; Barathidasan, Rajamani; Subhadra, Subhra; Sabat, Jyotsnamayee; Manjunath, M.J.; Kanta, Poonam; Mudhigeti, Nagaraja; Hazarika, Rahul; Mishra, Hricha; Abhishek, Kumar; Santhalembi, C.; Dikhit, Manas Ranjan; Vijay, Neetu; Narayan, Jitendra; Kaur, Harmanmeet; Giri, Sidhartha; Gupta, Nivedita

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. 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(t)) values was analyzed. 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(t) value ≤30 cycles and 95.5 per cent for C(t) 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(t) values ≤33 cycles, the concordance was ≥90 per cent across all laboratories for the 5-sample pools. 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.