Assessment of the feasibility of pool testing for SARS-CoV-2 infection screening

Abstract

Background

SARS-CoV-2 pandemic represented a huge challenge for national health systems worldwide. Pooling nasopharyngeal (NP) swabs seems to be a promising strategy, saving time and resources, but it could reduce the sensitivity of the RT-PCR and exacerbate samples management in terms of automation and tracing. In this study, taking advantage of the routine implementation of a screening plan on health workers, we evaluated the feasibility of pool testing for SARS-CoV-2 infection diagnosis in the presence of low viral load samples.

Method

Pools were prepared with an automated instrument, mixing 4, 6 or 20 NP specimens, including one, two or none positive samples. Ct values of positive samples were on average about 35 for the four genes analyzed.

Results

The overall sensitivity of 4-samples and 6-samples pools was 93.1 and 90.0%, respectively. Focussing on pools including one sample with Ct value ≥35 for all analyzed genes, sensitivity decreased to 77.8 and 75.0% for 4- and 6-samples, respectively; pools including two positive samples, resulted positive in any size as well as pools including positive samples with Ct values <35.

Conclusion

Pool testing strategy should account the balance between cost-effectiveness, dilution effect and prevalence of the infection. Our study demonstrated the good performances in terms of sensitivity and saving resources of pool testing mixing 4 or 6 samples, even including low viral load specimens, in a real screening context possibly affected by prevalence fluctuation. In conclusion, pool testing strategy represents an efficient and resources saving surveillance and tracing tool, especially in specific context like schools, even for monitoring changes in prevalence associated to vaccination campaign.

Keywords:

• SARS-CoV-2
• pooling
• molecular diagnosis
• COVID-19

Acknowledgement

No specific funding was received for the work reported here.

Ethical approval

The study was performed in accordance with the ethical standards as laid down in the 1964 Declaration of Helsinki and its later amendments. The beginning of this study was communicated to the local ethics committee in November 2020, but ethical approval was not needed because this feasibility project is included in the activities planned by Tuscany region on August 2020 (prot. N. 0287180).

Author contributions

FMC and GMR conceived the paper. IP, CS, BS, BE, CF, GP, JV, AA, CC and MC conducted the investigations. MB and FM perfomed statistical analysis. IP, CS, FC and MB wrote the first draft of the manuscript. All authors contributed to, and endorsed the final version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).