The Application of Sample Pooling for Mass Screening of SARS-CoV-2 in an Outbreak of COVID-19 in Vietnam

Abstract

We sampled nasal-pharyngeal throat swabs from 96,123 asymptomatic individuals at risk of SARS-CoV-2 infection, and generated 22,290 pools at collection, each containing samples from two to seven individuals. We detected SARS-CoV-2 in 24 pools, and confirmed the infection in 32 individuals after resampling and testing of 104 samples from positive pools. We completed the testing within 14 days. We would have required 64 days to complete the screening for the same number of individuals if we had based our testing strategy on individual testing. There was no difference in cycle threshold (Ct) values of pooled and individual samples. Thus, compared with individual sample testing, our approach did not compromise PCR sensitivity, but saved 77% of the resources. The present strategy might be applicable in settings, where there are shortages of reagents and the disease prevalence is low, but the demand for testing is high.

Figure 1.

An overview about the strategies of sampling and testing of the collected swabs for SARS-CoV-2. (A) Flowchart illustrating the strategy of obtaining the pooled nasal pharyngeal–throat swabs for primary screening of SARS-CoV-2, and follow-up sampling and testing of individuals of the pools who had a positive SARS-CoV-2 RT-PCR result. (B) Flowchart illustrating the mass community testing for SARS-CoV-2 leading to the detection of 32 cases, including eight belonging to two family clusters. Note to (B) *From the same family of five and three people, respectively, who were all positive for SARS-CoV-2, but were all asymptomatic. This figure appears in color at www.ajtmh.org.

Figure 2.

Plots showing real-time RT-PCR Ct values of pooled nasal pharyngeal–throat swab (NTS) samples and individual NTSs. A total of 24 pooled NTS samples and 32 individual NTS samples were included for analysis. Ct values (median, range): for pooled NTS samples: 30.86 (16–37), for individual NTS samples: 30.33 (15.36–34). P comparison = 0.23.