Self-collection and pooling of samples as resources-saving strategies for RT-PCR-based SARS-CoV-2 surveillance, the example of travelers in French Polynesia

Abstract

In French Polynesia, the first case of SARS-CoV-2 infection was detected on March 10th, 2020, in a resident returning from France. Between March 28th and July 14th, international air traffic was interrupted and local transmission of SARS-CoV-2 was brought under control, with only 62 cases recorded. The main challenge for reopening the air border without requiring travelers to quarantine on arrival was to limit the risk of re-introducing SARS-CoV-2. Specific measures were implemented, including the obligation for all travelers to have a negative RT-PCR test for SARS-CoV-2 carried out within 3 days before departure, and to perform another RT-PCR testing 4 days after arrival. Because of limitation in available medical staff, travelers were provided a kit allowing self-collection of oral and nasal swabs. In addition to increase our testing capacity, self-collected samples from up to 10 travelers were pooled before RNA extraction and RT-PCR testing. When a pool tested positive, RNA extraction and RT-PCR were performed on each individual sample. We report here the results of COVID-19 surveillance (COV-CHECK PORINETIA) conducted between July 15th, 2020, and February 15th, 2021, in travelers using self-collection and pooling approaches. We tested 5,982 pools comprising 59,490 individual samples, and detected 273 (0.46%) travelers positive for SARS-CoV-2. A mean difference of 1.17 Ct (CI 95% 0.93–1.41) was found between positive individual samples and pools (N = 50), probably related to the volume of samples used for RNA extraction (200 μL versus 50 μL, respectively). Retrospective testing of positive samples self-collected from October 20th, 2020, using variants-specific amplification kit and spike gene sequencing, found at least 6 residents infected by the Alpha variant. Self-collection and pooling approaches allowed large-scale screening for SARS-CoV-2 using less human, material and financial resources. Moreover, this strategy allowed detecting the introduction of SARS-CoV-2 variants of concern in French Polynesia.

An improvement of current hypercube pooling PCR tests for SARS-CoV-2 detection

“…The prevalence of infection is unknown when conducting large-scale screening. Therefore, we recommend to begin pooling with edge = 2, which produces the maximum dimension that satisfies Equation (2). Subsequently, the prevalence can be calculated, and the strategy for the rest of the tests can be adjusted.…”

“…In that case, we wondered the following: (1) if the quantization effect does influence efficiency, is hypercube pooling with edge three really the best strategy? And (2), if the answer is no, what is the best edge and dimension?…”

Perspective on the Use of Innovative Surveillance Strategies Implemented for COVID-19 to Prevent Mosquito-Borne Disease Emergence in French Polynesia

“…To prevent new viral introductions, travelers entering French Polynesia had the obligation to present a negative result in a SARS-CoV-2 RT-PCR test performed within the 3 days before departure. In addition, an innovative strategy consisting of using self-collected and pooled oral and nasal samples for RT-PCR-based surveillance of SARS-CoV-2 in travelers was implemented [ 14 , 15 ]. However, it could not prevent the re-introduction of SARS-CoV-2 in French Polynesia, and an outbreak started in August 2020 [ 12 ].…”

“…In order to increase testing capacity, biological samples from several travelers should be pooled before molecular diagnostics, as previously described for the surveillance of SARS-CoV-2 [ 14 , 15 ]. Adjustments to the pooling protocol (i.e., selection of the number and volume of individual samples to pool) might be required depending on the type of sample used (venous blood, capillary blood, saliva, or other).…”

SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability

“…Therefore, a widely used strategy for infection surveillance is PCR-based pool testing, which has been used in the educational setting as well. The advantage of this testing strategy is the higher sensitivity of the PCR test, and the pooling of individual samples makes the procedure more cost-effective and less resource-intensive [11][12][13][14]. Pool testing is especially effective when the infection prevalence is low [15,16].…”