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 B1.1.7 UK 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 in French Polynesia.

Real-time surveillance of international SARS-CoV-2 prevalence using systematic traveller arrival screening

“…To show how this approach can be used mid-pandemic, we analysed traveller data collected as part of the COVID-19 response in French Polynesia [15]. Between July 2020 and March 2022, more than 222,000 traveller tests were conducted as part of an arrival screening programme (Figure 3A).…”

“…Travel testing in French Polynesia was conducted in two distinct phases, with some additional adjustments to protocols during each phase. The first phase, between 15 th July 2020 and 30 th April 2021, was the ‘COV-CHECK’ system, with travellers required to perform a PCR test less than 72 hours before departure as well as a self-test four days after arrival in French Polynesia [15]. Mandatory quarantine was added to this protocol on 20 th February 2021.…”