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

  1. Maite Aubry
  2. Iotefa Teiti
  3. Anita Teissier
  4. Vaea Richard
  5. Teheipuaura Mariteragi-Helle
  6. Kiyojiken Chung
  7. Farah Deen
  8. Tuterarii Paoaafaite
  9. Van-Mai Cao-Lormeau

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Abstract

In French Polynesia, the first case of SARS-CoV-2 infection was detected on March 10 th , 2020, in a resident returning from France. Between March 28 th and July 14 th , 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 15 th , 2020, and February 15 th , 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 20 th , 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.

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  1. Version published to 10.1371/journal.pone.0256877
  2. ScreenIT

    SciScore for 10.1101/2021.06.17.21254195: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: The approval for the use of data produced within the framework of the COV-CHECK PORINETIA surveillance strategy was obtained from the ethics committee of French Polynesia (No. 90 CEPF of June 15th, 2021)
    Sex as a biological variablenot detected.
    RandomizationPooling of samples: Upon receipt at ILM, the barcode of each self-collected sample was scanned, and up to 10 self-collected samples were randomly grouped.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Travelers could refer to the instruction sheet received upon arrival and to the video tutorial posted online by the tourism department (available at: https://www.youtube.com/watch?v=pYcOp6tk9bo&feature=emb_logo).
    https://www.youtube.com/watch
    suggested: (GENEtics Video, RRID:SCR_004770)
    In the second protocol, 5 µL of each extracted RNA were added to 15 µL of reaction mixture containing 10 µL of 2X Reaction buffer and 0.5 µL of Reverse Transcriptase provided with iTaq Universal Probes One-Step kit (Bio-Rad, USA)
    iTaq Universal Probes
    suggested: None
    Partial sequences were cleaned and assembled using the Sequencher 4.10 software (Gene Codes Corporation, USA).
    Sequencher
    suggested: (Sequencher, RRID:SCR_001528)
    Statistical analysis: Data were analyzed with GraphPad Prism 7.04.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The COV-CHECK PORINETIA surveillance strategy had some limitations. Indeed, of the 61,397 travelers who were given a self-test kit on arrival, 1,907 (3.11%) did not return their self-collected samples, despite reminders. In addition, since self-collection was not supervised by a health worker, it was impossible to check whether the travelers had correctly collected their samples by strictly following the instructions supplied with the kit. Finally, the pooling samples strategy resulted in a slight loss of sensitivity of the RT-PCR assay compared to individual samples testing (on average 1.17 Ct for the detection of the E gene), probably related to the volume of sample extracted (50 µL versus 200 µL, respectively). Despite these limitations, the surveillance strategy contributed to protect most remote French Polynesia islands with limited health infrastructures from the introduction of SARS-CoV-2 [25]. In addition to the surveillance strategy implemented since July 15th, 2020, travelers were required to apply barrier measures during their stay, thus limiting the risk of contamination of the islands’ population, and to report to the health authorities any symptoms suggestive of COVID-19. Despite these obligations, an asymptomatic traveler whose self-collected sample tested positive but who had not complied with the barrier measures during the 4 days preceding the test generated the first cluster of COVID-19 cases in Tahiti [6]. As of February 15th, 2021, 18,293 cases of COVID-1...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2021.06.17.21254195v1 on medRxiv