SARS-CoV-2 RNA detection using pooling of self-collected samples: Simple protocol may foster asymptomatic surveillance

  1. Giselle Ibette Lopez-Lopes
  2. Rita de Cassia Compagnoli Carmona
  3. Valéria Oliveira Silva
  4. Cintia Mayumi Ahagon
  5. Lincoln Spinazola do Prado
  6. Fabiana Pereira dos Santos
  7. Daniela Bernardes Borges da Silva
  8. Katia Corrêa de Oliveira Santos
  9. Margarete Aparecida Benega
  10. Willian Nery Ribeiro
  11. Audrey Cilli
  12. Elaine Monteiro Matsuda
  13. Ana Maria Sardinha Afonso
  14. Maria do Carmo Sampaio Tavares Timenetsky
  15. Luís Fernando de Macedo Brígido

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Abstract

1

Background

Surveillance of COVID infection and isolation of infected individuals is one of the available tools to control the spread of SAR-CoV-2. Asymptomatic and pre symptomatic are responsible for substantial transmission. RNA or antigen tests are necessary to identify non-symptomatic individuals. We tested the feasibility of using samples pooling offering different collection alternatives (swab/throat wash/saliva) to volunteers of a public health institute.

Methods

We evaluated pool samples from frozen material from previously tested samples and a prospective collection from asymptomatic volunteers. Some collections were paired for comparison. Pools and some individual samples were extracted with QIAamp Viral RNA Mini Kit ( Qiagen , USA) and/or Lucigen Quick Extract DNA extraction solution (BioSearch, USA) and submitted to rtPCR (Allplex, Seegene, Korea).

Results

A total of 240 samples from 130 new collections and 37 samples with known result were evaluated. Pool CT was generally higher than individual samples. Lucigen extraction showed higher CT, including false negative results for samples with high CT at Qiagen extraction. Paired Swab and TW samples showed comparable results. No volunteer from negative pools reported any symptom in the 2-3 days after collection.

Conclusions

Clinical samples pooling to detect SARS-CoV-2 RNA is feasible and an economical way to test for COVID-19, especially in surveillance strategies targeting more infectiousness, higher viremia individuals. The use of Lucigen reagents show lower sensibility that may lead to false negative results with lower viremia samples. Combining throat wash with saliva may provide and interesting self-collection alternative, but more comparative work is needed.

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  1. ScreenIT

    SciScore for 10.1101/2020.10.05.20205872: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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:
    On the other hand, not only the relative high cost, especially to Low- and Middle-Income Countries (LMIC) of equipment and specialized molecular biology work force, but also the current limitations of these resources, as well as key reagents and demand for rt-qPCR machines, may suggest an important cost-effective advantage to the pooling option. We used relative small pools so we could process and give results in a same-day results, but some groups suggest larger pools, up to 32 individuals (Yelin 2020). Recently the FDA has recently stimulated the evaluation of pooling strategies (FDA 2020). One major drawback in pooling procedure is the number of times one will need to break a pool to identify one or more positive cases. In epidemiological scenarios with high prevalence, pooling may not be attractive, but in low prevalence scenarios, as among asymptomatic monitoring in environments were infection is not yet rampant (Yates, 2020). Pooling can provide cost effective surveillance and may actually increase testing capacity. Moreover, in some situations, pooling could be used to identify viral circulation, and the individual identification step could be omitted. This is especially true for pooling test of related people, as part of a same “epidemiological bubble”. For example, in some school returning activity, one positive test in a cohort of students may lead to home activities, for a couple of weeks, for all the group part of the pool, even in negative cases identified in ind...

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.10.05.20205872 on medRxiv