A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia

  1. Polina Alexandrovna Kuryntseva
  2. Kamalya Oktay Karamova
  3. Valentin Petrovich Fomin
  4. Svetlana Yurevna Selivanovskaya
  5. Polina Yurevna Galitskaya

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Abstract

The number of registered cases of COVID-19 is increasing in the world, and some countries are reporting a second wave of the pandemic. Accurate and real time information about epidemiological situation is therefore urgently needed for managing decisions in the countries, regions and municipalities which are affected. Massive testing of viral presence in people’s saliva, a smear from the nose, nasopharynx and / or oropharynx, bronchial lavage water obtained by fibrobronchoscopy (bronchoalveolar lavage), as well as from (endo) tracheal, nasopharyngeal aspirate, sputum, biopsy or autopsy material of the lungs, whole blood, serum or antibodies presence in blood cannot give relevant information about the COVID-19 infection rate in the community since simultaneous testing of the whole community is not technically possible, the information obtained in testing of specific groups is retarded and, in addition, such testing is expensive. The alternative to mass testing of the population is the testing of wastewater that could contain SARS-CoV-2 particles originating from excreta. Such testing has several limitations connected with the particularities of the testing procedure.

In the present study, a modified approach for detection of COVID-19 infection rate using wastewater analysis has been developed. The approach includes i) the creation of a calibration curve on the basis of the serial dilution of excreta collected from people who are infected with COVID-19 and ii) the analysis of the wastewater samples and their serial dilutions, the approach excludes usage of concentrating techniques before wastewater sample analysis as well as usage of external control in RT-PCR reactions for calculation of numbers of viral particles. The minimum infection rate that can be detected using this approach is 10-2%. The approach developed was used to investigate wastewater from eleven sewage inspection chambers in the city of Kazan (Russia). It was demonstrated that the average infection rate of people using these sewers was over 0.4% in July 2020.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.21.20197244: (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:
    However, the classical WBE approach that includes concentration of the sample, PCR based detection and calculation of the viral particle numbers has several limitations. There are additional limitations especially for SARS-CoV-2 viral particle determination, since this virus is an RNA-based one, and therefore RT reaction is included in the determination procedure, and the probability of RT efficiency may also differ depending on many factors. Thus, it has been shown that the detection efficiency of SARS-CoV-2 viral particles ranges from 8.5 to 71.6% depending on the concentration method and the volume of the concentrated sample (Hata et al.; Medema et al., 2020; Haramoto et al., 2020; Kitajima et al., 2020). The results obtained may be dependent on molecular process control that can strongly vary in different lab protocols and influence the final results. As such, a control of other coronaviruses as well as mouse hepatitis virus, coliphage MS2 (ATCC 15597-B1), tobacco mosaic virus, Pseudomonas phage Φ6 and Murine norovirus have been used in different studies (Hata et al.; Medema et al., 2020; Haramoto et al., 2020; Kitajima et al., 2020). The complexity of the wastewater matrix also limits the detection accuracy SARS-CoV-2. For example, organic components like fat, protein or humic substances are reported to influence the efficiency of RT and PCR reaction. Besides, viruses of the same family or genus can interfere during RT-PCR reaction (Sims & Kasprzyk-Hordern, 2020; Farkas ...

    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

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  2. Version published to 10.1101/2020.09.21.20197244v1 on medRxiv