Detection of SARs-CoV-2 in wastewater using the existing environmental surveillance network: A potential supplementary system for monitoring COVID-19 transmission

  1. Salmaan Sharif
  2. Aamer Ikram
  3. Adnan Khurshid
  4. Muhammad Salman
  5. Nayab Mehmood
  6. Yasir Arshad
  7. Jamal Ahmed
  8. Rana Muhammad Safdar
  9. Lubna Rehman
  10. Ghulam Mujtaba
  11. Jaffar Hussain
  12. Johar Ali
  13. Mehar Angez
  14. Muhammad Masroor Alam
  15. Ribqa Akthar
  16. Muhammad Wasif Malik
  17. Mirza Zeeshan Iqbal Baig
  18. Muhammad Suleman Rana
  19. Muhammad Usman
  20. Muhammad Qaisar Ali
  21. Abdul Ahad
  22. Nazish Badar
  23. Massab Umair
  24. Sana Tamim
  25. Asiya Ashraf
  26. Faheem Tahir
  27. Nida Ali

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Abstract

The ongoing COVID-19 pandemic is caused by SARs-CoV-2. The virus is transmitted from person to person through droplet infections i.e. when infected person is in close contact with another person. In January 2020, first report of detection of SARS-CoV-2 in faeces, has made it clear that human wastewater might contain this virus. This may illustrate the probability of environmentally facilitated transmission, mainly the sewage, however, environmental conditions that could facilitate faecal oral transmission is not yet clear. We used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value. A total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID 19 patients and quarantine center strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater. This study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as supplementary system to monitor viral tracking and circulation in cities with lower COVID-19 testing capacity or heavily populated areas where door-to-door tracing may not be possible. However, attention is needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.

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  1. Version published to 10.1371/journal.pone.0249568
  2. Version published to 10.1101/2020.06.03.20121426v3 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.03.20121426: (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

    Software and Algorithms
    SentencesResources
    The nucleotide sequences were assembled, edited and analyzed by Sequencher software v.4.9 (
    Sequencher
    suggested: (Sequencher, RRID:SCR_001528)
    The nucleotide sequence obtained was blasted against the available NCBI databank (https://blast.ncbi.nlm.nih.gov/Blast.cgi).
    https://blast.ncbi.nlm.nih.gov/Blast.cgi
    suggested: (TBLASTX, RRID:SCR_011823)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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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  4. Version published to 10.1101/2020.06.03.20121426v2 on medRxiv
  5. Version published to 10.1101/2020.06.03.20121426v1 on medRxiv