Viral surveillance in wastewaters: Improving sample processing steps and bioinformatics protocols

S.G. Seabra, M. Nunes, André F. Santos, Victor Pimentel, Aires Moura, Filipe Tomaz, Seixas G, Inês M. Alves, Mafalda Miranda, Daniela Alves, Diocreciano Bero, Sadia Pereira, A.P. Abílio, Carlos São-José, A Domingos, Marta Pingarilho, AB Abecasis, R Parreira

Research output: Contribution to conferencePosterpeer-review


Background: Wastewater monitoring is used worldwide for early detection of viral pathogens. A meta- genomic approach to virome sequencing in these complex samples would be relevant for surveillance of emerging and novel pathogenic viruses, including those of zoonotic origin. The WasteWaterVir exploratory project aimed to address the technical challenges of wastewater sample processing and virome bioinfor- matics analyses, with a focus on developing protocols for use in resource limited settings.
Methods: We tested the use of alternative processing methods, using samples from the influent of was- tewater treatment plants in Lisbon and Alentejo, as well as virus-spiked synthetic wastewater. We also tested a viral enrichment strategy using non-targeted amplification followed by nanopore sequencing and viral taxonomic identification using the CZ.ID cloud-based platform.
Results: The approach of using a hygienic tampon absorption method, followed by the use of Nanotrap Mi- crobiome Particles for virus capture, was successful in capturing viruses that had been spiked into synthe- tic wastewater, even after heat inactivation. The non-targeted amplification method was biased towards certain types of viruses, and a more targeted approach to families of viruses of interest, using a battery of degenerate primers, will be explored in the future.
Conclusions: The development of protocols for viral monitoring in wastewater will contribute to the appli- cation of a One Health approach to the detection of emerging infectious diseases based on environmental sampling, which is essential for the prevention and control of epidemics.
Funding: This work was funded by Fundação para a Ciência e Tecnologia (FCT) through funds to GHTM - UID/04413/2020 and LA-REAL – LA/P/0117/2020. S.G.S. was funded by FCT, Portugal, through contrato- -programa 1567 (CEECINST/00102/2018).
Original languageEnglish
Number of pages1
Publication statusPublished - 3 Dec 2023
Event2nd Egas Moniz One Health Symposium - Egas Moniz Campus, Monte da Caparica, Almada, Portugal
Duration: 3 Nov 20233 Nov 2023


Conference2nd Egas Moniz One Health Symposium
Internet address


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