Viral detection in wastewaters: Comparison of bioinformatic tools for virome analysis

André F. Santos, Mónica Nunes, Andreia Silva, Teresa Crespo, Victor Pimentel, Marta Pingarilho, Mafalda Miranda, Pieter Libin, R Parreira, AB Abecasis, S.G. Seabra

Research output: Contribution to conferencePoster


Analyses of viral genetic material in wastewaters provide community-level data that can be the basis for early warnings, and efficient tracking of viral pathogen emergence and spread. Unlike traditional species-specific diagnostic methods, a metavirome approach enables a more comprehensive overview of emergent and new potentially pathogenic viruses. By harnessing largescale sequence data collection with advanced algorithms, bioinformatics offers a more holistic
solution to disease surveillance using wastewaters, ensuring timely interventions and enhanced public health outcomes. For viral pathogens, wastewater analysis at the different steps of wastewater treatment is also relevant to understand their effectiveness in decreasing viral content.
In this study we used a random-primer-based sequencing approach combined with next-generation Illumina sequencing to characterize the viral content of influent and effluent waters from two wastewater treatment plants. For viral classification, we used the algorithms implemented in Genome Detective, Kraken2, CZ.ID and INSaFLU and compared the outcomes. The initial results
showed that sequencing throughput was highly variable between samples (ranging between 130,000 to 3,700,000 reads), that the percentage of remaining reads after quality control and human and contaminant filtering also ranged immensely (from 1.18% to 72.38%). Even using a viral enrichment amplification step in the experimental protocol, the proportion of viral reads was very low
(ranging between >0.001 and 8.44%) but a large number of virus families was found, including pathogenic viruses, across all stages of wastewater systems, adverting to inefficiency of removal or degradation of viruses by wastewater treatment processes.
Original languageEnglish
Number of pages1
Publication statusPublished - Dec 2023
EventCongress of Microbiology and Biotechnology 2023 - Covilhã, Portugal
Duration: 7 Dec 20239 Dec 2023


ConferenceCongress of Microbiology and Biotechnology 2023
Abbreviated titleMicrobiotec'23
Internet address


  • metavirome
  • wastewater
  • viral detection


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