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Application and development of viral Identification tools for metavirome analysis of wastewaters
Publication . Santos, André Filipe Bruno de Oliveira Tomás dos; Seabra, Sofia; Abecasis, Ana; Parreira, Ricardo
Wastewater surveillance has become an essential method for monitoring viral commu- nities, particularly in understanding the spread of human pathogenic viruses and bacterio- phages in the environment. This study aimed to assess the effectiveness and consistency of multiple bioinformatic pipelines in identifying viral communities from wastewater samples. Viral sequences were extracted from wastewater samples collected from two wastewater treat- ment plants (WWTPs) in Lisbon, Portugal, and analyzed using four bioinformatics tools: Ge- nome Detective, CZ.ID, INSaFLU-TELEVIR, and Kraken2. The comparison focused on viral occurrence, abundance, alpha and beta diversity metrics, and the proportion of viral reads related to the overall sequencing effort. Our results revealed significant variation between the tools in viral identification perfor- mance, with INSaFLU-TELEVIR and CZ.ID showing the highest rates of viral classification. Additionally, we explored the correlation between crAssphage, a marker for human fecal con- tamination, and other human pathogenic viruses. The findings highlighted the potential of wastewater metagenomics in identifying emerging and known pathogens, offering valuable insights into viral diversity and the reliability of various bioinformatic approaches. The study emphasizes the importance of tool selection and bioinformatics workflow in optimizing wastewater-based epidemiology for public health surveillance.
2024-11Dissertação de mestrado Acesso aberto Ver mais

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Fundação para a Ciência e a Tecnologia

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Concurso para Financiamento de Projetos de Investigação Científica e Desenvolvimento Tecnológico em Todos os Domínios Científicos - 2017

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PTDC/CTA-AMB/29586/2017

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