Abstract Title
Leveraging real-time genomics for fast and portable avian influenza sequencing.
Abstract
Real-time genomics through nanopore technology enables portable, rapid, and cost-efficient sequencing, which can enhance our understanding of viral disease and transmission dynamics, and improve global surveillance strategies. We here established real-time genomics for monitoring wetlands along global flyways as potential transmission hotspots of avian influenza virus (AIV), other RNA viruses, and antimicrobial resistances.
For AIV monitoring, we first benchmarked the latest direct viral RNA (vRNA) and complementary DNA (cDNA) nanopore chemistries and computational pipelines by genetically profiling a known low-pathogenicity AIV strain. We found that real-time genomic data of both, vRNA and cDNA, can be leveraged to create highly accurate viral consensus sequences, and that vRNA data can in addition describe RNA modifications which play crucial roles in host immune evasion. However, the application to dust samples from a H5N1-positive poultry farm showed us that only cDNA data was sensitive enough for taxonomic profiling of the responsible AIV strain. In an in vivo experiment where minks were infected with gull-origin AIV, we further showed that such real-time genomic data can detect low-frequency genetic variants that point to viral adaptation to mammalian hosts.
We finally employed our real-time genomics-based AIV monitoring protocols together with virome-agnostic SMART-9N for RNA virome profiling and metagenomics for antimicrobial resistance profiling to three wetland sites along the East Atlantic Flyway. We compared non-invasive sampling of water, air, and fecal material, and were able to make first recommendations for cost-efficient, rapid, and on-site real-time genomic surveillance of microbial threats to human and animal health.
For AIV monitoring, we first benchmarked the latest direct viral RNA (vRNA) and complementary DNA (cDNA) nanopore chemistries and computational pipelines by genetically profiling a known low-pathogenicity AIV strain. We found that real-time genomic data of both, vRNA and cDNA, can be leveraged to create highly accurate viral consensus sequences, and that vRNA data can in addition describe RNA modifications which play crucial roles in host immune evasion. However, the application to dust samples from a H5N1-positive poultry farm showed us that only cDNA data was sensitive enough for taxonomic profiling of the responsible AIV strain. In an in vivo experiment where minks were infected with gull-origin AIV, we further showed that such real-time genomic data can detect low-frequency genetic variants that point to viral adaptation to mammalian hosts.
We finally employed our real-time genomics-based AIV monitoring protocols together with virome-agnostic SMART-9N for RNA virome profiling and metagenomics for antimicrobial resistance profiling to three wetland sites along the East Atlantic Flyway. We compared non-invasive sampling of water, air, and fecal material, and were able to make first recommendations for cost-efficient, rapid, and on-site real-time genomic surveillance of microbial threats to human and animal health.
Co-Author(s)
Albert Perlas1,2, Tim Reska1,2,3, Alberto Sánchez-Cano 4, Crisitina Mejías 5,6, Ferran Tarrés-Freixas 11, Guillaume Croville 7, Marta Rusiñol 5,6, Jean-Luc Guérin 7, Natàlia Majó 9, 10, Ursula Höfle 4, Lara Urban 1,2,3
1-Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany
2-Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany
3-Technical University of Munich, School of Life Sciences, Freising, Germany
4-SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC, (CSIC-UCLM-JCCM), Ciudad Real, Spain
5-Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
6-The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
7-IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
9-Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
10-Unitat mixta d’investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain
11-IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
Abstract Category
Notable outbreaks, field and molecular epidemiology, and surveillance in wild birds