Leveraging real-time genomics for fast and portable avian influenza sequencing | LC 25

Biography

Albert Perlas is a postdoctoral researcher at Helmholtz Munich, specializing in avian influenza. His research focuses on understanding viral dynamics and evolution to enhance disease surveillance and preparedness. With a strong commitment to the One Health approach, he aims to improve global health by addressing the interconnections between human, animal, and environmental health. Through innovative sampling tools and sequencing technologies, Albert works towards developing better strategies for detecting, monitoring, and controlling avian influenza and other emerging infectious diseases.

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. Here, we established real-time genomics for monitoring wetlands along global flyways as potential transmission hotspots of avian influenza virus (AIV), other RNA viruses, and antimicrobial resistance. 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 an 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. Finally, we 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.