Biology subjects

Perlas, A.

Publications and source records attributed to Perlas, A..

3 recordsLinked to original sources

bioRxiv2025

Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems

Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens typically requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data, and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites, and used environmental DNA (eDNA) to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/674394v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1a006f2org.highwire.dtl.DTLVardef@12824c2org.highwire.dtl.DTLVardef@8554bdorg.highwire.dtl.DTLVardef@17e800e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Latest RNA and DNA nanopore sequencing allows for rapid avian influenza profiling

Avian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and wild mammals, thus posing a major threat to global health and underscoring the need for efficient monitoring of its distribution and evolution. Here, we utilized a well-defined AIV strain to systematically investigate AIV characterization through rapid, portable nanopore sequencing by (i) benchmarking the performance of fully portable RNA extraction and viral detection; (ii) comparing the latest DNA and RNA nanopore sequencing approaches for in-depth AIV profiling; and (iii) evaluating the performance of various computational pipelines for viral consensus sequence creation and phylogenetic analysis. Our results show that the latest RNA-specific nanopores can accurately genomically profile AIV from native RNA while additionally detecting RNA epigenetic modifications. We further identified an optimal laboratory and bioinformatic pipeline for reconstructing viral consensus genomes from nanopore sequencing data at various rarefaction thresholds, which we validated by application to real-world environmental samples for AIV monitoring in livestock. Author SummaryWe tested portable, rapid, and easy-to-use technology to obtain more information about the potentially zoonotic RNA virus avian influenza virus, or AIV. AIV has spread globally via the migratory paths of wild birds, and endangers domestic birds, mammals, and human populations given past evidence of infections of different animal species. We here used novel genomic technology that is based on nanopores to explore the genomes of the virus; we established optimized ways of creating the viral genome by comparing different laboratory and computational approaches and the performance of nanopores that either sequence the viral RNA directly or the converted DNA. We then applied the optimized protocol to dust samples which were collected from a duck farm in France during an AIV outbreak. We showed that we were able to use the resulting data to reconstruct the relationship between the virus responsible for the outbreak and previously detected AIV. Altogether, we showed how novel easy-to-use genomic technology can support the surveillance of potentially zoonotic pathogens by accurately recreating the viral genomes to better understand evolution and transmission of these pathogens.

genomics↗

bioRxiv2023

The Feather Epithelium Contributes to the Dissemination and Ecology of clade 2.3.4.4b H5 High Pathogenicity Avian Influenza Virus in Ducks

Immature feathers are known replication sites for high pathogenicity avian influenza viruses (HPAIVs) in poultry. However, it is unclear whether feathers play an active role in viral transmission. This study aims to investigate the contribution of the feather epithelium to the dissemination of clade 2.3.4.4b goose/Guangdong/1996 lineage H5 HPAIVs in the environment, based on natural and experimental infections of domestic ducks. During the 2016-22 outbreaks, H5 HPAIVs exhibited persistent and marked feather epitheliotropism in naturally infected commercial ducks. Infection of feathers resulted in epithelial necrosis, disruption, and the production and release of infectious virions. Viral and feather antigens colocalized in dust samples obtained from poultry barns housing naturally infected birds. In summary, the feather epithelium contributes to viral replication, and it is a likely source of environmental infectious material. This underestimated excretion route could greatly impact the ecology of HPAIVs, facilitating airborne and preening-related infections within a flock, and promoting prolonged viral infectivity and long-distance viral transmission between poultry farms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/550633v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@16f6b24org.highwire.dtl.DTLVardef@1e33c82org.highwire.dtl.DTLVardef@199b745org.highwire.dtl.DTLVardef@cf2024_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗