ArticleFrontiers in bioinformatics2025
Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples.
Article in Frontiers in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Co-detection and genomic characterization of avian rotavirus A, avian orthoreovirus, and chicken megrivirus-C using nontargeted metagenomic surveillance in Indian broiler chickens.Frontiers in cellular and infection microbiology · 2026Article
- An amplicon-based tiled PCR scheme for the enrichment of avian metapneumovirus subtype B genomes prior to next generation sequencing.Frontiers in cellular and infection microbiology · 2026Article
- IBDV-SSA, a novel molecular approach for the recovery of infectious bursal disease virus whole genomes from FTA cards.Microbiology spectrum · 2025Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Since viruses are obligate intracellular pathogens, sequencing their genomes results in metagenomic data from both the virus and the host. Virology researchers are constantly seeking new, cost-effective strategies and bioinformatic pipelines for the retrieval of complete viral genomes from these metagenomic samples. Avian orthoreoviruses (ARVs) pose a significant and growing threat to the poultry industry and frequently cause economic losses associated with disease in production birds. Currently available commercial vaccines are ineffective against new ARV variants and ARV outbreaks are increasing worldwide, requiring whole genome sequencing (WGS) to characterize strains that evade vaccines. This study compares the effectiveness of long-read and short-read sequencing technologies for obtaining ARV complete genomes. We used eight clinical isolates of ARV, each previously processed using our published viral genome enrichment protocol. Additionally, we evaluate three assembly methods to determine which provided the most complete and reliable whole genomes:
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