Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry

作者：Jeremy Ratcliff, Brian Merritt, Hannah Gooden, Jurre Y. Siegers, Abhinaya Srikanth, Sokhoun Yann, Sonita Kol, Sarath Sin, Songha Tok, Erik A. Karlsson, Peter Thielen · 发表于：Microbiology Spectrum · 年份：2024 · DOI：10.1128/spectrum.01880-24 · 被引用次数：9 · 研究领域：Influenza Virus Research Studies、Genomics and Phylogenetic Studies、RNA and protein synthesis mechanisms

ABSTRACT Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmission, and guiding interventions in near real-time. Oxford Nanopore sequencing holds promise for real-time influenza genotyping, but data quality from R9 chemistry has limited its adoption due to challenges resolving low-complexity regions such as the biologically critical hemagglutinin cleavage site, a homopolymer of basic amino acids that distinguish highly pathogenic strains. In this study, human and avian influenza isolates ( n = 45) from Cambodia were sequenced using both R9.4.1 and R10.4.1 flow cells and chemistries to evaluate performance between approaches. Overall, R10.4.1 yielded increased data output with higher average quality compared to R9.4.1, producing improved consensus sequences using a reference-based bioinformatics approach. R10.4.1 had significantly lower minor population insertion and deletion frequencies, driven by improved performance in low sequence complexity regions prone to insertion and deletion errors, such as homopolymers. Within the hemagglutinin cleavage site, R10.4.1 resolved the correct motif in 90% of genomes compared to only 60% with R9.4.1. Further examination showed reduced frameshift mutations in consensus sequences generated with R10.4.1 that could result in incorrectly classified virulence with...