Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry
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. Oxf...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2024-12-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01880-24 |
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| author | Jeremy D. Ratcliff Brian Merritt Hannah Gooden Jurre Y. Siegers Abhinaya Srikanth Sokhoun Yann Sonita Kol Sarath Sin Songha Tok Erik A. Karlsson Peter M. Thielen |
| author_facet | Jeremy D. Ratcliff Brian Merritt Hannah Gooden Jurre Y. Siegers Abhinaya Srikanth Sokhoun Yann Sonita Kol Sarath Sin Songha Tok Erik A. Karlsson Peter M. Thielen |
| author_sort | Jeremy D. Ratcliff |
| collection | DOAJ |
| description | 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 automated pipelines. Improved consensus genome quality from nanopore sequencing approaches, especially across biologically important low-complexity regions, is critical to reduce subjective hand-curation and will improve local and global genomic surveillance responses.IMPORTANCEThis study demonstrates significant advancement in the field of influenza virus genomic surveillance by showcasing the superior accuracy and data quality of the Oxford Nanopore R10 sequencing chemistry compared to the older R9 chemistry. Improved resolution, including in the critical hemagglutinin multi-basic cleavage site, enables more reliable monitoring and tracking of viral mutations. This accelerates the ability to respond quickly to outbreaks, potentially improving impacts on public health, agriculture, and the economy by enabling more accurate and timely interventions. |
| format | Article |
| id | doaj-art-02b80796ee7b40eaa6819833998fc75a |
| institution | OA Journals |
| issn | 2165-0497 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj-art-02b80796ee7b40eaa6819833998fc75a2025-08-20T02:19:12ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972024-12-01121210.1128/spectrum.01880-24Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistryJeremy D. Ratcliff0Brian Merritt1Hannah Gooden2Jurre Y. Siegers3Abhinaya Srikanth4Sokhoun Yann5Sonita Kol6Sarath Sin7Songha Tok8Erik A. Karlsson9Peter M. Thielen10Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USAJohns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USAJohns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USAVirology Unit, Institut Pasteur du Cambodge, Phnom Penh, CambodiaJohns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USAVirology Unit, Institut Pasteur du Cambodge, Phnom Penh, CambodiaVirology Unit, Institut Pasteur du Cambodge, Phnom Penh, CambodiaVirology Unit, Institut Pasteur du Cambodge, Phnom Penh, CambodiaVirology Unit, Institut Pasteur du Cambodge, Phnom Penh, CambodiaVirology Unit, Institut Pasteur du Cambodge, Phnom Penh, CambodiaJohns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USAABSTRACT 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 automated pipelines. Improved consensus genome quality from nanopore sequencing approaches, especially across biologically important low-complexity regions, is critical to reduce subjective hand-curation and will improve local and global genomic surveillance responses.IMPORTANCEThis study demonstrates significant advancement in the field of influenza virus genomic surveillance by showcasing the superior accuracy and data quality of the Oxford Nanopore R10 sequencing chemistry compared to the older R9 chemistry. Improved resolution, including in the critical hemagglutinin multi-basic cleavage site, enables more reliable monitoring and tracking of viral mutations. This accelerates the ability to respond quickly to outbreaks, potentially improving impacts on public health, agriculture, and the economy by enabling more accurate and timely interventions.https://journals.asm.org/doi/10.1128/spectrum.01880-24influenzaavian influenzaH5N1genomicsnext generation sequencingOxford Nanopore |
| spellingShingle | Jeremy D. Ratcliff Brian Merritt Hannah Gooden Jurre Y. Siegers Abhinaya Srikanth Sokhoun Yann Sonita Kol Sarath Sin Songha Tok Erik A. Karlsson Peter M. Thielen Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry Microbiology Spectrum influenza avian influenza H5N1 genomics next generation sequencing Oxford Nanopore |
| title | Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry |
| title_full | Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry |
| title_fullStr | Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry |
| title_full_unstemmed | Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry |
| title_short | Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry |
| title_sort | improved resolution of avian influenza virus using oxford nanopore r10 sequencing chemistry |
| topic | influenza avian influenza H5N1 genomics next generation sequencing Oxford Nanopore |
| url | https://journals.asm.org/doi/10.1128/spectrum.01880-24 |
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