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Bhamidipati SV, Surathu A, Chao H, Agustinho DP, Xiang Q, Kottapalli K, Santhanam A, Momin Z, Walker K, Menon VK, Weissenberger G, Emerick N, Mahjabeen F, Meng Q, Hu J, Sucgang R, Henke D, Sedlazeck FJ, Khan Z, Metcalf GA, Avadhanula V, Piedra PA, Ramani S, Atmar RL, Estes MK, Petrosino JF, Gibbs RA, Muzny DM, Cregeen SJ, Doddapaneni H. Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613242. [PMID: 39345650 PMCID: PMC11429736 DOI: 10.1101/2024.09.16.613242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. The Ct values of these samples ranged from 17.0-29.9 for RSV, and from 20.2-34.8 for HuNoV, with some HuNoV having below the detection limit. The mean percentage of post-processing reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries, respectively. Full-length genomes were>99% complete in all RSV positive samples and >96% complete in 47/55 HuNoV positive samples-a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data. Probe-based capture enrichment offers a comprehensive approach for RSV and HuNoV genome sequencing and monitoring emerging variants.
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Affiliation(s)
- Sravya V Bhamidipati
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anil Surathu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daniel P Agustinho
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qin Xiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Abirami Santhanam
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberly Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - George Weissenberger
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nathanael Emerick
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Faria Mahjabeen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Henke
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sasirekha Ramani
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Robert L Atmar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary K Estes
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sara Javornik Cregeen
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
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