Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Viruses, Cell Culture, and Clinical Samples
2.2. Sample Preparation, RNA Isolation, and Viral RNA Quantification by RT-PCR (RT-qPCR)
2.3. Library Generation and Sequencing
2.4. De Novo Assembly and Reference-Based Mapping
2.5. Single Nucleotide Variation Calling from NGS Reads and Confirmation by Pyrosequencing
2.6. GenBank Accession Number
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Reference Position a | Coding Region | Reference b | Change c | Coverage d | Frequency e | SNV Called by NGS f | Amino Acid Change g | SNV Identified by PYROSEQUENCING |
---|---|---|---|---|---|---|---|---|
1742 | 1C | G | A | 22,779 | 54.2 | mixed | mixed | |
2864 | 1D | T | A | 24,773 | 99.3 | single | single | |
4185 | 2C | G | A | 69,820 | 99.7 | single | AAA45465.1:p.[Glu1151Lys] | single |
5204 | 3A | G | A | 138,614 | 81.1 | mixed | single | |
6216 | 3D | T | C | 166,496 | 81.7 | mixed | single | |
6522 | 3D | T | A | 297,276 | 99.6 | single | AAA45465.1:p.[Ser1930Thr] | single |
6836 | 3D | C | T | 210,792 | 40.1 | mixed | mixed | |
7042 | 3D | - | A | 260,563 | 13.8 | mixed | AAA45465.1:p.[Gln2103fs] |
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Yang, Z.; Mammel, M.; Whitehouse, C.A.; Ngo, D.; Kulka, M. Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing. Viruses 2018, 10, 619. https://doi.org/10.3390/v10110619
Yang Z, Mammel M, Whitehouse CA, Ngo D, Kulka M. Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing. Viruses. 2018; 10(11):619. https://doi.org/10.3390/v10110619
Chicago/Turabian StyleYang, Zhihui, Mark Mammel, Chris A. Whitehouse, Diana Ngo, and Michael Kulka. 2018. "Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing" Viruses 10, no. 11: 619. https://doi.org/10.3390/v10110619
APA StyleYang, Z., Mammel, M., Whitehouse, C. A., Ngo, D., & Kulka, M. (2018). Inter- and Intra-Host Nucleotide Variations in Hepatitis A Virus in Culture and Clinical Samples Detected by Next-Generation Sequencing. Viruses, 10(11), 619. https://doi.org/10.3390/v10110619