Development of a low bias method for characterizing viral populations using next generation sequencing technology
| Autor: | Hélder A. M. Pedro, Lior Pachter, Adam P. Arkin, Stephanie M. Willerth, David V. Schaffer, Laurent Humeau |
|---|---|
| Přispěvatelé: | Vartanian, Jean-Pierre |
| Rok vydání: | 2010 |
| Předmět: |
General Science & Technology
Population lcsh:Medicine Genomics HIV Infections Viral quasispecies Genome Viral Biology Genome DNA sequencing Virus 03 medical and health sciences Virology Genetics 2.2 Factors relating to the physical environment 2.1 Biological and endogenous factors Humans Genomic library Viral Aetiology education lcsh:Science Illumina dye sequencing 030304 developmental biology 0303 health sciences education.field_of_study Multidisciplinary 030306 microbiology lcsh:R virus diseases HIV DNA Virology/Mechanisms of Resistance and Susceptibility including Host Genetics 3. Good health Infectious Diseases Good Health and Well Being Virology/Immunodeficiency Viruses DNA Viral HIV/AIDS lcsh:Q Infection Biotechnology Research Article |
| Zdroj: | PloS one, vol 5, iss 10 PLoS ONE, Vol 5, Iss 10, p e13564 (2010) PLoS ONE |
| Popis: | Background: With an estimated 38 million people worldwide currently infected with human immunodeficiency virus (HIV), and an additional 4.1 million people becoming infected each year, it is important to understand how this virus mutates and develops resistance in order to design successful therapies. Methodology/Principal Findings: We report a novel experimental method for amplifying full-length HIV genomes without the use of sequence-specific primers for high throughput DNA sequencing, followed by assembly of full length viral genome sequences from the resulting large dataset. Illumina was chosen for sequencing due to its ability to provide greater coverage of the HIV genome compared to prior methods, allowing for more comprehensive characterization of the heterogeneity present in the HIV samples analyzed. Our novel amplification method in combination with Illumina sequencing was used to analyze two HIV populations: a homogenous HIV population based on the canonical NL4-3 strain and a heterogeneous viral population obtained from a HIV patient's infected T cells. In addition, the resulting sequence was analyzed using a new computational approach to obtain a consensus sequence and several metrics of diversity. Significance: This study demonstrates how a lower bias amplification method in combination with next generation DNA sequencing provides in-depth, complete coverage of the HIV genome, enabling a stronger characterization of the quasispecies present in a clinically relevant HIV population as well as future study of how HIV mutates in response to a selective pressure. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|