Next-generation sequencing reveals large connected networks of intra-host HCV variants

Campo, David S; Dimitrova, Zoya; Yamasaki, Lilian; Skums, Pavel; Lau, Daryl TY; Vaughan, Gilberto; Forbi, Joseph C; Teo, Chong-Gee; Khudyakov, Yury

doi:10.1186/1471-2164-15-S5-S4

i

Next-generation sequencing reveals large connected networks of intra-host HCV variants

Supporting Files Public Domain

Jul 14 2014
By Campo, David S ; Dimitrova, Zoya ; Yamasaki, Lilian ; ...

Details

Alternative Title:

BMC Genomics
Personal Author:

Campo, David S ; Dimitrova, Zoya ; Yamasaki, Lilian ; Skums, Pavel ; Lau, Daryl TY ; Vaughan, Gilberto ; Forbi, Joseph C ; Teo, Chong-Gee ; Khudyakov, Yury
Description:

Background

Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.

Results

Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient.

Conclusions

Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.
Subjects:

Computer Simulation Genetic Variation Genotype Hepacivirus Hepatitis C High-Throughput Nucleotide Sequencing Humans Mutation Needle Sharing Research RNA, Viral Sequence Analysis, DNA
Source:

BMC Genomics. 2014; 15(Suppl 5):S4.
Document Type:

Journal Article
Volume:

15
Collection(s):

CDC Public Access
Main Document Checksum:

urn:sha256:fb2d918022983dbcda9437b9a7b9220ec670e897b663aaca7d76404c161848c8
Download URL:

https://stacks.cdc.gov/view/cdc/26771/cdc_26771_DS1.pdf
File Type:

[PDF - 1.34 MB ]

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