Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

被引：103

作者：

Di Giallonardo, Francesca ^{[1
,2
]}

Toepfer, Armin ^{[3
,4
]}

Rey, Melanie ^{[5
]}

Prabhakaran, Sandhya ^{[5
]}

Duport, Yannick ^{[1
]}

Leemann, Christine ^{[1
]}

Schmutz, Stefan ^{[1
]}

Campbell, Nottania K. ^{[1
,2
]}

Joos, Beda ^{[1
]}

Lecca, Maria Rita ^{[6
]}

Patrignani, Andrea ^{[6
]}

Daeumer, Martin ^{[7
]}

Beisel, Christian ^{[3
]}

Rusert, Peter ^{[8
]}

Trkola, Alexandra ^{[8
]}

Guenthard, Huldrych F. ^{[1
]}

Roth, Volker ^{[5
]}

Beerenwinkel, Niko ^{[3
,4
]}

Metzner, Karin J. ^{[1
]}

机构：

[1] Univ Zurich, Univ Zurich Hosp, Div Infect Dis & Hosp Epidemiol, CH-8091 Zurich, Switzerland

[2] Univ Zurich, Life Sci Zurich Grad Sch, CH-8057 Zurich, Switzerland

[3] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland

[4] SIB, CH-4058 Basel, Switzerland

[5] Univ Basel, Dept Math & Comp Sci, CH-4056 Basel, Switzerland

[6] Univ Zurich, Funct Genom Ctr Zurich, ETH Zurich, CH-8057 Zurich, Switzerland

[7] Inst Immunol & Genet, D-67655 Kaiserslautern, Germany

[8] Univ Zurich, Inst Med Virol, CH-8057 Zurich, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / 14期

基金：

瑞士国家科学基金会;

关键词：

GENERATION SEQUENCING DATA; RESISTANT HIV-1; DIVERSITY; ALGORITHMS; GENOMICS; ESCAPE; CCR5;

D O I：

10.1093/nar/gku537

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of similar to 8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Bio-sciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.

引用

页数：12

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