title: Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.
abstract: Whole HIV-1 genome sequences are pivotal for large-scale studies of inter- and intrahost evolution, including the acquisition of drug resistance mutations. The ability to rapidly and cost-effectively generate large numbers of HIV-1 genome sequences from different populations and geographical locations and determine the effect of minority genetic variants is, however, a limiting factor. Next-generation sequencing promises to bridge this gap but is hindered by the lack of methods for the enrichment of virus genomes across the phylogenetic breadth of HIV-1 and methods for the robust assembly of the virus genomes from short-read data. Here we report a method for the amplification, next-generation sequencing, and unbiased de novo assembly of HIV-1 genomes of groups M, N, and O, as well as recombinants, that does not require prior knowledge of the sequence or subtype. A sensitivity of at least 3,000 copies/ml was determined by using plasma virus samples of known copy numbers. We applied our novel method to compare the genome diversities of HIV-1 groups, subtypes, and genes. The highest level of diversity was found in the env, nef, vpr, tat, and rev genes and parts of the gag gene. Furthermore, we used our method to investigate mutations associated with HIV-1 drug resistance in clinical samples at the level of the complete genome. Drug resistance mutations were detected as both major variant and minor species. In conclusion, we demonstrate the feasibility of our method for large-scale HIV-1 genome sequencing. This will enable the phylogenetic and phylodynamic resolution of the ongoing pandemic and efficient monitoring of complex HIV-1 drug resistance genotypes.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Astrid
authors.initials: A
authors.lastname: Gall
authors.forename: Bridget
authors.initials: B
authors.lastname: Ferns
authors.forename: Clare
authors.initials: C
authors.lastname: Morris
authors.forename: Simon
authors.initials: S
authors.lastname: Watson
authors.forename: Matthew
authors.initials: M
authors.lastname: Cotten
authors.forename: Mark
authors.initials: M
authors.lastname: Robinson
authors.forename: Neil
authors.initials: N
authors.lastname: Berry
authors.forename: Deenan
authors.initials: D
authors.lastname: Pillay
authors.forename: Paul
authors.initials: P
authors.lastname: Kellam
mesh_terms: D024882:Drug Resistance, Viral; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020125:Mutation, Missense; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic
chemical_list: D012367:RNA, Viral