A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project.

ABSTRACT:

Background & methods

The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker.

Results

The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) fo

SUBMITTER: Yebra G 

PROVIDER: S-EPMC5794160 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature