title: A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.
abstract: To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies.
  
  
  
  Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies.
  
  
  
  At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100).
  
  
  
  A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies.
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada e Instituto de Investigación IBS, Granada, España. Electronic address: jose.angel.fernandez.caballero@gmail.com.
authors.forename: Jose Ángel
authors.initials: JÁ
authors.lastname: Fernández-Caballero Rico
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada e Instituto de Investigación IBS, Granada, España.
authors.forename: Natalia
authors.initials: N
authors.lastname: Chueca Porcuna
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada e Instituto de Investigación IBS, Granada, España.
authors.forename: Marta
authors.initials: M
authors.lastname: Álvarez Estévez
authors.affiliation: Servicio de Microbiología Clínica, Centro de Diagnóstico Biomédico, Hospital Clínic, Universidad de Barcelona, Barcelona, España.
authors.forename: María Del Mar
authors.initials: MDM
authors.lastname: Mosquera Gutiérrez
authors.affiliation: Servicio de Microbiología Clínica, Centro de Diagnóstico Biomédico, Hospital Clínic, Universidad de Barcelona, Barcelona, España.
authors.forename: María Ángeles
authors.initials: MÁ
authors.lastname: Marcos Maeso
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada e Instituto de Investigación IBS, Granada, España.
authors.forename: Federico
authors.initials: F
authors.lastname: García
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000494:pharmacology; D001483:Base Sequence; D016384:Consensus Sequence; D004279:DNA, Viral / Q000235:genetics*; D024882:Drug Resistance, Viral / Q000235:genetics; D015497:HIV-1 / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D019380:Anti-HIV Agents; D004279:DNA, Viral
keywords: Filogenia; Human immunodeficiency virus; Next generation sequencing; Phylogeny; Thresholds; Umbrales; Virus de la inmunodeficiencia humana