title: Automated sequence analysis and editing software for HIV drug resistance testing.
abstract: BACKGROUND
  Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue.
  
  
  OBJECTIVE
  To develop an automated sequence analysis and editing software to support high throughput automated sequencing.
  
  
  METHODS
  The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates.
  
  
  RESULTS
  The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT.
  
  
  CONCLUSIONS
  The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention.
authors.affiliation: Laboratory of Retrovirology, CRP-Santé, Luxembourg.
authors.forename: Daniel
authors.initials: D
authors.lastname: Struck
authors.forename: Carole L
authors.initials: CL
authors.lastname: Wallis
authors.forename: Gennady
authors.initials: G
authors.lastname: Denisov
authors.forename: Christine
authors.initials: C
authors.lastname: Lambert
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Servais
authors.forename: Raquel V
authors.initials: RV
authors.lastname: Viana
authors.forename: Esrom
authors.initials: E
authors.lastname: Letsoalo
authors.forename: Michelle
authors.initials: M
authors.lastname: Bronze
authors.forename: Sue C
authors.initials: SC
authors.lastname: Aitken
authors.forename: Rob
authors.initials: R
authors.lastname: Schuurman
authors.forename: Wendy
authors.initials: W
authors.lastname: Stevens
authors.forename: Jean Claude
authors.initials: JC
authors.lastname: Schmit
authors.forename: Tobias
authors.initials: T
authors.lastname: Rinke de Wit
authors.forename: Danielle
authors.initials: D
authors.lastname: Perez Bercoff
mesh_terms: D001331:Automation / Q000379:methods; D024882:Drug Resistance, Viral; D006678:HIV / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D015658:HIV Infections / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods*; D012984:Software; D013997:Time Factors