Automated sequence analysis and editing software for HIV drug resistance testing

Daniel Struck, Carole L. Wallis, Gennady Denisov, Christine Lambert, Jean Yves Servais, Raquel V. Viana, Esrom Letsoalo, Michelle Bronze, Sue C. Aitken, Rob Schuurman, Wendy Stevens, Jean Claude Schmit, Tobias Rinke de Wit, Danielle Perez Bercoff*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)


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. Objectives: To develop an automated sequence analysis and editing software to support high throughput automated sequencing. Study design: 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.

Original languageEnglish
Pages (from-to)30-35
Number of pages6
JournalJournal of Clinical Virology
Issue number1
Publication statusPublished - May 2012


  • Automated-sequence-analysis
  • HIV genotyping
  • HIV resistance
  • Software


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