Global HIV drug resistance laboratory network
National HIV drug resistance (DR) working groups coordinating WHO-recommended surveys should designate a national or regional WHO-accredited genotyping laboratory to provide quality-assured results for the surveys. WHO HIVResNet performs lab assessments for accreditation, which include lab reviews and an annual quality-assurance panel, and provides technical assistance.
WHO HIVDR Laboratory Guidance
The WHO/HIVResNet Laboratory Strategy functions to support national, regional, and global HIVDR surveillance and monitoring by the timely provision of accurate genotyping results in a standardized format that meets the WHO specifications. The aim of the WHO HIVDR laboratory strategy is to ensure the accurate collection, handling, shipment and storage of specimens collected in countries implementing HIVDR surveillance and monitoring surveys and to ensure the availability of quality-assured HIV genotyping laboratory services producing comparable and reliable results at the national, regional and global level.
WHO/HIVResNet drug resistance laboratory strategy (summary)
WHO/HIVResNet drug resistance laboratory strategy
HIVDR training package
An HIVDR training package has been developed in collaboration with the CDC Atlanta drug resistance laboratory.
SQUAT (Sequence Quality Assessment Tool)
SQUAT (sequence quality assessment tool) is a computerized stand-alone tool to assess quality of HIV protease (PR) and reverse transcriptase (RT) sequences prior to analyses. It was designed for Microsoft-Windows-running computers in an R statistical environment combined with Perl scripts. SQUAT steps include FASTA sequence file and related information submission; HIV PR and/or RT sequence identification; sequence alignment; screening for ambiguous nucleotides, frameshifts, insertions and deletions on the nucleic acid (NA) level; calculation of pairwise genetic distances and generation of a genetic distance histogram and a phylogenetic tree output; translation of NA into amino acids (AA); identification of ambiguous and atypical AA, stop codons and frameshifts on the AA level; and generation of a summary text file, aligned NA sequence output file, and two AA sequence output files of approved sequences, one with mixtures and one without mixtures.
The current version of SQUAT has not been extensively tested with Windows Vista or 7. Please follow the installation instructions carefully.
WHO manual for HIV drug resistance testing using dried blood spot specimens
The WHO HIVDR Dried Blood Spot (DBS) Working Group of HIVResNet developed the protocol for collecting and analyzing Dried Blood Spots for drug resistance testing. The genotyping protocol will be updated later this year.