Baseline Clinical HIV Genotypes Are a Valid Measure of Transmitted Drug Resistance Within the Treatment-Naive Population

Ragonnet-Cronin, Manon MSc*; Lee, Bonita E. MD, FRCPC; Plitt, Sabrina S. PhD; Zahariadis, George MD, FRCPC§,‖; Merks, Harriet BSc*; Sandstrom, Paul A. PhD*; Brooks, James I. MD, FRCPC*,¶,‖

JAIDS Journal of Acquired Immune Deficiency Syndromes: 15 December 2013 - Volume 64 - Issue 5 - p 443–447
doi: 10.1097/QAI.0b013e3182a4b991
Brief Report: Basic and Translational Science

Objective: To examine whether baseline clinical genotypes are equivalent to diagnostic serum genotypes for surveillance of HIV transmitted drug resistance (TDR).

Design: Current HIV TDR surveillance in Canada is conducted through genotyping remnant diagnostic sera from new HIV diagnoses. As part of routine care, baseline genotyping is now conducted on all newly diagnosed HIV infections, with TDR data being generated a second time on the same patients.

Methods: Surveillance genotyping, on HIV diagnostic serum, was performed on newly diagnosed HIV cases from 2007 to 2010 in Alberta, Canada. All subjects with a baseline clinical genotype result on file, and no evidence of antiretroviral therapy, were studied further. The HIV sequences from diagnosis and from the first clinical genotype were compared according to elapsed time between testing and by evaluating timing of infection based on BED capture enzyme immunoassay (BED-CEIA, abbreviated as BED in this article).

Results: Eighty-seven genotype pairs were available for analysis, most of which were subtype B. The time between genotypes ranged from 0 to 755 days, with a median of 36 days and an interquartile range of 155.25 days. Genetic distance between genotypes varied between 0 and 0.03389 substitutions per site and did not correlate with sampling times. There was a tendency for the genotypes of infections classified as recent by BED to be more similar to their clinical genotypes but this effect was lost when adjusted for elapsed time between tests. There was no difference in the identified drug resistance.

Conclusions: Baseline clinical genotypes from treatment-naive patients may be used for HIV TDR surveillance.

*National HIV and Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada;

Division of Infectious Diseases, Department of Pediatrics, University of Alberta, Alberta, Canada;

Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Canada;

§Division of Infectious Diseases, Department of Laboratory Medicine and Pathology, University of Alberta and Alberta Health Services, Alberta, Canada;

Division of Infectious Diseases, Department of Medicine, University of Western Ontario, London, Canada; and

Division of Infectious Diseases, Department of Medicine, University of Ottawa, Ottawa, Canada.

Correspondence to: James I. Brooks, MD, National HIV and Retrovirology Laboratories, Room 3172, Building 6, 100 Eglantine Driveway, AL0603A2, Tunney's Pasture, Ottawa, Ontario K1A 0K9, Canada (e-mail:

Supported by the Federal Initiative to Address HIV/AIDS in Canada.

The authors have no conflicts of interest to disclose.

Received February 22, 2013

Accepted July 11, 2013

© 2013 by Lippincott Williams & Wilkins