HIV Genotypic Testing in Rapid Initiation of ART

Clinical Rationale

Drug-resistance testing is recommended at entry into HIV care, to identify the presence of transmitted drug-resistant mutations. Untreated HIV replicates rapidly, and during the viral replication process there is a high mutation rate supporting the indication of initial resistance testing.

The NYSDOH, DHHS, IAS-USA and WHO clinical guidelines recommend HIV resistance testing for achieving viral suppression. The ART initiation should not be delayed pending resistance test results. Once the results are reported, the initial regimen can be modified if necessary.

Currently available RNA genotypic assays require a minimum viral load in the range of 500 to 2,000 copies/mL, depending on the assay, and generally require 2 weeks or less for results.

Two methods are used to determine drug resistance for HIV: genotyping, which detects treatment-resistant genetic mutations; and phenotyping, which assesses the viral response to ART agents. Genotyping is the preferred test in most clinical situations.


  • Include protease, reverse transcriptase, and integrase genes testing with initial bloodwork 
  • Genotype testing results might require updating the initial regimen  
  • Do not delay treatment initiation pending results  
  • Baseline testing is cost effective1

Determining HIV Drug Resistance

Standard genotypic resistance testing in treatment-naïve persons involves testing for mutations in the protease, reverse transcriptase, and integrase genes.

 In patients experiencing treatment failure or incomplete viral suppression; such testing should be performed while patients are still on therapy, but no later than 4 weeks after stopping ART, given the rapid return of wild-type virus. 

Perform co-receptor tropism testing prior to initiation of a CCR5 antagonist. 

If fusion inhibitor resistance is suspected that test should be obtained as a supplement to the other genotypic resistance tests.

For any questions regarding resistance tests or results, HIV experts are available through the Clinical Education Initiative line at 866-637-2342.


1. Sax PE, Islam R, Walensky RP, et al. Should resistance testing be performed for treatment-naive HIV-infected patients? A cost-effectiveness analysis. Clin Infect Dis. 2005;41(9):1316-1323. Available at:
2. Doyle T, Dunn DT, Ceccherini-Silberstein F, et al. Integrase inhibitor (INI) genotypic resistance in treatment-naive and raltegravir-experienced patients infected with diverse HIV-1 clades. J Antimicrob Chemother. 2015;70(11):3080-3086. Available at:
3. Menza TW, Billock R, Samoff E, Eron JJ, Dennis AM. Pretreatment integrase strand transfer inhibitor resistance in North Carolina from 2010–2016. AIDS. 2017;31(16):2235-2244. Available at: