January 10, 2011

Guidelines for the Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents Page 5 

Table 4. Recommendations for Using Drug-Resistance Assays (Updated January 10, 2011)

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Clinical Setting/Recommendation Rationale

Drug-resistance assay recommended

In acute HIV infection: Drug-resistance testing 

is recommended regardless of whether ART is 

initiated immediately or deferred (AIII). A 

genotypic assay is generally preferred (AIII).

If ART is to be initiated immediately, drug-resistance 

testing will determine whether drug-resistant virus was 

transmitted. Test results will help in the design of initial 

regimens or to modify or change regimens if results are 

obtained subsequent to treatment initiation.

Genotypic testing is preferable to phenotypic testing 

because of lower cost, faster turnaround time, and 

greater sensitivity for detecting mixtures of wild-type 

and resistant virus.

If ART is deferred, repeat resistance testing 

should be considered at the time therapy is 

initiated (CIII). A genotypic assay is generally 

preferred (AIII).

If ART is deferred, testing should still be performed 

because of the greater likelihood that transmitted 

resistance-associated mutations will be detected earlier 

in the course of HIV infection. Results of resistance 

testing may be important when treatment is initiated. 

Repeat testing at the time ART is initiated should be 

considered because the patient may have acquired a 

drug-resistant virus (i.e., superinfection).

In ART-naïve patients with chronic HIV 

infection: Drug-resistance testing is 

recommended at the time of entry into HIV care, 

regardless of whether therapy is initiated 

immediately or deferred (AIII). A genotypic 

assay is generally preferred (AIII).

Transmitted HIV with baseline resistance to at least 

one drug is seen in 6%–16% of patients, and 

suboptimal virologic responses may be seen in patients 

with baseline resistant mutations. Some drug-resistance 

mutations can remain detectable for years in untreated 

chronically infected patients.

If therapy is deferred, repeat resistance testing 

should be considered prior to the initiation of 

ART (CIII). A genotypic assay is generally 

preferred (AIII).

Repeat testing prior to initiation of ART should be 

considered because the patient may have acquired a 

drug-resistant virus (i.e., a superinfection).

Genotypic testing is preferable to phenotypic testing 

because of lower cost, faster turnaround time, and 

greater sensitivity for detecting mixtures of wild-type 

and resistant virus.

If an INSTI is considered for an ART-naïve 

patient and transmitted INSTI resistance is a 

concern, providers may wish to supplement 

standard resistance testing with a specific INSTI 

genotypic resistance assay (CIII).

Standard genotypic drug-resistance assays test only for 

mutations in the RT and PR genes.
January 10, 2011

Guidelines for the Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents Page 6 

Clinical Setting/Recommendation Rationale

In patients with virologic failure: Drug-resistance 

testing is recommended in persons on combination 

ART with HIV RNA levels >1,000 copies/mL (AI). In 

persons with HIV RNA levels >500 but <1,000 

copies/mL, testing may be unsuccessful but should 

still be considered (BII).

Testing can help determine the role of resistance 

in drug failure and maximize the clinician’s 

ability to select active drugs for the new 

regimen. Drug-resistance testing should be 

performed while the patient is taking prescribed 

ARV drugs or, if not possible, within 4 weeks 

after discontinuing therapy.

A standard genotypic resistance assay is generally 

preferred for those experiencing virologic failure on 

their first or second regimens (AIII).

Genotypic testing is preferable to phenotypic 

testing because of lower cost, faster turnaround 

time, and greater sensitivity for detecting 

mixtures of wild-type and resistant virus.

In patients failing INSTI-based regimens, genotypic 

testing for INSTI resistance should be considered to 

determine whether to include drugs from this class in 

subsequent regimens (BIII).

Standard genotypic drug-resistance assays test 

only for mutations in the RT and PR genes.

Addition of phenotypic assay to genotypic assay is 

generally preferred for those with known or suspected 

complex drug-resistance patterns, particularly to PIs 

(BIII).

Phenotypic testing can provide useful additional 

information for those with complex drugresistance mutation patterns, particularly to PIs.

In patients with suboptimal suppression of viral load: 

Drug-resistance testing is recommended for persons with 

suboptimal suppression of viral load after initiation of 

ART (AII).

Testing can help determine the role of resistance and thus 

assist the clinician in identifying the number of active 

drugs available for a new regimen.

In HIV-infected pregnant women: Genotypic resistance 

testing is recommended for all pregnant women prior to 

initiation of ART (AIII) and for those entering pregnancy 

with detectable HIV RNA levels while on therapy (AI).

The goal of ART in HIV-infected pregnant women is to 

achieve maximal viral suppression for treatment of 

maternal HIV infection and for prevention of perinatal 

transmission of HIV. Genotypic resistance testing will 

assist the clinician in selecting the optimal regimen for 

the patient.

Drug-resistance assay not usually recommended

After therapy discontinued: Drug-resistance testing is 

not usually recommended after discontinuation (>4 weeks) 

of ARV drugs (BIII).

Drug-resistance mutations might become minor species in 

the absence of selective drug pressure, and available 

assays might not detect minor drug-resistant species. If 

testing is performed in this setting, the detection of drug 

resistance may be of value; however, the absence of 

resistance does not rule out the presence of minor drugresistant species.

In patients with low HIV RNA levels: Drug-resistance 

testing is not usually recommended in persons with a 

plasma viral load <500 copies/mL (AIII).

Resistance assays cannot be consistently performed given 

low HIV RNA levels.

Table 4. Recommendations for Using Drug-Resistance Assays 

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