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HIV Genotyping and Phenotyping

Policy Number: MP-264

Latest Review Date: September 2020

Category: Laboratory

Policy Grade: Effective 02/06/2013: Active Policy but no longer scheduled for regular literature reviews and updates.


HIV drug resistance testing, either phenotypic or genotypic testing or combined phenotypic and genotypic testing in patients who have failed a course of antiviral therapy or who have suboptimal viral load reduction may be considered medically necessary.

HIV drug resistance testing, either phenotypic or genotypic, used in other applications including, but not limited to its use in patient with previously untreated HIV is considered not medically necessary and investigational.

Drug susceptibility phenotype prediction using genotypic comparison to known genotypic/phenotypic database, also known as virtual phenotype testing, (including, but not limited to Sentosa SQ HIV-1 Genotyping Assay) is considered not medically necessary and investigational.

*Refer also to medical policy #322 Laboratory Testing for HIV Tropism for additional information.


HIV is an RNA virus characterized by a high replication rate throughout all stages of infection. The reverse transcription enzyme required for replication is error prone, resulting in a high rate of mutations, further leading to a swarm of related viruses (termed quasi-species) within the host. In fact, it is estimated that every possible single point mutation occurs more than 10,000 times per day in infected individuals. While some of the mutations may be innocuous or render the virus unviable, others may confer resistance to anti-viral drugs. It is likely that clones of drug-resistant viruses exist even before any anti-viral therapy, but due to an associated replication or competitive disadvantage compared to the wild-type virus, the resistant clone only represents a small proportion of the total viral load. However, in the presence of anti-viral drugs that selectively eliminate the wild-type virus, a resistant clone may rapidly emerge as the dominant quasi-species. Over time, this resistant clone may accumulate additional secondary mutations that overcome the original replication or competitive disadvantage. Virological treatment failure (i.e., increasing viral loads) may result. Alternatively, due to the widespread use of anti-viral therapy, patients may become infected with a resistant strain.

Current recommendations for initial drug therapy suggest the use of combination therapy with antivirals with different mechanisms of action designed to reduce the viral load to as low a level as possible. The three classes of antivirals available include nucleoside reverse transcription inhibitors (NRTI), non-nucleoside reverse transcription inhibitors (NNRTI), and protease inhibitors (PI). This therapeutic principle is based on the concept that cessation of detectable HIV replication decreases the opportunity for accumulation of mutations that may give rise to drug-resistant viral variants. These regimens are referred to as HAART (highly active antiretroviral therapy). If initial drug therapy fails, as evidenced by rising HIV viral loads, it is likely that the emergent virus is drug resistant, unless failure is related to drug non-compliance. At this point, physicians must devise a salvage therapy, using drugs to which the virus likely remains sensitive. While drug resistance is most common in the setting of prior failed therapy, there have been reports of initial infection of drug-resistant strains, particularly to zidovudine, a drug that has been widely used since the 1980s.

HIV genotyping (i.e., gene sequencing) has revealed specific point mutations or combinations of mutations in the enzymes targeted by these drugs, i.e., viral protease and reverse transcriptase. These mutations may be associated with drug resistance. For example, a single-point mutation in HIV can confer high-level resistance to the antiviral lamivudine (a NRTI) and certain NNRTIs. In contrast, high-level resistance to zidovudine (a NRTI) and certain protease inhibitors requires accumulation of three or more mutations. When only a single mutation is required for resistance, resistance may emerge within one month of treatment initiation. For this reason, these drugs are never used as monotherapy. In contrast, when multiple mutations are required, resistance may emerge only after months to years of therapy. Mutations that are common to several different drugs within a group will confer cross-resistance. For example, cross-resistance among the protease inhibitor drugs is common.

HIV phenotyping directly measures drug resistance by identifying the drug concentration necessary to inhibit virus replications, usually by 50. While phenotyping is a more direct measure of drug resistance compared to genotyping, the technique is labor intensive and technically challenging. Results of genotypes have also been used to predict the phenotype by identifying similar genotypes from a large database of other HIV genotypes for which the phenotypes are known. This data analysis is known as the Virtual Phenotype™.

The evolving understanding of the clinical significance of drug resistance has created interest in both HIV genotyping and phenotyping to identify active drug regimens in the following clinical settings: 1) To determine the most effective salvage therapy in patients with drug resistance. For example, the virus seen during treatment failure may not be resistant to all drugs in a regimen. 2) To confirm that antiviral drug failure is due to drug resistance and not patient non-compliance. 3) To determine viral resistance at initial diagnosis of HIV infection.


This policy is based on evidence review of literature most recently performed on October 1, 2019.

Summary of Evidence

Three studies (Cingolani, Tural, Baxter) have been identified in which it is concluded that genotypic-resistance testing had a significant benefit on the virological response when choosing a therapeutic alternative. These trials reported that salvage antiviral therapy directed by genotyping had improved virologic outcomes compared with standard therapy. Even so, only about 30% of patients achieved undetectable viral loads, and in most cases, the sustained response was short lived. The evidence is accepted as sufficient to consider the technology medically necessary.

The prevalence of drug-resistant strains of HIV ranges geographically from 5% to 26% in this country and transmission of these strains has been documented.  There have been no controlled studies of resistance testing in treatment-naïve patients.  Some have recommended either genotypic or phenotypic resistance testing in patients with acute HIV infection in geographic areas where drug-resistant strains of HIV are prevalent.  In contrast, such testing is not generally recommended in patients with chronic, treatment-naïve HIV, based on the fact that genotypic or phenotypic testing may not detect drug-resistant species that were transmitted at the time of primary infection but have become a minor species in the absence of selective drug pressure.  An alternative approach would be to reserve genotypic or phenotypic testing to those patients with chronic HIV infection who have suboptimal response to initial therapy.

Randomized trials have suggested that genotype directed and, to a lesser extent, phenotype directed therapy may result in improved short-term virologic outcomes in patients failing or having suboptimal response to antiretroviral therapy. While guidelines suggest that either type of assay may be recommended in treatment-naïve patients with acute infection, particularly in geographic areas in which there is a high prevalence of resistant virus, this strategy has not been tested in controlled studies and therefore remains investigational. There are no randomized studies that have used combined genotype and phenotype directed therapy; therefore, this indication remains investigational. There have been no randomized studies that have compared genotype alone with predicted phenotype, i.e., “virtual phenotype”. The evidence is insufficient to support this technology at this time.

U.S. Preventive Services Task Force

Not applicable.


HIV drug resistance testing, phenotypic, genotypic, virtual phenotype, ART, antiretroviral therapy, HIV, drug susceptibility phenotype prediction, genotyping, phenotyping, viral load, virtual phenotype testing, Sentosa SQ HIV-1 Genotyping Assay, Vela Diagnostics


Clinical Guideline Recommendations

The Department of Health and Human Services and the International AIDS Society have published clinical guidelines regarding resistance testing. These were updated in 2003 and are summarized below:

Clinical Characteristic

IS-USA Recommendation

U.S. Treatment Guidelines Recommendation*

Rationale from U.S. Treatment Guidelines

Primary HIV Infection

Recommend testing

Recommend testing

“If the decision is made to initiate therapy in a person with acute HIV infection, using resistance testing to optimize the initial antiretroviral regimen is a reasonable, albeit untested strategy.”

Chronic HIV Infection

Recommend testing

Consider testing

Uncertain prevalence of resistant virus. Current assay may not detect minor drug-resistant species. Drug-resistant mutations may become minor species in the absence of selective drug pressure.

First or Multiple Regimen Failure

Recommend testing

Recommend testing

Determine the role of resistance in drug failure and maximize the number of active drugs in the new regimen, if indicated.

Determine the role of resistance and maximize the number of active drugs in the new regimen, if indicated.


Recommend testing if mother had detectable virus

With acute infection

With virologic failure

Suboptimal viral suppression

High likelihood of resistant virus**

Essentially the same indications as in non-pregnant patients.

These guidelines do not make a distinction between genotype or phenotype resistance assays. As noted in the text of the U.S. recommendations, “There are currently no prospective data to support the use of one type of resistance assay over the other (i.e., genotyping vs. phenotyping) in different clinical situations. Therefore, one type of assay is generally recommended per sample. However, in the setting of a complex prior treatment history, both assays may provide important and complementary information.” The text of the IAS-USA Panel states, “The clinical value of drug resistance testing is recognized and it is now considered standard-of-care in the management of treatment failure. Data are not yet available on which methods or type of resistance testing is superior in any given clinical setting.”

**High likelihood of resistant virus is based on community prevalence of resistant virus, known drug resistance in women’s sex partner, or other source of infection.


Coverage is subject to member’s specific benefits. Group specific policy will supersede this policy when applicable.

ITS: Home Policy provisions apply

FEP contracts: Special benefit consideration may apply. Refer to member’s benefit plan. FEP does not consider investigational if FDA approved and will be reviewed for medical necessity.


CPT codes:


Infectious agent drug susceptibility phenotype prediction using regularly updated genotypic bioinformatics


Infectious agent genotype, analysis by nucleic acid (DNA or RNA); HIV 1, reverse transcriptase and protease regions


Infectious agent, phenotype analysis by nucleic acid (DNA or RNA) with drug resistance tissue culture analysis, HIV 1; first through 10 drugs tested


   ;each additional drug tested


Infectious agent genotype analysis by nucleic acid (DNA or RNA); HIV-1, other region (e.g., integrase, fusion)


Infectious agent (human immunodeficiency virus), targeted viral next-generation sequence analysis (i.e., protease [PR], reverse transcriptase [RT], integrase [INT]), algorithm reported as prediction of antiviral drug susceptibility (Effective 10/1/2020)


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  3. Blue Cross Blue Shield Association. HIV genotyping and phenotyping. Medical Policy Reference Manual, June 2008.
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  5. Borroto-Esoda K, Waters JM, et al. Baseline genotype as a predictor of virological failure to emtricitabine or stavudine in combination with didanosine and efavirenz. AIDS Res Hum Retroviruses, August 2007; 23(8): 988-99
  6. CDC. (2014). Revised surveillance case definition for HIV infection--United States, 2014. MMWR Recomm Rep, 63(Rr-03), 1-10.
  7. Cingolani A. Usefulness of monitoring HIV drug resistance and adherence in individuals failing highly active antiretroviral therapy: A randomized study (ARGENTA), AIDS, February 2002; 16(3): 369-379.
  8. Coffin, J., & Swanstrom, R. (2013). HIV Pathogenesis: Dynamics and Genetics of Viral Populations and Infected Cells. In Cold Spring Harb Perspect Med (Vol. 3).
  9. Cohen CJ, et al. A randomized trial assessing the impact of phenotypic resistance testing on antiretroviral therapy, AIDS, March 2002; 16(4): 579-588.
  10. De Luca A, Di Giambenedetto S, et al. Three-year clinical outcomes of resistance genotyping and expert advice: Extended follow-up of the Argenta trial. Antiviral Therapy, January 2006; 11(3): 321-327. (Abstract)
  11. DHHS. (2018). Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. Retrieved from
  12. DHHS Panel on Antiretroviral Guidelines for Adults and Adolescents – A Working Group of the Office of AIDS Research Advisory Council (OARAC). Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. December 2007,
  13. Durant J, et al. Drug-resistance genotyping in HIV-1 therapy: The VIRADAPT randomised controlled trial, The Lancet, June 1999; 353(9171): 2195-2199.
  14. Dybul M, et al. Guidelines for using antiretroviral agents among HIV-infected adults and adolescents, Annals of Internal Medicine, September 2002; 137(5 Pt 2): 381-433.
  15. EACS. (2018). GUIDELINES. Retrieved from Eshleman SH, Husnik M, et al. Antiretroviral drug resistance, HIV-1 tropism, and HIV-1 subtype among men who have sex with men with recent HIV-1 infection. AIDS, May 2007; 21(9): 1165-1174.
  16. Evaluation of Resistance Assays (ERA) Trial Investigators. A randomized controlled trial of the value of phenotypic testing in addition to genotypic testing for HIV drug resistance. J Acquir Immune Defic Syndr, April 2005, Vol. 38, No. 5.
  17. Fox, Z. V., Geretti, A. M., Kjaer, J., Dragsted, U. B., Phillips, A. N., Gerstoft, J., . . . Lundgren, J.D. (2007). The ability of four genotypic interpretation systems to predict virological response to ritonavir-boosted protease inhibitors. Aids, 21(15), 2033-2042.doi:10.1097/QAD.0b013e32825a69e4
  18. Haubrich RH, et al. A randomised, prospective study of phenotype susceptibility testing versus standard of care to manage antiretroviral therapy: CCTG 575, AIDS, February 2005; 19(3): 295-302.
  19. Haubrich RH, et al. The clinical relevance of non-nucleoside reverse transcriptase inhibitor hypersusceptibility: A prospective cohort analysis, AIDS, October 2002; 16(15): F33-40.
  20. Hirsch MS, et al. Antiretroviral drug resistance testing in adult HIV-1 infection: Recommendations of an International AIDS Society-USA Panel, JAMA, May 2000; 283(18): 2417-2426.
  21. Hirsch MS, et al. Antiretroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society-USA Panel, Clinical Infectious Diseases, July 2003; 37(1): 113-128.
  22. Hirsch HH, et al. Genotypic and phenotypic resistance testing of HIV-1 in routine clinical care, European Journal of Clinical Microbiology and Infectious Diseases, November 2005; 24(11): 733-738.
  23. Kozal, M. (2018a). Interpretation of HIV drug resistance testing. Retrieved from sectionName=Viral%20fitness&topicRef=3769&anchor=H19102152&source=see_link#H 19102152
  24. Kozal, M. (2018b). Overview of HIV drug resistance testing assays - UpToDate. In J. Mitty (Ed.), UpToDate. Waltham. MA. Retrieved from source=search_result&search=hiv%20genotyping&selectedTitle=1~57.
  25. Kuritzkes DR, Lalama CM, Ribaudo HJ, et al. Preexisting resistance to nonnucleoside reverse-transcriptase inhibitors predicts virologic failure of an efavirenz-based regimen in treatment-naïve HIV-1-infected subjects. J Infect Disease, March 2008; 197(6): 867-870.
  26. Little SJ, Frost SDW, Wong JK, et al. Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. Journal of Virology, June 2008; 5510-5518.
  27. Mansky, L. M., & Temin, H. M. (1995). Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol, 69(8), 5087-5094.
  28. Mazzotta F, et al. Real versus virtual phenotype to guide treatment in heavily pretreated patients: 48-week follow-up of the Genotipo-Fenotipo di Resistenza (Gen Phe Rex) trial, Journal of Acquired Immune Deficiency Syndrome, March 2003; 32(3): 268-280.
  29. Meynard JL, et al. Phenotypic or genotypic resistance testing for choosing antiretroviral therapy after treatment failure: A randomized trial, AIDS, March 2002; 16(5): 727-736.
  30. Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. Department of Health and Human Services, January 29, 2008; 1-128. Available at Accessed February 8, 2010.
  31. Parker MM, Gordon D, Reilly A, et al. Prevalence of drug-resistant and nonsubtype B HIV strains in antiretroviral-naïve, HIV0-infection individuals in New York State. AIDS Patient Care STDS, September 12007; 21(9): 644-652.
  32. Parkin N, et al. Phenotypic and genotypic HIV-1 drug resistance assays provide complementary information, Journal of Acquired Immune Deficiency Syndromes, October 2002; 31(2): 128-136.
  33. Perez-Elias MJ, et al. Phenotypic or virtual phenotype for choosing antiretroviral therapy after failure: A prospective, randomized study, Antiretroviral Therapy, December 2003; 8(6): 577-584.
  34. Rosemary, A., Chika, O., Jonathan, O., Godwin, I., Georgina, O., Azuka, O., Emmanuel, I. (2018). Genotyping performance evaluation of commercially available HIV-1 drug resistance test. PLoS One, 13(6), e0198246. doi:10.1371/journal.pone.0198246
  35. Shen, C., Yu, X., Harrison, R. W., & Weber, I. T. (2016). Automated prediction of HIV drug resistance from genotype data. BMC Bioinformatics, 17 Suppl 8, 278. doi:10.1186/s12859-016- 1114-6
  36. Tural C, et al. Clinical utility of HIV-1 genotyping and expert advice: The Havana trial, AIDS, January 2002; 16(2): 209-218.
  37. U.S. Department of Health and Human Services: Panel on Clinical Practices for Treatment of HIV Infection. Guidelines for the use of antiretroviral agents in HIV-infected adults and adolescents, February 4, 2002. Available at
  38. U.S. Department of Health and Human Services: Panel on Clinical Practices for Treatment of HIV Infection. Guidelines for the use of antiretroviral agents in HIV-infected adults and adolescents, July 14, 2003. Available at
  39. Wegner SA, et al. Long-term clinical efficacy of resistance testing: Results of the CERT trial, 14th International AIDS Conference, July 2002.
  40. Wilson JW. Update on antiretroviral drug resistance testing: Combining laboratory technology with patient care, AIDS Read 2003; 13(1): 25-38.
  41. Yeni PG, et al. Antiretroviral treatment for adult HIV infection in 2002: Updated recommendations of the International AIDS Society-USA Panel, JAMA, July 2002; 288(2): 222-235.
  42. Yeni PG, et al. Treatment for adult HIV infection: 2004 Recommendations of the International AIDS Society-USA, JAMA, July 2004; 292(2): 251-265.
  43. Zhang, J., Rhee, S. Y., Taylor, J., & Shafer, R. W. (2005). Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays. J Acquir Immune Defic Syndr, 38(4), 439-444.
  44. Zolopa AR. Incorporating drug-resistance measurements into the clinical management of HIV-1 infection. Journal of Infectious Diseases 2006; 194: S59-S64.


Medical Policy Group, February 2006 (3)

Medical Policy Administration Committee, March 2006

Available for comment March 14-April 27, 2006

Updated Key Points, added references, February 2008 (1)

Medical Policy Group, February 2010 (1) Updated Key Points, added references

Medical Policy Group, December 2010 (1) Coding Update-Added new CPT code and updated verbiage

Medical Policy Group, February 2013: Effective 02/06/2013: Active Policy but no longer scheduled for regular literature reviews and updates.

Medical Policy Group, May 2015 (3): Editing update only; added cross-reference to medical policy #322 Laboratory Testing for HIV Tropism to Policy section; no change in policy statement; no literature review update done; policy status remains unchanged.

Medical Policy Group, October 2019 (9): Updates to Description, Key Points, References. Added key words: ART, antiretroviral therapy, HIV, drug susceptibility phenotype prediction, genotyping, phenotyping, viral load, virtual phenotype testing. No change to policy statement.

Medical Policy Group, September 2020: Quarterly coding update.  Added PLA code 0219U to Current Coding.

Medical Policy Group, September 2020 (9): For clarification purposes, added to the policy statement: "including, but not limited to Sentosa SQ HIV-1 Genotyping Assay". No change to policy statement intent. Added key words: Sentosa SQ HIV-1 Genotyping Assay, Vela Diagnostics

This medical policy is not an authorization, certification, explanation of benefits, or a contract. Eligibility and benefits are determined on a case-by-case basis according to the terms of the member’s plan in effect as of the date services are rendered. All medical policies are based on (i) research of current medical literature and (ii) review of common medical practices in the treatment and diagnosis of disease as of the date hereof. Physicians and other providers are solely responsible for all aspects of medical care and treatment, including the type, quality, and levels of care and treatment.

This policy is intended to be used for adjudication of claims (including pre-admission certification, pre-determinations, and pre-procedure review) in Blue Cross and Blue Shield’s administration of plan contracts.

The plan does not approve or deny procedures, services, testing, or equipment for our members. Our decisions concern coverage only. The decision of whether or not to have a certain test, treatment or procedure is one made between the physician and his/her patient. The plan administers benefits based on the member’s contract and corporate medical policies. Physicians should always exercise their best medical judgment in providing the care they feel is most appropriate for their patients. Needed care should not be delayed or refused because of a coverage determination.

As a general rule, benefits are payable under health plans only in cases of medical necessity and only if services or supplies are not investigational, provided the customer group contracts have such coverage.

The following Association Technology Evaluation Criteria must be met for a service/supply to be considered for coverage:

  1. The technology must have final approval from the appropriate government regulatory bodies;
  2. The scientific evidence must permit conclusions concerning the effect of the technology on health outcomes;
  3. The technology must improve the net health outcome;
  4. The technology must be as beneficial as any established alternatives;
  5. The improvement must be attainable outside the investigational setting.

Medical Necessity means that health care services (e.g., procedures, treatments, supplies, devices, equipment, facilities or drugs) that a physician, exercising prudent clinical judgment, would provide to a patient for the purpose of preventing, evaluating, diagnosing or treating an illness, injury or disease or its symptoms, and that are:

  1. In accordance with generally accepted standards of medical practice; and
  2. Clinically appropriate in terms of type, frequency, extent, site and duration and considered effective for the patient’s illness, injury or disease; and
  3. Not primarily for the convenience of the patient, physician or other health care provider; and
  4. Not more costly than an alternative service or sequence of services at least as likely to produce equivalent therapeutic or diagnostic results as to the diagnosis or treatment of that patient’s illness, injury or disease.