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CPT 87906: HIV-1 Genotype by Nucleic Acid (Non-RT/Protease Regions)

CPT code 87906 covers technical laboratory genotyping of HIV‑1 by nucleic acid methods for genomic regions other than reverse transcriptase and protease (for example, integrase or fusion genes). These targeted molecular assays support clinical decision‑making for antiretroviral resistance surveillance, epidemiologic characterization, and specialized patient management. Nationally, access to and coverage of such advanced genotyping tests affect infectious disease care pathways, public health reporting, and specialized laboratory workflows.

Key payers included in the analysis are Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise overview of the clinical context and typical sites of service, a summary of common modifiers and billing considerations, and an outline of where this service fits within laboratory molecular diagnostics. The publication also highlights benchmarking points and policy or coding updates where available. Data not available in the input is identified explicitly to avoid assumptions.

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Billing Code Overview

CPT code 87906 describes a laboratory technical procedure in which a lab analyst performs nucleic acid analysis to determine the genotype of an HIV‑1 virus for regions other than the reverse transcriptase and protease regions (for example, the integrase gene or fusion gene). This is a specialized molecular diagnostic test focused on sequencing or genotyping non‑RT/non‑protease regions of HIV‑1 to inform virologic characterization.

Service type: Molecular diagnostic laboratory test (technical component)
Typical site of service: Clinical laboratory or hospital laboratory performing molecular virology testing

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CPT 87906: HIV-1 Genotype by Nucleic Acid (Non-RT/Protease Regions)

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Get alerted when payer policies referencing 87906 are released or updated.

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Billing Code Overview

Service type: Molecular diagnostic laboratory test (technical component)
Typical site of service: Clinical laboratory or hospital laboratory performing molecular virology testing

Clinical & Coding Specifications

Clinical Context

A 42-year-old person with known HIV-1 infection presents for evaluation following suboptimal viral suppression on current antiretroviral therapy. The treating infectious disease clinician orders genotypic resistance testing focused on the HIV-1 integrase gene to detect mutations that confer resistance to integrase strand transfer inhibitors. A blood specimen (plasma) is collected in the outpatient infusion clinic or ambulatory lab and sent to a molecular diagnostics laboratory. The laboratory analyst performs nucleic acid extraction, sequencing or targeted genotyping of regions other than reverse transcriptase and protease (for example, the integrase gene), interprets the technical assay results, and reports detected resistance-associated substitutions to the ordering clinician. Typical site of service includes outpatient ambulatory clinics, hospital outpatient departments, and reference molecular laboratories. Typical workflow steps: specimen collection → specimen accessioning and nucleic acid extraction → amplification/sequencing or targeted assay of integrase/fusion regions → bioinformatic analysis and quality control → technical result reporting to the laboratory information system (with or without separate professional interpretation by a clinical molecular pathologist).

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	When billing only the physician/clinical interpretation portion if separated from the laboratory technical component.
`TC`	Technical component	When billing only the laboratory technical component (instrumentation, reagents, and personnel).
`90`	Reference (outside) laboratory	When the performing laboratory bills but testing was performed by an outside reference lab.
`91`	Repeat clinical diagnostic laboratory test	When the same test is repeated on the same day to confirm prior result.
`59`	Distinct procedural service	When another unrelated procedure or service on the same day is distinct and should not be bundled.
`52`	Reduced services	When the laboratory performed a reduced portion of the test procedure.
`53`	Discontinued procedure	When testing was started but discontinued for clinical reasons and partial work was performed.
`78`	Unplanned return to the operating/procedure room by same physician following initial procedure	Rare for lab testing but applicable if specimen collection required an unexpected return for additional sampling during the same encounter.
`91`	(listed again in CMS guidance) Repeat clinical diagnostic laboratory test	See above — used when results are repeated to confirm technical variability.
`QX`	Ordering physician certified no financial relationship (CLIA modifier)	When the performing laboratory is an independent diagnostic testing facility (IDTF) and the ordering provider meets modifier requirements.
`QY`	Ordering physician and lab within same group (CLIA modifier)	Applied when the ordering physician is a physician/clinic location that is part of the performing laboratory's Medicare-certified entity.
`59`	(distinct service)	See above — used selectively to indicate distinct service when bundling edits might deny.

Taxonomy Code	Specialty	Notes
1835G0001X	Infectious Disease	Clinicians ordering and interpreting genotypic resistance testing for HIV management.
207K00000X	Pathology & Laboratory Medicine	Medical directors and clinical pathologists providing interpretation and oversight of molecular testing.
363L00000X	Clinical Laboratory	Laboratory directors and technologists performing the technical testing.
207L00000X	Molecular Pathology	Specialists who interpret complex sequencing and resistance reports.
2084P0800X	Internal Medicine	Primary care or HIV specialty internists who order testing as part of antiretroviral management.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`B20`	Human immunodeficiency virus [HIV] disease	Primary diagnosis indicating HIV infection; genotypic resistance testing is performed to guide antiretroviral therapy.
`Z21`	Asymptomatic human immunodeficiency virus [HIV] infection status	Used when a patient is HIV-positive without symptoms; testing may be ordered if viral breakthrough or therapy change is considered.
`R75`	Inconclusive laboratory evidence of human immunodeficiency virus [HIV]	May prompt repeat or supplemental genotypic testing to clarify viral genetics.
`Z11.4`	Encounter for screening for human immunodeficiency virus [HIV]	Screening encounters that lead to confirmatory and subsequent resistance testing if infection is confirmed.
`B97.35`	Human immunodeficiency virus causing disease classified elsewhere	Used in some reporting conventions; relevant when HIV is listed as cause of other conditions and genotyping informs management.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`87491`	Infectious agent detection by nucleic acid (DNA or RNA); influenza virus, amplified probe technique, qualitative	Example of a nucleic acid amplification detection CPT used for viral identification; represents similar laboratory methodology (amplification platforms) though not specific to HIV genotyping.
`87536`	Infectious agent detection by nucleic acid (DNA or RNA), direct probe technique; HIV-1 quantification	Represents viral load testing often performed before or concurrently with genotypic resistance testing to assess viremia level.
`88260`	Tissue culture for viral isolation, any source; with identification of viral agent	Represents virology methods sometimes used in comprehensive viral testing workflows; less commonly used for modern genotypic assays.
`88342`	Immunohistochemistry or immunocytochemistry, per specimen; initial single antibody stain	Example laboratory code for ancillary testing workflows that may be bundled with pathology services when tissue-based viral testing is indicated.
`87907`	Laboratory analysis of genotype of HIV-1 virus by nucleic acid, reverse transcriptase and protease regions; (example companion code)	Related genotypic testing of different HIV-1 coding regions (reverse transcriptase and protease) commonly ordered alongside integrase genotyping to provide a full resistance profile.

CPT 87900: Viral Drug Susceptibility Testing, Genotype-to-Phenotype Prediction

CPT-87901-HIV-1-GENOTYPE-REVERSE-TRANSCRIPTASE-PROTEASE-ANALYSIS

CPT 87901: HIV-1 Genotype Analysis of Reverse Transcriptase and Protease

CPT-87902-HEPATITIS-C-GENOTYPE-NUCLEIC-ACID-TESTING-TECHNICAL

CPT 87902: Hepatitis C Genotype by Nucleic Acid, Technical Component

CPT-87903-HIV-1-DRUG-RESISTANCE-NUCLEIC-ACID-ANALYSIS

CPT 87903: HIV-1 Drug Resistance Nucleic Acid Analysis

CPT-87904-HIV-1-DRUG-RESISTANCE-ADDITIONAL-DRUG-TESTING

CPT 87904: HIV-1 Drug Resistance Analysis, Additional Drug

CPT-87905-ENZYMATIC-ACTIVITY-TESTING-INFECTIOUS-AGENT-TECHNICAL

CPT 87905: Enzymatic Activity Testing for Nonviral Infectious Agents

CPT-87910-CMV-GENOTYPE-NUCLEIC-ACID-ANALYSIS

CPT 87910: CMV Genotype Analysis by Nucleic Acid

CPT-87912-HEPATITIS-B-GENOTYPE-ANALYSIS-NUCLEIC-ACID

CPT 87912: Hepatitis B Virus Genotype Analysis, Nucleic Acid

CPT-87913-SARS-COV-2-GENOTYPE-ANALYSIS-NEXT-GENERATION-SEQUENCING

CPT 87913: SARS–CoV–2 Genotype Analysis by Next-Generation Sequencing

CPT-87999-UNLISTED-MICROBIOLOGY-PROCEDURE

CPT 87999: Unlisted Microbiology Procedure

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Jul 29, 2026.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.

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Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	When billing only the physician/clinical interpretation portion if separated from the laboratory technical component.
`TC`	Technical component	When billing only the laboratory technical component (instrumentation, reagents, and personnel).
`90`	Reference (outside) laboratory	When the performing laboratory bills but testing was performed by an outside reference lab.
`91`	Repeat clinical diagnostic laboratory test	When the same test is repeated on the same day to confirm prior result.
`59`	Distinct procedural service	When another unrelated procedure or service on the same day is distinct and should not be bundled.
`52`	Reduced services	When the laboratory performed a reduced portion of the test procedure.
`53`	Discontinued procedure	When testing was started but discontinued for clinical reasons and partial work was performed.
`78`	Unplanned return to the operating/procedure room by same physician following initial procedure	Rare for lab testing but applicable if specimen collection required an unexpected return for additional sampling during the same encounter.
`91`	(listed again in CMS guidance) Repeat clinical diagnostic laboratory test	See above — used when results are repeated to confirm technical variability.
`QX`	Ordering physician certified no financial relationship (CLIA modifier)	When the performing laboratory is an independent diagnostic testing facility (IDTF) and the ordering provider meets modifier requirements.
`QY`	Ordering physician and lab within same group (CLIA modifier)	Applied when the ordering physician is a physician/clinic location that is part of the performing laboratory's Medicare-certified entity.
`59`	(distinct service)	See above — used selectively to indicate distinct service when bundling edits might deny.

Taxonomy Code	Specialty	Notes
1835G0001X	Infectious Disease	Clinicians ordering and interpreting genotypic resistance testing for HIV management.
207K00000X	Pathology & Laboratory Medicine	Medical directors and clinical pathologists providing interpretation and oversight of molecular testing.
363L00000X	Clinical Laboratory	Laboratory directors and technologists performing the technical testing.
207L00000X	Molecular Pathology	Specialists who interpret complex sequencing and resistance reports.
2084P0800X	Internal Medicine	Primary care or HIV specialty internists who order testing as part of antiretroviral management.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`B20`	Human immunodeficiency virus [HIV] disease	Primary diagnosis indicating HIV infection; genotypic resistance testing is performed to guide antiretroviral therapy.
`Z21`	Asymptomatic human immunodeficiency virus [HIV] infection status	Used when a patient is HIV-positive without symptoms; testing may be ordered if viral breakthrough or therapy change is considered.
`R75`	Inconclusive laboratory evidence of human immunodeficiency virus [HIV]	May prompt repeat or supplemental genotypic testing to clarify viral genetics.
`Z11.4`	Encounter for screening for human immunodeficiency virus [HIV]	Screening encounters that lead to confirmatory and subsequent resistance testing if infection is confirmed.
`B97.35`	Human immunodeficiency virus causing disease classified elsewhere	Used in some reporting conventions; relevant when HIV is listed as cause of other conditions and genotyping informs management.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`87491`	Infectious agent detection by nucleic acid (DNA or RNA); influenza virus, amplified probe technique, qualitative	Example of a nucleic acid amplification detection CPT used for viral identification; represents similar laboratory methodology (amplification platforms) though not specific to HIV genotyping.
`87536`	Infectious agent detection by nucleic acid (DNA or RNA), direct probe technique; HIV-1 quantification	Represents viral load testing often performed before or concurrently with genotypic resistance testing to assess viremia level.
`88260`	Tissue culture for viral isolation, any source; with identification of viral agent	Represents virology methods sometimes used in comprehensive viral testing workflows; less commonly used for modern genotypic assays.
`88342`	Immunohistochemistry or immunocytochemistry, per specimen; initial single antibody stain	Example laboratory code for ancillary testing workflows that may be bundled with pathology services when tissue-based viral testing is indicated.
`87907`	Laboratory analysis of genotype of HIV-1 virus by nucleic acid, reverse transcriptase and protease regions; (example companion code)	Related genotypic testing of different HIV-1 coding regions (reverse transcriptase and protease) commonly ordered alongside integrase genotyping to provide a full resistance profile.

CPT 87900: Viral Drug Susceptibility Testing, Genotype-to-Phenotype Prediction

CPT-87901-HIV-1-GENOTYPE-REVERSE-TRANSCRIPTASE-PROTEASE-ANALYSIS

CPT 87901: HIV-1 Genotype Analysis of Reverse Transcriptase and Protease

CPT-87902-HEPATITIS-C-GENOTYPE-NUCLEIC-ACID-TESTING-TECHNICAL

CPT 87902: Hepatitis C Genotype by Nucleic Acid, Technical Component

CPT-87903-HIV-1-DRUG-RESISTANCE-NUCLEIC-ACID-ANALYSIS

CPT 87903: HIV-1 Drug Resistance Nucleic Acid Analysis

CPT-87904-HIV-1-DRUG-RESISTANCE-ADDITIONAL-DRUG-TESTING

CPT 87904: HIV-1 Drug Resistance Analysis, Additional Drug

CPT-87905-ENZYMATIC-ACTIVITY-TESTING-INFECTIOUS-AGENT-TECHNICAL

CPT 87905: Enzymatic Activity Testing for Nonviral Infectious Agents

CPT-87910-CMV-GENOTYPE-NUCLEIC-ACID-ANALYSIS

CPT 87910: CMV Genotype Analysis by Nucleic Acid

CPT-87912-HEPATITIS-B-GENOTYPE-ANALYSIS-NUCLEIC-ACID

CPT 87912: Hepatitis B Virus Genotype Analysis, Nucleic Acid

CPT-87913-SARS-COV-2-GENOTYPE-ANALYSIS-NEXT-GENERATION-SEQUENCING

CPT 87913: SARS–CoV–2 Genotype Analysis by Next-Generation Sequencing

CPT-87999-UNLISTED-MICROBIOLOGY-PROCEDURE

CPT 87999: Unlisted Microbiology Procedure

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Jul 29, 2026.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.

Published by

Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

OpenPayer

CPT 87906: HIV-1 Genotype by Nucleic Acid (Non-RT/Protease Regions)

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Billing Code Overview

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CPT 87906: HIV-1 Genotype by Nucleic Acid (Non-RT/Protease Regions)

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Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

References

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

References