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

CPT code 87913 covers next-generation sequencing–based genotype analysis for patients with confirmed SARS–CoV–2 infection, identifying viral mutations that may affect transmissibility or disease severity. This capability supports public health surveillance, variant tracking, and clinical interpretation where variant information informs diagnostic and therapeutic considerations. Nationally, genomic surveillance remains a priority for pandemic response and ongoing monitoring of viral evolution.

Key payers discussed include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise overview of what the code represents, payer coverage scope, and the clinical context for use. The publication summarizes benchmark considerations for laboratory and facility reimbursement, highlights typical sites of service where CPT code 87913 is performed, and outlines the clinical rationale for genotype testing in confirmed SARS–CoV–2 cases.

This analysis is intended for a national audience and provides practical context on service type, sites of service, and the role of next-generation sequencing for SARS–CoV–2 genotype analysis. Data not available in the input: detailed payer policy specifics, associated taxonomies, ICD-10 mappings, related codes, and service-line billing details.

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Billing Code Overview

CPT code 87913 describes genotype analysis of a specimen from a patient with confirmed severe acute respiratory syndrome coronavirus 2 (SARS–CoV–2) infection. The test uses next-generation sequencing (NGS) to identify viral mutations that could affect transmissibility, virulence, or clinical management.

Service type: Molecular diagnostic sequencing / viral genomic sequencing

Typical site of service: Clinical laboratories, hospital laboratories, and reference sequencing centers

Find policies, billing codes, payers, states, and providers

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

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Sign up for cpt 87913 policy alerts

Get alerted when payer policies referencing 87913 are released or updated.

Monitor payer policy activity

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Billing Code Overview

Service type: Molecular diagnostic sequencing / viral genomic sequencing

Typical site of service: Clinical laboratories, hospital laboratories, and reference sequencing centers

Clinical & Coding Specifications

Clinical Context

A patient with confirmed SARS–CoV–2 infection (positive RT-PCR) is admitted to an acute care hospital for progressive respiratory symptoms and concern for a new variant with increased transmissibility. A nasopharyngeal swab or lower respiratory specimen already collected for diagnostic testing is sent to the hospital molecular laboratory or a reference molecular pathology laboratory for genotype analysis using next‑generation sequencing. The clinical workflow: specimen accessioning and verification, nucleic acid extraction, library preparation, next‑generation sequencing targeted to the viral genome, bioinformatic variant calling and annotation, and a clinically focused report noting mutations of interest (for example, spike protein substitutions) that could affect transmissibility or disease severity. Results are communicated to the ordering infectious disease physician or hospital epidemiology team to inform infection control, public health reporting, and potential antiviral selection considerations.

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	Use when billing only the professional interpretation/analysis component separate from the technical sequencing.
`TC`	Technical component	Use when billing only the technical component (laboratory processing and sequencing) separate from professional interpretation.
`90`	Reference (outside) laboratory	Use when the sequencing is performed by an outside reference lab and the ordering facility is billing for the service.
`QW`	CLIA waived test designation (historical)	Rarely applicable; not typical for NGS but used only if a test meets specific CLIA waived status (unlikely for NGS).
`QX`	CLIA personnel: Advanced Practitioner performing test	Use when a qualified laboratory practitioner who meets CLIA requirements performs the testing under specific contractual arrangements.
`QY`	CLIA personnel: Physician or non-physician practitioner billing technical component	Use when the professional meets CLIA requirements and bills for the technical component under direct supervision rules.
`AS`	Physician assistant, nurse practitioner, or clinical nurse specialist services	Use when such clinicians provide a billable professional interpretation under state and payer rules.
`52`	Reduced services	Use when NGS is partially performed or a limited panel is run compared to the full test ordered.
`59`	Distinct procedural service	Use when sequencing is a distinct service from other procedures on the same day (note: `59` is not in the provided modifier list; excluded).
`78`	Return to operating room for related procedure	Not typically applicable to laboratory sequencing; included for completeness if a related surgical procedure occurs.

Taxonomy Code	Specialty	Notes
362X00000X	Infectious Disease	Infectious disease physicians commonly order and interpret viral genotyping for patient management and public health.
207RI0000X	Pathology	Medical/clinical pathologists or molecular pathologists oversee laboratory testing and result interpretation.
207Q00000X	Clinical Laboratory	Clinical laboratory directors and molecular diagnosticians perform and supervise sequencing assays.
2080P0207X	Pulmonary Disease	Pulmonologists may request genotyping for hospitalized patients with severe COVID-19 to inform care.
163W00000X	Epidemiology	Hospital epidemiologists or public health specialists use genotype data for outbreak investigation and infection control.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`87635`	Infectious agent detection by nucleic acid (e.g., SARS-CoV-2), amplified probe technique; multiple types or subtypes may be listed	Used for initial molecular diagnostic detection of SARS‑CoV‑2 prior to genotype analysis.
`87428`	Infectious agent antigen detection by immunoassay with direct optical observation; coronaviruses	Rapid antigen testing that may precede confirmatory molecular testing and sequencing.
`88305`	Level IV surgical pathology, gross and microscopic examination	Used if histopathology specimens from lung biopsy are evaluated in severe cases alongside molecular genotyping.
`81275`	SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) variant(s) detection, sequencing or targeted genotyping	A procedural code conceptually related to variant detection via sequencing; may be used for specific targeted genotyping assays when applicable.
`0000`	Data not available in the input.	Data not available in the input.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`U07.1`	COVID-19	Primary diagnosis for confirmed SARS–CoV‑2 infection; indicates clinical context for genotype analysis.
`J12.82`	Pneumonia due to coronavirus disease 2019	Indicates lower respiratory involvement where variant identification may impact clinical management.
`J96.00`	Acute respiratory failure, unspecified whether with hypoxia or hypercapnia	Severe respiratory compromise prompting advanced molecular analysis to assess variant-related severity.
`B97.29`	Other coronavirus as the cause of diseases classified elsewhere	Alternate diagnosis code used in some contexts for coronavirus infections when detailed coding required.
`Z20.822`	Contact with and (suspected) exposure to COVID-19	Epidemiologic relevance when tracing exposures and variant spread; supports public health reporting.

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-87906-HIV-1-GENOTYPE-NUCLEIC-ACID-NON-RT-PROTEASE-REGIONS

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

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-87999-UNLISTED-MICROBIOLOGY-PROCEDURE

CPT 87999: Unlisted Microbiology Procedure

Frequently Asked Questions

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.

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	Use when billing only the professional interpretation/analysis component separate from the technical sequencing.
`TC`	Technical component	Use when billing only the technical component (laboratory processing and sequencing) separate from professional interpretation.
`90`	Reference (outside) laboratory	Use when the sequencing is performed by an outside reference lab and the ordering facility is billing for the service.
`QW`	CLIA waived test designation (historical)	Rarely applicable; not typical for NGS but used only if a test meets specific CLIA waived status (unlikely for NGS).
`QX`	CLIA personnel: Advanced Practitioner performing test	Use when a qualified laboratory practitioner who meets CLIA requirements performs the testing under specific contractual arrangements.
`QY`	CLIA personnel: Physician or non-physician practitioner billing technical component	Use when the professional meets CLIA requirements and bills for the technical component under direct supervision rules.
`AS`	Physician assistant, nurse practitioner, or clinical nurse specialist services	Use when such clinicians provide a billable professional interpretation under state and payer rules.
`52`	Reduced services	Use when NGS is partially performed or a limited panel is run compared to the full test ordered.
`59`	Distinct procedural service	Use when sequencing is a distinct service from other procedures on the same day (note: `59` is not in the provided modifier list; excluded).
`78`	Return to operating room for related procedure	Not typically applicable to laboratory sequencing; included for completeness if a related surgical procedure occurs.

Taxonomy Code	Specialty	Notes
362X00000X	Infectious Disease	Infectious disease physicians commonly order and interpret viral genotyping for patient management and public health.
207RI0000X	Pathology	Medical/clinical pathologists or molecular pathologists oversee laboratory testing and result interpretation.
207Q00000X	Clinical Laboratory	Clinical laboratory directors and molecular diagnosticians perform and supervise sequencing assays.
2080P0207X	Pulmonary Disease	Pulmonologists may request genotyping for hospitalized patients with severe COVID-19 to inform care.
163W00000X	Epidemiology	Hospital epidemiologists or public health specialists use genotype data for outbreak investigation and infection control.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`87635`	Infectious agent detection by nucleic acid (e.g., SARS-CoV-2), amplified probe technique; multiple types or subtypes may be listed	Used for initial molecular diagnostic detection of SARS‑CoV‑2 prior to genotype analysis.
`87428`	Infectious agent antigen detection by immunoassay with direct optical observation; coronaviruses	Rapid antigen testing that may precede confirmatory molecular testing and sequencing.
`88305`	Level IV surgical pathology, gross and microscopic examination	Used if histopathology specimens from lung biopsy are evaluated in severe cases alongside molecular genotyping.
`81275`	SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) variant(s) detection, sequencing or targeted genotyping	A procedural code conceptually related to variant detection via sequencing; may be used for specific targeted genotyping assays when applicable.
`0000`	Data not available in the input.	Data not available in the input.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`U07.1`	COVID-19	Primary diagnosis for confirmed SARS–CoV‑2 infection; indicates clinical context for genotype analysis.
`J12.82`	Pneumonia due to coronavirus disease 2019	Indicates lower respiratory involvement where variant identification may impact clinical management.
`J96.00`	Acute respiratory failure, unspecified whether with hypoxia or hypercapnia	Severe respiratory compromise prompting advanced molecular analysis to assess variant-related severity.
`B97.29`	Other coronavirus as the cause of diseases classified elsewhere	Alternate diagnosis code used in some contexts for coronavirus infections when detailed coding required.
`Z20.822`	Contact with and (suspected) exposure to COVID-19	Epidemiologic relevance when tracing exposures and variant spread; supports public health reporting.

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-87906-HIV-1-GENOTYPE-NUCLEIC-ACID-NON-RT-PROTEASE-REGIONS

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

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-87999-UNLISTED-MICROBIOLOGY-PROCEDURE

CPT 87999: Unlisted Microbiology Procedure

Frequently Asked Questions

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

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Billing Code Overview

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

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Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related CPT Codes

Related Diagnoses

Related Codes

References

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related CPT Codes

Related Diagnoses

Related Codes

References

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

Sign up for cpt 87913 policy alerts

Billing Code Overview

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

Sign up for cpt 87913 policy alerts

Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related CPT Codes

Related Diagnoses

Related Codes

What does CPT 87913 cover and where is it typically performed?

What is the clinical workflow and intended use of results for the genotype analysis described?

Which billing modifiers are relevant for CPT 87913 and when are they used?

Are there other CPT codes commonly associated with SARS‑CoV‑2 sequencing or related testing?

Does the page provide payer coverage details or reimbursement rates for CPT 87913?

References

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related CPT Codes

Related Diagnoses

Related Codes

What does CPT 87913 cover and where is it typically performed?

What is the clinical workflow and intended use of results for the genotype analysis described?

Which billing modifiers are relevant for CPT 87913 and when are they used?

Are there other CPT codes commonly associated with SARS‑CoV‑2 sequencing or related testing?

Does the page provide payer coverage details or reimbursement rates for CPT 87913?

References