Molina Healthcare nucleic acid probe Coverage Update

Coverage Determinations and Criteria

Organism/probe coverage table

Coverage determinations by organism and probe type (Direct Probe, Amplified Probe, Quantification). "MCC" = meets coverage criteria; "DNMCC" = does not meet coverage criteria.

Organism-level statuses: Each organism in the policy table is assigned a coverage status per probe type (Direct Probe, Amplified Probe, Quantification). Examples from the table: Chlamydia pneumoniae — Direct Probe (87485) = DNMCC; Amplified Probe (87486) = MCC; Quantification (87487) = DNMCC. Cytomegalovirus — Direct Probe (87495) = DNMCC; Amplified Probe (87496) = MCC; Quantification (87497) = MCC.

All direct probe entries in the policy were changed to DNMCC in the 10/15/2025 revision; see revision history.

Selected organism entries (representative): Bartonella henselae/quintana: Amplified Probe = 87471 (MCC); Quantification = 87472 (DNMCC). Clostridium difficile: Amplified Probe = 87493 (MCC). Enterovirus: Amplified Probe = 87498 (MCC). Legionella pneumophila: Amplified Probe = 87541 (MCC). Mycoplasma pneumoniae: Amplified Probe = 87581 (MCC). Respiratory syncytial virus: Amplified Probe = 87634 (MCC). Staphylococcus aureus and MRSA: Amplified Probes = 87640, 87641 (MCC). Orthopoxvirus (e.g., mpox): Amplified Probe = 87593 (MCC). Herpes virus-6: Quantification = 87533 (MCC); Direct and Amplified probes = 87531, 87532 (DNMCC).

Direct probe columns contain many DNMCC entries per revision.

Ordering restriction: Simultaneous ordering of an amplified probe test and quantification for the same organism in a single encounter does not meet coverage criteria and will be denied.

Do not order amplified probe and quantification for the same organism on the same encounter.

Extracted coverage logic and clinical-use criteria

Explicit clinical-use and coverage statements extracted from the policy and authoritative guidance.

Mpox—diagnostic specimen guidance: Mpox is diagnosed by PCR on a viral swab taken from one or more vesicles or ulcers; collect lesion swab(s) in viral transport or viral culture medium. If pharyngeal lesions are present, also collect a throat swab. Clinicians should collect two swabs from each lesion (generally from 2–3 lesions) to allow for additional testing such as clade confirmation.

Source: UKHSA and CDC guidance.

Mpox—follow-up and additional specimens: If follow-up testing is required for clinical deterioration or to inform discharge, additional samples should include lesion swab(s), throat swab (in viral transport medium), blood in an EDTA tube, and urine in a sterile container.

Source: UKHSA guidance.

Mpox—semen testing post-recovery: Perform MPXV PCR on semen (and, if necessary, oropharyngeal and/or rectal swabs) following the initial 12 weeks and up to 6 months after recovery when the patient is undergoing fertility treatment or planning pregnancy, for planned semen storage, when the partner is immunocompromised (including pregnant partners), or when the patient requests testing due to transmission concerns.

Per the policy, simultaneous ordering of an amplified probe and quantification for the same organism in a single encounter DOES NOT MEET COVERAGE CRITERIA. Providers ordering both an amplified probe (MCC-type test) and a quantification assay for the same organism on the same date of service should expect denial of coverage.

The policy revision clarifies that direct probe (direct probe technique) tests for listed organisms do not meet coverage criteria (DNMCC). This change is reflected in the revision history and in the coverage table where direct probe entries were changed to DNMCC; direct probe assays listed in the table should not be ordered as covered tests.

Specific CPT procedure codes and probe categories in the policy table are designated DNMCC (DOES NOT MEET COVERAGE CRITERIA) for the probe type listed. Examples from the table include direct probe entries such as 87485 (Chlamydia pneumoniae, Direct Probe), 87495 (Cytomegalovirus, Direct Probe), 87540 (Legionella pneumophila, Direct Probe), and 87580 (Mycoplasma pneumoniae, Direct Probe), which are shown as DNMCC in the coverage table.

Direct probe assays in the revised policy are designated as not meeting coverage criteria (DNMCC). Operationally, this means direct probe entries listed in the policy table are considered not covered and will be denied when billed; ordering clinicians and laboratories should rely on amplified probe or quantitative assays only where those probe types are indicated as MCC in the table.

When Testing is Covered

Diagnostic testing where amplified probe (MCC) is indicated

Diagnostic testing indicated where the policy table assigns Amplified Probe = MCC and where authoritative guidance (CDC/WHO/UKHSA/IDSA) recommends NAAT/PCR.

CDC-recommended NAAT/PCR diagnostics: Per CDC, NAATs (including real-time PCR) are preferred for certain pathogens: Chlamydia pneumoniae (preferred for acute infection), Clostridioides difficile (FDA-approved PCR assays are sensitive and specific for toxin gene detection), and Cytomegalovirus (PCR on saliva with urine confirmation for congenital CMV). Where the policy table marks Amplified Probe as MCC (e.g., C. pneumoniae 87486; C. difficile 87493; CMV quant 87497), NAAT/PCR testing is indicated consistent with guidance.

References: CDC statements and table match MCC assignments.

Other organism-specific MCC indications: Amplified probe tests designated MCC in the table include: Bartonella henselae/quintana (87471), Enterovirus (87498), Enterococcus vanA/vanB (87500), Legionella pneumophila (87541), Mycoplasma pneumoniae (87581), RSV (87634), Staphylococcus aureus/MRSA (87640, 87641), and Orthopoxvirus (mpox) amplified probe (87593). These represent covered indications for NAAT/ PCR per the policy table.

Providers should reference the table for organism-specific probe coverage.

Procedure Codes and Coding Rules

Listed organism probe codesCPT

87471	Bartonella henselae or quintana, Amplified Probe
87472	Bartonella henselae or quintana, Quantification
87485	Chlamydia pneumoniae, Direct Probe
87486	Chlamydia pneumoniae, Amplified Probe
87487	Chlamydia pneumoniae, Quantification
87493	Clostridium difficile, Amplified Probe
87495	Cytomegalovirus, Direct Probe
87496	Cytomegalovirus, Amplified Probe
87497	Cytomegalovirus, Quantification
87500	Enterococcus vancomycin-resistant (vanA, vanB), Amplified Probe

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Representative Covered/Listed CPT Codes (part 1)CPT

87471	Infectious agent detection by nucleic acid (DNA or RNA); Bartonella henselae and Bartonella quintana, amplified probe technique.
87472	Infectious agent detection by nucleic acid (DNA or RNA); Bartonella henselae and Bartonella quintana, quantification.
87485	Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia pneumoniae, direct probe technique.
87486	Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia pneumoniae, amplified probe technique.
87487	Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia pneumoniae, quantification.
87493	Infectious agent detection by nucleic acid (DNA or RNA); Clostridium difficile, toxin gene(s), amplified probe technique.
87495	Infectious agent detection by nucleic acid (DNA or RNA); cytomegalovirus, direct probe technique.
87496	Infectious agent detection by nucleic acid (DNA or RNA); cytomegalovirus, amplified probe technique.
87497	Infectious agent detection by nucleic acid (DNA or RNA); cytomegalovirus, quantification.
87498	Infectious agent detection by nucleic acid (DNA or RNA); enterovirus, amplified probe technique, includes reverse transcription when performed.

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Representative Covered/Listed CPT Codes (part 2)CPT

87525	Infectious agent detection by nucleic acid (DNA or RNA); hepatitis G, direct probe technique.
87526	Infectious agent detection by nucleic acid (DNA or RNA); hepatitis G, amplified probe technique.
87527	Infectious agent detection by nucleic acid (DNA or RNA); hepatitis G, quantification.
87531	Infectious agent detection by nucleic acid (DNA or RNA); Herpes virus-6, direct probe technique.
87532	Infectious agent detection by nucleic acid (DNA or RNA); Herpes virus-6, amplified probe technique.
87533	Infectious agent detection by nucleic acid (DNA or RNA); Herpes virus-6, quantification.
87540	Infectious agent detection by nucleic acid (DNA or RNA); Legionella pneumophila, direct probe technique.
87541	Infectious agent detection by nucleic acid (DNA or RNA); Legionella pneumophila, amplified probe technique.
87542	Infectious agent detection by nucleic acid (DNA or RNA); Legionella pneumophila, quantification.
87580	Infectious agent detection by nucleic acid (DNA or RNA); Mycoplasma pneumoniae, direct probe technique.

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Representative Covered/Listed CPT Codes (part 3)CPT

87634	Infectious agent detection by nucleic acid (DNA or RNA); respiratory syncytial virus, amplified probe technique.
87640	Infectious agent detection by nucleic acid (DNA or RNA); Staphylococcus aureus, amplified probe technique.
87641	Infectious agent detection by nucleic acid (DNA or RNA); Staphylococcus aureus, methicillin resistant, amplified probe technique

Simultaneous ordering limit — amplified probe + quantification

RuleSimultaneous ordering of an amplified probe test and a quantitative test for the same organism in a single clinical encounter DOES NOT MEET COVERAGE CRITERIA and will be denied.

ScopeApplies to nucleic acid amplified probe (e.g., CPT entries listed as amplified probe) plus quantification for the identical organism in the same encounter.

Action for orderingOrder either amplified probe OR quantification on a single encounter for a given organism; separate encounters required for both modalities if clinically necessary and supported by documentation.

Documentation noteCoverage application depends on individual benefit coverage at time of request; providers should verify benefits prior to ordering.

Provider Responsibilities and Billing Implications

Billing Rule

Code-specific coverage verification

Providers must verify coverage for the CPT/HCPCS procedure codes listed in this policy prior to ordering or billing. Coverage status varies by code (covered vs not covered) and is dependent on the member's benefits and applicable Medicare/Medicaid rules.

Affected codes include (but are not limited to): 87471, 87472, 87485, 87486, 87487, 87493, 87495, 87496, 87497, 87498, 87500, 87525, 87526, 87527, 87531, 87532, 87533, 87540, 87541, 87542, 87580, 87581, 87582, 87593, 87634, 87640, 87641

Denial Risk

Direct probe testing exclusion — denial risk

Direct probe technique tests (direct probe CPT codes) do not meet coverage criteria per the current policy revision. Ordering or billing for direct probe tests for organisms covered by this policy is at risk for denial.

How to Order and Laboratory Requirements

Note

Ordering requirements: benefit verification and specimen collection

Verify member benefits prior to ordering and follow specimen collection guidance (for example, collect lesion swabs in viral transport medium for suspected mpox) to ensure compliance with policy and public health recommendations.

For suspected mpox, collect two swabs from each lesion (CDC recommendation) and document collection details in the medical record.
Confirm benefits and coverage for the specific CPT code to avoid denials.

Documentation Required

Ordering requirements: LDT validation and CLIA/facility-level compliance

Ensure laboratory-developed tests (LDTs) used for these assays are validated and performed under CLIA as high-complexity tests; FDA clearance is not required for clinical use but LDTs remain CMS/CLIA-regulated.

Document that the performing laboratory validated the LDT and operates under appropriate CLIA certification.

Tests and Codes Not Covered

Codes and probe types marked as DNMCC in the policy table are not covered under this policy. The table identifies multiple direct probe and some quantification codes with a DNMCC designation; these codes should be treated as non-covered for benefit determination and prior authorization purposes.

As detailed in the revision history, direct probe testing (direct probe technique) for certain organisms does not meet coverage criteria. The policy explicitly states that all direct probes in the policy do not meet coverage criteria following the update, and direct probe CPT entries in the coverage table reflect this exclusion.

Clinical and Technical Background

Nucleic acid hybridization technologies — including nucleic acid amplification tests (NAATs) such as PCR, ligase/helicase-dependent amplification, and transcription-mediated amplification — are highly sensitive and specific methods for pathogen detection across specimen types. The policy recognizes these methods’ advantages (rapid turnaround and high throughput) and limitations (contamination risk, assay standardization, interpretation complexity, and cost) when describing coverage of direct probe, amplified probe, and quantification testing.

Terminology and Specimen Definitions

Selected terminology

NAATsNucleic acid amplification tests.

PCRPolymerase chain reaction.

qPCRQuantitative polymerase chain reaction.

rRT-PCRReal-time reverse transcriptase-polymerase chain reaction.

FRETFluorescent resonance energy transfer.

Lesion swab — definition and collection notes

DefinitionLesion swab: a viral swab taken from a vesicle, ulcer, or crusted lesion and placed in viral culture medium or viral transport medium for PCR testing.

Frequency and Timing Limits

Frequency limits — absence of explicit caps

Frequency limitsNo explicit numeric frequency limits are provided in this policy extract for routine ordering of the listed nucleic acid tests.

ImplicationAbsent stated caps, coverage evaluation will follow per-test coverage criteria and clinical justification on each request.

Provider actionVerify member benefits and document clinical necessity for repeat testing as appropriate.

MPXV PCR on semen — testing window and indications

MPXV semen testing windowPerform MPXV PCR on semen between 12 weeks and up to 6 months after recovery for specified indications.

IndicationsIndicated for patients undergoing fertility treatment or planning pregnancy, planned semen storage, immunocompromised partner (including pregnant), or patient request due to transmission concerns.

Policy Revision History

2025-10-15Policy revisionLatest

Updated background, guidelines, and references; removed 'Non-vaginal Candida species' and associated codes; changed direct probe testing for Chlamydia pneumoniae, Cytomegalovirus, Legionella pneumophila, and Mycoplasma pneumoniae from MCC to DNMCC and designated all direct probes as not meeting coverage criteria; reorganized criteria to specify that simultaneous ordering of amplified probe and quantification for the same organism in a single encounter does not meet coverage criteria; removed CPT codes 87480, 87481, and 87482.

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Identification of Microorganisms using Nucleic Acid Probes