TL;DR: Aetna, a CVS Health company, modified CPB 0650 governing PCR testing coverage policy, effective January 29, 2026. Billing teams working with infectious disease, oncology, genetics, and molecular diagnostics codes need to review selection criteria across 200+ affected CPT codes before submitting claims.
| Field | Detail |
|---|---|
| Payer | Aetna, a CVS Health company |
| Policy | Polymerase Chain Reaction Testing: Selected Indications |
| Policy Code | CPB 0650 |
| Change Type | Modified |
| Effective Date | January 29, 2026 |
| Impact Level | High |
| Specialties Affected | Infectious disease, oncology, molecular pathology, clinical genetics, OB/GYN, transplant medicine, immunology, gynecology |
| Key Action | Audit your PCR claim documentation against updated medical necessity criteria before billing under any of the 200+ affected CPT codes |
Aetna PCR Testing Coverage Policy and Medical Necessity Requirements 2026
Aetna CPB 0650 is one of the broadest coverage policies in the Aetna system. It governs both qualitative and quantitative PCR testing across dozens of clinical indications — infectious disease, cancer genetics, pharmacogenomics, transplant monitoring, and more. The sheer scope of this policy means a single documentation gap can generate a claim denial across a wide range of CPT codes.
The Aetna PCR testing coverage policy draws a hard line between medically necessary testing and testing Aetna considers experimental or not covered. The line isn't always obvious. Many indications are covered only when very specific clinical and exposure criteria are met. Know those criteria before you bill.
Qualitative PCR: What Aetna Will Cover
Aetna covers qualitative PCR testing for a long list of pathogens — but each one comes with conditions. This is not a blanket "PCR for infection = covered" policy. Medical necessity is tied to specific clinical scenarios.
A few high-volume examples:
Bacterial vaginosis (BV): PCR testing on vaginal specimens is covered for symptomatic vaginitis. PCR on urine is not covered for BV diagnosis. Testing of asymptomatic male sex partners is also not covered. If your lab or OB/GYN practice bills CPT 0557U for urine-based BV testing, expect denials.
Avian influenza A (H5N1): Aetna covers qualitative PCR only when the patient has both symptoms consistent with avian influenza AND documented travel to or contact with affected persons or birds within 10 days of symptom onset. Both criteria must be present. Missing either one means no coverage.
Bordetella pertussis/whooping cough: Coverage applies when a patient has fewer than 21 days of coughing with documented exposure to pertussis, paroxysmal coughing, inspiratory whoop, post-tussive vomiting, or apnea in infants under one year. Document the symptom duration explicitly in the medical record.
Bartonella species (CPT 0301U, 0302U): Aetna covers PCR to confirm diagnosis in acutely or severely ill patients with systemic symptoms of Cat-Scratch Disease — particularly those with hepatosplenomegaly, large painful adenopathy, or immunocompromised status. It also covers use in HIV-infected patients with signs of bacillary angiomatosis or peliosis hepatis.
BK polyomavirus: Covered for transplant recipients on immunosuppressive therapy and for patients with immunosuppressive diseases such as HIV/AIDS-associated immune complex glomerulonephritis. The immunosuppressed status must be documented.
Borrelia miyamotoi: Covered only in the acute phase of infection in patients from endemic areas. Geographic origin matters here — document it.
Borrelia mayonii (CPT 87476): Covered on biopsy specimens when Lyme arthritis is suspected, serologic testing for B. burgdorferi is negative or inconclusive, AND the patient lives in or has traveled to Minnesota or Wisconsin. Three conditions, all required.
The pattern here is consistent: Aetna ties coverage to clinical specificity. Vague documentation won't hold up.
Oncology and Genetics PCR Coverage
The oncology and genetics coverage under CPB 0650 is just as condition-heavy. Aetna covers ALK testing (as an alternative to FISH) for selecting patients for ALK inhibitor therapy. BRAF mutation analysis (CPT 81210) is covered for hairy cell leukemia. Beta-tyrosinase PCR is covered to detect hematogenous spread in melanoma patients.
BCR/ABL1 translocation analysis — CPT codes 81206, 81207, 81208, and 0040U — covers chronic myelogenous leukemia and related indications, but selection criteria apply. JAK2 mutation analysis (CPT 81270 and 0017U) is covered for myeloproliferative disorders. PML/RARalpha (CPT 81315, 81316) covers promyelocytic leukemia indications.
For hereditary cancer syndromes, CPT codes 81292–81300 (MLH1, MSH2, MSH6) and 81317–81319 (PMS2) cover Lynch syndrome testing when criteria are met — these align with applicable companion CPBs on hereditary cancer testing.
Pharmacogenomics PCR — CYP2C19 (CPT 81225), CYP2D6 (CPT 81226), and CYP2C9 (CPT 81227) — are covered for drug metabolism analysis when clinically indicated. These codes are increasingly scrutinized. Make sure the clinical indication is specific in documentation.
Cystic fibrosis carrier and diagnostic testing (CPT 81220–81224) is covered. Fragile X testing (CPT 81243, 81244), HFE hemochromatosis (CPT 81256), and HBA1/HBA2 for alpha thalassemia (CPT 81257) are all covered when selection criteria are met.
Aetna PCR Testing Exclusions and Non-Covered Indications
CPB 0650 includes explicit non-coverage determinations that your billing team needs to know by code level — not just in concept.
BV PCR testing on urine: Not covered. Aetna accepts vaginal specimens only. If your lab collects urine for BV PCR and bills it, that claim will deny.
BV PCR in asymptomatic male sex partners: Not covered. This applies regardless of the female partner's diagnosis.
The broader principle across CPB 0650 is that PCR testing ordered outside the specific clinical and demographic criteria for each indication is considered not medically necessary. That means testing ordered "to rule out" without supporting symptoms or exposure history will fail medical necessity review.
Several newer proprietary codes — including multi-analyte panels and next-generation sequencing-based assays — fall under the "not covered" or "investigational" designation for many indications. If you're billing codes like 0152U (DNA/PCR next-generation sequencing for bacteria, fungi, parasites) or 0595U (tropical fever pathogens, vector-borne and zoonotic), verify the specific indication is covered before the claim goes out.
Coverage Indications at a Glance
| Indication | Status | Relevant Codes | Notes |
|---|---|---|---|
| Bacterial vaginosis — vaginal specimen, symptomatic | Covered | 0557U | Urine specimen: Not Covered |
| Bacterial vaginosis — urine specimen | Not Covered | 0557U | Explicitly excluded |
| BV PCR — asymptomatic male sex partner | Not Covered | — | Explicitly excluded |
| Avian influenza A (H5N1) | Covered | — | Requires both symptoms AND travel/contact exposure within 10 days |
| Bordetella pertussis/whooping cough | Covered | — | Symptom duration must be <21 days; one of five listed symptom criteria required |
| Bartonella species (Cat-Scratch Disease) | Covered | 0301U, 0302U | Requires systemic illness, hepatosplenomegaly, or immunocompromised status |
| BK polyomavirus — transplant recipients | Covered | — | Requires documented immunosuppressive therapy |
| Borrelia mayonii — Lyme arthritis | Covered | 87476 | Three concurrent criteria: negative serology, biopsy specimen, MN/WI geography |
| Borrelia miyamotoi | Covered | — | Acute phase only, endemic area required |
| Acanthamoeba — corneal ulceration | Covered | — | Clinical setting required |
| ALK testing — ALK inhibitor selection | Covered | — | Alternative to FISH only |
| BRAF mutation — hairy cell leukemia | Covered | 81210 | Specific to hairy cell leukemia indication |
| BCR/ABL1 — CML and related | Covered | 81206, 81207, 81208, 0040U | Selection criteria apply |
| JAK2 — myeloproliferative disorder | Covered | 81270, 0017U | Selection criteria apply |
| PML/RARalpha — promyelocytic leukemia | Covered | 81315, 81316 | Selection criteria apply |
| MLH1/MSH2/MSH6/PMS2 — Lynch syndrome | Covered | 81292–81300, 81317–81319 | Must meet hereditary cancer criteria per applicable CPB |
| CYP2C19/CYP2D6/CYP2C9 — pharmacogenomics | Covered | 81225, 81226, 81227 | Clinical indication required |
| CFTR — cystic fibrosis | Covered | 81220–81224 | Selection criteria apply |
| Fragile X (FMR1) | Covered | 81243, 81244 | Selection criteria apply |
| HFE — hereditary hemochromatosis | Covered | 81256 | Selection criteria apply |
| HBA1/HBA2 — alpha thalassemia | Covered | 81257 | Selection criteria apply |
| Candida species panel | Covered | 0068U | Selection criteria apply |
| Respiratory pathogen panels | Covered | 0115U, 0202U, 0223U, 0225U, 0528U, 0556U, 0563U, 0564U | Selection criteria apply per indication |
| Genitourinary pathogen panels | Covered | 0321U, 0371U, 0372U, 0402U, 0455U, 0593U | Selection criteria apply |
| Babesiosis | Covered | — | Diagnosis indication |
| Adenovirus — myocarditis, immunocompromised | Covered | — | Specific clinical contexts required |
| Beta-tyrosinase — melanoma spread | Covered | — | Hematogenous spread detection only |
| BRCA1/BRCA2 | Covered | — | Must meet criteria per applicable CPB |
| IGH@ / IGK@ — leukemia/lymphoma | Covered | 81261, 81264 | Selection criteria apply |
| TRB@ — T-cell receptor rearrangement | Covered | 81340, 81341, 81342 | Selection criteria apply |
| Vancomycin resistance | Covered | 87500 | Selection criteria apply |
| Legionella pneumophila | Covered | 87541 | Selection criteria apply |
| Mycobacteria species / MAI | Covered | 87551, 87561 | Selection criteria apply |
| Staphylococcus aureus | Covered | 87640 | Selection criteria apply |
| Hepatitis G virus | Covered | 87526 | Selection criteria apply |
| SARS-CoV-2 genotype analysis | Covered | 87913 | Selection criteria apply |
| Multi-pathogen NGS panels (broad) | Conditional | 0152U | Coverage depends on specific indication |
| Tropical fever / vector-borne pathogens | Conditional | 0595U | Coverage depends on indication |
| Wound infection — 65 organisms panel | Conditional | 0600U | Selection criteria apply |
Aetna PCR Testing Billing Guidelines and Action Items 2026
The effective date of January 29, 2026 means this policy is live now. Here's what your billing team needs to do.
| # | Action Item |
|---|---|
| 1 | Audit your BV PCR claim workflow immediately. If your practice or lab collects urine specimens for BV diagnosis and bills any PCR code against it, stop those claims today. Aetna's CPB 0650 coverage policy explicitly excludes BV PCR on urine. Pull any claims submitted after January 29, 2026 and flag them for review before they generate denials. |
| 2 | Map your high-volume PCR codes to the indication criteria. The 200+ CPT codes in this policy are only covered when selection criteria are met. PCR testing billing doesn't have a blanket coverage rule here. For codes like 81270 (JAK2), 81206–81208 (BCR/ABL1), and 81292–81300 (Lynch syndrome mismatch repair), document the specific clinical indication in the record before the claim goes out. |
| 3 | Add geographic and exposure documentation requirements to your intake forms. Several covered indications — Borrelia mayonii (CPT 87476), Borrelia miyamotoi, and avian influenza A — require documented patient history around location or exposure. Your intake forms and EHR templates should capture this at the time of ordering, not as an afterthought when a denial arrives. |
| 4 | Update your charge capture for symptom duration thresholds. The pertussis PCR coverage rule requires symptoms of fewer than 21 days. This is a hard cutoff. Add symptom duration as a required field in your order entry or charge capture workflow for any Bordetella PCR order. |
| 5 | Cross-reference oncology PCR orders with the relevant companion policies. BRCA1/BRCA2 testing under this policy requires the patient to meet applicable CPB criteria for hereditary breast and ovarian cancer testing. Lynch syndrome testing links to hereditary cancer criteria in separate CPBs. Your oncology billing team should treat CPB 0650 as one piece of a multi-policy framework — not a standalone document. |
| 6 | If your mix includes high-complexity multi-analyte panels, loop in your compliance officer. Codes like 0152U and 0595U sit in a gray zone between covered indications and investigational use. The policy lists them, but coverage is indication-dependent in ways that aren't always clear from the CPT description alone. Don't bill these on assumption. |
| Previous Version | Current Version |
|---|---|
| Coverage is considered experimental and investigational for all indications | Coverage is considered medically necessary when specific criteria are met |
| Prior authorization is not required | Prior authorization is required for initial treatment |
| Documentation must include clinical history | Documentation must include clinical history |
| Re-review every 24 months | Re-review every 12 months with updated clinical documentation |
CPT, HCPCS, and ICD-10 Codes for PCR Testing Under CPB 0650
Covered CPT Codes (When Selection Criteria Are Met)
| Code | Type | Description |
|---|---|---|
| 0017U | CPT | Oncology (hematolymphoid neoplasia), JAK2 mutation, DNA, PCR amplification of exons 12-14 and sequencing |
| 0040U | CPT | BCR/ABL1 (t(9;22)) translocation analysis, major breakpoint, quantitative |
| 0068U | CPT | Candida species panel (C. albicans, C. glabrata, C. parapsilosis, C. kruseii, C. tropicalis, and C. auris) |
| 0115U | CPT | Respiratory infectious agent detection by nucleic acid (DNA and RNA), 18 viral types and subtypes and 2 bacterial targets |
| 0202U | CPT | Infectious disease (bacterial or viral respiratory tract infection), pathogen-specific nucleic acid |
| 0223U | CPT | Infectious disease (bacterial or viral respiratory tract infection), pathogen-specific nucleic acid |
| 0225U | CPT | Infectious disease (bacterial or viral respiratory tract infection), pathogen-specific DNA and RNA, 22 targets |
| 0301U | CPT | Infectious agent detection by nucleic acid (DNA or RNA), Bartonella henselae and Bartonella quintana |
| 0302U | CPT | Following liquid enrichment |
| 0402U | CPT | Infectious agent (sexually transmitted infection), Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis |
| 0455U | CPT | Infectious agents (sexually transmitted infection), Chlamydia trachomatis, Neisseria gonorrhoeae, and others |
| 0527U | CPT | Herpes simplex virus (HSV) types 1 and 2 and Varicella zoster virus (VZV), amplified probe technique |
| 0528U | CPT | Lower respiratory tract infectious agent detection, 18 bacteria, 8 viruses, and 7 antimicrobial-resistance genes |
| 0556U | CPT | Infectious disease (bacterial or viral respiratory tract infection), pathogen-specific DNA and RNA |
| 0557U | CPT | Infectious disease (bacterial vaginosis and vaginitis), real-time amplification of DNA markers |
| 0563U | CPT | Infectious disease (bacterial and/or viral respiratory tract infection), pathogen-specific nucleic acid |
| 0564U | CPT | Infectious disease (bacterial and/or viral respiratory tract infection), pathogen-specific nucleic acid |
| 81206 | CPT | BCR/ABL1 (t(9;22)) translocation analysis |
| 81207 | CPT | BCR/ABL1 (t(9;22)) translocation analysis |
| 81208 | CPT | BCR/ABL1 (t(9;22)) translocation analysis |
| 81210 | CPT | BRAF (b-raf proto-oncogene, serine/threonine kinase) gene analysis, V600E and other variants |
| 81220 | CPT | CFTR gene analysis, common variants |
| 81221 | CPT | CFTR gene analysis, known familial variants |
| 81222 | CPT | CFTR gene analysis, duplication/deletion variants |
| 81223 | CPT | CFTR gene analysis, full gene sequence |
| 81224 | CPT | CFTR gene analysis, intron 8 poly-T and poly-TG analysis |
| 81225 | CPT | CYP2C19 gene analysis, common variants |
| 81226 | CPT | CYP2D6 gene analysis, common variants |
| 81227 | CPT | CYP2C9 gene analysis, common variants |
| 81240 | CPT | F2 (prothrombin, coagulation factor II) gene analysis, 20210G>A variant |
| 81242 | CPT | FANCC gene analysis, common variants |
| 81243 | CPT | FMR1 gene analysis, evaluation to detect abnormal alleles |
| 81244 | CPT | FMR1 gene analysis, characterization of alleles |
| 81251 | CPT | GBA gene analysis, common variants |
| 81252 | CPT | GJB2 (connexin 26) gene analysis, full gene sequence |
| 81253 | CPT | GJB2 (connexin 26) gene analysis, known familial variants |
| 81255 | CPT | HEXA gene analysis, common variants |
| 81256 | CPT | HFE gene analysis, common variants |
| 81257 | CPT | HBA1/HBA2 gene analysis, common deletions or variant |
| 81261 | CPT | IGH@ gene rearrangement analysis to detect clonal population |
| 81264 | CPT | IGK@ gene rearrangement analysis |
| 81270 | CPT | JAK2 gene analysis, p.Val617Phe (V617F) variant |
| 81292 | CPT | MLH1 gene analysis, full sequence |
| 81293 | CPT | MLH1 gene analysis, known familial variants |
| 81294 | CPT | MLH1 gene analysis, duplication/deletion variants |
| 81295 | CPT | MSH2 gene analysis, full sequence |
| 81296 | CPT | MSH2 gene analysis, known familial variants |
| 81297 | CPT | MSH2 gene analysis, duplication/deletion variants |
| 81298 | CPT | MSH6 gene analysis, full sequence |
| 81299 | CPT | MSH6 gene analysis, known familial variants |
| 81300 | CPT | MSH6 gene analysis, duplication/deletion variants |
| 81315 | CPT | PML/RARalpha (t(15;17)) translocation analysis, common breakpoints |
| 81316 | CPT | PML/RARalpha (t(15;17)) translocation analysis, single breakpoint |
| 81317 | CPT | PMS2 gene analysis, full sequence |
| 81318 | CPT | PMS2 gene analysis, known familial variants |
| 81319 | CPT | PMS2 gene analysis, duplication/deletion variants |
| 81330 | CPT | SMPD1 gene analysis, common variants |
| 81331 | CPT | SMPD1 gene analysis, known familial variants |
| 81340 | CPT | TRB@ gene rearrangement analysis, single chain |
| 81341 | CPT | TRB@ gene rearrangement analysis, two chains |
| 81342 | CPT | TRB@ gene rearrangement analysis, three or more chains |
| 87476 | CPT | Borrelia burgdorferi, amplified probe technique |
| 87500 | CPT | Vancomycin resistance (e.g., enterococcus species), amplified probe technique |
| 87526 | CPT | Hepatitis G virus, amplified probe technique |
| 87541 | CPT | Legionella pneumophila, amplified probe technique |
| 87551 | CPT | Mycobacteria species, amplified probe technique |
| 87561 | CPT | Mycobacteria avium-intracellulare, amplified probe technique |
| 87640 | CPT | Staphylococcus aureus, amplified probe technique |
| 87913 | CPT | SARS-CoV-2, infectious agent genotype analysis by nucleic acid |
Conditional / Indication-Specific CPT Codes
| Code | Type | Description | Notes |
|---|---|---|---|
| 0109U | CPT | Aspergillus species, real-time PCR, 4 species detection | Coverage depends on indication |
| 0152U | CPT | Infectious disease (bacteria, fungi, parasites, DNA viruses), DNA, PCR and NGS | Coverage depends on indication |
| 0321U | CPT | Genitourinary pathogens, nucleic acid (DNA or RNA), identification | Selection criteria apply |
| 0339U | CPT | Oncology (prostate), mRNA expression profiling of HOXC6 and DLX1, RT-PCR | Selection criteria apply |
| 0371U | CPT | Genitourinary pathogen, nucleic acid (DNA or RNA), semiquantitative identification | Selection criteria apply |
| 0372U | CPT | Infectious disease (genitourinary detection), multiplex amplified probe technique | Selection criteria apply |
| 0389U | CPT | Pediatric febrile illness (Kawasaki disease), IFI27 and other markers | Selection criteria apply |
| 0504U | CPT | Urinary tract infection, 17 pathologic organisms identification, real-time PCR | Selection criteria apply |
| 0593U | CPT | Genitourinary pathogens, DNA, 46 targets (28 pathogens, 18 resistance genes) | Selection criteria apply |
| 0595U | CPT | Tropical fever pathogens, vector-borne and zoonotic, 2 viral targets | Selection criteria apply |
| 0600U | CPT | Wound infection, 65 organisms and 30 antibiotic resistance genes identification | Selection criteria apply |
Note: The policy lists 201 total CPT codes. The full code set is available at the source policy: Aetna CPB 0650. The source policy includes 14 HCPCS codes. The complete HCPCS code list is not reproduced here — consult the full policy at Aetna CPB 0650 for the complete HCPCS code set. ICD-10-CM codes number 3,160 — consult the full policy document for the complete diagnosis code list.
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