CPT code 87631 – Respiratory virus panel nucleic acid detection

Key takeaways

CPT code 87631 covers multiplex nucleic acid detection of 3 to 5 respiratory virus targets in a single panel run.

Choose the tier by counting targets: 87631 covers 3 to 5, 87632 covers 6 to 11, and 87633 covers 12 to 25.

A dedicated four-target assay for SARS-CoV-2, influenza A/B and RSV reports under its own code, 87637.

Every 87631 claim needs an ICD-10 diagnosis code that establishes medical necessity, such as J06.9, R05.9 or R50.9.

Pabau’s claims management software submits 87631 claims electronically through Claim.MD, which checks claims for common errors before they reach the payer.

What is CPT code 87631?

CPT code 87631 is the code for multiplex nucleic acid testing that detects 3 to 5 respiratory virus targets in one run. The American Medical Association’s CPT Editorial Panel maintains it. It sits in the Microbiology subsection (87001-87999) of the Pathology and Laboratory section.

“Multiplex amplified probe technique” means the test looks for several viruses at once in a single specimen. That specimen is usually a nasopharyngeal swab, and the method is a nucleic acid amplification test (NAAT) such as PCR.

The phrase “types or subtypes” decides how you count. Influenza A and influenza B are two separate targets, not one. RSV A and RSV B also count as two. So a panel detecting influenza A, influenza B and RSV A reports as 87631, with three targets.

• Code range: 87631 belongs to the 87471-87801 range for infectious agent detection by nucleic acid.
• Test method: Multiplex nucleic acid amplification (PCR, NAAT or an equivalent platform).
• Specimen type: Nasopharyngeal swab, throat swab or another respiratory specimen, as documented by the ordering physician.
• Analyte count rule: Count individual types and subtypes, not assay brand names or panel trade names.
• Code category: Pathology and Laboratory section, Microbiology subsection.

Pathogens detected by the CPT 87631 respiratory virus panel

Any respiratory virus combination that totals 3 to 5 targets falls under 87631. The most common is influenza A, influenza B and RSV, a three-target panel found on many point-of-care and rapid NAAT platforms.

Adding SARS-CoV-2 to that trio changes the code. A dedicated influenza A/B, RSV and SARS-CoV-2 assay reports as 87637. Other combinations of 3 to 5 targets stay with 87631, such as influenza A/B and RSV plus parainfluenza or human metapneumovirus. A sixth target pushes the claim to 87632.

Panels detecting six or more targets fall outside 87631. Adding adenovirus and rhinovirus to a flu, RSV, COVID-19 and metapneumovirus combination is one example. Report those as 87632 or 87633, depending on the total target count.

CPT 87631 vs 87632 vs 87633: Panel size and code selection

The three respiratory panel codes share the same NAAT method and differ only by the number of targets detected. Picking the wrong tier is the most common coding error on these claims. It usually happens when coders go by the test’s brand name instead of counting the analytes reported.

The chart below turns that rule into two checks: first rule out the dedicated 87637 assay, then count.

Where 87637 fits: CPT code 87637 covers simultaneous detection of SARS-CoV-2, influenza A/B and RSV as a dedicated combination assay. It sits outside the 87631/87632/87633 tier structure, so the codes are not interchangeable.

A lab running a dedicated assay for exactly those four targets reports 87637. When the same four sit inside a broader respiratory panel, count every target on the report. Report 87631 if the total is 3 to 5 targets, and 87632 if it is 6 to 11.

Medicare reimbursement rates for CPT code 87631

Medicare pays CPT code 87631 under the Clinical Laboratory Fee Schedule (CLFS), which CMS updates every year. The CLFS pays national limit amounts, with no geographic adjustment.

For the current allowed amount, look up 87631 in the files on the CMS Clinical Laboratory Fee Schedule page. CMS posts a downloadable rate file for each quarter there.

We don’t reproduce a dollar figure for 87631 here, because the CLFS rate changes under PAMA (Protecting Access to Medicare Act) reporting cycles. A stale figure leads to wrong write-off calculations and patient cost estimates. Pull the rate from the current CMS CLFS file for the payment year instead.

How to bill CPT code 87631: Documentation and coding requirements

Billing CPT code 87631 correctly takes documentation that ties the physician’s clinical decision to the panel ordered and the pathogens the assay targets. Five elements carry most of that weight.

1. Ordering physician documentation: The ordering provider documents the clinical signs or symptoms that justify testing for several respiratory pathogens at once. Examples include fever, cough, upper respiratory symptoms or a known exposure. Blanket orders without clinical context are a leading denial trigger.
2. Specimen and methodology notation: The lab report names the specimen type (nasopharyngeal swab, throat swab or bronchoalveolar lavage). It also lists the analytes in the panel and the testing platform or method used.
3. Analyte count verification: Before choosing between 87631 and 87632, count the distinct targets on the result report. Record that count in the lab’s billing notes if your practice management system supports it.
4. ICD-10 diagnosis code assignment: Link a supporting ICD-10-CM code that establishes medical necessity. See the diagnosis code table in the next section.
5. Place-of-service code: Report the POS code that matches where the specimen was collected. That is POS 11 (office), POS 22 (outpatient hospital) or POS 81 (independent laboratory).

Required ICD-10 codes to support medical necessity

A clean claim for 87631 pairs the CPT code with an ICD-10-CM diagnosis that reflects the clinical reason for testing. The table below lists commonly accepted diagnosis codes. Payer-specific LCDs may expand or restrict this list.

Always check that your MAC’s active LCD for respiratory panel testing includes the diagnosis codes you plan to use. Novitas Solutions (JH and JL jurisdictions) publishes billing article A58575, which accompanies its Respiratory Pathogen Panel Testing LCD (L38916). National Government Services (J6 and JK jurisdictions) maintains its own coverage policy for the same code family.

Payer coverage policies: Medicare, Medicaid, and commercial insurers

Coverage for respiratory pathogen panels depends on the payer, and the LCD criteria a practice must meet differ by MAC jurisdiction and plan year. Check the policy that applies to your patient before you bill these tests routinely.

• Medicare (CMS): Coverage is set by MAC LCDs. Standard LCD rules apply now that PHE-era flexibilities have expired.
• Novitas Solutions (JH/JL jurisdictions): Billing article A58575 accompanies the Novitas Respiratory Pathogen Panel Testing LCD (L38916). In the outpatient setting, the LCD generally limits coverage to panels of five or fewer pathogens, which is the 87631 range. A non-covered diagnosis on the order leads to denial, even when the CPT code itself is right.
• National Government Services (J6/JK): NGS maintains a parallel coverage policy. Check the current version, because LCD language for respiratory panels has changed several times since 2020.
• Medicaid: State Medicaid programs set their own policies and prior authorization rules. Confirm the applicable state policy before assuming Medicaid covers 87631.
• Commercial payers: Regional commercial carriers also set their own policies and prior authorization rules. Many require prior authorization for larger respiratory panels, particularly outside an acute care setting.

Common reasons CPT 87631 claims are denied

Denials for 87631 trace back to three causes. The diagnosis fails the payer’s LCD criteria, the panel size was miscoded, or a bundled code went out alongside it. Solid denial management workflows catch each of these before remittance. A guide to denial codes in medical billing helps coders read the CARC reason codes that come back with these rejections.

• Non-covered or unsupported ICD-10 diagnosis code: The most frequent denial. The diagnosis isn’t on the MAC’s covered list for respiratory panel testing, or the ordering documentation doesn’t support it.
• Medical necessity not established: The ordering provider’s note doesn’t document clinical signs or symptoms that justify multiplex testing. A brief order without supporting documentation falls short of most LCD criteria.
• Panel size mismatch: 87631 was billed when the result report shows six or more analytes, so the claim should have used 87632. Payers audit result reports against the billed tier.
• Missing or invalid ordering provider NPI: The claim must carry the ordering physician’s NPI, not only the performing lab’s NPI. A missing NPI triggers automatic rejection before clinical review.
• Place-of-service error: Billing POS 11 (office) when an independent reference lab collected the specimen calls for a different billing arrangement. Match the POS to the collection site.
• Duplicate testing denial: 87631 billed on the same date of service as 87636 or 87637 raises a duplicate-testing flag. Only documentation of distinct clinical reasons for each test gets past it.

Can CPT 87631 be billed with other respiratory codes?

Only when the second test adds clinical information the 87631 panel didn’t already provide. Bundling follows CCI (Correct Coding Initiative) edits and each payer’s own policy, and overlapping targets count as duplicate testing.

87631 and 87635 (SARS-CoV-2 nucleic acid detection)

CPT code 87635 is a standalone COVID-19 NAAT code. If the 87631 panel already detects SARS-CoV-2, billing 87635 on the same date is duplicate testing, and the payer will deny one of the two.

87635 can stand alongside 87631 when the panel leaves SARS-CoV-2 out. One example is a three-target flu and RSV panel plus a separate COVID-19 test, ordered because the panel result was equivocal. Document that clinical reason clearly.

87631 and 87636 or 87637

CPT code 87636 (SARS-CoV-2 and influenza A/B) and 87637 (SARS-CoV-2, influenza A/B and RSV) conflict with 87631 on the same date. Both detect some of the same analytes, so payers treat the pair as unbundling and deny the lower-paid code.

If the clinical picture calls for more targets than 87631 covers, choose the single tier code that fits (87632 or 87633). Don’t stack 87631 with 87636 or 87637.

How claims management software keeps 87631 claims moving

Many labs and practices raise the invoice in one system, then re-key the claim into a clearinghouse portal. Each re-keyed field is another chance to send the wrong tier code or drop the ordering NPI.

Pabau, the practice management platform with insurance billing built in, turns the invoices you already raise into electronic CMS-1500 claims. Its claims management software submits 87631 claims through Claim.MD, which checks claims for common errors before they reach the payer.

Your front desk can check a patient’s coverage in real time before the swab is taken. Claim statuses and electronic remittance advice then flow back into Pabau, so you can see which panel claims are paid, pending or denied. Our Claim.MD clearinghouse guide explains that submission cycle step by step.

Submit cleaner respiratory panel claims

Pabau turns your invoices into electronic claims sent through Claim.MD, with real-time eligibility checks and claim status tracking. See how 87631 claims move from order to payment in your practice.

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Conclusion

Treat the result report as the source of truth for 87631. Count the targets it lists, rule out the dedicated 87637 assay, and pair the claim with a diagnosis your MAC’s LCD accepts.

That habit costs a coder a minute per claim. Skipping it costs a denial, a resubmission and weeks of delay before the lab is paid.

Are respiratory panel denials running high at your practice? Book a demo to see how Pabau takes a claim from invoice to payment without re-keying.

Continue your research

Billing the combined COVID, flu and RSV assay? CPT code 87637 covers the dedicated four-target assay that sits outside the 87631 tier structure.

Coding the cough behind the order? ICD-10 code R05.9 covers the unspecified cough code that often sits behind a respiratory panel order.

Need to understand how clearinghouse submission works? Claim.MD clearinghouse overview explains how electronic claim routing, eligibility checks and ERA retrieval work together in one submission cycle.

Looking for denial reason code definitions? Denial codes in medical billing maps the most common CARC and RARC codes to their root causes and the documentation fixes for each.

Want a walkthrough of the 837P claim format? 837P electronic claim filing covers loop structure and segment requirements for electronic professional claims.

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