What Is CPT Code 87798 for Infectious Agent Detection?

CPT code 87798 is a billing code used by laboratories to report the molecular detection of an infectious agent that does not have its own dedicated CPT code. In plain terms, when a lab runs a DNA- or RNA-based test to look for a specific germ and there is no unique billing code assigned to that particular germ, the lab reports the work under 87798. The American Medical Association’s full descriptor for 87798 reads “Infectious agent detection by nucleic acid (DNA or RNA), not otherwise specified; amplified probe technique, each organism.” That phrase “not otherwise specified” is the key: 87798 is a catch-all, and understanding what that means for patients, clinicians, and laboratories clears up a lot of confusion around test bills and insurance coverage.

What the Code Actually Describes

Every molecular diagnostic test that hunts for a pathogen’s genetic material falls under a family of CPT codes in the 87471–87801 range. Many common infections have their own dedicated code. Chlamydia, for example, has 87491; influenza has 87502. But hundreds of less common organisms lack a pathogen-specific code. When a lab uses a nucleic acid amplification technique, such as PCR, to detect one of those organisms, 87798 is the code it bills. The code is billed once per organism detected or tested for, so a single patient encounter can generate more than one line of 87798 if the lab is looking for multiple organisms that all fall under the “not otherwise specified” umbrella.

The word “amplified” in the code descriptor matters. It distinguishes 87798 from codes like 87797 (direct, non-amplified probe technique) and 87799 (quantification, meaning the test measures how much of the pathogen is present rather than simply whether it is there). If the lab is running a PCR or similar amplification-based method to give a yes-or-no answer on whether a pathogen’s DNA or RNA is in the sample, 87798 is the appropriate code.

Why a Catch-All Code Exists

The CPT code system is updated annually, but the pace of molecular diagnostics moves faster than the code committees can keep up with. New pathogens emerge, laboratories develop tests for uncommon organisms, and multiplex panels that screen for dozens of targets at once have become routine. The result is a permanent gap between what labs can test for and what the code set specifically names. Code 87798 fills that gap. It was designed as a flexible placeholder so that labs could bill for legitimate diagnostic work even when the CPT catalog had not yet created a dedicated code for the organism in question.

That flexibility comes at a cost. Because the code does not name the organism, the same 87798 line item on a bill could represent a test for BK virus, human herpesvirus 6, Babesia, Bartonella, varicella-zoster virus, or any number of other pathogens. A study examining STI testing patterns in the United States noted that varicella-zoster virus testing, for instance, is reported under 87798, and because the code is not specific to VZV, results filed under it could actually reflect testing for other organisms entirely.¹ That ambiguity makes 87798 harder to track in public-health databases and harder for insurers to evaluate at a glance.

How Multiplex Panels Complicate the Picture

Modern respiratory and gastrointestinal panels can test for 20 or more pathogens from a single specimen in one run. Many of those targets lack their own CPT codes. When a lab bills for such a panel, it may need to submit 87798 multiple times on the same claim, once for each organism that falls under the generic code. This is technically correct billing, but it creates practical headaches that affect laboratories, insurers, and sometimes patients.

A review of FDA-cleared molecular respiratory tests highlighted this problem directly: because there are no specific CPT codes for each individual target in a multiplex assay, laboratories must bill for multiple targets using the same generic amplified probe code. Many hospital billing systems do not recognize multiple identical CPT codes on a single claim and will only drop one charge through. Some insurance payers cover only the first instance of 87798 and deny the rest, and there are limits on how many times the same code can be billed per day.² The consequence is that a lab running a single sophisticated test may be reimbursed for only a fraction of the work it performed, which in turn affects which tests laboratories choose to offer and how aggressively they pursue newer, broader panels.

For patients, this sometimes shows up as a confusing bill. You might see the same code listed several times with different charges or partial payments, and without additional context it is nearly impossible to tell which line corresponds to which pathogen. If you are trying to understand a bill that lists 87798 multiple times, asking the laboratory for the specific test order and the organisms included is the most direct way to decode it.

Common Pathogens Billed Under 87798

The list of organisms that lack their own CPT code and therefore fall under 87798 shifts over time as the AMA adds new pathogen-specific codes. As of recent code updates, some of the organisms you are most likely to see billed under 87798 include:

BK virus: A polyomavirus that causes problems mainly in kidney transplant recipients and other immunosuppressed patients. Labs have developed quantitative and qualitative PCR assays for BK virus on high-throughput platforms, but the qualitative detection piece still bills under 87798.³
Human herpesvirus 6 (HHV-6): Relevant in transplant medicine and occasionally in encephalitis workups.
Varicella-zoster virus (VZV): The virus behind chickenpox and shingles, when tested by molecular methods rather than serology.
Bartonella species: The bacteria responsible for cat-scratch disease and other syndromes.
Babesia species: A tick-borne parasite increasingly recognized in parts of the northeastern and upper midwestern United States.
Respiratory viruses in panels: Several respiratory pathogens included in syndromic panels, such as certain coronaviruses (non-SARS-CoV-2), bocavirus, and some parainfluenza subtypes, may still bill under 87798 depending on whether specific codes have been assigned.

The common thread is that these are organisms where molecular testing is clinically useful but not so high-volume that the AMA has created a standalone code. When the AMA does assign a new pathogen-specific code, laboratories switch to it and 87798 is no longer appropriate for that organism.

How 87798 Differs from Related Codes

Patients and clinicians sometimes confuse 87798 with a handful of neighboring codes. The differences are straightforward once you know what to look for.

Code 87797 covers detection of an unspecified infectious agent by a direct (non-amplified) probe technique. The distinction is the method: if the lab amplifies the pathogen’s DNA or RNA before detecting it (as in PCR), it is 87798. If it uses a probe that binds directly to the genetic material without amplification, it is 87797. Amplified methods are far more sensitive and are the standard for most clinical molecular testing today, so 87798 appears on bills much more often than 87797.

Code 87799 is the quantitative version: it reports not just whether the organism’s nucleic acid is present but how much of it is in the sample. Viral load testing for BK virus in transplant patients is a common example. If the test gives a number (copies per milliliter, for instance), the lab bills 87799. If the test gives only a positive-or-negative result, 87798 applies.

Then there are the pathogen-specific codes. When an organism has its own CPT code, the lab should use that code rather than 87798, even if the method is the same. Billing 87798 for an organism that has a dedicated code is incorrect coding and can trigger claim denials or compliance issues.

Insurance Coverage and Medical Necessity

Because 87798 is a generic code, insurance payers often apply extra scrutiny before approving payment. Most commercial and government payers require the ordering clinician to demonstrate medical necessity, meaning there should be a clear clinical reason to test for the specific organism. A diagnosis code (ICD-10) that matches the suspected infection is typically required alongside the CPT code.

Denials are more common with 87798 than with pathogen-specific codes for several reasons. First, the vagueness of the code makes automated adjudication harder; the payer’s system cannot tell from 87798 alone whether the test was for something reasonable or something esoteric. Second, as noted in the multiplex panel context, some payers cap the number of times 87798 can appear on a single claim or a single day.² Third, certain payers maintain lists of organisms they consider investigational or not medically necessary for molecular testing, and because the payer cannot always tell which organism 87798 refers to, the claim may be flagged for manual review.

If you receive a denial for a test billed under 87798, the most effective route is to ask the ordering physician’s office to provide a letter of medical necessity along with clinical documentation explaining why molecular detection of that particular organism was warranted. Many denials are overturned on appeal when the clinical context is clear.

Lab-Developed Tests and the Role of 87798

A substantial portion of tests billed under 87798 are lab-developed tests, sometimes called LDTs. These are assays designed and validated by a specific laboratory rather than manufactured as a commercial kit with FDA clearance. Laboratories create LDTs when no commercial test exists for a particular organism, or when they want to run the test on a platform that does not have a manufacturer-provided kit for that target. A laboratory evaluating a custom-designed primer and probe set for BK virus on a high-throughput cobas platform is a representative example of this workflow.³

LDTs are regulated differently from FDA-cleared tests, and the billing implications matter. An FDA-cleared test for a specific organism typically has a well-established reimbursement pathway. An LDT billed under the generic 87798 may face additional hurdles: payers sometimes require proof that the test has been validated according to laboratory accreditation standards, and some Medicare contractors have local coverage determinations that restrict which organisms they will reimburse under 87798. Laboratories that run LDTs billed under this code often maintain detailed validation documentation and keep it readily available for payer audits.

What Shows Up on Your Bill

If you are a patient trying to interpret a lab bill or an explanation of benefits, here is what to look for. A line item reading “87798” with a charge next to it means the lab performed a molecular test for an infectious organism that does not have its own billing code. The charge typically covers the technical work of extracting nucleic acid from your specimen, amplifying it, and detecting whether the target organism’s genetic material is present.

The amount you owe depends on your insurance plan, your deductible status, and whether the payer considers the test medically necessary. Molecular tests are not cheap; a single 87798 charge can range from roughly $50 to over $200 depending on the laboratory and the payer’s fee schedule. If multiple organisms were tested under 87798 on the same specimen, the charges can stack. Some patients are surprised to see what looks like the same test listed several times at full price. In those cases, it is worth confirming with the lab that each charge represents a distinct organism and not a billing error.

When an insurer denies one or more lines of 87798, the remaining balance may be passed to you. Before paying, check whether the lab is in-network (which limits what you can be billed) and whether the denial was for medical necessity or for a coding technicality. Coding-related denials can often be resolved between the lab and the payer without any cost to you.

Why Public Health Researchers Find 87798 Frustrating

Epidemiologists and public health analysts rely on billing data to estimate how often certain infections are tested for and diagnosed across large populations. Pathogen-specific codes make this straightforward: if you count how many times CPT 87491 was billed in a region, you have a reasonable proxy for the volume of chlamydia molecular testing. But 87798 is a black box. A spike in 87798 claims could represent an outbreak of monkeypox testing, a wave of BK virus screening in transplant centers, or simply a new multiplex panel gaining market share.

Research examining real-world STI testing patterns has run into this limitation directly. When the investigators looked at VZV testing volumes, they had to acknowledge that the 87798-based counts might include testing for entirely different pathogens, because the code does not specify which organism was targeted.¹ This kind of noise in the data makes it harder to track testing trends, identify gaps in screening, and allocate public health resources accurately. It is one of the quieter consequences of the coding system’s failure to keep pace with molecular diagnostics, and it affects the quality of population-level health data in ways that are difficult to quantify.

When Organisms Graduate to Their Own Code

The AMA’s CPT Editorial Panel reviews proposals for new codes regularly, and high-volume organisms do eventually get their own billing codes. SARS-CoV-2 is a dramatic example: before the pandemic, a coronavirus PCR would have been billed under 87798. Within months of COVID-19’s emergence, a dedicated code (87635) was fast-tracked. Similar transitions have happened over the years for organisms like Zika virus and certain sexually transmitted pathogens as testing volume grew large enough to justify a standalone code.

When an organism gets its own code, laboratories must update their billing systems to use the new code and stop reporting that organism under 87798. The transition is not always smooth. Reference labs with thousands of test menus may take weeks to update, and during the gap, claims can be denied under either code. For the patient, though, the shift is almost always positive: pathogen-specific codes are easier for payers to process, less likely to be flagged for review, and more likely to be reimbursed without a fight.

The organisms that remain under 87798 are generally those tested in lower volumes or in specialized clinical settings. Transplant medicine, infectious disease consultations, and immunocompromised patient care generate a disproportionate share of 87798 claims, simply because those are the contexts where clinicians need molecular testing for uncommon pathogens that have not yet earned their own code.