Your pathology report for polyomavirus nephropathy

Jason Wasserman MD PhD FRCPC
June 18, 2025

Polyomavirus nephropathy (PVN) is a condition that affects kidney transplant patients. It happens when a common virus called BK virus becomes active and causes inflammation and injury to the transplanted kidney. If untreated, PVN can damage the kidney and affect its function. A kidney biopsy can help doctors diagnose and manage PVN early.

What causes polyomavirus nephropathy?

Polyomavirus nephropathy develops when the BK virus reactivates in people who have received a kidney transplant. After transplantation, patients take medications that suppress the immune system to prevent the body from rejecting the new kidney. These medications lower the body’s defenses, allowing the BK virus, which normally stays dormant, to become active and multiply, causing kidney damage.

What are the symptoms of polyomavirus nephropathy?

Most people with polyomavirus nephropathy do not experience symptoms early on. However, as the condition progresses, it may lead to signs of kidney dysfunction, such as:

• Elevated creatinine levels (seen in blood tests).

• Blood in the urine (hematuria).

• Reduced kidney function.

• Occasionally, pain or discomfort around the kidney transplant site.

Usually, doctors find PVN by monitoring routine blood tests and urine samples rather than through specific symptoms.

How is this diagnosis made?

The diagnosis of polyomavirus nephropathy is typically made after examining a kidney biopsy tissue sample under a microscope. A kidney biopsy is a procedure in which a tiny piece of kidney tissue is removed with a needle. The pathologist closely examines the tissue to look for characteristic changes caused by the BK virus. They may also use special stains (such as SV40 staining) to confirm the presence of viral infection.

How is polyomavirus nephropathy classified?

Polyomavirus nephropathy is classified using two systems designed to help doctors understand how serious the condition is and predict how well the kidney will function in the future. The two classification systems are called AST-IDCOP and Banff.

AST-IDCOP Classification

The AST-IDCOP classification divides polyomavirus nephropathy into five groups (Class A, B1, B2, B3, and C) based on how severe the viral damage and scarring appear under the microscope. Pathologists evaluate how much virus is in the kidney, inflammation, scarring, and the Banff ‘ti’ (tubulitis) score, which measures how much inflammation there is in kidney tubules.

The AST-IDCOP classes include:

• Class A (early or minimal infection):
  There are signs of early viral infection. Viral changes are limited, affecting less than 10% of the biopsy. Inflammation and scarring are minimal. The Banff ti score is usually 0 or 1. Patients generally have the best outcomes.

• Class B (established disease):
  Viral infection is clearly visible. Class B is further divided based on how extensive the infection, inflammation, and scarring are:

  • Class B1: Mild infection with viral changes in less than 25% of kidney tissue and minimal inflammation (Banff ti ≤1). Patients generally do well with careful monitoring.

  • Class B2: Moderate infection affecting 25–50% of kidney tissue, with moderate inflammation (Banff ti ≥2). Kidney function is often more affected, but treatment can help stabilize it.

  • Class B3: Severe infection involving more than 50% of kidney tissue, along with significant inflammation (Banff ti ≥2). Patients have a higher risk of permanent kidney damage.

• Class C (Advanced scarring):
  Significant scarring (fibrosis) is present, reflecting extensive and longstanding injury. Viral changes might be less obvious because of extensive scarring. This stage has the poorest prognosis, with a high risk of long-term kidney function loss.

Higher AST-IDCOP classes generally indicate more severe kidney damage and predict a greater risk of kidney problems in the future.

Banff Classification

The Banff classification is another way to categorize PVN based primarily on the severity of viral infection (“pvl”) and scarring (“ci” score). It divides PVN into three main classes:

• Class 1: Low virus presence and minimal scarring. People in this class typically respond well to treatment, with good kidney function long-term.

• Class 2: Moderate viral infection or scarring. Patients have an intermediate prognosis but can still improve if treated early.

• Class 3: Severe viral infection or extensive scarring. This class has the highest risk of significant and lasting kidney damage, and recovery of kidney function can be difficult even with treatment.

What are the microscopic features of polyomavirus nephropathy?

Under the microscope, pathologists look for several features that suggest PVN, including:

• Viral inclusions: Enlarged kidney cells with clear virus-related changes in their nuclei.

• Tubular injury (tubulitis): Inflammation within kidney tubules, scored using the Banff ‘ti’ system.

• Interstitial inflammation: Inflammatory cells surrounding kidney tubules.

• Interstitial fibrosis: Scarring indicating chronic or longstanding injury.

• Positive viral staining: Special staining (SV40) confirms BK virus presence.

These features help determine the severity of the condition.

What is the treatment for polyomavirus nephropathy?

Treatment for polyomavirus nephropathy usually involves:

• Reducing immunosuppressive medications: Allowing your body’s immune system to fight off the BK virus.

• Antiviral medications: Sometimes used, although their effectiveness varies and they are not always recommended.

• Monitoring and supportive care: Regular blood tests and monitoring kidney function closely.

• Surgical intervention: Rarely, surgery may be required if the virus causes severe damage or complications, such as blocked urine drainage.

Early diagnosis and close monitoring greatly improve outcomes.

Questions to ask your doctor

• What AST-IDCOP class or Banff class is indicated in my pathology report, and what does this mean for my kidney?

• Do I need changes to my medication to reduce my risk of further kidney damage?

• How often should I have blood tests or repeat biopsies?

• Are antiviral medications recommended for my condition?

• What can I do to help protect my kidney and prevent further damage?