Viral Sequencing Helps Identify Hidden Hepatitis C

ADVANCED viral sequencing could help clarify some cases of hepatitis of unknown origin by identifying infections missed during initial diagnostic testing, according to a study involving 49 patients in China.

Researchers detected hepatitis C virus (HCV) in one patient whose initial antibody and RNA tests were negative. Subsequent testing confirmed acute HCV infection, allowing the case to be reclassified. However, no common novel pathogen was identified across the wider cohort.

Investigating Unexplained Hepatitis

Hepatitis of unknown origin remains a diagnostic challenge when conventional testing fails to identify an underlying cause of liver inflammation.

Researchers at Beijing Ditan Hospital investigated 49 patients, comprising 48 adults and one adolescent aged 16 years, enrolled between June and December 2024.

All participants had undergone initial investigations excluding recognised causes, including hepatitis A–E, alcohol-related liver disease, drug-induced liver injury, autoimmune hepatitis, metabolic disorders, and biliary obstruction.

The team analysed 59 clinical specimens, including 44 plasma and 15 faecal samples, using two complementary sequencing approaches.

Targeted RNA sequencing screened for 139 viruses, while unbiased metagenomic sequencing examined a broader range of viral genetic material.

Sequencing Identifies Previously Missed Hepatitis C

Targeted sequencing detected HCV in one plasma sample, while the remaining 58 specimens tested negative for the viruses included in the targeted panel.

The patient had initially tested negative for HCV antibodies and RNA, leading to a diagnosis of hepatitis of unknown origin.

Metagenomic sequencing subsequently identified a near-complete HCV genome, covering 94.5% of the reference sequence.

Follow-up testing 14 days after enrolment confirmed HCV RNA positivity, with a viral load of 420,000 IU/mL, alongside antibody seroconversion.

These results established that the patient had experienced an early, initially undetected HCV infection.

The finding demonstrates how additional molecular testing may improve diagnostic resolution when initial results are inconclusive.

Other Viral Signals Remain Uncertain

Metagenomic sequencing also detected hepatitis B virus (HBV) sequences in another patient, despite negative conventional HBV testing at enrolment.

Researchers suggested this could represent occult HBV infection, although they could not establish whether it caused the patient’s hepatitis.

A goose circovirus-like sequence was identified in one faecal sample, but there is currently no evidence that goose circovirus causes human hepatitis.

An additional low-level influenza A-like signal was detected in one plasma sample. However, it fell below the study’s confirmation threshold and could not be verified using follow-up PCR testing.

Overall, researchers found no common pathogenic virus capable of explaining the cohort’s unexplained hepatitis cases.

Improving Diagnostic Accuracy

Viral community analysis revealed differences between plasma and faecal specimens, suggesting that analysing multiple sample types could provide complementary information.

However, the exploratory study had several limitations, including its small sample size, absence of a healthy control group, and lack of liver biopsy specimens.

The findings therefore do not establish new viral causes of hepatitis or support routine metagenomic testing for every patient.

Instead, researchers suggest that sequencing could complement established diagnostic methods in selected unresolved cases, particularly when early infection or inconclusive conventional testing is suspected.

Larger controlled studies are needed to establish its clinical utility and determine whether broader sequencing can reduce the number of hepatitis cases remaining unexplained.

Reference

Li X et al. Metagenomic study in a predominantly adult cohort with hepatitis of unknown etiology. Biosafety and Health. 2026. DOI:10.1016/j.bsheal.2026.09.003.