Groundbreaking research reveals unexpected HPV genotypes in oral squamous cell carcinoma, reshaping our understanding of oral cancer causes and prevention.
For decades, oral cancer has been predominantly linked to lifestyle factors like tobacco use and alcohol consumption. However, a silent and surprising contributor has been emerging from the shadows—the human papillomavirus, or HPV. While HPV is widely recognized for causing cervical cancer, its role in oral cancers is less known and often misunderstood. Recent groundbreaking research has uncovered that the story is more complex than we imagined, involving not just the usual suspects like HPV 16 and 18, but also less common, yet equally concerning, genotypes.
This article explores the fascinating discovery of high-risk HPV genotypes 58 and 59 in patients with oral squamous cell carcinoma, a finding that could reshape our understanding of what causes oral cancer and how we might prevent it.
Human papillomavirus is a common family of viruses with over 200 identified genotypes. Approximately a dozen of these are classified as "high-risk" (HR-HPV) due to their strong link to various cancers. The virus is strictly epitheliotropic, meaning it infects the skin and mucosal layers 1 .
The cancer-causing mechanism of high-risk HPV is particularly insidious. The virus produces oncoproteins E6 and E7, which act as master saboteurs within human cells 1 . The E6 protein targets and degrades p53, a crucial tumor suppressor protein often called "the guardian of the genome." Simultaneously, the E7 protein neutralizes another tumor suppressor, the retinoblastoma protein (pRb). This double assault dismantles the cell's critical defense systems, leading to uncontrolled cell division and, ultimately, cancer .
E6 Protein
Degrades p53
E7 Protein
Neutralizes pRb
The connection between HPV and oropharyngeal cancers (those affecting the tonsils and base of the tongue) is well-established, with HPV implicated in up to 70% of cases in Western countries 1 3 . However, the role of HPV in oral cavity cancers (those affecting the front of the tongue, gums, cheeks, and roof of the mouth) remains controversial and less clear 3 .
A recent comprehensive meta-analysis of 31 studies found that the prevalence of HPV in oral cavity squamous cell carcinomas varies dramatically worldwide—from 0% to 37%—with an overall prevalence of just 6% 3 . This suggests that while HPV may not be a primary driver of most oral cavity cancers, it likely plays a significant role in a distinct subset of cases.
In 2025, a revealing study conducted at a tertiary care hospital in Mangalore, India, set out to detect different high-risk HPV genotypes among oral and oropharyngeal cancer patients 1 5 . The research involved 25 patients, predominantly male (96%), with a mean age of 57.4 years 1 .
The results surprised the scientific community. Among the 25 biopsy samples tested, three (12%) were positive for high-risk HPV. But the real surprise came from the genotyping results. Through sophisticated Sanger sequencing and bioinformatic analysis, researchers discovered that two samples contained HPV type 58, and one contained type 59 1 5 .
This finding was significant because most previous studies from India had consistently reported HPV 16 and 18 as the predominant subtypes. The discovery of types 58 and 59 highlighted a previously overlooked dimension of the oral cancer problem 1 .
The study also uncovered important clinical correlations. All HPV-positive patients were male with low socioeconomic status. Clinical analysis revealed a significant association between HPV-positive oral cancer and habits of high alcohol consumption and tobacco chewing 1 . This suggests that HPV infection might work in concert with traditional risk factors rather than acting alone.
Interestingly, the tumors in HPV-positive cases showed a tendency toward certain characteristics. Another study noted that HPV DNA positive cases were more prevalent in poorly-differentiated oral cancers, which are typically more aggressive .
| Characteristic | HPV-Positive Oral Cancer | HPV-Negative Oral Cancer |
|---|---|---|
| Primary Risk Factors | HPV infection, plus alcohol and tobacco | Primarily tobacco and alcohol |
| Common Genotypes | 16, 18, 58, 59 | Not applicable |
| Typical Patient Profile | Younger, fewer co-morbidities | Older, more co-morbidities |
| Tumor Biology | Often poorly-differentiated | Varies |
| Response to Treatment | Possibly better prognosis (more research needed) | Standard prognosis |
Table 1: Characteristics of HPV-Positive vs. HPV-Negative Oral Cancer Patients
The detection of HPV 58 and 59 in oral cancer tissues requires sophisticated laboratory techniques. Here's how the researchers accomplished this feat:
The process began with collecting 3–5 mm tissue samples from surgically removed tumors or diagnostic biopsies. These samples were carefully transported in cold chain conditions to preserve the genetic material 1 .
Scientists used specialized kits to extract nucleic acids from the processed biopsy samples. This involved pulverizing the tissue with a pestle in a lysis buffer to break open cells and release their genetic content 1 .
The extracted DNA was then tested using two complementary methods:
The PCR products from HPV-positive samples were purified and sequenced for the HPV L1 gene using the Sanger sequencing method. The resulting sequences were then analyzed using bioinformatics software and compared to reference sequences to identify the specific genotypes 1 .
| Reagent/Equipment | Function in HPV Detection |
|---|---|
| Trueprep® Auto v2 DNA Extraction Kit | Extracts and purifies DNA from tissue samples for analysis |
| Trunat® HPV-HR Kit | Detects the presence of high-risk HPV DNA through real-time PCR |
| PGMY and MGP Primers | Target and amplify the L1 region of the HPV genome for genotyping |
| Thermal Cycler | Equipment that performs PCR by cycling temperatures to amplify DNA |
| Big Dye Terminator Cycle Sequencing Kit | Enables Sanger sequencing of PCR products to identify specific genotypes |
| 3500XL Genetic Analyzer | Analyzes sequenced DNA fragments to determine genetic code |
| Nickel;niobium | |
| Gold;mercury | |
| 6-Azido-9H-purine | |
| nickel;titanium | |
| Holmium;indium |
Table 2: Key Research Reagents for HPV Detection in Oral Cancer
Detecting HPV in the oral cavity presents unique challenges. A 2024 study called "The Oromouth study" compared different sampling methods and found that while oral rinse samples had the highest detection rates for HPV (16% for any HPV), they missed a staggering 73% of high-risk HPV infections that were detected by sampling other oral sites 4 .
When researchers combined samples from oral rinse, pharyngeal wall, tongue base, and tonsil tissue, they improved high-risk HPV detection by 38% compared to oral rinse alone 4 .
This highlights the importance of sampling methodology in accurately assessing HPV's role in oral diseases.
Data from "The Oromouth study" 4
In cervical and oropharyngeal cancers, the p16 protein is used as a reliable surrogate marker for HPV infection. However, this relationship appears to be different in oral cavity cancers 3 .
A 2025 study found that using p16 as a marker for HPV DNA infection in oropharyngeal cancer had a sensitivity of only 62.5%, with a kappa coefficient of 0.67 between HPV DNA and p16 . The relationship was even weaker for oral cavity cancers. This suggests that p16 overexpression does not reliably indicate HPV infection in oral cavity cancers, complicating diagnosis and highlighting the need for more direct detection methods 3 .
| Detection Method | Mechanism | Advantages | Limitations |
|---|---|---|---|
| HPV DNA PCR | Detects viral DNA | Highly sensitive, can genotype | May detect transient, non-cancerous infections |
| p16 Immunohistochemistry | Detects p16 protein overexpression | Simple, widely available, inexpensive | Poor surrogate marker for HPV in oral cavity cancers |
| E6/E7 mRNA Testing | Detects viral oncogene expression | Confirms transcriptionally active virus | Expensive, technically challenging, requires frozen tissue |
Table 3: Comparison of HPV Detection Methods
The discovery of HPV 58 and 59 in oral cancers is particularly relevant given their classification in cervical cancer screening. One study categorized HPV genotypes by their positive predictive value for high-grade cervical lesions, placing HPV 33 and 16 in the highest risk group, while HPV 58 was grouped with types 31, 18, 52, 35, and 51 as "highly predictive," and HPV 59 was categorized with types 68, 45, 39, 66, and 56 as "intermediately predictive" of precancerous changes 2 .
Based on positive predictive value for high-grade cervical lesions 2
While this hierarchy was developed for cervical cancer, it highlights the concerning potential of types 58 and 59 to cause malignancy, underscoring why their discovery in oral cancers is significant.
The detection of HPV genotypes 58 and 59 in oral squamous cell carcinoma represents a significant shift in our understanding of oral cancer's complex etiology. These findings demonstrate that the landscape of HPV-related oral cancers is more diverse than previously appreciated, extending beyond the well-known HPV 16 and 18.
HPV vaccination may help prevent not just cervical cancer but possibly certain oral cancers as well.
Improved detection methods can identify high-risk HPV genotypes in oral cancers earlier.
Ongoing research continues to uncover the complex relationship between HPV and oral cancer.
While traditional risk factors like tobacco and alcohol remain critically important, recognizing the role of various HPV genotypes provides a more complete picture of why oral cancer develops—and how we might stop it.