Clinical overview
Human papillomavirus (HPV) is the single most important infectious cause of cancer in the female genital tract, and in South Africa — where cervical cancer is the leading cause of cancer death in women and where HIV co-infection is endemic — understanding its pathology is not academic. Almost every squamous cervical cancer, the large majority of vulvar and vaginal high-grade lesions, most anal cancers, and a substantial fraction of oropharyngeal cancers share a common molecular driver: persistent infection with a high-risk HPV genotype and the integration of its oncogenes into the host epithelial cell. The clinical spectrum runs from clinically silent transient infection (the rule, cleared by most immunocompetent women within 1–2 years), through benign productive lesions (condylomata acuminata, low-grade squamous intraepithelial lesions), to high-grade precancer (HSIL/CIN 2–3) and frank invasive carcinoma.
For the registrar, the pathology of HPV is the conceptual spine that connects the screening programme, the colposcopy clinic, and the oncology ward. The reason we screen with HPV-DNA tests, the reason we treat HSIL but observe much LSIL, the reason an HIV-positive woman needs more frequent surveillance, and the reason a single-dose prophylactic vaccine can plausibly eliminate the disease — all flow directly from how the virus behaves inside the epithelium. This chapter describes those pathological features: the virology, the gross and microscopic morphology of each lesion grade, the molecular carcinogenesis, and the WHO 2020 terminology that has reshaped how we report them. See also cin-pathophysiology and cervical-carcinogenesis for the dysplasia/invasion sequence in more depth, and cervical-screening-sa for the South African programme that operationalises all of this.
Core knowledge
The virus and its targets
Figure D7.1 — The HPV virion and its ~8 kb circular genome: the roles of E6, E7, E2 and L1, and high-risk (16/18) vs low-risk (6/11) types.
HPV is a small, non-enveloped, double-stranded circular DNA virus (~8 kb) of the Papillomaviridae. Over 200 genotypes are described; the genital tract is colonised by the alpha-papillomaviruses. The clinically critical division is by oncogenic potential:
- High-risk (oncogenic) types: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and others. HPV 16 and 18 alone cause roughly 70% of cervical cancers worldwide; HPV 16 dominates squamous carcinoma and HSIL, while HPV 18 is over-represented in adenocarcinoma.
- Low-risk types: 6 and 11 cause ~90% of anogenital warts (condylomata acuminata) and recurrent respiratory papillomatosis, and are associated with LSIL but essentially never with invasion.
The virus genome encodes early (E) and late (L) proteins. The oncogenes E6 and E7 are the engine of malignant transformation; E1 and E2 regulate replication and transcription (E2 represses E6/E7); L1 and L2 are the capsid proteins (L1 self-assembles into the virus-like particles that are the basis of the vaccine).
The vulnerable cell: the transformation zone
HPV infects basal keratinocytes reached through micro-abrasions, but the cell type that matters most is the metaplastic squamous epithelium of the cervical transformation zone (TZ) — the dynamic interface between the original squamous epithelium of the ectocervix and the columnar epithelium of the endocervical canal. The squamocolumnar junction migrates with hormonal status (everted and exposed in adolescence and pregnancy, receding into the canal after menopause). Immature metaplastic cells of the TZ are uniquely susceptible to HPV-driven transformation, which is why cervical precancer and cancer overwhelmingly arise here, and why the position of the TZ governs colposcopic adequacy and the choice of ablative versus excisional treatment (see colposcopy and cin-management).
Productive infection: the cytopathic signature
Figure D7.2 — The HPV life cycle tied to squamous maturation: basal infection, episomal amplification, koilocyte formation, and surface shedding.
In a permissive (productive) infection, the viral life cycle is coupled to keratinocyte differentiation. The virus maintains its genome as a low-copy episome in basal cells, then amplifies and assembles capsids as the cells differentiate towards the surface. This produces the diagnostic cytopathic effect:
- Koilocytosis — the morphological hallmark of productive HPV infection. A koilocyte is a superficial/intermediate squamous cell with a large, sharply demarcated perinuclear halo (clear cytoplasmic cavity), a condensed peripheral rim of cytoplasm, and an enlarged, hyperchromatic, irregular ("raisinoid") nucleus, often binucleation. The halo reflects cytoskeletal collapse driven by the E4 protein.
- Dyskeratosis, parakeratosis and acanthosis accompany koilocytosis in warts and LSIL.
- These features are most florid in LSIL/CIN 1 and condylomata, where viral replication is most active.
Gross and microscopic morphology by lesion
Figure D7.3 — Histopathology of HPV disease: koilocytes, and LSIL (CIN1) vs HSIL (CIN2–3) with the WHO-2020/LAST two-tier system and p16.
Condyloma acuminatum (genital wart) — gross: soft, sessile or pedunculated, papillary/cauliflower-like exophytic growths, usually multiple, on vulva, perineum, perianal skin, vagina and occasionally cervix; commonly low-risk HPV 6/11. Microscopy: papillomatosis with fibrovascular cores, acanthosis, hyperkeratosis/parakeratosis and koilocytes in the upper layers; the basal layer is orderly and the basement membrane intact.
LSIL (low-grade squamous intraepithelial lesion = CIN 1, flat condyloma) — the morphological correlate of a productive infection. Microscopy: koilocytosis plus mild basal/parabasal proliferation confined to the lower third of the epithelium; nuclear atypia is mild; maturation is preserved in the upper two-thirds; mitoses are basal and normal in form. Most LSIL is transient and regresses, mirroring the natural history of the infection.
HSIL (high-grade squamous intraepithelial lesion = CIN 2–3) — the morphological correlate of a transforming infection. Microscopy: loss of normal maturation and stratification with atypical, crowded, hyperchromatic cells extending into the middle and upper thirds (CIN 2) or full thickness (CIN 3/carcinoma in situ); increased nuclear:cytoplasmic ratio, nuclear pleomorphism, and mitoses above the basal layer including atypical (abnormal) mitotic figures. Koilocytosis is often inconspicuous because the productive cycle is suppressed by integration. The basement membrane remains intact (no stromal invasion) — this is what separates HSIL from invasive carcinoma.
Invasive squamous cell carcinoma — defined by malignant squamous cells breaching the basement membrane into the stroma, eliciting a desmoplastic stromal reaction; earliest invasion (microinvasion) is the basis of FIGO 2018 stage IA, defined microscopically by stromal invasion ≤5 mm in depth. Keratinising and non-keratinising patterns are described.
HPV-associated adenocarcinoma and AIS — HPV (especially 18 and 45) also drives glandular precancer (adenocarcinoma in situ, AIS) and the usual-type endocervical adenocarcinoma. WHO 2020 separates HPV-associated endocervical adenocarcinoma from HPV-independent types (e.g. gastric-type), which behave more aggressively and are not detected by HPV-targeted screening — a deliberate, clinically important distinction.
Molecular carcinogenesis: E6, E7 and integration
Figure D7.4 — The molecular mechanism: integration disrupts E2, unleashing E6 (→ p53 degradation) and E7 (→ pRb inactivation), with p16 over-expression as the surrogate marker.
Transformation depends on a shift from episomal, productive infection to integration of the viral genome into the host chromosome. Integration typically disrupts the E2 open reading frame; because E2 normally represses E6/E7 transcription, its loss causes deregulated, constitutive over-expression of E6 and E7:
- E7 binds and inactivates the retinoblastoma protein (pRb), releasing E2F and driving the cell through G1/S into unscheduled proliferation. The resulting feedback de-repression causes accumulation of p16^INK4a^, which is why diffuse, strong block-positive p16 immunohistochemistry is the surrogate marker of transforming high-risk HPV infection.
- E6 binds p53 and, via the E6AP ubiquitin ligase, targets it for proteasomal degradation, abrogating apoptosis and cell-cycle checkpoints. E6 also activates telomerase (hTERT), conferring replicative immortality.
The combined loss of pRb and p53 control produces genomic instability, accumulation of secondary mutations, and progression from HSIL to invasion. Crucially, persistent infection with a high-risk type is necessary — the great majority of HPV infections are cleared by the immune system and never integrate. Persistence, not mere acquisition, is the driver. This molecular logic underpins the two key biomarkers used in modern pathology: p16 IHC (a marker of E7-driven transformation; the LAST/WHO criteria use diffuse block-positive p16 to upgrade an equivocal lesion to HSIL) and HPV-DNA/mRNA testing (which detects the causal agent itself).
WHO 2020 / LAST terminology
The WHO Classification of Tumours of the Female Genital Tract, 5th edition (2020), adopting the Lower Anogenital Squamous Terminology (LAST), replaced the three-tier CIN system with a two-tier system that reflects the underlying biology:
| WHO 2020 / LAST | CIN equivalent | Biology | p16 |
|---|---|---|---|
| LSIL | CIN 1 (and flat condyloma/HPV effect) | Productive infection | Negative or patchy |
| HSIL | CIN 2 and CIN 3 | Transforming infection | Diffuse block-positive |
The same two-tier LSIL/HSIL nomenclature is applied across the lower anogenital tract — cervix, vagina, vulva, anus, perianus. p16 is the arbiter for the ambiguous CIN 2 category: a morphologically borderline lesion that is block-positive is classified HSIL, while a p16-negative lesion defaults to LSIL. This biology-anchored language is the standard for reporting and should be used in answers; quote the CIN equivalent in parentheses for clarity.
Vulvar and vaginal lesions: two distinct pathways
The vulva illustrates that not all genital squamous cancer is HPV-driven, and the distinction is examinable. There are two carcinogenic pathways:
- HPV-associated (usual-type) — arises in younger women from vulvar HSIL (usual-type VIN, formerly VIN 2–3), HPV 16-predominant, p16 block-positive, basaloid/warty histology.
- HPV-independent — arises in older women on a background of lichen sclerosus and differentiated VIN (dVIN), is p53-mutant (often aberrant p53 IHC), keratinising, and carries a higher risk of rapid progression to invasion than usual-type VIN. See vulval-carcinoma and lichen-sclerosus.
The same HPV-associated versus HPV-independent dichotomy applies to cervical adenocarcinoma and is formalised in WHO 2020 across sites.
HIV co-infection — the South African dimension
In a setting of high HIV prevalence this is central pathology, not a footnote. HIV-mediated CD4 depletion impairs clearance of HPV, so HIV-positive women have higher HPV prevalence, more multi-type infection, higher rates of persistence, faster progression from infection to HSIL, higher recurrence after treatment, and earlier invasive cancer. Cervical cancer is an AIDS-defining malignancy. Antiretroviral therapy (TLD — tenofovir/lamivudine/dolutegravir per SA ART guidelines) improves but does not fully normalise this risk. The pathology is the same lesion set, but it presents more often, more extensively, and younger — which is exactly why South African screening policy treats HIV status as a key modifier (see hiv-gynaecology and cervical-screening-sa).
Assessment
How HPV pathology is detected and worked up:
- Primary HPV-DNA testing — South Africa is moving to HPV-DNA primary screening (informed by the DiaVACCS trial), the high-performance test endorsed by the WHO elimination strategy. It detects the causal agent before morphological change and is more sensitive than cytology. A positive test is triaged (by genotyping for 16/18, reflex cytology, or visual inspection with acetic acid, VIA) before treatment.
- Cervical cytology (Pap) — reports the LSIL/HSIL morphology described above (ASC-US/ASC-H/LSIL/HSIL/AGC in the Bethesda framework). Historic SA public-sector policy was cytology-based, screening women 30–50, three smears 10-yearly from age 30 (confirm current algorithm against the BetterGyn 2024 / NDoH policy document).
- Colposcopy — directed examination after a positive screen: acetowhite epithelium, abnormal vessels (punctation, mosaicism, atypical vessels), and Lugol's-iodine-negative areas guide biopsy. The TZ type is assessed for treatment planning.
- Histology — the definitive diagnosis, from punch biopsy or excision (LLETZ/cone). p16 immunohistochemistry resolves equivocal CIN 2 and confirms HSIL; p53 helps separate HPV-independent dVIN from usual-type vulvar HSIL.
- HIV testing — offered to every woman with HPV-related disease in the SA context, as it directs surveillance frequency.
Management
This is a pathology objective, so only the principles that follow from the morphology are summarised; detail lives in cin-management, cervical-screening-sa and the staging/treatment chapters.
- Prevention (the upstream answer) — prophylactic L1 virus-like-particle vaccines generate neutralising antibody and prevent acquisition; the 9-valent (nonavalent) vaccine gives the broadest cover. The WHO-endorsed single-dose schedule (2022; adopted across Africa via SAGE/RITAG 2023) underpins the South African school-based programme running since 2014 for girls 9–14. This is the first pillar of the WHO 90-70-90 elimination strategy.
- LSIL/CIN 1 — usually observed, as most regresses spontaneously, mirroring transient productive infection; persistent lesions may be treated.
- HSIL/CIN 2–3 — treated to interrupt progression, by ablation (thermal/cryo) for a fully visualised TZ or excision (LLETZ/cone) where excision/diagnosis is needed. AIS generally warrants excision because of skip lesions.
- Invasive disease — staged by FIGO 2018 and managed per ESGO/ESTRO/ESP 2023: fertility-sparing or radical surgery for early disease; concurrent chemoradiation (weekly cisplatin) plus image-guided brachytherapy (EMBRACE-II/GEC-ESTRO standards) for locally advanced disease; pembrolizumab + chemoradiation (KEYNOTE-A18) for high-risk locally advanced disease and pembrolizumab + chemo ± bevacizumab (KEYNOTE-826) for recurrent/metastatic disease (PD-L1 CPS ≥1).
Red flags / pitfalls
- Do not equate HPV positivity with disease. Most infections are transient and clear; only persistent high-risk infection matters. Over-treating a single positive test causes harm.
- Koilocytosis is a marker of LSIL/productive infection, not of HSIL. Expecting florid koilocytes in HSIL is a trap — the productive cycle is suppressed once the virus integrates.
- Beware HPV-independent lesions. Gastric-type endocervical adenocarcinoma and HPV-independent (p53-mutant, dVIN-associated) vulvar carcinoma are HPV-negative, are missed by HPV-targeted screening, and the vulvar variant progresses faster — keep a low threshold for biopsy of lichen sclerosus that changes.
- CIN 2 is biologically heterogeneous — use p16 to resolve it rather than treating every CIN 2 reflexively; block-positivity defines HSIL.
- HIV-positive women progress faster and recur more. A "normal" interval in an immunocompetent woman is not safe in an immunocompromised one — follow the HIV-specific surveillance (screen at HIV diagnosis, then more frequently regardless of age).
- An intact basement membrane defines precancer; its breach defines cancer. The most consequential single judgement the pathologist makes is invasion versus in-situ disease — do not under-call early stromal invasion.
- The post-menopausal endocervical TZ recedes into the canal, so an inadequate colposcopy in an older woman can miss disease — favour excision/diagnosis when the TZ is not fully seen.
Evidence anchors
- WHO Classification of Tumours of the Female Genital Tract, 5th edition (2020) — the source for histological typing, the two-tier LSIL/HSIL (LAST) terminology with CIN equivalence, p16 criteria, and the HPV-associated versus HPV-independent distinction across cervix and vulva.
- South African cervical cancer screening — SASOG / BetterGyn Clinical Guideline (2024) and the NDoH National Cervical Cancer Screening / Prevention & Control Policy — the SA source of truth: the move to HPV-DNA primary screening (informed by the DiaVACCS trial), the historic cytology pathway (women 30–50, 3 smears 10-yearly from 30), and HIV-positive women screened at diagnosis and more frequently regardless of age. Confirm exact intervals/algorithm against the current PDF before quoting numbers.
- WHO Cervical Cancer Elimination Strategy (2020) — 90-70-90 by 2030, the WHO-endorsed single-dose HPV schedule (2022), the 9-valent vaccine, and the SA school-based programme (since 2014).
- ESGO/ESTRO/ESP Guidelines for cervical cancer — Update 2023 (Int J Gynecol Cancer) with FIGO 2018 staging (microinvasion IA ≤5 mm depth; nodal disease = IIIC) — the framework linking pathology to staging and treatment.
- Radiation and medical oncology anchors (relevant to invasive sequelae of HPV disease): concurrent chemoradiation with image-guided brachytherapy (EMBRACE-II / GEC-ESTRO); KEYNOTE-A18 (pembrolizumab + chemoradiation, high-risk locally advanced) and KEYNOTE-826 (pembrolizumab + chemo ± bevacizumab, recurrent/metastatic, PD-L1 CPS ≥1).
- South African HIV / ART Consolidated Guidelines (2023) — TLD first-line; the basis for the HIV-modifier in HPV pathology and surveillance.