Prevalence of human papillomavirus types and phylogenetic analysis of HPV-16 L1 variants from Southern India

Systematic Literature Review on the Burden of Human Papillomavirus Infection and Related Diseases in India

Human papillomavirus (HPV)-related diseases pose public health concerns for both genders, yet their understanding remains limited in India. This review outlines HPV incidence and prevalence, genotype distribution, and attribution rates across different HPV-related disease types. A comprehensive literature search was performed to identify observational studies on individuals aged 15 years and older, and a total of 3702 publications were identified. A total of 139 studies were included in this review, involving 607,425 subjects aged 15.8-82.2 years, with a gender distribution of 38.13% males and 61.86% females. The prevalence of HPV infection in the anogenital area among healthy males and females was 41.07% and between 0.4% and 41.8%, respectively. Among individuals with HPV-related diseases, HPV infection prevalence was 26.1%-100% in unhealthy cervixes and cervical lesions, 3.1%-41% in anal lesions, 71.4% in vulva and vaginal lesions, and 0%-92.3% in head and neck cancer. The review highlights the variability in HPV prevalence across genders and age groups in India, likely due to population heterogeneity and testing differences. This study highlights the need for rigorous and uniform studies in India on the HPV disease burden and the importance of gathering evidence with a special focus on males.

Identification of differentially expressed MiRNA clusters in cervical cancer

BACKGROUND

Aberrant miRNA expression has been associated with cervical cancer (CC) progression. The present study aimed to identify the miRNA clusters (MCs) altered in CC, identify their clinical utility, and understand their biological functions via computational analysis.

METHODS

We used small RNA sequencing and qRT‒PCR to identify and validate abnormally expressed MCs in cervical squamous cell carcinoma (CSCC) samples. We compared our data with publicly available CC datasets to identify the differentially expressed MCs in CC. The potential targets, pathways, biological functions, and clinical utility of abnormally expressed MCs were predicted via several computational tools.

RESULTS

Small RNA sequencing revealed that 229 miRNAs belonging to 48 MCs were significantly differentially expressed in CSCC (p-value ≤ 0.05). Validation by qRT‒PCR confirmed the downregulation of members of the miR-379/656, namely, hsa-miR-376c-3p (2.8-fold; p-value 0.03), hsa-miR-494-3p (3.4-fold; p-value 0.02), hsa-miR-495-3p (eightfold; p-value 0.01), and hsa-miR-409-3p (fivefold; p-value 0.03), in CSCC samples compared with normal samples. The prognostic model generated via miRNA expression and random forest analysis showed robust sensitivity and specificity (0.88 to 0.92) in predicting overall survival. In addition, we report 22 prognostically important miRNAs in CC. Pathway analysis revealed the enrichment of several cancer-related pathways, notably p53, the cell cycle, viral infection and MAPK signalling. CDC25A, CCNE1, E2F1, CCNE2, RBL1, E2F3, CDK2, RBL2, E2F2 and CCND2 were identified as the top ten gene targets of MC. Drug‒gene interaction analysis revealed enrichment of 548 approved drugs and 62 unique genes.

CONCLUSION

Our study identified MCs, their target genes, their prognostic utility, and their potential functions in CC and recommended their usefulness in CC management.

Molecular epidemiology of human papillomavirus variants in cervical cancer in India

Background & objectives Cervical cancer (CC) has been documented as the fourth most common cancer worldwide. Persistent infections with high-risk human papillomavirus (hr-HPV) have been suggested in the development of CC. Although prophylactic vaccines are available for the prevention of prevalent hr-HPV types, intra-type variations exist within a particular HPV type that has varying oncogenic potential as well as the mechanism of pathogenicity and varying neutralization by antibodies. Therefore, we carried out a systematic review to determine the distribution of HPV intra-typic variations in different geographical locations of India and their reported implications. Methods Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed to retrieve relevant articles from the standard databases using appropriate keywords. Consequently, 17 articles were included in the current review after screening based on inclusion and exclusion criteria. Results The majority of articles included in this review reported variations within the HPV16 E6 gene, followed by the L1 and E7 genes. Analysis of available data indicated the differential regional distribution of some variations. These variations have also been reported to impact the biological functions of various viral proteins. Interpretation & conclusions The distribution of lineages varied with the different genomic regions sequenced. Additionally, there were certain unique and common variations in the HPV genome with respect to geographical regions. Hence, we suggest the identification of region-specific variations for the development of diagnostic and prognostic interventions.

A Study to Assess the Impact of Education on the Knowledge and Attitude Toward Cervical Cancer and HPV (Human Papillomavirus) Vaccination Among Female Healthcare Students

Background Cervical cancer ranks among the top five cancers in India, with human papillomavirus (HPV) types 16 and 18 causing up to 70% of related lesions. HPV infection, acquired through various routes, poses risks for both men and women, especially in the age group of 16 to 25 years. Effective prevention is possible through HPV vaccination, with Cervarix and Gardasil approved for use in India. Despite its proven efficacy, HPV vaccine use remains minimal. This study aims to evaluate awareness, willingness, and barriers among female healthcare students while assessing the impact of a health education program on their knowledge and attitude. Methods The present study is an educational interventional study conducted on 489 female students in the healthcare sector in the age group of 19-25 years. Two questionnaires (pre-lecture and post-lecture) were used. After the pre-lecture questionnaire, a session on cervical cancer and vaccine education was delivered by the subject expert. Afterward, the post-lecture questionnaire was given and the impact of session was analyzed using various statistical tools. Result A total of 489 students across MBBS (Bachelor of Medicine, Bachelor of Surgery), BAMS (Bachelor of Ayurvedic Medicine and Surgery), BHMS (Bachelor of Homoeopathic Medicine and Surgery), paramedical, and nursing courses participated in the study. Prior to the lecture, knowledge regarding cervical cancer and vaccines was generally low across subgroups, witnessing improvements ranging from 60% to 100% in various questionnaire sections post-education. Understanding of the importance of a Pap smear (Papanicolaou test) increased significantly from 21% to 79% after the educational session. The most preferred measure to boost coverage was the inclusion of the HPV vaccine in the National Immunization Schedule, with lack of awareness identified as the most significant barrier. Conclusion An educational session not only enhances knowledge but also boosts willingness for cervical cancer vaccination. Inclusion of the vaccine in the National Immunization Schedule not only increases acceptability but also indirectly raises awareness.

Trends in Co-circulation of Oncogenic HPV Genotypes in Single and Multiple Infections among Unvaccinated Community

Cocirculation of multiple human papillomavirus (HPV) infections with low, probably high, and high‐risk genotypes are to be associated with various grades of infections and cancer progression. The oncogenic high‐risk HPVs are distributed and cocirculated throughout the world. This study was investigated to identify HPV genotypes related to genital disorders in unvaccinated women. The subjects were referred from clinics to a molecular lab for HPV testing in Iran as a low‐coverage vaccinated country. HPVs DNAs of cervical scrapping and genital tissue specimens of 1,133 un‐vaccinated women were genotyped using an in vitro diagnostic line probe (reverse hybridization) assay. In addition, phylogenetic trees were constructed on 100 MY09/MY11 polymerase chain reaction (PCR) amplicons of common genotypes of HPV L1 gene by Sanger sequencing. The mean age of the population study was 32.7 ± 8.0 and the mean age of HPV‐positive cases was 31.6 ± 7.8. HPV DNA was detected in 57.8% (655/1133) of women subjects and 42.2% (478/1133) of cases were undetected. Among 655 HPV‐positive cases, 639 subjects (56.4%) were related to defined genotypes and 16 subjects (1.4%) were untypeable. The highest prevalence rate of HPV genotypes was identified in the 25–34 years. The top 6 dominant HPVs in single and multiple genotypes were HPV6 (284/655 [43.4%]), HPV16 (111/655 [16.9%]), HPV31 (72/655 [11%]), HPV53 (67/655 [10.2%]), HPV11 (62/655 [9.5%]), and HPV52 (62/655 [9.5%]). Moreover, single, multiple and untypeable HPV genotypes were diagnosed as follows: 1 type (318/655 [48.5%]), 2 types (162/655 [24.8%]), 3 types (83/655 [12.7%]), 4 types (42/655 [6.5%]), more than 5 types (34/655 [5.3%]), and 1.4% un‐typeable subjects. The sequenced partial L1 gene of HPV genotypes (GenBank databases under the accession numbers: MH253467‐MH253566) confirmed and determined the cocirculated HPV genotypes' origins and addressed helpful insights into the future viral epidemiology investigations. Multiple HPV infections and cocirculation of various oncogenic HPV genotypes among the normal population (women and men) with asymptomatic forms are still challenging in unvaccinated communities. The preventive and organized surveillance programs for HPV screening are needed to be considered and compiled by health policy makers of low or unvaccinated countries.

Human papilloma and other DNA virus infections of the cervix: A population based comparative study among tribal and general population in India

BACKGROUND

Despite being preventable, cervical cancer remains a major health concern among women. Persistent Human Papillomavirus (HPV) and other viral co-infections may influence cervical dysplasia. We determined and compared the prevalence and risk factors of cervical viral infections among the tribal and general population of southern coastal Karnataka, India.

METHODS

A population-based cross-sectional survey was conducted among 1140 and 1100 women from tribal and general population, respectively. Cervical infections with HPV, Epstein-Barr Virus (EBV), Cytomegalovirus (CMV) and Herpes-Simplex Virus (HSV) were examined using polymerase chain reactions (PCR) and DNA sequencing.

RESULTS

HPV prevalence was higher among tribal women (40.6%) than general population (14.3%) while the prevalence of EBV (55.1%) and CMV (49.4%) were lower among tribal women than general population (74.3% and 77.5%, respectively). HSV infection was observed in tribal women only (1.8%). Among HR-HPV strains, HPV-18 was predominant among tribal population (28.3%) while, HPV-16 was predominant among the general population (9.1%). Infections were associated with age, educational status, unemployment and personal hygiene of tribal women. Phylogenetic analysis revealed that HPV-16 variants of tribal participants were closely related to non-European sublineages indicating greater risk of HPV persistence and carcinogenesis.

CONCLUSION

The study provides a comparative estimate for DNA virus infections of the cervix among women from general as well as tribal population in this region and also reveals a different type-specific pattern of viral infection. Further research is required to delineate the role of specific interactions between multiple virus infections and their role in carcinogenesis.

Phylogeny and Classification of Human Papillomavirus (HPV)16 and HPV18 Variants Based on E6 and L1 genes in Tunisian Women with Cervical Lesions

Background:

High-risk human papillomavirus (HPV) types are the main etiological factors for cervical cancer. HPV16 and HPV18 are generally the most common forms associated with development of high-grade cervical lesions. This study was undertaken to identify intratypic variants of HPV16 and HPV18 among women with cervical lesions in Tunisia.

Materials and Methods:

DNA was extracted from cervical samples collected from 49 women. using a PureLinkTM Genomic DNA mini Kit (Invitrogen). E6 and L1 open reading frames (ORF) were amplified by PCR and viral DNA amplicons were subjected to automated sequencing using Big Dye Terminators technology (Applied Biosystems). The obtained sequences were analyzed using an appropriate software program to allow phylogenetic trees to be generated.

Results:

HPV16 and HPV18 were detected in 15 and 5 cases, respectively. HPV16 E6 sequences clustered with the European German lineage (A2) whereas one isolate diverged differently in the L1 region and clustered with the African sub-lineage (B1). HPV 18 E6 sequences clustered with the European sub-lineage (A1) but L1 sequences clustered as a new clade which diverged from A1-A5.

Conclusions:

Our results suggest that the distribution of HPV16 and HPV18 sequences in women with cervical lesions in Tunisia is mainly related to European epidemiological conditions and point to the presence of recombinant HPV forms.

Prevalence and age-wise distribution of Human Papillomavirus type 16/18 infections among hospital screened women of a peri-urban area in West Bengal: Impact of socio-demographic factors

BACKGROUND

We undertook the current study on cervical Human Papillomavirus (HPV) prevalence along with cytology in women visiting the Gynecology Out-patient Department of a hospital for common gynecological ailments, subsequent to our earlier population-based study on HPV prevalence from India.

METHODS

We analyzed data on cervical-cytology (Pap smears) and PCR-based molecular detection of HPV infection along with socio-demographic variables (N = 696).

RESULTS

We identified 36.84% HPV-positive women amongst whom, HPV16 and 18 together predominated (79.37%) over other HPV types (20.63%). Contrarily, only 6.4% women revealed abnormal cytological lesions, of which, 46.51% were HPV-positive and 95% of such women harbored HPV16/18, while 5% harbored other HPV types. Individuals with normal cytology portrayed 36.09% HPV infections, of which, 77.97% were HPV16/18-positive and 22.03% harbored other HPV types. Overall HPV prevalence decreased significantly (p_trend  = 0.047) with increase in age, but HPV16/18 infections were significantly over-represented compared to the other HPV types across all age-groups. Specifically, HPV16 prevalence increased (p _trend < 0.01) with increase in severity of cervical lesions. HPV16 prevalence did not differ between the Hindus and Muslims but HPV18 was significantly higher among the cytologically normal Muslim women (24.14%, p = 0.02), compared to the Hindus (11.91%), specifically among those ≥ 30 years of age. There was a significant (p < 0.05) overrepresentation of HPV16 prevalence among women who were users of oral contraceptive-pills, irrespective of cytology.

CONCLUSIONS

Our study highlights the need for HPV16/18-based screening of cervical cancers in India considering the immense socio-cultural and genetic diversity at the population level.

Gene promoter-associated CpG island hypermethylation in squamous cell carcinoma of the tongue

The present study was undertaken to explore and validate novel hypermethylated DNA regions in squamous cell carcinoma of the tongue (SCCT). Genome-wide methylation changes were identified by differential methylation hybridization (DMH) microarray and validated by bisulfite genome sequencing (BGS). The results were compared against datasets from The Cancer Genome Atlas head and neck squamous cell carcinoma (TCGA-HNSCC), Gene Expression Omnibus (GSE26549), and ArrayExpress (E-MTAB-1328). DMH identified 116 hypomethylated and 241 hypermethylated regions. Of the latter, 24 were localized to promoter or 5'-UTR regions. By BGS, promoter sequences of DAPK1, LRPPRC, RAB6C, and ZNF471 were significantly hypermethylated in tumors when compared with matched normal tissues (P < 0.0001). A TCGA-HNSCC dataset (516 cases of cancer and 50 normal tissue samples) further confirmed hypermethylation of DAPK1, RAB6C, and ZNF471. Sensitivity and specificity of methylation markers for a diagnosis of cancer were in the range of 70-100% in our study and from TCGA-HNSCC datasets, with an area under curve (AUC) of 0.83 and above. Kaplan-Meier survival analysis of TCGA-HNSCC expression data revealed that patients with low expressions of DAPK1, RAB6C, and ZNF471 showed poorer survival than patients with high expression (P = 0.02). Human papillomavirus (HPV) was found in 55% of cases, HPV16 being the predominant genotype. DAPK1 immunohistochemical staining was lower in SCCT than in normal buccal epithelial cells. This is the first study to report hypermethylation of LRPPRC, RAB6C, and ZNF471 in SCCT and its diagnostic and prognostic potentials in a specific head and neck squamous cell carcinoma.

Aberrant gene-specific DNA methylation signature analysis in cervical cancer

Multicomponent molecular modifications such as DNA methylation may offer sensitive and specific cervical intraepithelial neoplasia and cervical cancer biomarkers. In this study, we tested cervical tissues at various stages of tumor progression for 5-methylcytosine and 5-hydroxymethylcytosine levels and also DNA promoter methylation profile of a panel of genes for its diagnostic potential. In total, 5-methylcytosine, 5-hydroxymethylcytosine, and promoter methylation of 33 genes were evaluated by reversed-phase high-performance liquid chromatography, enzyme-linked immunosorbent assay based technique, and bisulfate-based next generation sequencing. The 5-methylcytosine and 5-hydroxymethylcytosine contents were significantly reduced in squamous cell carcinoma and receiver operating characteristic curve analysis showed a significant difference in (1) 5-methylcytosine between normal and squamous cell carcinoma tissues (area under the curve = 0.946) and (2) 5-hydroxymethylcytosine levels among normal, squamous intraepithelial lesions and squamous cell carcinoma. Analyses of our next generation sequencing results and data from five independent published studies consisting of 191 normal, 10 low-grade squamous intraepithelial lesions, 21 high-grade squamous intraepithelial lesions, and 335 malignant tissues identified a panel of nine genes ( ARHGAP6, DAPK1, HAND2, NKX2-2, NNAT, PCDH10, PROX1, PITX2, and RAB6C) which could effectively discriminate among the various groups with sensitivity and specificity of 80%-100% (p < 0.05). Furthermore, 12 gene promoters (ARHGAP6, HAND2, LHX9, HEY2, NKX2-2, PCDH10, PITX2, PROX1, TBX3, IKBKG, RAB6C, and DAPK1) were also methylated in one or more of the cervical cancer cell lines tested. The global and gene-specific methylation of the panel of genes identified in our study may serve as useful biomarkers for the early detection and clinical management of cervical cancer.

Detection of Genital HPV Infection Using Urine Samples: a Population Based Study in India

BACKGROUND

Cervical cancer is the second commonest cancer among Indian women and its association with human papilloma virus (HPV) is well established. This preventable cancer accounts for the maximum number of cancer related deaths among rural Indian women. Unlike in developed countries there are no organized cervical cancer screening programmes in India due to lack of resources and manpower.

OBJECTIVE

To detect genital HPV infection using urine samples among asymptomatic rural women in the age group of 18-65 years.

MATERIALS AND METHODS

The study area chosen was Perdoor village in Udupi Taluk, Karnataka State and all the women in the age group of 18-65 years formed the study cohort. A cross sectional study was conducted by house visits and 1,305 women were enrolled in the study. After taking written informed consent a data sheet was filled and early stream random urine samples were collected, transported to a laboratory at 4OC and aliquoted. Samples were tested using nested HPV PCR with PGMY09/11 and GP5+/6+ primers. Positive cases were genotyped by sequence analysis.

RESULTS

Study participants included 1,134 sexually active and 171 unmarried women with a mean age at marriage of 22.1 (SD=3.9) years. Study area showed high female literacy rate of 86.6%. Five urine samples tested positive for HPV DNA (0.4%).

CONCLUSIONS

We found very low genital HPV infection rate among women from monogamous community. This is the first major population based study carried out among asymptomatic rural women to detect genital HPV infectio from Karnataka using urine samples.

Genomic diversity and phylogenetic relationships of human papillomavirus 16 (HPV16) in Nepal

OBJECTIVES/BACKGROUND

Sequence variants in HPV16 confer differences in oncogenic potential; however, to date there have not been any HPV sequence studies performed in Nepal. The objective of this study was to characterize HPV16 viral genome sequences from Nepal compared to a reference sequence in order to determine their lineages. Additionally, we sought to determine if five High-grade Squamous Intraepithelial Lesion (HSIL) subjects were genetically distinct from the non-HSIL subjects.

METHODS

DNA was isolated from exfoliated cervical cells from 17 individuals in Nepal who were previously identified to be HPV16-positive. A custom HPV16 Ion Ampliseq panel of multiplexed degenerate primers was designed that generated 47 overlapping amplicons and covered 99% of the viral genome for all known HPV16 variant lineages. All sequence data were processed through a custom quality control and analysis pipeline of sequence comparisons and phylogenetic analysis.

RESULTS

There were high similarities across the genomes, with two major indels observed in the non-coding region between E5 and L2. Compared to the PAVE reference HPV16 genome, there were up to 9, 4, 38, 27, 8, 7, 52, and 32 nucleotide variants in the E6, E7, E1, E2, E4, E5, L2, and L1 genes in the Nepalese samples, respectively. Based on sequence variation, HPV16 from Nepal falls across the A, C, and D lineages in this study. We found no evidence of genetic distinctness between HSIL and non-HSIL subjects.

CONCLUSIONS

The evolutionary and pathological characteristics of the representative HPV16 genomes from Nepal seem similar to results from other parts of the world and provide the basis for further studies.