Human Papillomavirus Variants Research Articles

Distribution of HPV types among women with HPV-related diseases and exploration of lineages and variants of HPV 52 and 58 among HPV-infected patients in China: A systematic literature review

ABSTRACT To summarize the distribution of types of human papillomavirus (HPV) associated with HPV-related diseases and investigate the potential causes of high prevalence of HPV 52 and 58 by summarizing the prevalence of lineages, sub-lineages, and mutations among Chinese women. We searched PubMed, EMBASE, CNKI, and WanFang from January, 2012 to June, 2023 to identify all the eligible studies. We excluded patients who had received HPV vaccinations. Data were summarized in tables and cloud/rain maps. A total of 102 studies reporting HPV distribution and 15 studies reporting HPV52/HPV58 variants were extracted. Among Chinese women, the top five prevalent HPV types associated with cervical cancer (CC) were HPV16, 18, 58, 52, and 33. In patients with vaginal cancers and precancerous lesions, the most common HPV types were 16 and 52 followed by 58. For women with condyloma acuminatum (CA), the most common HPV types were 11 and 6. In Chinese women with HPV infection, lineage B was the most prominently identified for HPV52, and lineage A was the most common for HPV58. In addition to HPV types 16, which is prevalent worldwide, our findings revealed the unique high prevalence of HPV 52/58 among Chinese women with HPV-related diseases. HPV 52 variants were predominantly biased toward lineage B and sub-lineage B2, and HPV 58 variants were strongly biased toward lineage A and sub-lineage A1. Further investigations on the association between the high prevalent lineage and sub-lineage in HPV 52/58 and the risk of cancer risk are needed. Our findings underscore the importance of vaccination with the nine-valent HPV vaccine in China.

Cervical Cancer Treatment Update: A Society of Gynecologic Oncology Clinical Practice Statement

ABSTRACT Despite increased screening and human papillomavirus (HPV) vaccination in high-income countries, cervical cancer represents the fourth most diagnosed cancer in women worldwide and the second highest cause of cancer mortality among women in low- and middle-income countries. This clinical practice statement describes therapies for cervical cancer by treatment setting, as well as quality of life, financial toxicity, and disparities associated with the disease. Persistent HPV infection, particularly types 16 and 18, are the main factor in the development of cervical cancer. High-risk HPV variants integrate HPV DNA into the host genome to upregulate two viral oncoproteins, E6 and E7, which in turn inhibit the tumor suppressor proteins p53 and Rb. Certain driver mutations including PIK3CA, KRAS, and EGFR are frequently seen in cervical cancer, however further research is needed to identify an actionable biomarker based on targetable oncogenic alterations. Locally advanced cervical cancer is defined as clinically visible tumor exceeding 4 cm or invading beyond the cervix, extending to the pelvic sidewalls, vagina, bladder, rectum, or involving pelvic and/or paraaortic lymph nodes. Standard treatment for locally advanced cervical cancer is external beam radiation therapy and concurrent weekly cisplatin. Standard treatment for advanced, recurrent, or metastatic cervical cancer is cisplatin, paclitaxel, and bevacizumab (possibly adding pembrolizumab). Several studies have shown that checkpoint inhibitors, when combined or sequenced with chemoradiation, may provide survival benefit in both locally advanced and recurrent/metastatic cervical cancer. Given these findings, immunotherapy should be incorporated in treatment of advanced or recurrent disease. Negative effects on quality of life (QOL) in patients with cervical cancer often begin in people who receive negative Papanicolaou test results or positive HPV DNA tests. Negative body image, self-esteem, and relationships with partners contribute to an overall decrease in QoL. Surgical, radiation-induced, and chemotherapy-induced treatment effects further impact survivors’ physical health, body-image, and sexual function. Economic burdens of cancer diagnosis and treatment may disproportionally affect cervical cancer patients due to the intensity of curative treatment, decreases in QoL and functional status, and unique population including younger patients, those with poor access to health care at baseline, and those who identify as racial or ethnic minorities.

Unravelling the Impact of Human Papillomavirus (HPV): A Comprehensive Exploration of its Role in Cancer Progression and Global Health Challenges

HPV represents a large group of double stranded DNA viruses that are highly involved with different types of human cancers. This synopsis describes the complexities surrounding HPV virology, classifications, and genomic variation, especially focusing on high-risk strains such as HPV16 and HPV18, the main causative factors for cervical cancers. The International Committee on Taxonomy of Viruses specifies more than 200 HPV types each associated with a respective disease and indicated in Table 1. HPV spread is mostly due to direct skin-to-skin contact between individuals’ sex organs causing infections on the mucous membrane and keratinized epithelial cells. Although majority of the infections are asymptomatic, some chronic HRHPV infections may progress into cancers because of oncoproteins E6 and E7. The high-risk variants of HPV lead to cervical, anal, and oropharyngeal cancers whereas the low-risk types cause harmless genital warts. While integrating HPV DNA into the host genome, orchestrated by oncoproteins E6 and E7 disrupts the cell regulatory mechanism; this leads to abnormal control over cell multiplication–one of the major elements of the process that develops to HPV induced cancer. A classic case is cervical cancer that has been extensively investigated as one of the highly documented HPV associated malignancies. Pap smears and HPV DNA tests are among the screening means that lower the incidents and deaths associated with cervical cancers. HPV-associated cancers of the head and neck, anus, penis, vulva, and vagina all show a characteristic profile in terms of the pathogen aetiology and risks involved. HPV-related head and neck cancers affect non-smokers and show good response to standard therapies. HPV poses increased anal cancer risk for immunocompromised individuals highlighting the complexity of interdependence of immunity and cancer development. Penile cancer results from poor hygiene and non-circumcision. Vulvar and virginal cancer mostly affects women, and the risk factors involve HPV infection and smoking. Therefore, various types of multidisciplinary approach that may include surgeries, radiotherapy, and chemotherapy are necessary to ensure proper treatment. Certain cancers are strongly associated with some high-risk HPV genotypes, such as HPV-16 and HPV-18; thus, vaccination is important. HPV infection outcomes are determined by the immune response as well as clearance of HPV infection. Screening and immunological understanding for early detection of HPV related health risks is fundamental. However, this encompassing review highlights the multi-dimensional impact of HPV encompassing virology of HPV, cancer specific presentation of HPV and control including prevention of HPV infection, screening, and research on cancer attributable by HPV and strategies towards mitigation of this global health problem.

Screening of High and Low-risk Human Papillomavirus Variants in Cervical Cancer Patients by Polymerase Chain Reaction: A Cross-sectional Study

Introduction: Cervical cancer is the second most common gynaecological malignancy worldwide. Persistent Human Papillomavirus (HPV) infection is the principal risk factor leading to cervical carcinogenesis and causes a large number of casualties. Aim: To estimate the risk factors and symptoms related to cervical carcinoma and to check for mono-infection or co-infections of low-risk and high-risk HPVs in Northern Indian females. Materials and Methods: This cross-sectional study was conducted from January 2019 to January 2021 on 110 confirmed cervical cancer tissue samples collected from the Department of Obstetrics and Gynaecology at Pandit BD Sharma University of Health Sciences, Rohtak, Haryana, India. Information about risk factors and symptoms was collected using a semistructured proforma. Detection of HPV infection and HPV genotyping (16, 18, 33, 58, 6, and 11) was done by using type-specific Polymerase Chain Reaction (PCR). Fisher’s exact test was applied to determine the association of high- risk HPV infection with other risk factors using GraphPad Prism Version 6 (La Jolla, California, USA). A p-value of ≤0.05 was considered significant. Results: Of all the studied cases, 68 (62%) were above 55 years old, 67 (61%) were in a postmenopausal state, and 86 (78%) were from a rural background. Irregular menstruation was observed in 99 (90%) cases, bleeding after menopause in 59 (54%) cases, and early age at first intercourse in 57 (52%) cases were the most common symptoms. HPV infection was found in all cases of cervical carcinoma. The incidence of high- risk-HPV16 (84%) and HPV18 (73%) was the most prominent, while the incidence of low-risk-HPV6 (7.2%) and HPV11 (6%) was the lowest. Co-infection of HPV16/18 was the Highest in 60 (54.5%) cases, followed by HPV16/33 in 13 (11.8%) cases. Multi-infection of HPV types 16/18/33 was found in 10 (9.1%) cases, and multi-infection of HPV types 16/18/33/6/11, except HPV58, was found in one patient. Conclusion: Higher age, postmenopausal status, early age at intercourse, and poor menstrual hygiene were significantly associated with high-risk HPV co-infection. Educating women about the risk factors and symptoms of cervical cancer and screening for high-risk HPVs in rural women are required to reduce the prevalence of cervical cancer in Northern India.

Evaluation of anticancer activity of Gmelina asiatica leaves, in-vitro and in-silico studies

Cervical cancer poses a major threat to women’s health worldwide, constituting the fourth most prevalent cancer among the female population. High-risk variants of human papillomavirus (HPV) with its oncogenic proteins are a necessary cause of cervical cancer. Due to the resistance of cancer cells to the current treatment, there is a need for new medicines with new strategies to treat cervical cancer. Gmelina asiatica Linn. is a medicinal plant with various traditional uses and biological activities. Its anticancer potential against breast cancer and lymphoma has been demonstrated in the literature. In view of this, our study aims to investigate the anticancer activity of Gmelina asiatica leaves against cervical cancer. Various extracts of Gmelina asiatica leaves were prepared by soxhletation and maceration methods. The cytotoxic activity of the extracts was evaluated through in-vitro studies against SiHa cell line using MTT assay and fluorescence imaging. The most potent extract (GAME) phytochemical profile was analysed by UHPLC-HRMS. Further, in-silico studies were performed on its phytoconstituents against E6 oncoprotein, and the DFT studies were conducted on the active component to assess the physicochemical properties. In-vitro studies revealed that methanolic extract (GAME) showed the highest inhibition on the SiHa cell line compared to the other extracts and the control (p < 0.0001). In-silico studies indicated high affinity with stable interaction of the compound 5 (JC5ABDR) at E6 binding sites. This study revealed the importance of Gmelina asiatica plant as a potential source of anticancer molecules with a specific mode of action against cervical cancer. Communicated by Ramaswamy H. Sarma

Impact of HPV-16 Lineages Infection in Response to Radio-Chemotherapy in Cervical Cancer.

HPV is strongly related to cervical cancer. HPV lineages can contribute to a response to cervical cancer therapy. The aim of this research was to estimate the frequency of human papillomavirus (HPV)-16 lineages in specimens of cervical cancer, relate the pathological factors in these variants, and assess their response to treatment with radical chemoradiotherapy. Samples of cervical cancer were collected from women who were referred to a reference cancer hospital to test the presence of human papillomavirus-type DNA. The standard protocol of this service consisted of cisplatin-based chemotherapy of 40 mg/m2, plus conventional pelvic irradiation in doses of 45-50.4 Gy and high dose-rate brachytherapy of 28-30 Gy to Point A. The response to chemotherapy was evaluated after three months in patients with the HPV-16 lineage. HPV DNA was detected in 104 (88.1%) of the 118 patients. HPV-16 was present in 63 patients (53%). Lineages of HPV-16 were identified in 57 patients and comprised 33 instances of (57.8%) lineage A, 2 instances of lineage B (3.5%), 2 instances of lineage C (3.5%), and 20 instances of (35.0%) lineage D. The median age of the patients was 48.4 years (range 25-85 years). Squamous cell carcinoma was detected 48 times (84.2%). Adenocarcinoma was more likely to occur in lineage D, as three of the four cases occurred in this lineage. A total of 11 patients with the HPV-16 variant were treated with chemoradiotherapy. After three months, it was observed that nine of the eleven patients (81.8%) achieved a complete response, five with the lineage A type, two with the lineage C type, and two with the lineage D type. The two cases of partial response and disease progression, one of each, occurred in lineage A. In addition to the small number of patients and HPV variants, we noticed a better response in patients with the HPV-16 lineage A. Increasing the sample size could be helpful to better assess the impact of HPV variants on cervical cancer treatment.

Diversity of cervicovaginal human papillomavirus (HPV) genotypes and naturally occurring E6/E7 DNA polymorphisms of HPV-16 in Ghana

Human papillomavirus (HPV) E6 and E7 oncogene expression is essential for cervical carcinogenesis. Evidence exists that E6/E7 variants may have different transforming activities while the risk of HPV-16 variants (A/D) differs by race/ethnicity. We determined the type-specific diversity of HPV infection in women with high grade cervical disease or cervical cancer in Ghana and investigated naturally occurring E6/E7 DNA variants in this population. HPV genotyping was carried out on 207 cervical swab samples collected from women referred to a gynaecology clinic at two teaching hospitals in Ghana. HPV-16, HPV-18 and HPV-45 were detected in 41.9%, 23.3% and 16.3% of cases respectively. HPV-16 E6/E7 DNA sequencing was performed in 36 samples. Thirty samples contained E6/E7 variants of the HPV-16-B/C lineage. 21/36 samples were of the HPV-16C1 sublineage variant and all contained the E7 A647G(N29S) single nucleotide polymorphism (SNP). This study reveals the diversity of E6/E7 DNA and the dominance of HPV16 B/C variants in cervicovaginal HPV infection in Ghana. Type-specific HPV diversity analysis indicates that most Ghanaian cervical disease cases are vaccine preventable. The study provides an important baseline from which for the impact of vaccine and antivirals on clinically relevant HPV infection and associated disease can be measured.

Excurve and Emit Lobular Endocervical Glandular Hyperplasia

Lobular endocervical glandular hyperplasia of uterine cervix is a benign, exceptional lesion with a characteristic proliferation of miniature, spherical glands accompanied by gastric type differentiation. The discrete lobules incriminate upper endocervical canal of predominantly premenopausal women. Lobular endocervical glandular hyperplasia and gastric subtypes of cervical glandular lesions appear non concurrent to persistent infection with high risk variants of human papilloma virus (HPV). Cytological examination depicts mono-layered sheets of tall, columnar, mucinous cells demonstrating smooth nuclear outline with absent cellular or nuclear atypia or mitotic figures. Papanicolaou stained smears exemplify extracellular or intracellular, golden yellow mucin, indicative of gastric subtype of cellular differentiation. The well-defined lobular or acinar lesion is comprised of a centric crypt with circumscribing glandular articulations and miniature, spherical cysts which configure a floret-like pattern. Centric and peripheral glands are layered with columnar epithelial cells pervaded with pale, eosinophilic cytoplasm, bland, miniature, basal nuclei with mild nuclear atypia. Atypical cytological and architectural features may progress into the malignant ‘atypical lobular endocervical glandular hyperplasia’, currently contemplated as a category of gastric type adenocarcinoma in situ (GAIS). The lesion is immune reactive to pyloric gland mucin (HIK1083), MUC6, PAX2 or chromogranin A. Lobular endocervical glandular hyperplasia of uterine cervix requires segregation from neoplasms such as human papilloma virus (HPV) independent endocervical adenocarcinoma, gastric type, pyloric type metaplasia, gastric type adenocarcinoma in situ, type A tunnel clusters, micro glandular hyperplasia and mesonephric remnants or mesonephric hyperplasia of uterine cervix. Lesions detected upon surgical tissue sampling, cervical loop electrosurgical excision procedure (LEEP) or conisation may be optimally managed with total abdominal hysterectomy

Attitude and practice on Human Papillomavirus, Human Papillomavirus Vaccine and associated factors among population in the Republic of Kosova

Аpproximately 50–80% of sexually active women are exposed to at least one HPV variant during their lifetime. Based on the 2015 annual report of the National Institute of Public Health of Kosova, 68 new cases of cervical cancer were detected. The aim of the study was to investigate the attitude and practice regarding Human Papillomavirus (HPV) infections and the Human Papillomavirus vaccine in the population of the Republic of Kosova. Material and methods: A cross-sectional survey was conducted to assess the knowledge concerning HPV infections among the population aged 18 to 35+ years. The study was conducted during the period of time June 2021 –to August 2021. The sample included 500 participants. The questionnaire was anonymous, and participants were free to end their participation any time, without completing the questionnaire. Results: Regarding the claim "The HPV vaccine is safe", more than half of the respondents, respectively58.6% declare that they do not know, 33.4% of the respondents agree, 6.0% gave an incorrect answer / disagree, and 2.0% did not answer. The percentage difference between the unknown and correct answers is statistically significant for p&lt;0.05. Conclusion: This study found out that the attitude towards the HPV vaccine among people of the Republic of Kosova is low to moderate. HPV vaccines should be included in the national immunization programs, since there is not still established national vaccination program for HPV vaccination.

Cervical human papillomavirus genotypes in a high HIV setting: A scoping review of a decade of human papillomavirus epidemiological research in Botswana.

Cervical cancer burden is still high in low- and middle-income countries, including Botswana. Persistent human papillomavirus (HPV) infection is the leading cause of cervical cancer. Accurate knowledge of HPV diversity associated to cervical cancer in sub-Saharan Africa may provide accurate understanding of the natural history of HPV infection in these contexts. The goal of this review was to consolidate existing evidence on cervical HPV infection and to conduct a pooled analysis of data from all eligible Botswana studies. After a successful review of twelve studies on cervical HPV genotypes that met the inclusion criteria, HPV-16 genotype was the most frequently discovered in women with pre-cancerous and cancer lesions, followed by HPV-18. HPV-16 in HIV-positive women with precancerous lesions to cancer is between 45% and 47.7%, and between 4.5% and 26.1% for HPV-18. With reference to other HPV genotypes, the proportion of HPV-35 and HPV-58 (13-16%) seems relatively consistent among the studies, however HPV-58 appears to be more common in HIV-positive subjects compared to HIV-negative women. Indeed, HPV-45 seems to be frequently detected in women with cervical cancer compared to women with precancerous lesions. Regarding the low-risk HPV genotypes, an appropriate breakdown has been provided. In conclusion, the current prophylactic vaccines against HPV-16 and HPV-18, which have demonstrated good immunogenicity in HIV-infected populations, may still prevent infection and ultimately cancer.

Epidemiology and Molecular Biology of HPV Variants in Cervical Cancer: The State of the Art in Mexico.

Cervical cancer (CC) continues to be a major public health problem in Mexico, ranking second among cancers in women. A persistent infection with human papillomaviruses (HPV) is the main risk factor for CC development. In addition, a significant fraction of other cancers including those of the anus, oropharynx, and penis are also related to HPV infection. In CC, HPV-16 is the most prevalent high-risk HPV type, followed by HPV-18, both being responsible for 70% of cases. HPV intratype variant lineages differ in nucleotide sequences by 1–10%, while sublineages differ by 0.5–1%. Several studies have postulated that the nucleotide changes that occur between HPV intratype variants are reflected in functional differences and in pathogenicity. Moreover, it has been demonstrated that HPV-16 and -18 intratype variants differentially affect molecular processes in infected cells, changing their biological behavior that finally impacts in the clinical outcome of patients. Mexico has participated in providing knowledge on the geographical distribution of intratype variants of the most prevalent HPVs in premalignant lesions of the cervix and cervical cancer, as well as in other HPV-related tumors. In addition, functional studies have been carried out to assess the cellular effects of intratype variations in HPV proteins. This review addresses the state of the art on the epidemiology of HPV-16 and HPV-18 intratype variants in the Mexican population, as well as their association with persistence, precancer and cervical cancer, and functional aspects related to their biological behavior.

Identifying risk factors for post-operative bleeding in women undergoing loop electrosurgical excision procedure for cervical dysplasia.

Loop electrosurgical excision is a procedure utilised in the treatment of high-grade squamous intraepithelial lesion (HSIL) of the cervix. Post-operatively women may experience immediate and/or delayed per vaginal bleeding. The objective of this prospective pilot study was to assess the feasibility of identifying and quantifying patients' subjective experiences of post-operative bleeding following a loop electrosurgical excision procedure (LEEP) for HSIL. In addition, an analysis of demographical, lifestyle and surgical factors was undertaken to assess for any statistically significant correlation with post-operative bleeding. This study included 110 patients who underwent a LEEP for biopsy-proven or suspected HSIL between 2017 and 2020. Subjective data were collected from weekly post-operative surveys and correlated with procedural data. Primary outcome assessed was the subjective rate of bleeding experienced. Baseline demographics were age, body mass index (BMI), specimen size, human papilloma virus variant and histopathology. Other variables of interest collected were exercise intensity, and alcohol intake. No association of statistical significance was discovered between age, BMI, or day of menstrual cycle. There was a statistically significant association between exercise intensity or specimen size (greater than the median) and increased bleeding, primarily in the first 2 weeks. Women who undergo intense or prolonged exercise in the post-operative period may experience heavier bleeding particularly in the first 2 weeks post-LEEP. Heavy bleeding was also associated with a larger specimen size. There was no correlation between BMI, age or any other demographical factor.

Skin Cancer Back to Basics

ABSTRACT Anogenital squamous cell carcinoma is rare but an often-invasive malignancy that is becoming an increasingly prevalent public health problem. Infection with high-risk human papillomavirus variants plays a critical role in disease progression and occurrence. Immunosuppressive treatment, positive HIV status, number of sexual partners, and history of smoking increase neoplastic progression. Early diagnosis and treatment are pivotal in managing anogenital malignancies to improve quality of life and minimize extensive surgical excision. This article reviews lesion categorization, epidemiology, human-papillomavirus-driven dysplastic epithelial changes, risk factors, diagnostic criteria, treatment options, and prophylactic measures to improve patient outcomes.

Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan.

Human papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes, together with geographical differences in the distribution of genotypes and variants. Here, by employing a maximum likelihood method, we performed phylogenetic analyses of the complete genome sequences of HPV16, HPV18 and HPV58 available from GenBank (n = 627, 146 and 157, respectively). We found several characteristic clusters that exclusively contain HPV genomes from Japan: two for HPV16 (sublineages A4 and A5), one for HPV18 (sublineage A1) and two for HPV58 (sublineages A1 and A2). Bayesian phylogenetic analyses of concatenated viral gene sequences showed that divergence of the most recent common ancestor of these Japan-specific clades was estimated to have occurred ~98,000 years before present (YBP) for HPV16 A4, ~39,000 YBP for HPV16 A5, ~38,000 YBP for HPV18 A1, ~26,000 for HPV58 A1 and ~25,000 YBP for HPV58 A2. This estimated timeframe for the divergence of the Japan-specific clades suggests that the introduction of these HPV variants into the Japanese archipelago dates back to at least ~25,000 YBP and provides a scenario of virus co-migration with ancestral Japanese populations from continental Asia during the Upper Paleolithic period.

Genetic diversity in L1 ORF of human papillomavirus in women with cervical cancer with and without human immunodeficiency virus in Botswana and Kenya

BackgroundThe variation of human papillomavirus (HPV) genotypes shapes the risks of cervical cancer and these variations are not well defined in Africa. Nucleotide changes within the L1 gene, nucleotide variability, and phylogeny were explored in relation to HIV in samples from Botswana and Kenya.MethodsA total of 98 HPV-positive cervical samples were sequenced to identify different HPV variants. Phylogenetic inferences were used to determine HPV genotypes and investigate the clustering of sequences between women living with HIV (WLWHIV) and -women not living with HIV (WNLWHIV).ResultsOut of 98 generated sequences, 83.7% (82/98) participants had high-risk (HR) HPV genotypes while 16.3% (16/98) had low-risk (LR) HPV genotypes. Among participants with HR-HPV genotypes, 47.6% (39/82) were coinfected with HIV. The prevalence of HR-HPV genotypes was statistically higher in the Botswana population compared to Kenya (p-value < 0.001). Multiple amino acid mutations were identified in both countries. Genetic diversity differed considerably among WLWHIV and WNLWHIV. The mean pairwise distances between HPV-16 between HIV and HIV/HPV as well as for HPV-18 were statistically significant. Six (6) new deleterious mutations were identified in the HPV genotypes based on the sequencing of the L1 region, HPV-16 (L441P, S343P), HPV-18 (S424P), HPV-45 (Q366H, Y365F), and HPV-84 (F458L). The majority of the patients with these mutations were co-infected with HIV.ConclusionsGenomic diversity and different genomic variants of HPV sequences were demonstrated. Candidate novel mutations within the L1 gene were identified in both countries which can be further investigated using functional assays.

Genetic Diversity of HPV 16 and HPV 18 Based on Partial Long Control Region in Iranian Women.

Background Human papillomavirus (HPV) 16 and HPV 18 account for 75% of all cervical cancers. The L1 gene, encoding the major surface protein (MSP), is used to classify HPV types (lineages and sublineages), genotypes, and intratypic variants. Therefore, this study aimed to investigate the lineages, sublineages, genetic variabilities, and mutation effects on transcription factor binding sites by using partial sequences of the HPV 16 and HPV 18 long control regions (LCRs) in these samples. Materials and Methods After DNA isolation from 56 positive samples, the LCR of HPV 16 and HPV 18 were amplified using specific primers, and phylogenetic trees were drawn through MEGA X. Compared to the reference sequences, single nucleotide polymorphisms (SNPs) were identified. The transcription binding sites were also evaluated using the online PROMO database. Results The LCRs of 52 samples were successfully sequenced. Overall, 81.58% of all HPV 16 variants belonged to the D1 sublineage, followed by A4 (13.16%), A1 (2.63%), and C1 (2.63%) sublineages. All HPV 18 isolates belonged to A sublineage, 92.85% to A3 sublineage, and 7.15% to A4 sublineage. Out of 27 SNPs in the HPV 16 LCR, A7382T, T7384G, C7387T, C7393G, A7431G, T7448C, and C7783A were HPV 16-specific. Also, among 14 SNPs in the HPV 18 LCR, C7577A and A7943T were not previously reported. An insertion (C) between 7432 and 7433 positions was identified in all studied HPV 16 variants. Besides, most of the HPV 16 mutations were embedded in the YY1, TFIID, Oct-2, and NF-1 binding sites, while c-Fos and MBF1, as the most common binding sites, were affected by HPV 18 LCR mutations. Conclusion The present results showed that D1 and A3 were the dominant sublineages of HPV 16 and HPV 18, respectively. Therefore, women infected with these variants need to be examined in further longitudinal studies to obtain more information about the oncogenic potential of these dominant variants in Iran. Besides, YY1, TFIID, Oct-2, NF-1, c-Fos, and MBF1 were the most frequent binding sites, which were influenced by the mutations.

Identification of Genetic Variants of Human Papillomavirus in a Group of Mexican HIV/AIDS Patients and Their Possible Association with Cervical Cancer.

Infections caused by the human immunodeficiency virus (HIV) and human papillomavirus (HPV) cause thousands of deaths worldwide each year. So far, there has been no consensus on whether there is a direct relationship between the incidence of neoplasms and the immunosuppression caused by HIV that could help understand if coinfection increases the likelihood of cervical cancer. The objective of the study was to identify the presence of genetic variants of HPV in a group of HIV-positive women and their possible association with cervical cancer. Cervical samples were taken from HIV-positive patients for cytological analysis to identify the HPV genotype by polymerase chain reaction (PCR) and sequencing. The most prevalent L1 capsid protein mutations in the HPV genotype were analyzed in silico. Various types of HPV were identified, both high-risk (HR) and low-risk (LR). The most prevalent genotype was HPV51. Analysis of the L1 gene sequences of HPV51 isolates showed nucleotide variations. Of the samples analyzed in Puebla, Mexico, HPV51 had the highest incidence (17.5%, 7/40). Different mutations, which could be used as population markers, were detected in this area, and they have not been reported in the L1 databases for HPV51 in Mexico. Genotypes 6, 14, 86, 87, 89, and 91, not detected or reported in samples from patients with HPV in Mexico, were also identified. Data from the population analyzed suggest no direct relationship between HIV immunosuppression and cervical cancer, regardless of the high- or low-risk HPV genotype. Furthermore, it is possible to develop regional population markers for the detection of HPV based on the mutations that occur in the sequence of nucleotides analyzed.

Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures.

Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.

E6/E7 Variants of Human Papillomavirus 16 Associated with Cervical Carcinoma in Women in Southern Mexico.

Persistent infection with the human papillomavirus 16 (HPV 16) is the cause of half of all cervical carcinomas (CC) cases. Moreover, mutations in the oncoproteins E6 and E7 are associated with CC development. In this study, E6/E7 variants circulating in southern Mexico and their association with CC and its precursor lesions were evaluated. In total, 190 DNA samples were obtained from scrapes and cervical biopsies of women with HPV 16 out of which 61 are from patients with CC, 6 from patients with high-grade squamous intraepithelial lesions (HSIL), 68 from patients with low-grade squamous intraepithelial lesions (LSIL), and 55 from patients without intraepithelial lesions. For all E7 variants found, the E7-C732/C789/G795 variant (with three silent mutations) was associated with the highest risk of CC (odd ratio (OR) = 3.79, 95% confidence interval (CI) = 1.46–9.85). The analysis of E6/E7 bicistron conferred to AA-a*E7-C732/C789/G795 variants revealed the greatest increased risk of CC (OR = 110, 95% CI = 6.04–2001.3), followed by AA-c*E7-C732/C789/G795 and A176/G350*E7-p. These results highlight the importance of analyzing the combinations of E6/E7 variants in HPV 16 infection and suggest that AA-a*E7-C732/C789/G795, AA-c*E7-C732/C789/G795, and A176/G350*E7-p can be useful markers for predicting CC development.

Laboratorio molecular en virus del papiloma humano (VPH) y cáncer

No hace muchos años la aproximación hacia las neoplasias malignas en seres humanos tenía un enfoque diagnóstico principalmente basado en los hallazgos morfológicos, y aunque teníamos conocimiento de la oncogénesis por virus desde hace casi medio siglo, este conocimiento no se había logrado integrar al diagnóstico, prevención y manejo oncológico [1]. En la década de los cincuenta, el entendimiento de la historia natural del cáncer de cuello uterino, con tiempos largos de evolución, permitió la implementación de protocolos de tamización, que hasta hace menos de una década, estaban basados en citologías cervicovaginales seriadas y regulares [2,3], sin mucho protagonismo en los algoritmos diagnósticos de la detección de variantes de alto riesgo del virus del papiloma humano (VPHAR) [4]. A pesar de que las pruebas moleculares se encuentran aprobadas para uso clínico desde aproximadamente el año 2001 [5], solo hasta el 2014 en paísescomo Estados Unidos, se incorporó la detección de genotipos de VPH-AR como prueba de tamización principal, que determina la necesidad de estudios adicionales para la detección temprana del cáncer cervicouterino [6].