Genetic diversity and phylogenetic analysis of HPV 16 & 18 variants isolated from cervical specimens of women in Saudi Arabia

Genetic variability of human papillomavirus type 18 based on E6, E7 and L1 genes in central China

BACKGROUND

High-risk human papillomavirus (HR-HPV) infection is an important factor for the development of cervical cancer. HPV18 is the second most common HR-HPV after HPV16.

METHODS

In this study, MEGA11 software was used to analyze the variation and phylogenetic tree of HPV18 E6-E7 and L1 genes. The selective pressure to E6, E7 and L1 genes was estimated using pamlX. In addition, the B cell epitopes of L1 amino acid sequences and T cell epitopes of E6-E7 amino acid sequences in HPV18 were predicted by ABCpred server and IEDB website, respectively.

RESULTS

A total of 9 single nucleotide variants were found in E6-E7 sequences, of which 2 were nonsynonymous variants and 7 were synonymous variants. Twenty single nucleotide variants were identified in L1 sequence, including 11 nonsynonymous variants and 9 synonymous variants. Phylogenetic analysis showed that E6-E7 and L1 sequences were all distributed in A lineage. In HPV18 E6, E7 and L1 sequences, no positively selected site was found. The nonconservative substitution R545C in L1 affected hypothetical B cell epitope. Two nonconservative substitutions, S82A in E6, and R53Q in E7, impacted multiple hypothetical T cell epitopes.

CONCLUSION

The sequence variation data of HPV18 may lay a foundation for the virus diagnosis, further study of cervical cancer and vaccine design in central China.

Distribution of human papillomavirus among Vietnamese women with cervical cancer and unusual genetic variability of HPV16

HPV16, with typical mutations that differ in geographical distribution and carcinogenic potency, has implications for cervical cancer screening, clinical diagnosis, and treatment. DNASTAR and MEGA were used to identify HPV16 variants and construct a phylogenetic tree. The most prevalent HPV genotypes were HPV16 (63.9%), HPV18 (26.7%), and other HPV (6.9%). HPV16 alterations were found in all E6, E7, and L1 genes, including 15 missense and 18 synonymous mutations. Missense mutations include R10G, Q14H, D25E, H78Y, L83V (E6); M29V, R35K, L78R, L95P (E7); H73Y, T176 N, N178T, T317P, T386S, L472F/I (L1). HPV16 sublineages include A1 (17.2%), A2 (0.9%), A3 (56.0%), A4 (19.0%), D1 (4.3%), and D3 (2.6%). Although several mutations in the oncoproteins E6, E7, and L1 have been detected, mutations known to be associated with cervical cancer risk, such as D25E and L83V, occur at a relatively low frequency. This suggests that HPV16 mutations are associated with cervical cancer through a complicated mechanism.

Type distribution of human papillomaviruses in ThinPrep cytology samples and HPV16/18 E6 gene variations in FFPE cervical cancer specimens in Fars province, Iran

BACKGROUND

There exists strong evidence that human papillomavirus (HPV) is associated with cervical cancer (CC). HPV E6 is a major oncogene whose sequence variations may be associated with the development of CC. There is not sufficient data on the distribution of HPV types in ThinPrep cytology specimens and HPV 16/18 E6 gene variations among CC patients in the southwest of Iran. This study was conducted to contribute to HPV screening and vaccination in Iran.

METHODS

A total of 648 women screened for cervicitis, intraepithelial neoplasia or CC were included in the study. All participants underwent ThinPrep cytology testing, single-step HPV DNA detection and allele-specific reverse hybridization assays. Moreover, a total of 96 specimens previously tested positive for single infection with HPV16 or 18 were included for variant analysis. HPV16/18 lineages and sublineages were determined by PCR assays followed by sequencing the E6 gene and the construction of neighbor-joining phylogenetic trees.

RESULTS

Overall, HPV DNA was detected in 62.19% of all the screened subjects. The detection rates of HPV DNA among individuals with normal, ASC-US, ASC-H, LSIL, and HSIL cervical cytology were 48.9%, 93.6%, 100%, 100%, and 100%, respectively. Low-risk HPVs were detected more frequently (46.9%) than high-risk (38.9%) and possible high-risk types (11.1%). Of 403 HPV-positive subjects, 172 (42.7%) had single HPV infections while the remaining 231 (57.3%) were infected with multiple types of HPV. Our results indicated a remarkable growth of high-risk HPV66 and 68 and low-risk HPV81 which have rarely been reported in Iran and HPV90 and 87 that are reported for the first time in the country. In addition, 3 lineages (A, D, and C) and 6 sublineages (A1, A2, A4, C1, D1, and D2) of HPV16, and one lineage and 4 sublineages (A1, A3, A4, and A5) of HPV18 were identified. The studied HPV16 and 18 variants mainly belonged to the D1 and A4 sublineages, respectively.

CONCLUSION

The present study suggests that the prevalence of HPV infection in women of all age groups with or without premalignant lesions in the southwestern Iran is high and the predominant HPV types in the southwest of Iran may differ from those detected in other parts of the country. This study also highlights the necessity of not only initiating HPV vaccination for the general population but also developing new vaccines that confer immunity against the prevalent HPV types in the area and national cervical screening programs using a combination of thinPrep cytology test and HPV detection assays in order to improve the accuracy of the screening.

Genotypic distribution of human papillomavirus and phylogenetic analysis of E6 and E7 gene of HR-HPV variants isolated from Pakistani population

High-risk-human papillomavirus (HR-HPV)-induced cervical cancer is the second most common cause of death among females worldwide. HPV16 is the most prevalent HR-HPV infection worldwide. This study found the genotypic distribution of HR-HPV in the local population and investigated the sequence variations among the E6 and E7 oncogenes of the local HPV16 genotype to the E6 and E7 oncogenes of the foreign HPV16 genotypes and constructed a phylogenetic relationship based on nucleotide sequence comparison among the variants identified in our study along with previously reported isolates that were obtained from different regions of the world. The samples were collected from patients with cervical cancer. Genomic DNA was extracted, and HR-HPV genotypes were determined using real-time PCR. The HPV16 E6 and E7 genes were amplified and sequenced. A HPV16 phylogenetic tree was constructed using the maximum likelihood method with MEGA 7. HPV16 was the most prevalent human papillomavirus (HPV) type identified in the present study. HPV16 isolates belonged to the A1 sublineage of the European branch. Twenty-one nucleotide sequences were included in this analysis. The first, second, and third codon positions are also included. The final dataset included 776 positions.

Genetic Variability in the E6, E7, and L1 Genes of Human Papillomavirus Types 16 and 18 among Women in Saudi Arabia

Cervical cancer is the eighth most frequent cancer in Saudi Arabia, and most cases are associated with human papillomavirus (HPV) types 16 and 18. HPV-induced carcinogenesis may be associated with the intra-type variant, genetic mutation, or the continuous expression of viral oncogenes E6 and E7. Infection efficiency and virus antigenicity may be affected by changes in the L1 gene. Thus, this retrospective cohort study analyzed E6, E7, and L1 gene mutations in cervical specimens collected from Saudi women positive for HPV16 or HPV18 infection. HPV16 and HPV18 lineages in these specimens were predominantly from Europe. The L83V mutation in the E6 gene of HPV16 showed sufficient oncogenic potential for progression to cervical cancer. By contrast, the L28F mutation in the E7 gene of HPV16 was associated with a low risk of cervical cancer. Other specific HPV16 and HPV18 mutations were associated with an increased risk of cancer, cancer progression, viral load, and age. Four novel mutations, K53T, K53N, R365P, and K443N, were identified in the L1 gene of HPV16. These findings for HPV16 and HPV18 lineages and mutations in the E6, E7, and L1 genes among women in Saudi Arabia may inform the design and development of effective molecular diagnostic tests and vaccination strategies for the Saudi population.

Knowledge, attitudes, and perception toward human papillomavirus among health profession students: A cross-sectional study in King Saud Bin Abdulaziz University for Health Sciences

BACKGROUND

Human papillomavirus (HPV) infection is the major risk factor for cervical cancer (CC) in women of reproductive age. Despite advances in treatment and prevention of CC by HPV vaccination, very few women utilize them because of a lack of awareness about HPV.

MATERIALS AND METHODS

We conducted this cross-sectional study among Health Professions Students (HPS) at King Saud Bin Abdul Aziz University for Health Sciences, Jeddah. Data were collected using a predesigned and validated study questionnaire to assess the knowledge, attitude, and perception of HPS toward HPV.

RESULTS

A total of 580 HPS responded to the survey; 128 (22.1%) were male, while 452 (77.9%) were female with the mean age ± standard deviation 20.36 ± 1.74 years. There was no significant difference between males and females related to screening of HPV and CC (82.8%; 82.3%). A minority (30.3%) of participants thought that HPV infection leads to CC, while 38.3% did not know about it. Furthermore, knowledge about HPV screening and vaccination was poor.

CONCLUSIONS

Students from the college of medicine had more knowledge and awareness about HPV (34.9%, P < 0.001). Thus, it is important to implement effective education programs, curricular activities, and awareness campaigns for health professions to augment the learning process effectively.

Cervical Cancer and Human Papillomavirus Awareness among Women in Saudi Arabia

Background and Objectives: Cervical cancer (CC) is the eighth most common cancer among Saudi women of all ages. With limited national data, we aimed to evaluate the public awareness of cervical cancer, CC risk factors, HPV infection, and HPV vaccines in different regions of Saudi Arabia. Materials and Methods: This was a survey-based cross-sectional study that encompassed 564 Saudi women over a period of a month. A self-administrated questionnaire was distributed through different social media platforms. Results: The collected data included sociodemographic variables and questions assessing awareness of CC, and the attitudes toward CC screening and human papillomavirus (HPV) vaccination. Most respondents were aware of CC (84.0%), although their primary source of information was the internet. However, only 45 females (8.0%) had a history of cervical screening. Furthermore, most females did not know that HPV was transmitted sexually (78.9%), or that it caused genital warts (81.7%) and CC (81.9%). Regarding the HPV vaccine, 100 females (17.7%) had heard about it, but only 11 (2.0%) took the vaccine, although more than half of the respondents (54.1%) were willing to take the vaccine after being informed about it. Conclusions: We noticed a remarkable lack of awareness among the respondents regarding HPV's clinical implications; and the HPV vaccine, and its importance and availability. The main source of information for most of the Saudi women in this study was the internet, which may be an unreliable source, or provide misleading information that may delay screening or discourage vaccination. Thus, organized campaigns by the Ministry of Health or other health-advocating agencies, in addition to screening and vaccination programs, are strongly encouraged.

Fifteen new nucleotide substitutions in variants of human papillomavirus 18 in Korea : Korean HPV18 variants and clinical manifestation

High-risk human papillomavirus (HPV) infection is an essential factor for the development of cervical cancer. HPV18 is the second most common carcinogenic HPV type following HPV16, but the lineages of HPV18 have been less well studied than those of HPV 16. The purpose of this study was to analyze the nucleotide variants in the E6, E7, and L1 genes of HPV18, to assess the prevalence of HPV18 variants in Korea and to explore the relationship between HPV18 genetic variants and the risk for cervical cancer.

A total of 170 DNA samples from HPV18-positive cervical specimens were collected from women admitted to a secondary referral hospital located in Seoul. Among them, the lineages of the 97 samples could be successfully determined by historical nomenclature.

All the studied HPV 18 variants were lineage A. Sublineages A1 and A4 comprised 91.7% (89/97) and 1.0% (1/97), respectively. Sublineages other than A1 or A4 comprised 7.2% (7/97). We identified 15 new nucleotide substitutions among 44 nucleotide substitutions: C158T, T317G, T443G, A560G, A5467G, A5560C, A5678C, A6155G, G6462A, T6650G, G6701A, T6809C, A6823G, T6941C and T6953C. Among them, 6 substitutions at positions 317, 443, 5467, 5560, 6462, and 6823 resulted in amino acid changes (E6: F71L and N113K; L1: H13R, H44P, A345T, and N465S, respectively). The pathologic results were classified as normal in 25.8% (25/97) of the women, atypical squamous cells of undermined significance (ASCUS) in 7.2% (7/97), cervical intraepithelial neoplasia (CIN) 1 in 36.1% (35/97), CIN2/3 in 19.6% (18/97), and carcinoma in 12.4% (12/97). There was no significant association between the HPV18 sublineages and the severity of pathologic lesion or the disease progression.

This study is the first to analyze the distribution of HPV18 variants in Korean and to associate the results with pathologic findings. Although the HPV18 variants had no significant effect on the degree and progression of the disease, the newly discovered nonsynonymous mutation in L1 might serve as a database to determine vaccine efficacy in Korean women.

Human papillomavirus: present and future perspective in Saudi Arabia

Human papillomavirus (HPV) is a widely dispersed DNA double-stranded carcinogenic virus worldwide. Many cancers have been attributed to HPV subtypes as a major aetiological factor. Around 90% of cervical cancers have been attributed to the HPV infection, in addition to other cancers such as head and neck cancer, breast cancer and other cancers. As the carcinogenic high risk and low-risk, HPV subtypes are sexually transmitted viruses, and the Saudi community is religiously conservative, lots of measures of the precise burden of the HPV and its related cancers are still obscure. With the absence of cervical-screening programmes and in-depth research in HPV-related cancers, there a lack of literature except for literature pertained to awareness and perceptions. Consequently, the present review is deemed to explore the present state of the HPV-related issues, the future perspective in light of the current scientific evidence, as well as, Saudi community practices, and health policies in this regard. Making accessible data on HPV-related cancers can assist in designing HPV-related early detection and control sustainable programmes. Therefore, this review aimed to discuss the most important magnitudes related to the HPV, concerning the available literature from Saudi Arabia and the data in the neighbouring Arab countries interrelated to Saudi Arabia. The review depended on searching Electronic databases using strongly considered indexes including PubMed, Medline, Web of Science, Scopus, ABSCO, EMBASE, and others. In conclusion, though Saudi Arabia is pronounced as a conservative community with low sexual transmitted diseases, there is an alarming menace of HPV-attributable diseases necessitating a quick intervention.

Saudi Women's Knowledge and Attitude toward Cervical Cancer Screening, Treatment, and Prevention: A Cross-Sectional Study in Qassim Region (2018-2019)

Background:

Cervical cancer is a preventable and curable disease if early diagnosed; however, most of the cases present late; hence, there is a need to raise the awareness about cervical cancer and to establish screening programs. We aimed to assess the knowledge and attitudes toward screening and to determine the current status of awareness among women.

Methods:

We conducted a cross-sectional study among 2,220 Saudi women in the Qassim region using a validated questionnaire that gathers data on socio-demographics, knowledge and attitude domains.

Results:

Among the participants, 952 (42.9%) were between 31 and 45 years old; most were married and highly educated 1,754 (79%), and showed moderate knowledge about cervical cancer symptoms, prevention, and screening. The most reported symptom was non-cyclic bleeding by 511 (23%), while prolonged use of contraceptives 289 (13%) was the more selected risk factor by participants. We found that 1,881 (84.7%) of women had not undergone a Pap smear test, and 805 participants (42.8%) expressed their refusal to attend for it, citing various reasons; the most reported was that they do not know someone who tried pap smear. A significant negative correlation was found between the level of knowledge and acceptance to vaccinate daughters at school age against human papillomavirus.

Conclusion:

Saudi women in the Qassim region have moderate awareness of cervical cancer but negative attitudes toward screening. Awareness campaigns are needed to promote knowledge and improve pap smear attendance to eliminate negative perceptions and beliefs.