Archives of Virology

HPV genotypes in Africa: comprehensive analysis of genetic diversity and evolutionary dynamics

Human papillomavirus (HPV) is a widespread and diverse group of viruses that are responsible for various clinical conditions, including cervical cancer, one of the most common cancers among women worldwide. In Africa, the prevalence and distribution of HPV genotypes vary significantly across different regions. In this study, we analyzed the genetic diversity, geographical distribution, and evolutionary dynamics of HPV genotypes across various African countries to provide insights into the prevalence and transmission patterns of HPV. A total of 9203 genome sequences of HPV isolates from cervical samples from 21 African countries were obtained from the GenBank database. Of these, 184 were identified as unique sequences and were used for further analysis. Phylogenetic analysis demonstrated that the African HPV sequences share genetic ancestry with European sequences, whereas American isolates are less closely related. Migration analysis revealed a significant asymmetry in HPV flow, with migration rates from Africa to Europe consistently exceeding those in the opposite direction, suggesting that Africa is a major source of HPV genetic variants entering Europe. This interconnectedness underscores the intricate interplay of historical, regional, and cultural determinants that have collectively contributed to shaping the genomic landscape of African strains. The geographically variable HPV genotypes 35, 31, 16, 18, 58, 45, 7, and 66 are the most common in Africa. Algeria, Morocco, Rwanda, and Guinea have diverse genotypes, and the rates of infection are highest in the Republic of Congo and Chad.

High prevalence of human papillomavirus type 66 in low-grade cervical lesions of Mexican women

Our aim was to analyze the prevalence of high-risk human papillomavirus (HR-HPV) and its association with risk factors related to cervical lesions. We used 362 cervical samples from a transversal study to detect nineteen types from the high-risk HPV clade by highly sensitive PCR. Unexpectedly, we found a very high prevalence of HPV type 66 (32.8%), particularly in low-grade squamous intraepithelial lesions. A significant association of HPV66 with previously sexually transmitted disease was observed (p < 0.05). Our results strongly suggest that HPV66 might be indicative of cervical lesions that will not progress to cancer. HPV genotyping by methods that grouped type 66 with other HR-HPV clade types should be interpreted with caution.

Prevalence and genotype distribution of human papillomavirus in Zhengzhou, China, in 2016

In this study, the prevalence and genotype distribution of human papillomavirus (HPV) in 49,793 women aged 25-64 years were determined by fluorescent real-time polymerase chain reaction (PCR) assay. HPV was detected in 6,020 women, giving a prevalence of 12.09% (6020/49,793). Single and multiple infections accounted for 71.81% (4323/6020) and 28.19% (1697/6020) of total infections, respectively. The most commonly found genotypes were HPV52 (19.90%, 1198/6020) and HPV16 (19.17%, 1154/6020), followed by HPV58 (13.11%, 789/6020), HPV81 (10.10%, 608/6020) and HPV56 (9.00%, 542/6020). The prevalence of HPV increased with age and was highest in the 54- to 64-year-old age group. The genotypes covered by the nonavalent HPV vaccine accounted for 39.32% (2367/6020) and 22.81% (1373/6020) of the total monoinfections and polyinfections, respectively. This study indicates a high HPV infection rate in women in the city of Zhengzhou and a large percentage of women are infected with single or multiple high-risk HPV genotypes that cannot be prevented using the current nonavalent HPV vaccine. Vaccines incorporating more HPV genotypes and extended age coverage for the current nonavalent vaccine might be necessary to better prevent HPV-related cervical cancer.

Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C

Human papillomavirus 31 (HPV31) is the fourth most frequent high-risk HPV (HR-HPV) genotype identified in cervical cancer (CC) worldwide and in Mexico. It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 - C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. This is the first report on the whole-genome diversity of HPV31 in Mexico.

Different types of adjuvants in prophylactic and therapeutic human papillomavirus vaccines in laboratory animals: a systematic review

Human papillomavirus (HPV) causes cervical carcinoma, which and is the third most common cancer, accounting for 275,000 deaths annually worldwide. Adjuvants have a key role in promotion of vaccine efficacy; therefore, using prophylactic and therapeutic vaccines combined with adjuvant could be of great benefit in prevention and treatment of cervical cancer. There are different types of adjuvants, including MF59

Distribution of human papillomavirus genotypes in western China and their association with cervical cancer and precancerous lesions

The aim of this study was to describe the distribution of human papillomavirus (HPV) genotypes among cervical cancers and pre-cancers in Shaanxi province of western China. A total of 17,341 women who were screened for cervical cancer from January 2014 to December 2016, using HPV genotyping and ThinPrep cytologic test were included. The prevalence and attribution of HPV genotypes were stratified by cervical lesion and age group. Of the subjects, 26.3% were infected with HPV, 28.0% of whom had multiple infections. The crude HPV prevalence increased from atypical squamous cells of undetermined significance/low-grade squamous intraepithelial lesions (ASCUS/LSIL, 64.3%) to high-grade squamous intraepithelial lesions (HSIL, 79.8%) and to invasive cervical cancer (ICC, 89.7%, P < 0.001). The three most prevalent genotypes were HPV 16 (8.0%), 58 (4.2%), and 52 (4.0%), and HPV 16, 31 and 33 were positively correlated with increased severity of cervical lesions. Additionally, the divalent vaccine genotypes HPV 16 and 18 accounted for 68.2% of ICC cases. Although 78.5% of ICC and 60.3% of HSIL cases were attributed to 9-valent vaccine genotypes, the other genotypes not covered by any vaccine still resulted in increases in coverage, with 1.5% for ICC, 5.3% for HSIL, and 13.5% for ASCUS/LSIL. HPV prevalence in western China was consistent with other regions of China. Early vaccination with 9-valent HPV vaccine is recommended in this locality for females younger than 26 years with no prior infection, while divalent the vaccine is more appropriate for women between 26 and 45 years, considering the efficacy, safety and cost-effectiveness of vaccines.

Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses

Simple and standardized approaches for genome analysis of human papillomavirus (HPV) by next-generation sequencing are needed. The aim of the study was to develop a protocol for direct deep sequencing of high-risk (hr) HPV strains, based on the widely used commercial Hybrid Capture 2 (QIAGEN) test, without any additional probe design. This protocol was applied to 15 HPV-positive and two HPV-negative cervical samples or cell lines and validated at the genotype level by comparing the sequencing results to those obtained using a commercial genotyping kit. The performance of our protocol, presented in this proof-of-principle study, supports its use for accurate characterization of genetic variants of hrHPV.

Development of a simplified and cost-effective sample preparation method for genotyping of human papillomavirus by next-generation sequencing

High-risk human papillomavirus (HPV) infection is the most common cause of cervical cancer, but low-risk HPV strains can sometimes also be involved. Although HPV genotyping techniques used in clinical diagnosis cannot detect low-risk HPV, next-generation sequencing (NGS) can detect both types. However, DNA library preparation is complicated and expensive. The aim of this study was to develop a simplified, cost-effective sample preparation procedure for HPV genotyping based on next-generation sequencing (NGS). After DNA extraction, a first round of PCR was performed using modified MY09/11 primers specific for the L1 region of the HPV genome, followed by a second round of PCR to add the indexes and adaptors. Then, the DNA libraries were purified and quantified, and high-throughput sequencing was performed using an Illumina MiSeq platform. The sequencing reads were compared with reference sequences for HPV genotyping. The limit of detection for HPV amplification was 100 copies/µl. Analysis of the correlation of pathological cytology with the HPV genotype in individual clinical samples showed that HPV66 was the most common genotype found in the normal stage, whereas HPV16 was the main genotype found in low-grade squamous intraepithelial lesions, high-grade squamous intraepithelial lesions, and cervical cancer. This NGS method can detect and identify several HPV genotypes with 92% accuracy and 100% reproducibility, and it shows potential as a simplified and cost-effective technique for large-scale HPV genotyping in clinical samples.