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Scientific Reports Aug 2022The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve...
The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.
Topics: Alphapapillomavirus; Genotype; Humans; Papillomaviridae; Papillomavirus Infections; Real-Time Polymerase Chain Reaction
PubMed: 35977949
DOI: 10.1038/s41598-022-14730-9 -
Viruses Sep 2021HPV-related head and neck squamous cell carcinoma (HNSCC) has emerged as a diverse clinical and biological disease entity, mainly in young patients with oropharyngeal... (Review)
Review
HPV-related head and neck squamous cell carcinoma (HNSCC) has emerged as a diverse clinical and biological disease entity, mainly in young patients with oropharyngeal tumors who are nonsmokers and nondrinkers. Indeed, during the past few years, the pendulum has shifted towards a new epidemiological reality, the "HPV pandemic", where the majority of oropharyngeal squamous cell carcinomas (OPSCCs) are attributed to HPV. The oncogenic potential of the virus is associated to its capacity of integrating oncogenes and into the host cell, leading to the inactivation of several tumor suppressor genes, such as Rb. HPV status can affect prognosis in OPSCC, but its role as a predictive biomarker remains to be elucidated. Given the favorable prognosis associated with HPV-positive disease, the concept of de-escalation treatment strategies has been developed with the primary intent being the reduction of treatment-related long-term toxicities. In this review, we aim to depict current data regarding treatment de-escalation in HPV-associated OPSCC and discuss ongoing clinical trials.
Topics: Carcinoma, Squamous Cell; Head and Neck Neoplasms; Humans; Oncogenes; Oropharyngeal Neoplasms; Papillomaviridae; Papillomavirus E7 Proteins; Papillomavirus Infections; Prognosis; Repressor Proteins; Squamous Cell Carcinoma of Head and Neck
PubMed: 34578368
DOI: 10.3390/v13091787 -
Journal of Clinical Virology : the... Apr 2018Accurate and internationally comparable human papillomavirus (HPV) DNA detection and typing services are essential for HPV vaccine research and surveillance.
BACKGROUND
Accurate and internationally comparable human papillomavirus (HPV) DNA detection and typing services are essential for HPV vaccine research and surveillance.
OBJECTIVES
This study assessed the proficiency of different HPV typing services offered routinely in laboratories worldwide.
STUDY DESIGN
The HPV Laboratory Network (LabNet) has designed international proficiency panels that can be regularly issued. The HPV genotyping proficiency panels of 2013 and 2014 contained 43 and 41 coded samples, respectively, composed of purified plasmids of sixteen HPV types (HPV 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68a and 68b) and 3 extraction controls. Proficient typing was defined as detection in both single and multiple infections of 50 International Units of HPV 16 and HPV 18 and 500 genome equivalents for the other 14 HPV types, with at least 97% specificity.
RESULTS
Ninety-six laboratories submitted 136 datasets in 2013 and 121 laboratories submitted 148 datasets in 2014. Thirty-four different HPV genotyping assays were used, notably Linear Array, HPV Direct Flow-chip, GenoFlow HPV array, Anyplex HPV 28, Inno-LiPa, and PGMY-CHUV assays. A trend towards increased sensitivity and specificity was observed. In 2013, 59 data sets (44%) were 100% proficient compared to 86 data sets (59%) in 2014. This is a definite improvement compared to the first proficiency panel, issued in 2008, when only 19 data sets (26%) were fully proficient.
CONCLUSION
The regularly issued global proficiency program has documented an ongoing worldwide improvement in comparability and reliability of HPV genotyping services.
Topics: Female; Genotyping Techniques; Global Health; Health Services Research; Humans; International Cooperation; Laboratories; Laboratory Proficiency Testing; Papillomaviridae; Papillomavirus Infections; Sensitivity and Specificity; Virology
PubMed: 29433017
DOI: 10.1016/j.jcv.2018.01.016 -
Viruses Apr 2024A massive mortality event concerning farmed Chinese tongue soles occurred in Tianjin, China, and the causative agent remains unknown. Here, a novel papillomavirus...
A massive mortality event concerning farmed Chinese tongue soles occurred in Tianjin, China, and the causative agent remains unknown. Here, a novel papillomavirus (CsPaV) and parvovirus (CsPV) were simultaneously isolated and identified from diseased fish via electron microscopy, virus isolation, genome sequencing, experimental challenges, and fluorescence in situ hybridization (FISH). Electron microscopy showed large numbers of virus particles present in the tissues of diseased fish. Viruses that were isolated and propagated in flounder gill cells (FG) induced typical cytopathic effects (CPE). The cumulative mortality of fish given intraperitoneal injections reached 100% at 7 dpi. The complete genomes of CsPaV and CsPV comprised 5939 bp and 3663 bp, respectively, and the genomes shared no nucleotide sequence similarities with other viruses. Phylogenetic analysis based on the L1 and NS1 protein sequences revealed that CsPaV and CsPV were novel members of the Papillomaviridae and Parvoviridae families. The FISH results showed positive signals in the spleen tissues of infected fish, and both viruses could co-infect single cells. This study represents the first report where novel papillomavirus and parvovirus are identified in farmed marine cultured fish, and it provides a basis for further studies on the prevention and treatment of emerging viral diseases.
Topics: Animals; Fish Diseases; China; Phylogeny; Flatfishes; Parvoviridae Infections; Parvovirus; Genome, Viral; Papillomaviridae; Papillomavirus Infections; In Situ Hybridization, Fluorescence
PubMed: 38793587
DOI: 10.3390/v16050705 -
Virology Jun 2018The International Human Papillomavirus (HPV) Reference Center supports quality and order in HPV research and diagnostics. Notably, the center assigns HPV type numbers to...
The International Human Papillomavirus (HPV) Reference Center supports quality and order in HPV research and diagnostics. Notably, the center assigns HPV type numbers to novel HPV types, maintains a reference clone repository, and issues international proficiency panels for HPV genotyping. The established HPV types, currently up to HPV225, belong to 5 different genera: alpha (65 types), beta (54 types), gamma (98 types), mu (3 types) and nu (1 type). Since 2014, 23 novel types have been established, 82.6% of which belong to the gamma genus. Reference clones have been provided to 44 different research laboratories and the global proficiency program for HPV genotyping has seen an increasing participation (currently 146 laboratories) and complete proficiency has increased over time (from 26% to 59% of datasets). In summary, an increasing complexity of the HPVs requires international efforts to support a recognized quality and order among HPV types.
Topics: Biological Specimen Banks; Biomedical Research; Genotype; Humans; Internationality; Papillomaviridae; Papillomavirus Infections; Virology
PubMed: 29679790
DOI: 10.1016/j.virol.2018.04.003 -
Journal of Applied Microbiology Oct 2019The diversity and the geographical distribution of swine papillomaviruses (PVs) are virtually unknown. The occurrence and the diversity of swine PV were therefore...
AIMS
The diversity and the geographical distribution of swine papillomaviruses (PVs) are virtually unknown. The occurrence and the diversity of swine PV were therefore investigated in pig slurry collected in Italy, to contribute towards filling this gap in knowledge.
METHODS AND RESULTS
Twenty-two slurry samples underwent analysis by nested PCR and DNA sequencing using published and newly designed specific primer pairs for Sus scrofa papillomavirus (SsPV) type 1 and 2 (SsPV1 and 2), along with degenerate PV-specific primers targeting the major coat protein L1 and the helicase protein E1. Overall, three samples (13·6%) were positive for SsPV1 by specific primers, and nucleotide (nt) sequences showed 99-100% nt identity with SsPV1 variant a (EF395818), while SsPV2 was not found in any sample. Using generic primers, eight samples (36·4%) were tested positive for human papillomavirus (HPV), and were characterized as follows: β1-HPV8, β1-HPV14, β1-HPV206, β2-HPV113, β2-HPV120 and γ1-HPV173. Moreover, one unclassified γ-type was detected.
CONCLUSIONS
Both swine and human PVs were detected in pig slurry in this study. The unexpected presence of HPV in pig waste could be explained as the result of an improper use of the sewage collection pits and/or with improper procedures of the operators.
SIGNIFICANCE AND IMPACT OF THE STUDY
This study reports the first detection of SsPV1 in Italy, along with the first detection of HPVs in pig slurry samples in Italy, and expands our knowledge about PV diversity and geographic distribution.
Topics: Animals; DNA, Viral; Humans; Italy; Manure; Papillomaviridae; Papillomavirus Infections; Polymerase Chain Reaction; Sequence Analysis, DNA; Swine
PubMed: 31251456
DOI: 10.1111/jam.14363 -
Epidemiology and Infection Aug 2014A series of observational studies were evaluated concerning the risk of human papillomavirus (HPV) infection in pregnancy; however, the results were controversial. We... (Meta-Analysis)
Meta-Analysis Review
A series of observational studies were evaluated concerning the risk of human papillomavirus (HPV) infection in pregnancy; however, the results were controversial. We systematically reviewed and collected data on studies regarding HPV prevalence published up to 30 April 2013, in which HPV was detected in pregnant women or both in pregnant and non-pregnant women. In total, 28 eligible studies were included that provided data on HPV infection concerning 13 640 pregnant women. The overall HPV prevalence in pregnant and age-matched non-pregnant women was 16·82% [95% confidence interval (CI) 16·21-17·47] and 12·25% (95% CI 11·50-13·01), respectively. The prevalence in the in three trimesters was 18·20%, 14·38%, and 19·32%, respectively. HPV-16 was the most frequently observed type, with a prevalence of 3·86% (95% CI 3·40-4·32). The overall HPV prevalence varied by study region, age, and HPV type. The meta-analysis showed a significantly increased risk of HPV infection in pregnant women, with a summary odds ratio (OR) of 1·42 (95% CI 1·25-1·61), especially for those aged <25 years (OR 1·79, 95% CI 1·22-2·63). The results suggest that pregnant women, especially those aged <25 years, are more susceptible to HPV infection.
Topics: Female; Genotype; Humans; Papillomaviridae; Papillomavirus Infections; Pregnancy; Pregnancy Complications, Infectious; Prevalence; Risk Assessment
PubMed: 24667102
DOI: 10.1017/S0950268814000636 -
Viruses Jul 2023Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding...
Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.
Topics: Phylogeny; Papillomaviridae; Alphapapillomavirus; Genetic Drift; Codon Usage
PubMed: 37631973
DOI: 10.3390/v15081631 -
Head & Neck Aug 2020Human papillomavirus (HPV) in oropharyngeal squamous cell carcinoma (SCC) is a well-known cause and prognostic indicator, and the utility of p16 as a surrogate marker...
Human papillomavirus (HPV) in oropharyngeal squamous cell carcinoma (SCC) is a well-known cause and prognostic indicator, and the utility of p16 as a surrogate marker for HPV status has been established. P16 and its relationship with HPV have not been defined in sinonasal malignancy nor has a link with outcomes been established. Patients with sinonasal SCC from 2011 to 2017 were identified from our pathology database. P16 immunohistochemistry and HPV RNA in situ hybridization were performed on tissue specimens. Forty-seven patients were included. Disease-free survival for p16+ patients was significantly higher than p16- patients (P = .043). Fewer HPV+ patients died (P = .052) or experienced recurrence (P = .0437). Odds ratio between p16 and HPV status was 14.19 (95% CI: 1.72, 442.03). Our findings demonstrate improved survival in both the p16+ and HPV+ groups and a positive association between p16 and HPV. There may be similar potential for modifying classification for HPV+ sinonasal SCC.
Topics: Alphapapillomavirus; Carcinoma, Squamous Cell; Cyclin-Dependent Kinase Inhibitor p16; Humans; Neoplasm Recurrence, Local; Papillomaviridae; Papillomavirus Infections
PubMed: 32149447
DOI: 10.1002/hed.26134 -
Journal of Medical Virology Jan 2018To describe the prevalence of human papillomavirus (HPV) and its genotype distribution among females in the suburb of Shanghai. A total of 33 562 participants were...
To describe the prevalence of human papillomavirus (HPV) and its genotype distribution among females in the suburb of Shanghai. A total of 33 562 participants were enrolled in this study from January to December 2016. HPV GenoArray test kit was used to perform HPV genotyping and was also used in DNA amplification and HybriBio's proprietary flow-through hybridization technique. The overall prevalence of HPV was 18.98% and the top ten genotypes of HPV infection were HPV 16 (3.36%), HPV 58 (2.65%), HPV 52 (2.48%), HPV 51 (1.58%), HPV 54 (1.40%), HPV 68 (1.32%), HPV 18 (1.23%), HPV 6 (1.15%), HPV 56 (1.10%), and HPV 33 (1.07%). Single infection (4749, 14.15%) was the most common types among all the infected cases. Significant differences were found among age groups and month groups in terms of simple and multiple infection (P < 0.05), pure HR, LR and mixed HPV infection (P < 0.05). The prevalence of HR and LR HPV infection among females in the suburb of Shanghai is high, prevalence of single and multiple infection, pure HR, LR and mixed infection is correlated with the age and month.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Cervix Uteri; Child; China; Coinfection; DNA, Viral; Female; Genotype; Genotyping Techniques; Human papillomavirus 16; Human papillomavirus 18; Humans; Middle Aged; Nucleic Acid Hybridization; Papillomaviridae; Papillomavirus Infections; Prevalence; Young Adult
PubMed: 28700089
DOI: 10.1002/jmv.24899