Protein sequence-based risk classification for human papillomaviruses

Human papillomaviruses (HPVs) are small DNA tumor viruses which infect epithelial tissues and induce hyperproliferative lesions. Infection by high-risk genital HPVs is associated with the development of anogenital cancers. Classification of risk types is important in understanding the mechanisms in infection and in developing novel instruments for medical examination such as DNA microarrays. The sequence-based classification methods are useful in classifying risk types by considering residues in conserved positions. In this paper, we present a machine learning approach to the classification of HPV risk types by using the protein sequences. Our approach is based on the hidden Markov model and the kernel method. The former searches informative subsequence positions and the latter computes efficiently to classify protein sequences. In the experiments, the classifier predicted four unknown HPV types exactly. An additional result shows that the kernel-based classifiers learned with more informative subsequences outperform the classifiers learned with the whole sequence or random subsequences.     

Human papillomavirus update with a particular focus on cervical disease

Human papillomavirus (HPV) is a common viral infection of squamous epithelial tissues, but its importance has only recently been recognised by the medical community. HPVs are now realised to consist of many genotypes and are associated with a diverse spectrum of clinical manifestations. Within the genital tract, some diseases have been recognised since antiquity; for example, genital warts which are caused by HPV types distinct from those causing genital cancer. However, others (such as cervical cancer), although recognised centuries ago as linked to sexual activity, have only been associated with oncogenic HPVs relatively recently, with the tools of molecular biology. We now understand that genital HPV infections are the most common sexually transmitted viral infections, are largely transient, asymptomatic and of no consequence. This virus manifests as more than just benign warts. Chronic carriage of with oncogenic genotypes (over years and in a minority of patients), together with other cofactors (host and/or exogenous) in complex pathways not totally understood, result in severe dysplasia or, ultimately, carcinogenesis. As it takes time for precursor lesions to develop and there are effective screening programmes for their detection and treatment, HPV-related neoplastic disease of the cervix is largely a preventable reproductive health issue of women. Yet, on a global scale, cervical cancer is the second most common cancer of women, with the majority of cases occurring in developing countries. Although HPV is noncultivatable by traditional diagnostic virological methods, successfully applied molecular biology techniques have underpinned development of vaccines which are now in phase II/III clinical trials. Successful vaccination ultimately has the greatest potential to impact upon the global burden of disease from genital HPV infection. However, the outcome from reduction in incidence of dysplasia and neoplasia will take years to eventuate; consequently, various cervical cancer prevention strategies still need to be endorsed and maintained in the meantime.     

Could human papillomaviruses be spread through blood?

The human papillomaviruses (HPVs) are epitheliotropic viruses that require the environment of a differentiating squamous epithelium for their life cycle. HPV infection through abrasion of the skin or sexual intercourse causes benign warts and sometimes cancer. HPV DNA detected in the blood has been interpreted as having originated from metastasized cancer cells. The present study examined HPV DNA in banked, frozen peripheral blood mononuclear cells (PBMCs) from 57 U.S. human immunodeficiency virus (HIV)-infected pediatric patients collected between 1987 and 1996 and in fresh PBMCs from 19 healthy blood donors collected in 2002 to 2003. Eight patients and three blood donors were positive mostly for two subgroups of the HPV type 16 genome. The HPV genome detected in all 11 PBMC samples existed as an episomal form, albeit at a low DNA copy number. Among the eight patients, seven acquired HIV from transfusion (three associated with hemophilia) and one acquired HIV through vertical transmission; this patient also had received a transfusion before sampling. Our data suggest that PBMCs may be HPV carriers and might spread the virus through blood.     

Trichomonas vaginalis: paradigm of a successful sexually transmitted organism

Trichomonas vaginalis (TV) is one of the most successful protozoan pathogens and one of the most common sexually transmitted organism in females, yet it is also one of the most poorly investigated. By producing a wide array of glycosidases and cysteine proteinase enzymes, the organism can easily adapt to the environment, harvesting host proteins and DNA for metabolism. With the ability to cause lesions, vaginitis and acute inflammatory disease of the genital mucosa, TV acts as a potential catalyst in the acquisition of secondary infections including human immunodeficiency virus (HIV) and human papillomavirus (HPV), the organism responsible for the pathogenesis of cervical cancer. Treatment of TV infection is relatively easy and could dramatically reduce the transmission of HIV in areas where TV is endemic.     

Management of genital herpes in HIV-infected patients

The management of genital herpes in patients infected with human immunodeficiency virus (HIV) differs from that in individuals with genital herpes because of the significant interaction between the two viruses involved. HIV-induced immunodeficiency increases the frequency and severity of recurrent anogenital herpes simplex virus (HSV) shedding and disease as well as the risk of developing drug-resistant HSV infection. HSV infection, in turn, increases HIV replication and the risk of HIV transmission. The advent of highly active antiretroviral therapy has facilitated therapy for genital herpes, but important unanswered questions remain about the optimal therapy of drug-sensitive and -resistant genital herpes and the role of antiherpes drugs in reducing HIV disease progression and the risk of HIV transmission.     

Prevalence and risk factors of the whole spectrum of sexually transmitted diseases in male incoming prisoners in France

Sexually transmitted diseases (STD) are a public health issue in prison. As inmates are eventually released, it is also a community concern. There are very few data on the entire spectrum of STDs, particularly condyloma among prisoners. To determine the prevalence of all STDs: infection with human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), herpes simplex virus (HSV), Chlamydia trachomatis, Neisseria gonorrhoea, syphilis, and condyloma among entering inmates. A cross-sectional study was conducted in France from November 2000 to June 2003. Male adults entering a prison remand center in Caen had a medical consultation and physical examination including external genital organs and perianal area for condyloma and herpes infection, a urethral swab for Chlamydia trachomatis and Neisseria gonorrhoea detection, and a blood sample for HBV, HCV, HIV, and syphilis serology. Five hundred and ninety-seven inmates agreed to participate in the study. Sixteen percent had at least one STD: 4.0% had condyloma, 4.0% chlamydia infection, and 4.9% were positive for HCV antibodies. Two had early syphilis and 1 had acute HBV, but no HIV infection, neither genital herpes nor gonorrhea. The analysis of the STD risk behaviors did not show any difference between the infected and uninfected participants, except that HCV-positive participants were more likely to be intravenous drug users. Results suggest that a systematic screening of all STDs should be at least proposed to every entering inmate since no demographic or sexual characteristics are consistently associated with STDs. L. Verneuil and J.-S. Vidal are equal contributors to this work.     

Human papillomavirus infection and cervical abnormalities in Nairobi, Kenya, an area with a high prevalence of human immunodeficiency virus infection

Human papillomavirus (HPV) infection and cervical abnormalities, and their association with human immunodeficiency virus (HIV) infection were studied in 488 women who visited a health center in Nairobi. PCR-based HPV and cervical cytology tests were carried out on all participants, and peripheral CD4+ T cells and plasma HIV RNA were quantitated in HIV positive women. HIV were positive in 32% (155/488) of the women; 77% of these were untreated, and the others had been treated with anti-retroviral drugs within 6 months. Cervical HPV infection was detected in 17% of HIV negative and 49% of HIV positive women. Low-grade squamous intraepithelial lesions were observed in 6.9% of HIV negative and 21% of HIV positive women, while high-grade squamous intraepithelial lesions and cancer were seen in 0.6% and 5.8%, respectively. Multivariate analysis revealed that HIV and HPV infections were associated with each other. Cervical lesions were significantly associated with high-risk HPVs and with HIV infection, depending on HPV infection. HPV infection increased in accordance with lower CD4+ T cell counts and higher HIV RNA levels, and high-grade lesions were strongly associated with high-risk HPV infection and low CD4+ T cell counts. Immunosuppression as a result of HIV infection appears to be important for malignant progression in the cervix. Nationwide prevention of HIV infection and cervical cancer screening are necessary for the health of women in this area. High-risk HPV infection and low CD4+ T cell counts are the risk factors for cervical cancer.     

International standard reagents for HPV detection

Human papillomavirus is the commonest genital viral infection in healthy sexually active subjects, and the presence of chronic or persistent HPV types in genital cells may constitute a prognostic marker of underlying, or predict future HPV-associated diseases. A variety of novel tests for detecting the presence of oncogenic HPV types in biological specimens have been reported. These are based on the various stages of infection and viral life cycle. HPV infects squamous epithelium with expression of various gene products intimately linked to epithelial cell differentiation. Hence, there are basically three classes of detectable markers directly derived from HPVs: molecular markers based on detection of nucleic acid sequences, serological markers based on detection of antibodies against viral proteins, and cellular markers based on detection of proteins expressed intracellularly, upon either infection or carcinogenesis. The nature of various assays and the development of international standard reagents for qualitative and quantitative assessment of assay performance are outlined. There is an increasing demand to develop standard tools to assess the quality of HPV detection systems, for regulatory and clinical management purposes. International standard reagents for HPV will help defining the analytical sensitivity and specificity of various detection methods, and will allow assuring that laboratory services used to evaluate disease burden, HPV vaccines, and cancer prevention strategies are accurate and comparable worldwide. The advancement of prophylactic vaccine candidates against HPV infections and related diseases stresses the increasing importance of HPV assays in monitoring the impact of HPV vaccination on disease burden.     

Malpighian epithelia and papillomavirus infections]

Human papillomaviruses (HPV) are a large group of DNA viruses, with over 60 types identified to date, which can cause the development of benign tumors in the skin and mucosal squamous epithelia. Most of these tumors regress spontaneously but some, especially in the mucosal membranes, become malignant. HPV types with a high risk for inducing malignancies (e.g. 16 and 18) are the subject of increasing interest. HPVs are both host-specific and tissue-specific: some types preferentially infect specific epithelia, giving rise to lesions with distinct topographic characteristics. HPVs are difficult to study because they do not replicate in available in vitro models. In vivo, HPVs replicate well in epithelial cells undergoing terminal differentiation, e.g. in keratinized cells. Some 40 different types have been reported in epidermal keratinocytes, the most common being types 1 and 2 which produce large amounts of viral antigens and viral particles. In contrast, HPVs replicate poorly in the weakly keratinized squamous epithelia which line the digestive, respiratory, and genital tracts. Junctional epithelia, e.g. on the uterine cervix, are especially prone to HPV infection. The most prevalent HPV types in benign genital lesions are types 6 and 11, whose characteristic features include extrachromosomal DNA and production of only small amounts of viral antigens. The profound nuclear and cytoplasmic changes induced by HPVs lead to the formation of ko?locytes which are found mainly in the granular layer of epithelia and have been especially well described in the uterine cervix and vagina. HPV epithelial tumors are squamous cell carcinomas that often harbor HPV types 16 and 18; this is especially true of cervical intraepithelial neoplasias.(ABSTRACT TRUNCATED AT 250 WORDS)     

Search for cellular partners of human papillomavirus type 16 E2 protein

Human papillomaviruses (HPVs) are small, double-stranded DNA viruses that infect cutaneous and mucosal epithelia. Type 16 (HPV16) displays tropism to genital epithelia, giving rise to genital warts and cervical intraepithelial neoplasia (CIN), which is a precursor lesion to invasive carcinoma of the cervix. The great majority of human cervical cancers contain integrated HPV DNA where the E2 gene is usually disrupted, suggesting that the loss of the E2 protein is an important step in HPV-induced carcinogenesis. The HPV16 E2 protein is a regulatory protein that seems to be essential for creating favourable conditions for establishment of infection and proper completion of the viral life cycle. Recently, diverse activities of the E2 proteins have been described, but the molecular basis of these processes has not beenfully elucidated. Using a yeast two-hybrid system, we have identified epithelial cellular proteins that bind to the E2 protein of HPV16.     

Basic concepts and practical applications of recombinant DNA techniques in detection of human papillomavirus (HPV) infection. Review article

Recent studies on the role of infectious agents in the pathogenesis of malignancy have demonstrated a strong association between HPV and several human benign and malignant epithelial neoplasms. There are 60 distinct types of HPV, of which HPV 16, 18, 31, 33, 35 and 39 have been associated with squamous cell neoplasia of the genital tract. Rapid progress in the field of recombinant DNA technology with the availability of specific probes has enabled the detection of HPV genomic sequences in characteristic HPV lesions. In addition, HPV sequences have been found in malignant squamous cell lesions, and even in normal tissues lacking the morphologic signs of HPV infection. Currently, hybridization analysis of the nucleic acid is the most reliable method for diagnosis of HPV infections, also permitting the genotyping of these viruses. A variety of hybridization procedures have been developed with different sensitivities and specificities. Despite the divergent technical modifications, however, all hybridization tests working according to the same basic principles. The double helix of DNA composed of two complementary polynucleotide chains can be opened by heating or by increasing pH. Cooling of the two strands allows reassociation. Labeled HPV DNA or RNA probe hybridizes with the complementary sequences allowing the detection of HPV sequences in the samples. Hybridization assays can be conducted under conditions in which virtually all HPVs will be detected, but not specifically typed (low stringency) or under conditions in which the type can be identified (high stringency). Widely divergent results have been reported both in prevalence of HPV infection and distribution of different HPV types in the genital tract. These discordant results have been explained on the basis of sampling effects, differences in histopathological diagnosis, geographical variations in HPV types and interlaboratory variation in HPV detection and typing techniques. In this review the various procedures for detecting HPV sequences by hybridization and related techniques are shortly described.     

Serologic investigations in a New York City cohort of parenteral drug users

Human immunodeficiency virus (HIV) infection continues to be a major health problem for society. Intravenous drug users are the second largest risk group for HIV infection. The disease primarily affects immunologic functioning. This study examined the inherent immunologic dysfunction by measuring the seroprevalence of infection against pathogens often associated with HIV infection. Additionally, chi square analysis was used to compare intravenous drug users with a non-drug-using control group to see if any difference existed in the prevalence of antinuclear antibody, rheumatoid factor, abnormal titer of antibody to Toxoplasma gondii, cytomegalovirus, and herpes simplex virus (types 1 and 2). The intravenous drug users had a significantly greater level of antibody titers for antinuclear antibody and Toxoplasma gondii than did controls. Abnormal serologic results were not significantly associated with HIV seropositivity. The findings of this study suggest that intravenous drug users experience a greater prevalence of alteration in serologic markers unrelated to HIV exposure.     

Detection of human papillomavirus type 16 DNA in consecutive genital samples does not always represent persistent infection as determined by molecular variant analysis

Persistent human papillomavirus (HPV) infection of the uterine cervix is a risk factor for progression to high-grade squamous intraepithelial lesions. Detection in consecutive genital samples of HPV-16 DNA, a frequently encountered HPV type, may represent persistent infection or reinfection. We undertook a study using PCR-single-strand conformation polymorphism (SSCP) analysis and sequencing of PCR products (PCR-sequencing) to determine if consecutive HPV-16-positive samples contained the same HPV-16 variant. Fifty women (36 human immunodeficiency virus [HIV] seropositive, 14 HIV seronegative) had at least two consecutive genital specimens obtained at 6-month intervals that contained HPV-16 DNA as determined by a consensus L1 PCR assay. A total of 144 samples were amplified with two primer pairs for SSCP analysis of the entire long control region. Fifteen different SSCP patterns were identified in our population, while 22 variants were identified by PCR-sequencing. The most frequent SSCP pattern was found in 75 (53%) samples from 27 (54%) women. The SSCP patterns obtained from consecutive specimens were identical for 46 (92%) of 50 women, suggesting persistent infection. Four women exhibited in consecutive specimens different HPV-16 SSCP patterns that were all confirmed by PCR-sequencing. The additional information on the nature of persistent infection provided by molecular variant analysis was useful for 6% of women, since three of the four women who did not have identical consecutive specimens would have been misclassified as having persistent HPV-16 infection on the basis of HPV typing.     

Macrophage-tropic HIV: critical for AIDS pathogenesis?

Human immunodeficiency virus (HIV) occurs as a number of genetic and biological variants. Of these, transmission of macrophage-tropic HIV variants appears to be favored, although most infected individuals also harbor T-cell-tropic cytopathic viruses and macrophage-tropic non-cytopathic viruses. Recent evidence regarding CD4⁺ T-cell depletion in vivo suggests that macrophage-tropic HIV isolates may be necessary and sufficient for the development of AIDS. This review summarizes the recent findings on macrophage-tropic viruses, and compares matched sets of experiments in HIV-infected humanized severe combined immunodeficiency (SCID) mice with a computer simulation of the lymph node microenvironment. This may help to understand why HIV infection of macrophages may have profound effects on the immune system.     

Postmodern cancer: the role of human immunodeficiency virus in uterine cervical cancer.

The association between cervical cancer and human papillomavirus (HPV) is well known, but its association with human immunodeficiency virus (HIV) is controversial. Coinfection with HPV and HIV is to be expected and recent epidemiological data from Africa show that cervical cancer is the most common AIDS defining neoplasm in women. Unlike other AIDS defining neoplasms, the occurrence of cervical cancer is not dependent on immune compromise. HIV alters the natural history of HPV infection, with decreased regression rates and more rapid progression to high grade and invasive lesions, which are refractory to treatment, requiring more stringent intervention and monitoring. The more aggressive behaviour is mirrored by a different molecular pathway. HIV associated cervical cancers are thought to progress through the microsatellite instability pathway, whereas HIV negative ones progress through loss of heterozygosity. Interaction is probably via viral proteins, with HIV proteins enhancing effectiveness of HPV proteins, and perhaps contributing to cell cycle disruption. Dysregulation of the cellular and humoral arms of the local and systemic immune systems may ensure disease progression. Furthermore, HPV infection may predispose to HIV infection and facilitate its progression.     

Presence of human papillomavirus and Epstein-Barr virus in the cervix of women infected with the human immunodeficiency virus

The presence of human papillomavirus (HPV) and Epstein-Barr virus (EBV) was sought in cervical scrapings from 110 human immunodeficiency virus (HIV)-infected women to evaluate the role of these viruses as risk factors for squamous intraepithelial lesions of the cervix. By using PCR, presence of HPV-DNA and EBV-DNA was found in 60.9% (67/110) and in 10% (11/110) of clinical samples, respectively. Identification of oncogenic group of HPV by hybrid capture (HC II, Murex-Digene) indicated the presence of low-risk HPV in 13 (19.4%) patients, high-risk HPV in 28 (41.8%), and both types of HPV in 26 (38.8%) patients. Squamous intraepithelial lesions were present in 59 cases, being low-grade (n = 52) and high-grade (n = 7) lesions. HPV was detected in 84.7% of patients with lesions, in association with low-grade (43/52) and high-grade lesions (7/7), and in 33% of patients without lesions. EBV-DNA was detected in 8 patients with low-grade lesions and in 3 patients without lesions. Concurrent genital HPV and EBV infection was observed in 9 cases. HPV was associated with detection of squamous intraepithelial lesions [OR = 3.55; 95% CI = (1.96; 6.48)]. No significant association was found between presence of EBV and detection of lesions, both in case of EBV infection alone [OR = 1.4; 95% CI = (0. 93; 2.12)] and in case of HPV/EBV combined infection [OR = 0.87; 95%CI = (0.54; 1.42)]. These data confirm the significant role of HPV as risk factor for squamous intraepithelial lesions and suggest that EBV could not be involved in the pathogenesis of the lesions that arise in the cervix of HIV-positive women.     

Human papillomavirus vaccines

A wealth of epidemiological and molecular evidence has led to the conclusion that virtually all cases of cervical cancer and its precursor intra-epithelial lesions are a result of infection with one or other of a subset of genital human papillomaviruses (HPVs) suggesting that prevention of infection by prophylactic vaccination would be an effective anti-cancer strategy. The papillomaviruses cannot be grown in large amounts in culture in vitro, but the ability to generate HPV virus like particles (VLPs) by the synthesis and self-assembly in vitro of the major virus capsid protein L1 provides for a potentially effective sub unit vaccine. HPV L1 VLP vaccines are immunogenic and have a good safety profile. Published data from proof of principle trials and preliminary reports from large Phase III efficacy trials suggest strongly that they will protect against persistent HPV infection and cervical intra epithelial neoplasia. However, the duration of protection provided by these vaccines is not known, the antibody responses induced are probably HPV type specific and immunisation should occur pre-exposure to the virus. Second generation vaccines could include an early antigen for protection post-exposure and alternative delivery systems may be needed for the developing world.     

Diagnosis of HIV infection and laboratory monitoring of its therapy.

BACKGROUND: Serological diagnosis of human immunodeficiency virus (HIV) infection became available in 1985, with the rapid increase in sensitivity and specificity of enzyme-linked immunosorbent assays (ELISAs) and the supplement tests. Molecular tests for detection of HIV in the diagnosis of HIV infection in special settings and monitoring of HIV-1 infection followed this. OBJECTIVE AND DESIGN: In this review it is intended to give a brief overview of the diagnosis and monitoring of HIV infection. Results and conclusion: Serological methods and molecular methods for the detection and quantitation of HIV are discussed.     

Comparison of papillomavirus and immunodeficiency virus evolutionary patterns in the context of a papillomavirus vaccine.

In contemplating a vaccine for human papillomaviruses (HPVs), it is important to consider the evolutionary context in which such a vaccine would be deployed. The human immunodeficiency virus, having been the subject of even more extensive study than HPV, shares certain salient features with regards to phylogenetic structure, and may serve as a model for contemplation of possible difficulties with HPV vaccination. However, there are also striking differences in the evolutionary potentials and histories of the viruses that permit an optimistic outlook for HPV. These similarities and differences, as well as their implications for vaccination studies, are reviewed.     

Neutrophil extracellular traps prevent HIV infection in the female genital tract

Women acquire human immunodeficiency virus (HIV) mainly through sexual intercourse. However, low transmission rates per sexual act indicate that local immune mechanisms contribute to HIV prevention. Neutrophils represent 10–20% of the genital immune cells in healthy women. Neutrophils mediate mucosal protection against bacterial and fungal pathogens through different mechanisms, including the release of neutrophil extracellular traps (NETs). NETs are DNA fragments associated with antimicrobial granular proteins. Despite neutrophil abundance and central contributions to innate immunity in the genital tract, their role in protection against HIV acquisition is unknown. We found that stimulation of human genital neutrophils with HIV viral-like particles (HIV-VLPs) induced NET release within minutes of viral exposure, through reactive oxygen species-independent mechanisms that resulted in immediate entrapment of HIV-VLPs. Incubation of infectious HIV with pre-formed genital NETs prevented infection of susceptible cells through irreversible viral inactivation. HIV inactivation by NETs from genital neutrophils could represent a previously unrecognized form of mucosal protection against HIV acquisition.