Sequence variants of human papillomavirus type 16 from couples suggest sexual transmission with low infectivity and polyclonality in genital neoplasia

Exploring the roles of HPV16 variants in head and neck squamous cell carcinoma: current challenges and opportunities

The incidence of squamous cell carcinomas of the head and neck (HNSCC) is consistently increasing, in association with human papillomavirus (HPV) infection, especially HPV16. HPV variants show heterogeneity in the pathogenicity of cervical cancer, but little has been established about their relevance on HNSCC. This review addresses the distribution of HPV16 variants in HNSCC and their potential contribution to clinical practice. A search was performed in PubMed using the keywords HNSCC HPV16 variants. Sixty articles were identified between 2000 and 2020 and 9 articles were selected for a systematic analysis. Clinical cohorts comprised 4 to 253 patients aged between 17 and 91 years with confirmed HPV16-positive HNSCC. Samples were collected from fresh biopsies of the tumour, oral rinse or formol fixed/paraffin embedded tissue, from the oral cavity, oropharynx, hypopharynx, larynx and Waldeyer's tonsillar ring. HPV16 variants were identified using Sanger sequencing techniques. Seven studies addressed the HPV16 E6 gene, one studied E6 and E7, another studied L1 and one focused on the long control region. European variants represent 25-95%, Asian-American 5-57% and African 2-4% of the total isolates, suggesting a marked predominance of European strains. No correlations could be drawn with patient prognosis, partly because many studies relied on small patient cohorts. Additional studies are needed, particularly those employing next generation sequencing techniques (NGS), which will allow faster and accurate analysis of large numbers of samples.

Genetic variants of HPV-16 and their geographical and anatomical distribution in men: A systematic review with meta-analysis

BACKGROUND

The prevalence of Human Papillomavirus type 16 (HPV-16) variants in men and the association with tumor development has not been fully investigated. We estimated the prevalence of genital, anal, and oral HPV-16 infections in men through a systematic review and meta-analysis.

METHODS

Seven databases were searched and included studies that identified HPV-16 positive males, HPV-16 variants (lineages/sublineages), and indicated the sample's anatomical origin. This protocol is registered in PROSPERO (CRD42020178013).

RESULTS

The database searches yielded 14 studies including 445 HPV-16 positive samples classified as lineage A (n = 390), lineage D (n = 43), lineage B (n = 10), and lineage C (n = 2) variants. Lineage A variants predominated among the anatomical sites and the diverse geographical regions.

CONCLUSIONS

HPV-16 lineages vary according to anatomical and geographical region. According to this preliminary evaluation of the current literature, we hypothesize that, similar to women, specific HPV-16 variants may also be associated to increased cancer risk in men.

Human Papillomavirus Infection and Transmission Among Couples Through Heterosexual Activity (HITCH) Cohort Study: Protocol Describing Design, Methods, and Research Goals

BACKGROUND

Human papillomavirus (HPV) epidemiological research has generally been individual based, typically focusing on women, with couple-based research mostly consisting of cross-sectional assessment of prevalent HPV infection in both partners.

OBJECTIVE

The HPV Infection and Transmission among Couples through Heterosexual activity (HITCH) study was set up to investigate the transmissibility of HPV among young, recently formed couples in Montreal, Canada. This paper provides an overview of the HITCH cohort study design and procedures as well as a narrative summary of the most important findings.

METHODS

HITCH is a longitudinal investigation of HPV transmission in recently formed heterosexual partnerships initiated within 6-month pre-enrollment, a time at which considerable transmission is believed to occur. A total of 549 newly formed dyads were recruited (2005-2011) from postsecondary institutions, including 502 young women and their male partners. An additional 46 males were enrolled at follow-up, as some women enrolled a subsequent partner at follow-up. Women aged 18-24 years were followed for 24 months for acquisition of HPV types not present at enrollment, whereas men returned for a single follow-up visit at month 4, for a sum total of 3361 clinic visits. The last follow-up visit occurred in January 2014. Extensive sociodemographic, sexual behavioral, and medical history data were collected every 2-4 months using computer-assisted, self-administered questionnaires. Furthermore, participants provided genital, blood, oral, and hand specimens for HPV assessment.

RESULTS

Although in its early analysis stage, HITCH has produced important publications. Findings from HITCH have increased the available knowledge about the natural history of HPV transmission and its determinants, provided further evidence regarding oral-oral and oral-genital routes of HPV transmission, and supplied empirically valid epidemiological parameters of HPV transmission to assist mathematical modelers in health economic assessments. In addition, HITCH data were made available to several multistudy collaborations evaluating new HPV detection assays and evidence for-or-against HPV type replacement following the introduction of HPV vaccination.

CONCLUSIONS

HITCH will continue to offer a unique resource for research on HPV transmission.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR1-10.2196/11284.

E6 molecular variants of human papillomavirus (HPV) type 16: an updated and unified criterion for clustering and nomenclature

Reports on taxonomic identification of E6/HPV 16 variants, don't have a worldwide, updated and unified criterion for clustering and nomenclature. Our aim was to update the existing criterion and propose a new one for clustering and nomenclature for E6/HPV 16 molecular variants based on the descriptive and comparative analyses of nucleotide sequences. A systematic search of the publications between 1991 and 2010 was carried out in PUBMED and manually. 240 E6/HPV 16 variants were identified. 157 were classified as European (E), 24 as Asian (As), 14 as Asian American (AA), 11 as North American 1 (NA 1), 19 as African 1 (Af 1) and 15 as African 2 (Af 2). Three classes were determined for the E, 3 each for the As, Af 2 and AA branches, 4 classes for the NA 1 and 6 for the Af 1 branch. This study reports our results and proposes an updated criterion for clustering and nomenclature that will be useful for E6 variant identification.

Meta-analysis of human papillomavirus infection concordance

BACKGROUND

Estimates of human papillomavirus (HPV) concordance among sexual partners are important for various public health activities, from counseling individual patients to predicting the effect of HPV vaccination.

METHODS

We systematically searched the PubMed and EMBASE databases for studies of HPV concordance among heterosexual couples published through 2008 in English. Two coders independently abstracted data using standardized forms. We integrated concordance data using random-effects meta-analysis.

RESULTS

Thirty studies (33 study populations) that met inclusion criteria reported concordance data for 2,972 couples. Most studies were cross-sectional cohort studies conducted in Europe or Asia that used DNA hybridization to test for HPV, sometimes in conjunction with PCR. Overall, 25.5% (95% confidence interval, 17.2-36.1%) of couples were infected with 1 or more of the same HPV types. Among couples with both members HPV-positive, 63.2% (95% confidence interval, 49.1-75.3%) were infected with 1 or more of the same viral types. Positive concordance was higher for female partners of men with HPV infections than for male partners of women with HPV infections. Positive concordance was also higher for studies using PCR and for the few studies that recruited men with HPV-related disease.

CONCLUSIONS

Sexual partners of HPV-infected individuals had high rates of HPV infection, suggesting a need for increased attention to this group.

IMPACT

Our refined estimates of HPV concordance can inform clinical encounters and public health planning. Future HPV concordance studies should use more rigorous research designs, characterize their participants in greater detail, and study more meaningful populations.

Human papillomavirus infections among couples in new sexual relationships

BACKGROUND

No studies have examined human papillomavirus (HPV) infections among couples early in their sexual relationships when transmission is most likely. Our objective was to describe the distribution of HPV infections among recently formed couples, using the partnership as the unit of analysis.

METHODS

Women aged 18-24 years attending a university or junior college in Montreal enrolled in a longitudinal study with their new male partners. Self-collected vaginal swabs and clinician-collected swabs from the penis and scrotum were tested for 36 HPV genotypes. Participants self-reported sexual behavior in computerized questionnaires. We analyzed patterns of genital HPV infection in 263 couples using data obtained at enrollment.

RESULTS

Couples had engaged in vaginal sex for a median of 3.9 months. HPV was detected in 64% (169/263) of couples. In 41% (109/263), both partners harbored the same HPV type-nearly 4 times more than expected if HPV status of partners were uncorrelated. There were 583 type-specific HPV infections among 169 couples for whom at least one partner was infected. Of these, 42% were of the same type for both partners (95% confidence interval = 36%-47%). This rose from 25% among those engaging in vaginal sex for less than 2 months to 68% among those at 5 to 6 months.

CONCLUSIONS

Although HPV is common, detection of the same type in persons initiating a sex relationship would be rare given type-specific prevalence rates. The high degree of concordance we found suggests a high probability of transmission.

A new approach for the evaluation of the human papillomavirus type 16 variability with high resolution melting analysis

Studies on the variability of human papillomavirus (HPV) type 16 are based mostly on DNA sequencing of the viral oncogenes E6 and E7. In order to simplify variant identification, high resolution melting (HRM) analysis, which has been shown to distinguish amplicons differing in a single nucleotide, was employed. Optimised HRM analysis was applied to 255 anogenital samples positive for HPV 16. The E6/E7 region of the HPV 16 genome was amplified using nested PCR with subsequent melting of the amplicons. Samples giving ambiguous melting profiles were melted again in the presence of reference HPV 16 DNA to define and confirm the novel melting profiles. Out of 219 samples of Croatian origin, 65 reference variants, 119 E6-360G variants and 35 novel melting profiles were found. Samples containing unusual profiles were sequenced for identification. In addition, a subset of samples with two common variants, 23 reference and 34 E6-350G variants, was also sequenced to confirm the findings of high resolution melting. Concordance between the melting analysis and sequencing was 93.9%, while HRM sensitivity and specificity were 92.9% and 94.7%, respectively. This study showed that HRM analysis can be useful for the identification of HPV 16 variants. The HRM method will be useful in low resource settings as it saves considerable time and resources compared to sequencing.

Transmission of human papillomavirus in heterosexual couples

We examined the transmission of human papillomavirus (HPV) in 25 heterosexual, monogamous couples (25 men, 25 women), followed up over an average of 7.5 months. A total of 53 heterosexual transmission events were observed among 16 couples (14 male-to-female and 39 female-to male). Sexual transmission involved 13 different oncogenic and nononcogenic HPV types; 8% were vaccine-covered types transmitted between partners. The overall rate of HPV transmission from the penis to the cervix was 4.9/100 person-months, which was substantially lower than that from the cervix to the penis (17.4/100 person-months). Transmission between the hands and genitals, as well as apparent self-inoculation events (primarily in men), were also observed. Couples who transmitted HPV were more sexually active and used condoms less frequently. These results have implications for HPV prevention and control strategies, including the targeting of prophylactic vaccines.

Transmission of human papillomavirus in heterosexual couples

We examined the transmission of human papillomavirus (HPV) in 25 heterosexual, monogamous couples (25 men, 25 women), followed up over an average of 7.5 months. A total of 53 heterosexual transmission events were observed among 16 couples (14 male-to-female and 39 female-to male). Sexual transmission involved 13 different oncogenic and nononcogenic HPV types; 8% were vaccine-covered types transmitted between partners. The overall rate of HPV transmission from the penis to the cervix was 4.9/100 person-months, which was substantially lower than that from the cervix to the penis (17.4/100 person-months). Transmission between the hands and genitals, as well as apparent self-inoculation events (primarily in men), were also observed. Couples who transmitted HPV were more sexually active and used condoms less frequently. These results have implications for HPV prevention and control strategies, including the targeting of prophylactic vaccines.

High grade cervical lesions are caused preferentially by non-European variants of HPVs 16 and 18

The intratypic variability of HPVs 16 and 18 has been extensively studied and has been used as an important tool in epidemiological studies of viral transmission, persistence and progression to clinically relevant cervical lesions. Infections by non-European variants of HPVs 16 and 18 are associated with an increased risk for the development of high grade squamous intraepithelial lesions (HSIL). Our aim was to correlate the intratypic molecular variability of both HPV types and risk of persistent infection and lesion outcome in a cohort study conducted in Brazil. We characterized molecular variants of HPV types 16 and 18 by sequencing a fragment of the LCR, and of the E6 and L1 genes, for HPV-16 variants only. For both types, European variants composed the most prevalent and diverse group. Persistent infections with HPV-18 were associated with continuous detection of European variants. However, risk for simultaneous detection of HSIL and HPV DNA was higher in women harboring non-European variants of HPV-16. The same trend was observed with HSIL detected during follow-up. Our study confirms the association between non-European variants and risk of cervical neoplasia, and highlights the importance of their geographic distribution for cervical cancer risk assessment.

Genome variation of human papillomavirus types: phylogenetic and medical implications

Human papillomaviruses (HPVs) are described as "types" based on their genome sequences and identified by a number. For example, HPV-6 is associated with genital warts, and HPV-16 with anogenital cancers. The genomes of many HPV types have been reisolated, sequenced and compared to reference "prototypes" countless times by laboratories throughout the world. It was found that each HPV type occurs in the form of "variants", identified by about 2% nucleotide differences in most genes and 5% in less conserved regions. Less than 100 variants of any HPV type have been detected, a scenario that is very different from the quasi-species formed by many RNA viruses. The variants of each HPV type form phylogenetic trees, and variants from specific branches are often unique to specific ethnic groups. Immigrant populations contain, depending on their respective ethnic origins, mixtures of variants. The absence of HPV genomes intermediate to specific types show that all HPV types existed already when humans became a species. Consequently, humans had always suffered from lesions like anogenital cancer, genital warts and common warts. A growing number of epidemiological, etiological and molecular data suggest that variants of the same HPV type are biologically distinct and may confer differential pathogenic risks. Since the distribution of some variants of HPV-16 and 18 correlates with the distribution of human populations that have an increased risk to develop anogenital cancer, the study of HPV type variation may point to one of the reasons for the higher incidence rates of these lesions in specific cohorts.

Flat penile lesions: The infectious “invisible” link in the transmission of human papillomavirus

Although it has been widely accepted that high-risk human papillomavirus (hrHPV) is sexually transmitted, limited insight is available about the clinical manifestations of hrHPV infection in men and their contribution in the viral spread. Here, we reviewed the literature on the relationship between hrHPV and the presence of penile lesions. Flat penile lesions have similar predilection sites as HPV, often contain hrHPV as identified by DNA in situ hybridization in biopsy specimens, show a high association with hrHPV as identified by PCR in penile scrapes of lesional sites and are associated with high viral copy numbers. Absence of flat lesions is generally associated with very low HPV copy numbers or absence of HPV. Therefore, we argue that these lesions form the reservoir of hrHPV in men and contribute to the viral spread. Their bare visibility with the naked eye and their high degree of spontaneous healing explain why flat penile lesions have slipped the attention of the clinician. Combining an HPV DNA test with a visual inspection after acetic acid application offers a more reliable interpretation of a positive HPV test in men, as it helps to distinguish positivity that is very likely to reflect a productive HPV infection from potentially HPV infections with very low copy numbers or HPV contamination by the sex partner. Future trials of HPV vaccines in men should take into account not only the presence of penile HPV but also the presence of flat penile lesions as an outcome measure for the efficacy of a vaccine.

Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses

Human papillomavirus type 16 (HPV16) is the primary etiological agent of cervical cancer, the second most common cancer in women worldwide. Complete genomes of 12 isolates representing the major lineages of HPV16 were cloned and sequenced from cervicovaginal cells. The sequence variations within the open reading frames (ORFs) and noncoding regions were identified and compared with the HPV16R reference sequence. This whole-genome approach gives us unprecedented precision in detailing sequence-level changes that are under selection on a whole-viral-genome scale. Of 7,908 base pair nucleotide positions, 313 (4.0%) were variable. Within the 2,452 amino acids (aa) comprising 8 ORFs, 243 (9.9%) amino acid positions were variable. In order to investigate the molecular evolution of HPV16 variants, maximum likelihood models of codon substitution were used to identify lineages and amino acid sites under selective pressure. Five codon sites in the E5 (aa 48, 65) and E6 (aa 10, 14, 83) ORFs were demonstrated to be under diversifying selective pressure. The E5 ORF had the overall highest nonsynonymous/synonymous substitution rate (omega) ratio (M3 = 0.7965). The E2 gene had the next-highest omega ratio (M3 = 0.5611); however, no specific codons were under positive selection. These data indicate that the E6 and E5 ORFs are evolving under positive Darwinian selection and have done so in a relatively short time period. Whether response to selective pressure upon the E5 and E6 ORFs contributes to the biological success of HPV16, its specific biological niche, and/or its oncogenic potential remains to be established.

Detection and typing of human papillomavirus in anal epidermoid carcinomas: sequence variation in the E7 gene of human papillomavirus Type 16

INTRODUCTION

Human papillomavirus, particularly Type 16, plays a central role in the development of anogenital squamous-cell carcinomas. A common sequence variation of human papillomavirus Type 16 in cervical cancer cell lines and in cervical cancer tissues from Korean patients was recently reported. The present study was performed to determine the integration type of human papillomavirus DNA in anal epidermoid carcinoma and to identify the common sequence variations in the human papillomavirus Type 16 E7 gene that had been previously reported.

METHODS

Twenty-one formalin-fixed, paraffin-embedded specimens collected from 29 patients with anal epidermoid carcinomas treated at the Seoul National University Hospital over a ten-year period (1989-1998) were investigated. Genomic DNA from the 21 specimens was extracted and analyzed using the polymerase chain reaction with a general primer and a type-specific primer for human papillomavirus Types 16 and 18. Direct sequencing was performed. As a control, 13 normal anal epithelia available from these patients were microdissected. As another control, 21 hemorrhoidal squamous epithelia obtained from a demographically adjusted group were also analyzed.

RESULTS

Human papillomavirus Type 16 DNA was present in all 21 anal epidermoid carcinomas. All controls were negative for human papillomavirus DNA. Sequence analysis revealed that 57 percent (12/21) specimens showed two types of sequence variation in the E7 gene. One variant with a single nucleotide change at position 647 (amino acid 29, AAT-->AGT, asparagine to serine) was found in 38 percent (8/21) of the samples. This variant has been detected in cervical cancers from Korean patients: 19 (39 percent) of 49 cervical cancer tissues and 6 (50 percent) of 12 cervical cancer cell lines. Another single nucleotide change at position 645 (amino acid 28, TTA-->TTC, leucine to phenylalanine) was found in 19 percent (4/21) of the samples. These two variants exhibit a change of amino acid affecting the critical sites for Rb binding.

CONCLUSION

Human papillomavirus Type 16 was found to be present in all 21 anal epidermoid carcinomas. Furthermore, in the Korean population, the most common sequence variant found in cervical

Molecular variants of human papillomavirus types 16 and 18 preferentially associated with cervical neoplasia

In order to determine geographically related intratypic variation in human papillomavirus (HPV) type 16 and 18 isolates that could be associated with lesion development, data were analysed from an ongoing cohort study of the natural course of infection of HPVs and cervical neoplasia. Testing for HPVs was carried out by PCR and molecular variants of these HPVs were characterized by sequence analysis of the long control region and by dot blot hybridization of the E6 and L1 genes. Tests for HPV were done in multiple first-year specimens from 1690 women enrolled in a cancer screening program from 1993 to 1997. Subjects were followed-up by cytology and cervicography for detection of cervical lesions. Seven variants of HPV-16 and four of HPV-18 were detected in one or more specimens from 65 subjects. The same variant was found in specimens taken on different visits from each case of persistent infection. Overall, non-European variants tended to persist more frequently [odds ratio (OR)=4.5; 95% confidence interval (CI), 1.6-12.4] than European (E) variants (OR=2.5; 95% CI, 1.3-4.9), relative to the risk of persistence for non-oncogenic HPVs. In addition, non-E variants were more strongly associated with risk of both prevalent (age- and race-adjusted OR=172.2; 95% CI, 47.1-630.1) and incident [relative risk (RR)=22.5; 95% CI, 6.0-83.9] high-grade lesions than E variants (prevalent lesions OR=46.3; 95% CI, 15.5-138.0 and incident lesons RR=6.1; 95% CI, 1.3-27.4), relative to the risk for HPV-negative women. Although consistent, the latter differences were not statistically significant. If confirmed in other populations, measurement of intratypic variation of HPV-16 and -18 has the potential to serve as an ancillary tool in cervical cancer screening.

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.

High risk genital papillomavirus infections are spread vertically

It is well recognised that high-risk human papillomaviruses (HPVs) are spread by sexual activity, but the possibility of non-sexual transmission remains controversial. We present evidence for vertical transmission from at least 30% HPV positive mothers to their infants, resulting in persistent infection in children. That the mother is the source of infant infection has been confirmed by DNA sequencing. We also discuss the evidence for oral HPV-16 infection in children. In our own studies, HPV-16 DNA was detected in buccal cells from 48% children, aged 3-11 and transcriptionally active infection was confirmed in some children. Other studies have reported prevalences of 19%-27% among children less than 11 years of age. Studies that have failed to detect high-risk HPVs in children have used techniques which were insufficiently sensitive to detect the low levels of virus present. Serological studies also suggest that < or = 45% prepubertal children have acquired HPV-16. Thus, convincing evidence is now available for vertical transmission of high risk HPVs, which probably results in widespread infection among children. The consequences of such infections remain to be elucidated.

Human papillomavirus type 16 sequence variation in cervical cancers: a worldwide perspective

We examined intratype human papillomavirus type 16 (HPV-16) sequence variation in tumor samples that were collected and analyzed in an international study of invasive cervical cancer. The collection included tumors from 22 countries in five continents. Using our recently developed E6 and L1 PCR-based hybridization systems to distinguish HPV-16 variant lineages, we analyzed material from tumors previously found to contain HPV-16 DNA. Of 408 specimens analyzed in the E6 hybridization assay, 376 (92.2%) belonged to previously reported HPV-16 variant lineages. The remaining 32 specimens (7.8%) harbored HPV-16 variants with novel hybridization patterns, novel nucleotide changes, or both. Nucleotide sequences (1,203 bp) were determined for the E6, the MY09/11 region of L1, and the long control region of each novel variant and representative specimens from each hybridization pattern observed. Based on E6 hybridization patterns, most of the variants from European and North American samples were phylogenetically classified as European prototype (E) while samples from Africa contained primarily African 1 (Af1) or African 2 (Af2) variants. The majority of Asian (As) variants were observed in Southeast Asia, and almost all Asian American (AA) variants were from Central and South America or Spain. A single North American 1 (NA1) variant was detected in a tumor from Argentina. Nucleotide changes previously shown to covary between the MY09/11 region of L1 and the E6 coding region were examined in a subset of 249 specimens. We observed 22 combined E6-L1 hybridization patterns, of which 11 (in 21 samples) were novel. No unanticipated nucleotide covariation was observed between the E class and the AA-Af1-Af2-NA1 classes, suggesting the absence or rarity of genomic recombination between HPV-16 lineages. This extensive description of HPV-16 variants forms a basis for further examining the relationship between intratype variation and basic functional differences in biological activities. HPV-16 variants may prove important for the determination of the risk of cervical neoplasia and for the design of HPV-16 vaccine strategies.

Human papillomaviruses and cervical cancer

Molecular and epidemiological studies conducted over the last 20 years led to the recognition of certain types of human papillomavirus (HPV) as the etiological agents of cervical cancer, a very common neoplasia, particularly in developing countries. More than 70 HPVs have been described, including both cutaneous and mucosal types. About half of the known HPVs, and an even higher number of variants, have been isolated from genital mucosas. The association of certain types primarily with normal tissues and benign lesions, as opposed to cancer-associated types, has led to the concept of low and high oncogenic risk HPVs, respectively. The latter express oncogenic proteins that interfere with cell growth control functions. As a consequence of the continuous expression of these viral genomes, chromosome instability may occur, leading to fully transformed cells. Studies indicate that persistence of high-risk HPVs may determine progression to more severe stages of cervical disease, while the majority of HPV infections are transient and do not seem to be important in cervical carcinogenesis. The risk for disease progression seems also to be associated with viral burden. Prospective epidemiological studies will contribute to the knowledge of the natural history of HPV infections and provide information on the determinants of viral persistence. Data derived from these studies may define the clinical utility of HPV testing and its use in cervical cancer prevention programs.

Natural variants of the human papillomavirus type 16 E6 protein differ in their abilities to alter keratinocyte differentiation and to induce p53 degradation

Three naturally occurring variant human papillomavirus type 16 (HPV-16) E6 proteins, which contained amino acid substitutions predominantly near the N terminus, exhibited significant differences in their abilities to abrogate keratinocyte differentiation in response to serum and calcium and to induce the degradation of p53 in vitro. One variant surpassed the reference E6 protein in its ability to abrogate keratinocyte differentiation responses, whereas another showed a reduction in this activity. Interestingly, the biological activities of the HPV-16 E6 proteins and their abilities to induce p53 degradation in vitro were directly correlated. These results demonstrate that naturally occurring variants of HPV-16 differ in biological and biochemical properties which might result in differences in pathogenicity.

Low-stringency single specific primer PCR, DNA sequencing and single-strand conformation polymorphism of PCR products for identification of genetic variants of human papillomavirus type 16

Two fragments from within the long control region of the genome of human papillomavirus type 16 (HPV16) were amplified using the polymerase chain reaction (PCR). Putative genetic variation among the parent viruses was assessed by complete sequence analysis and single-strand conformation polymorphism (SSCP) analysis of one of the fragments and by application of the recently described low-stringency single specific primer (LSSP) PCR to both PCR products. The study comprised 34 HPV16 positive samples, derived from seventeen different individuals. It is demonstrated that under experimentally standardised conditions the LSSP PCR-, sequencing- and SSCP-data display differing degrees of resolution. Based on combined LSSP PCR analyses, 33 out of 34 samples can be discriminated, whereas SSCP and direct sequencing identify 4 and 8 types, respectively. Although the variability observed among LSSP PCR patterns may be the consequence of small quantities of mutated viral amplimers, no concordant grouping of strains, identical by sequencing and SSCP analysis, can be established by either of the four theoretically possible LSSP PCR assays. Results are discussed in the context of experimental variability of the procedures or genetic heterogeneity of HPV16 pools derived from cervical swabs.

Genotyping human papillomavirus type 16 isolates from persistently infected promiscuous individuals and cervical neoplasia patients

Nucleotide sequence variation in the noncoding region of the genome of human papillomavirus type 16 (HPV16) was determined by direct sequencing and single-strand conformation polymorphism analysis of DNA fragments amplified by PCR. Individuals of diverse sexual promiscuity and/or cervicopathology were studied. In a group of 14 healthy, monogamous HPV16-positive females, only two HPV16 sequence variants could be documented. Among 17 females and 3 males with multiple sex partners and living in the same geographical region, nine sequence variants were found, whereas among 7 patients with cervical neoplasia from another region, five variants were detected. Although numbers are limited, in the group of individuals at high risk of acquiring a sexually transmitted disease or with cervical neoplasia, a larger number of HPV16 sequence variants was encountered (two types among 14 individuals versus nine types among 20; Fisher's exact test, P = 0.07). Seven of the individuals were sampled repeatedly over time. For these persistently infected women, no differences in HPV16 sequences were detected, irrespective of promiscuity, and persistence of a single viral variant, spread over multiple anatomic sites, for more than 2 years could be demonstrated. This indicates that viral persistence may be a common feature and that successful superinfection with a new variant may be rare, despite a potentially high frequency of viral reinoculation.

Perinatal infection and persistence of human papillomavirus types 16 and 18 in infants

Perinatal transmission of genital human papillomaviruses (HPVs), including HPV-16 and -18 which are associated with anogenital carcinomas have been described previously [Pakarian et al. (1994): British Journal of Obstetrics and Gynaecology 101:514-517; Kaye et al. (1994) Journal of Medical Virology 44:415-421]. A study was undertaken to investigate whether HPV-16 and -18 DNA in infants contaminated at delivery persists until they are 6 months of age. Of 61 pregnant women recruited, 42 (68.8%) were HPV-16 and 13 (21.3%) were HPV-18 DNA positive. At 24 hr there were transmission rates from HPV DNA positive mothers to their infants of about 73% (HPV-16: 69%; HPV-18: 76.9%). Ten mothers who were both HPV-16 and -18 DNA positive produced six (60%) infants who were also doubly positive at 24 hr. HPV DNA persisted to 6 weeks in 79.5% (HPV-16: 84%; HPV-18: 75%) of those infants who were positive at birth. At 6 months of age, persistent HPV-16 DNA was detected in 83.3% of cases, but HPV-18 DNA persistence at this time was 20%. To extend these observations over a greater age range of children HPV-16 L1 and L2 proteins were expressed in insect cells via recombinant baculoviruses and sera from 229 children were examined to determine at what age IgM antibodies to HPV were acquired. There was a bimodal distribution of IgM seropositivity which peaked between 2 and 5 and 13 and 16 years of age, suggesting that two distinct modes of transmission may occur. The observation that infection with high cancer risk genital HPVs may occur in early life and persist is of considerable importance for HPV vaccine strategies.

Variation of human papillomavirus type 6 (HPV-6) and HPV-11 genomes sampled throughout the world

We examined the genomic diversity of human papillomavirus type 6 (HPV-6) and HPV-11 isolates from different parts of the world by comparing the nucleotide sequences of part of the long control region of three reference clones and 62 HPV-6 and 40 HPV-11 isolates from Africa, Europe, Asia, and North and South America. The genomic sequence of the HPV-6b reference type had to be amended by inclusion of a 94-bp segment, which is also present with minor differences in HPV-6a. Aside from two small inserts typical of all variants related to HPV-6a and three inserts found in HPV-11 variants, no major alterations to the size of the long control regions of these viruses were observed. This corrects the previous impression that these two HPV types are highly polymorphic. Altogether, 19 HPV-6 and 10 HPV-11 variant genomes could be distinguished, and most of the differences were due to point substitutions. The variants of either type were continuously connected in phylogenetic trees rather than clustered separately into subtype groups. Thirteen mutations, namely, the two HPV-6a inserts and 11 substitutions in HPV-6 or HPV-11 variants, reduced the dissimilarity between the types, but they bridged only a small fraction of the genetic distance between the two types. Genomes more obviously intermediate between HPV-6 and HPV-11 were not found and probably do not exist any more. A single HPV-11 variant was found in Africa, but otherwise, no significant correlations of HPV-6 or HPV-11 variants with geography or ethnicity of the patient cohort were found. Functional analysis of diverse enhancer variants showed activities that differed two-to threefold, and it must be considered that transcriptional differences may alter the biology or pathology of these viruses. Similar variants were found in lesions from anatomically different sites and in both benign and malignant lesions.

Human papillomaviruses and cervical neoplasia. I. Classification, virology, pathology, and epidemiology

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