Oligonucleotide primers for DNA amplification of the early regions 1, 6, and 7 from human papillomavirus types 6, 11, 16, 18, 31, and 33

Summary Human papillomavirus (HPV) type-specific sequences required for polymerase chain reaction (PCR) mediated amplification of HPV DNA sequences are presented. One primer pair within the E1 open reading frame (ORF) was shared by HPV 6, HPV 11, HPV 16, and HPV 31, whereas the other primer pair within the E1 ORF was specific for HPV 16. Eight primer pairs from the E6 and E7 ORFs specifically detected HPV 6, HPV 16, HPV 18, and HPV 33 sequences. This system has been used for detection of HPV DNA in biopsies, cytological smears and sections of formalin-fixed tissues.     

Human papillomavirus detection in adenocarcinoma of the anus.

Human papillomavirus (HPV) is associated with carcinoma of the cervix but not with carcinoma of the endometrium. HPV 16 is the type most commonly detected in squamous cell carcinomas from this site, whereas HPV 18 predominates in adenocarcinomas. We analyzed eight anal carcinomas for HPV DNA using the polymerase chain reaction and type-specific (open reading frame E6) primers for HPV 16, 18, 31, and 35. HPV DNA sequences were amplified in two of six anal adenocarcinomas and, in each case, the type was HPV 18. Sequences homologous to HPV 16 were amplified in each of two anal squamous cell carcinomas; one also contained HPV 18. No amplification was detected in any of seven adenocarcinomas of the rectum or colon or in three adenomatous polyps of the colon. It is concluded that HPV is associated with anal adenocarcinomas but not colorectal adenocarcinomas. The reason(s) why HPV is associated with adenocarcinoma of the anus and cervix but not with the rectum and endometrium, despite the close proximity, requires further study.     

Detection of low level of human papilloma virus type 16 DNA sequences in cancer cell lines derived from two well-differentiated nasopharyngeal cancers

Human papilloma virus type 16 (HPV16) related sequences were detected in two EBV-negative nasopharyngeal carcinoma (NPC) cell lines derived from two well-differentiated NPC by polymerase chain reaction. E2 and E6 related sequences of HPV16 were demonstrated using two pairs of primers derived from these two regions. DNA sequence analysis of amplified products excluded the possibility of laboratory viral DNA contamination. © 1993 Wiley-Liss, Inc.     

Evaluation of immunoassays for the detection and typing of PCR amplified human papillomavirus DNA.

AIMS: To evaluate different hybridisation techniques to detect and type human papillomavirus (HPV) DNAs amplified by consensus primer polymerase chain reaction (PCR) in biopsy and cytological specimens. METHODS: A hybrid capture-immunoassay in microtitre wells was performed to detect HPV sequences amplified by PCR and typed by specific oligoprobes. Consensus primers were used to amplify a sequence within the L1 open reading frame, and direct digoxigenin labelling of amplified products was performed during the amplification reaction. The amplified product was separately hybridised with six biotinylated type specific probes (HPV6, 11, 16, 18, 31, and 33); hybrids were then captured into streptavidin coated microtitre wells and detected by a spectrophotometer as an ELISA using antidigoxigenin Fab fragment labelled with peroxidase and a colorimetric substrate. The results were compared with the dot-blot immunoassay used to detect and type PCR amplified HPV DNA sequences. Consensus primers were used to generate the same unlabelled PCR product; digoxigenin labelled type specific probes for HPV6, 11, 16, 18, 31, and 33 were used and hybrids visualised by colorimetric immunoenzymatic reaction. Thirty nine biopsy specimens and 31 cytological samples were tested by the PCR-ELISA and by standard PCR followed by dot-blot hybridisation. RESULTS: The PCR-ELISA proved to be more sensitive than standard PCR with dot-blot hybridisation typing. All samples positive for HPV-DNA in standard PCR with dot-blot hybridisation method were confirmed positive by the PCR-ELISA assay; however, seven samples were positive only by PCR-ELISA. CONCLUSIONS: The PCR-ELISA assay, which can be performed in one day, is easily standardised and therefore seems to be a practical, sensitive, and reliable diagnostic tool for the detection and typing of HPV genomes in biopsy and in cytological specimens in the routine diagnostic laboratory.     

Analysis of prostate tissue DNA for the presence of human papillomavirus by polymerase chain reaction,cloning, and automated sequencing

We have analysed the DNA from 24 prostate tissue biopsies, spanning a range of Gleason grading from benign to grade 5 and mixed randomly with cervical cancer samples of known human papillomavirus (HPV) status, for the prevalence of HPV DNA, in a double-blind study to ensure complete objectivity. Polymerase chain reactions (PCR) were performed using general E1 open reading frame primers for HPV under low stringency conditions, in addition to reactions containing primers specific for HPV16, E2, and E6 open reading frames under higher, more stringent PCR conditions. The presence of cellular DNA was verified by the use of primers for hypoxanthine guanine phosphoribosyl transferase. DNA bands were not detected in the prostate biopsies using the HPV16-specific primers under high-stringency PCR conditions, however a predominant band in the 400 bp region was observed in 15 of the prostate biopsies using the general primers and the low annealing temperature of 40°C. This fragment was excised and cloned into the pT7 blue vector and the sequence of the insert determined. Although the cloned sequences initiated and terminated with the two authentic PCR primers, they did not contain a significant HPV-related open reading frame. Our results indicate that HPV type 16 and closely related types, as detected by the general primer pair, are unlikely initiators of prostate carcinogenesis within our population. J. Med. Virol. 52:8–13, 1997. © 1997 Wiley-Liss, Inc.     

Single primer pair for amplifying segments of distinct Shiga-like-toxin genes by polymerase chain reaction.

By using a single synthetic oligonucleotide primer pair in the polymerase chain reaction, we amplified specific Shiga-like-toxin (SLT) gene segments from DNAs of 20 clinical Escherichia coli isolates, irrespective of whether they produce SLT-I, SLT-II, or heretofore uncategorized SLTs. These segments were not detectable in any of 20 nontoxigenic E. coli strains. The primers deduced from a conserved region among SLT genes are so-called degenerate-sequence primers; i.e., they contain intentionally introduced sequence ambiguities to overcome minor sequence variations within different SLT genes. In direct gel hybridization with genomic DNA, both primers recognized SLT-I and SLT-II DNA sequences. Amplified sequences of target DNA obtained by polymerase chain reaction were visualized after gel electrophoresis by ethidium bromide staining, and definitive identification of the amplification product as an SLT gene segment was achieved by hybridization to SLT-I- and SLT-II-specific 20-base oligonucleotide probes complementary to a portion of the amplified sequences but not to the primers. The detecting oligonucleotide probes shared only 30% base homology and were shown to recognize specifically SLT-I or SLT-II sequences within genomic DNA. Moreover, they were used to distinguish whether the amplified sequence originated from SLT-I or SLT-II genes. The PCR system with the primers described here is a powerful technique to amplify SLT sequences in E. coli strains that produce serologically distinct SLTs and will facilitate identification of these pathogens, particularly among a multitude of nonpathogenic E. coli strains.     

Polymerase chain reaction for fast, nonradioactive detection of high- and low-risk papillomavirus types in routine cervical specimens and in biopsies

A polymerase chain reaction (PCR) procedure capable of amplifying specific DNA sequences by up to a millionfold was developed for detection of infection by human papillomaviruses (HPVs) of low (HPV6, HPV11) or high (HPV16, HPV18, HPV33) oncogenic potential. For high-risk HPVs the region chosen was within the E6 open reading frame, which can become integrated into genomic DNA. A region corresponding to this was chosen for low-risk HPVs. After repeated cycles of specific oligonucleotide-primed extension of viral DNA with Klenow or thermophilic DNA polymerase, the type of HPV present was then determined on the basis of the size of the ethidium-bromide-stained band visible after polyacrylamide gel electrophoresis: for HPV6 or 11 the band was approximately 120 bp, for HPV 16 or 33 it was approximately 200 bp, and for HPV18 it was approximately 100 bp. Specific hybridization to the relevant band was seen using radioactive or nonradioactive (alkaline-phosphatase-linked) target oligonucleotide probes. Using the PCR method, we have determined, within as little as a few hours, the infection status of a variety of clinical specimens, including cervical scrapes and lavages, anal scrapes, and anogenital biopsies. The PCR steps can be automated, adding to the potential of PCR for widespread use in the detection of HPV, which is becoming increasingly popular in cervical screening.     

Congenital infection by human cytomegalovirus with a 65 bp deletion in the morphological transforming region II

Summary Human cytomegalovirus (HCMV) infection is an important cause of neonatal death. Using primers derived from sequences within the morphological transforming region II (mtrII), HCMV DNA was amplified by polymerase chain reaction (PCR) from fixed tissues of infants who had died of congenital HCMV infection. In one neonate, HCMV DNA with reduction in the expected size was detected in the liver, spleen, kidney, adrenal, und thyroid tissues by gel electrophoresis. Nucleotide sequencing of the PCR product revealed a 65bp frame-shift deletion within the 79 amino acid open reading frame (ORF) of themtrII. Based upon this observation, it is likely that viral genomic rearrangement involving themtrII may occur in some cases of congenital HCMV infection.     

Comparison of L1 consensus primers with E6 type specific primers for detection of human papillomaviruses in paraffin sections of cervical neoplasia.

In our comparative study of L1 consensus primers with E6 type-specific primers for detection of human papillomavirus (HPVs) by polymerase chain reaction (PCR) in 35 cases of cervical neoplasia, the detection rate by E6 primers (54%; 19/35) was significantly higher than that by L1 primers (25%; 9/35) (p < 0.01). And all specimens HPV-positive with L1 primers were also positive by E6 primers. HPV DNA could be amplified in 36% (9 of 25) of tissue by L1 consensus primers from which beta-globin gene was amplified as compared with 64% (16 of 25) of tissue by E6 type-specific primers. With the L1 consensus primers, 8 cases were positive for HPV-16 and 1 case was positive for HPV-33. These results show that the L1 consensus primers have inferior sensitivity to the E6 type-specific primers for the detection of HPV by PCR. But the L1 consensus primers have great value in making simultaneous detection of various HPV types in a single tube reaction, thus they permit reduction of time and the economic burden of the experiment.     

Consensus polymerase chain reaction and enzyme-linked immunosorbent assay for human papillomavirus detection and typing in cervical specimens.

Human papillomavirus (HPV) infection is common in cervical intraepithelial neoplasia (CIN). This study investigates HPV detection and typing assay based on polymerase chain reaction amplification of L1 open reading frame with general primers GP5/GP6, followed by enzyme-linked immunosorbent assay detection with type-specific DNA probes. To determine the sensitivity of this assay, formalin-fixed CaSki cells were used as reference cell lines. Fifty copies of viral DNA diluted in DNA from 100,000 noninfected cells could be detected. This assay was also investigated for HPV detection and typing of 67 cervical specimens diagnosed with with CIN III or carcinoma in situ (CIS) and their adjacent squamous epithelium. The CIN III lesions were infected in approximately 80% of the samples, 81% in the neighboring CIN II, and 68% in CIN I. The HPV infection was even detectable in 54% of nondysplastic epithelium located near a CIN III lesion.     

TT virus infection in patients with chronic liver disease of unknown etiology

The role of a novel virus, designated as TT virus (TTV), as a cause of chronic liver disease has not been well defined. We investigated the prevalence of TTV among 69 patients with chronic liver disease of unknown etiology and 50 volunteer blood donors with normal transaminase levels. TTV DNA was amplified by polymerase chain reaction (PCR) by using two different sets of primers: one based on the sequence of the original N22 clone within the open reading frame 1 (set A) and the other derived from the untranslated region (set B). The prevalence of TTV detected by PCR primers set A only, set B only, and in total (by either set A or B) was 11 (31%), 31 (86%), and 31 (86%) of 36 patients with chronic hepatitis; 2 (40%), 4 (80%), and 4 (80%) of 5 with cirrhosis; 11 (39%), 17 (61%), and 22 (79%) of 28 with hepatocellular carcinoma; and 9 (18%), 39 (78%), and 40 (80%) of 50 volunteer blood donors, respectively. Of the interpretable 25 PCR products amplified with primers set A, 9 were classified as genotype 1a, 10 as genotype 1b, 4 as genotype 2, 1 as genotype 3, and 1 as genotype 4. Molecular evolutionary analysis did not suggest any particular strains of TTV that might be associated with chronic liver disease. The nucleotide sequences of the untranslated region on which PCR primers set B were designed were highly conserved, and the interpretable 22 PCR products amplified with primers set B were not clearly divisible into distinct genotypes. Our findings provided no evidence that TTV is a causative agent of chronic liver disease.     

Human papillomavirus DNA is present in a subset of unselected breast cancers

OBJECTIVE: The major molecular events in the genesis of most breast cancers are unknown. However, human papillomaviruses (HPV) have been reported to be found in a significant portion of breast cancers of women with concomitant cervical intraepithelial neoplasia III. To investigate a potential HPV-breast cancer link, we carried out a small survey to identify HPV in unselected, general breast cancer tissues. STUDY DESIGN/METHODS: Deoxyribonucleic acid (DNA) was isolated from 17 breast cancer tissues (and one cervical swab) taken from our local, randomly selected patient population. Two different previously characterized broad-spectrum primer sets (targeting the E6/E7 or L1 regions) were used to amplify HPV DNA, and another primer set was used to amplify the ColE1/pBR322 origin of replication by polymerase chain reaction amplification. The polymerase chain reaction product DNA was analyzed by dot blot hybridization with HPV-16, -18, -31, or pRB322 DNA probes. Total cellular DNA was also analyzed by one- and two-dimensional Southern blot analysis. Finally, the E6/E7 polymerase chain reaction products were cloned, sequenced, and compared to previously cloned HPV types. RESULTS: Polymerase chain reaction/dot blot analysis by both the HPV E6-E7 and L1 primer sets identified the same 6 out of 17 (35%) breast cancers as being HPV positive. ColE1/pBR322 origin targeted polymerase chain reaction/dot blot analysis failed to identify plasmid contamination. One- and two-dimensional Southern blot analysis showed that the breast cancers specimens contained significant levels of HPV DNA and that the viral DNA was largely episomal. The sequences of the HPV clones demonstrated that HPV-16, -18, and possibly type 11 were present within the breast cancer specimens. Furthermore, the HPV sequences cloned from the cervical swab and breast cancer of the same patient were found to be identical. CONCLUSIONS: These data suggest that HPV may be associated with a significant subset of breast cancers, and further suggest that additional studies are warranted.     

Sequence comparison of JSRV with endogenous proviruses: envelope genotypes and a novel ORF with similarity to a G-protein-coupled receptor.

Ovine pulmonary carcinoma, a contagious lung cancer of sheep, is caused by the oncogenic jaagsiekte sheep retrovirus (JSRV) that is closely related to a family of endogenous sheep retroviral sequences (ESRVs). By using exogenous virus-specific U3 oligonucleotide primers, the entire JSRV proviral genome or its 3' part was amplified from tumor DNA. Analysis of these proviral sequences revealed a novel open reading frame (ORF) within the pol coding region, designated ORF X, which was well conserved in ESRV and JSRV sequences. Deduced amino acids of ORF X showed similarity to a portion of the mammalian adenosine receptor subtype 3, a member of the G-protein-coupled receptor family. Comparison of deduced env amino acids of six JSRV strains from three continents identified 15 residues that defined two distinct genotypes of JSRVs. Sequence analysis identified two highly variable regions between JSRV and ESRV in the transmembrane domain of env (TM) and the 3' unique sequence (U3) of the long terminal repeat, from which JSRV-specific DNA probes were derived. By using these DNA probes in Southern hybridization, for the first time we successfully identified JSRV proviral sequences in tumor genomic DNA in the presence of multiple ESRV loci, validating the use of exogenous virus-specific DNA probes in the analysis of oncogenic proviral integration sites and identification of integrated exogenous proviral sequences.     

Rapid method for distinguishing clonal from polyclonal B cell populations in surgical biopsy specimens.

The polymerase chain reaction (PCR) was used to detect clonal rearrangements of the immunological heavy chain gene in frozen samples of human lymphoid tissue. DNA sequences in rearranged genes were amplified using oligomeric primers predicted from conserved sequences in the variable (VH) and joining (JH) regions. On polyacrylamide gel electrophoresis, polyclonal B cell proliferations showed a "smear", probably due to the variable lengths of the diversity (DH) region genes and the N regions separating the VH and DH and JH regions. In contrast, DNA from B cell lymphomas showed a clear single band in eight out of 10 cases. PCR undertaken on germ line DNA from non-lymphoid tumours showed no detectable bands or smears. The method can be completed within one day of biopsy, compared with several days in the case of conventional DNA blot analysis. Furthermore, it is cheaper, simpler, avoids the need for radioactive materials and requires very small amounts of DNA (about 1 micrograms).     

Geographically Distinct HHV-8 DNA Sequences in Saudi Arabian Iatrogenic Kaposi’s Sarcoma Lesions

A new member of the γ-herpesvirus family, HHV-8 (also known as Kaposi’s sarcoma (KS)-associated herpesvirus), has been linked to KS and body cavity-based lymphoma. Other members of this family, eg, Epstein-Barr virus, were originally thought to have only one strain, but subsequent analysis revealed different strains correlating to cellular patterns of infectivity and geographical location. To determine whether multiple strains of HHV-8 exist, we compared DNA sequences among KS and body cavity-based lymphoma-derived HHV-8 and examined differences in HHV-8 subgroups between American and Saudi Arabian iatrogenic KS patients. Samples were analyzed by polymerase chain reaction using multiple primer sets to five different open reading frames from HHV-8, and DNA sequencing was performed. HHV-8 DNA was present in all of our KS and body cavity-based lymphoma samples by polymerase chain reaction. HHV-8 DNA was detected in each body cavity-based lymphoma sample using a majority of the primers, whereas only two primer sets consistently amplified HHV-8 DNA derived from KS lesions. DNA sequencing within open reading frames 26 and 27 indicate the existence of at least three variants of HHV-8, with the majority of iatrogenic KS patients in Saudi Arabia containing unique nucleotide changes that may define a distinct, previously unidentified subgroup we term SA, whereas those from America were of Group A or B. Thus, although the sequencing data within open reading frames 26 and 27 did not permit discrimination between patients with lymphoma versus KS disease processes, HHV-8 derived from Saudi Arabian KS lesions were shown to have a distinct nucleotide sequence not seen in any of the other clinical samples examined.