1
|
Kuiken CL, Cornelissen MT, Zorgdrager F, Hartman S, Gibbs AJ, Goudsmit J. Consistent risk group-associated differences in human immunodeficiency virus type 1 vpr, vpu and V3 sequences despite independent evolution. J Gen Virol 1996; 77 ( Pt 4):783-92. [PMID: 8627267 DOI: 10.1099/0022-1317-77-4-783] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Human immunodeficiency virus 1 type vpr, vpu and V3 sequences from 15 homosexual men and 19 intravenous drug users in the Amsterdam Cohort studies were analysed. Previously, we reported that V3 domains of viruses from drug users are distinguishable from those of homosexual men on the basis of two silent mutations. Phylogenetic analysis of vpr, vpu and V3 shows that differences in all three regions correlate with risk group. Two positions in both vpr and vpu were found to differ significantly between the risk groups. The distinguishing positions were confirmed for sequences from 11 Scottish and four German samples. The three regions show relatively independent evolution patterns; they resulted in different phylogenies, the only stable clustering being that based on the risk group distinction. Pairwise differences between sequences of the genes were moderately correlated (around 0.30). Surprisingly, when only silent changes are counted, the correlations dropped almost to zero, indicating that the evolution towards independence was more advanced in the silent than in the non-silent positions. This suggests that selection at the amino acid level is not the primary driving force for the independent evolutionary behaviour of the genes. Recombination, combined with restrictions on certain amino acids because of epistatic interactions between the genes, could be an alternative explanation of this phenomenon.
Collapse
Affiliation(s)
- C L Kuiken
- Department of Human Retrovirology, University of Amersterdam, The Netherlands.
| | | | | | | | | | | |
Collapse
|
2
|
Lukashov VV, Cornelissen MT, Goudsmit J, Papuashvilli MN, Rytik PG, Khaitov RM, Karamov EV, de Wolf F. Simultaneous introduction of distinct HIV-1 subtypes into different risk groups in Russia, Byelorussia and Lithuania. AIDS 1995; 9:435-9. [PMID: 7639968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To investigate genotypes and serotypes of HIV-1 variants in Russia, Byelorussia and Lithuania. PATIENTS AND METHODS Sera from 20 HIV-1-infected individuals were tested in an enzyme-linked immunosorbent assay (ELISA) with 19 V3 synthetic peptides, and serum HIV-1 V3 RNA was amplified and sequenced. RESULTS Sequence comparison of the envelope V3 region among specimens tested revealed a 2-29% range nucleotide divergence, with a mean of 19%. Phylogenetic analysis from the homosexual men were shown to belong to subtype B, and all of the heterosexually infected individuals to subtype C. Sequences from the parenterally infected individuals were more heterogeneous. IOn the peptide ELISA three reactivity patterns were found. Serum samples from six out of seven homosexual men showed reactivity to peptides p108 or p110 representing V3 amino-acid sequences found in US/West European HIV-1 isolates. Serum samples from six of seven individuals who had acquired HIV-1 through heterosexual contacts were reactive to peptide p169. Four out of six parenterally infected patients had peak reactivity to p168. CONCLUSION Distinct HIV-1 variants were found in Russia, Byelorussia and Lithuania, which were introduced simultaneously in the mid-1980s. This diversity was shown to be associated with the route of transmission. Homosexual men appeared to be infected with subtype B and heterosexually infected individuals with subtype C HIV-1 variants. HIV-1 subtypes A, C, D and G were found among parenterally infected individuals.
Collapse
Affiliation(s)
- V V Lukashov
- Human Retrovirus Laboratory, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
3
|
Zwart G, van der Hoek L, Valk M, Cornelissen MT, Baan E, Dekker J, Koot M, Kuiken CL, Goudsmit J. Antibody responses to HIV-1 envelope and gag epitopes in HIV-1 seroconverters with rapid versus slow disease progression. Virology 1994; 201:285-93. [PMID: 7514319 DOI: 10.1006/viro.1994.1293] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We studied the relationship between the rate of disease progression after HIV-1 seroconversion and the level of IgG antibody response to HIV-1 envelope and core epitopes. This was done by comparing a group of fast-progressing individuals and a group of slow-progressing individuals for serum IgG titers to peptides from the gp120-V3 neutralization domain, to a peptide from the immunodominant gp41 epitope (residues 590 to 607), and to recombinant gp120 and p24. The two groups displayed a large overlap in titers to the envelope epitopes, which precluded their differentiation at most time points after seroconversion. Low responsiveness to envelope antigens was not only found in a few fast-progressors but also in one individual who remained asymptomatic for at least 92 months after seroconversion. The only significant differences between the groups were found in the first months after seroconversion when the responses to the V3 domain and the gp41 epitope were more vigorous in the group of fast-progressors. Furthermore, on evaluating ratios of anti-V3 antibody titers to anti-gp120 antibody titers we found no indication that fast disease progression was associated with a restriction in antibody response to the V3 epitope. We did confirm the finding that fast disease progression is associated with low levels of p24-directed antibodies, both early after seroconversion and at later stages. These data demonstrate that levels of IgG antibodies to envelope epitopes are poor predictors of rapid disease progression and suggest that the role of V3-directed neutralizing antibodies in preventing subversion of the immune system is not decisive in natural HIV-1 infection.
Collapse
Affiliation(s)
- G Zwart
- Department of Virology, Academic Medical Center, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Cornelissen MT, Bots T, Briët MA, Jebbink MF, Struyk AP, van den Tweel JG, Greer CE, Smits HL, ter Schegget J. Detection of human papillomavirus types by the polymerase chain reaction and the differentiation between high-risk and low-risk cervical lesions. ACTA ACUST UNITED AC 1992; 62:167-71. [PMID: 1357817 DOI: 10.1007/bf02899679] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
By means of a consensus polymerase chain reaction (PCR) method, the prevalence of HPV types was determined in cervical biopsies from 137 women referred to the gynecological outpatient clinic for colposcopy because of an abnormal cervical smear. The prevalence of HPV was 80.3%. There was a statistically highly significant rise in the prevalence of the oncogenic HPV types (16, 18, 31, 33) with increasing severity of cervical intraepithelial neoplasia (CIN I to III), indicating a role for these HPV types in the pathogenesis of cervical cancer. The prevalence of other HPV types decreased significantly with the severity of the lesion, suggesting that these HPV types play a less significant role in this process. These data indicate that HPV typing with PCR may be a valuable tool for distinguishing between high-risk and low-risk cervical lesions. Furthermore, our results suggest that the detection of HPV types by consensus PCR in the cervix of patients with an abnormal smear but without histologically detectable CIN is a useful tool for predicting which of these patients will eventually develop CIN. Finally, a relatively low percentage (3%) of HPV double infections is reported in this study.
Collapse
Affiliation(s)
- M T Cornelissen
- Department of Virology, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Smits HL, Cornelissen MT, Jebbink MF, van den Tweel JG, Struyk AP, Briët M, ter Schegget J. Human papillomavirus type 16 transcripts expressed from viral-cellular junctions and full-length viral copies in CaSki cells and in a cervical carcinoma. Virology 1991; 182:870-3. [PMID: 1850935 DOI: 10.1016/0042-6822(91)90632-l] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have mapped using the RNA PCR the viral-cellular junctions of HPV16 viral-cellular cotranscripts expressed in CaSki cells and a cervical carcinoma to nt 3728 and 881, respectively. Both junctions were located within the E1-E2 region. Examination of the cellular sequences of the cotranscripts showed the presence of a polyadenylation signal in each of the transcripts. In CaSki cells and in the cervical carcinoma transcripts derived from the full-length early region including the E2 transcript were also detected. Our results suggest that the utilization of a cellular polyadenylation site could be important in the development of cancer by HPV.
Collapse
Affiliation(s)
- H L Smits
- Department of Medical Microbiology, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
6
|
Resnick RM, Cornelissen MT, Wright DK, Eichinger GH, Fox HS, ter Schegget J, Manos MM. Detection and typing of human papillomavirus in archival cervical cancer specimens by DNA amplification with consensus primers. J Natl Cancer Inst 1990; 82:1477-84. [PMID: 2167986 DOI: 10.1093/jnci/82.18.1477] [Citation(s) in RCA: 363] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We developed a polymerase chain reaction DNA amplification system using two distinct consensus oligonucleotide primer sets for the improved detection and typing of a broad spectrum of human genital papillomavirus (HPV) sequences, including those of novel viruses. The system incorporates one primer set designed to amplify a highly conserved L1 domain and a second primer set designed to amplify a domain within the E6 gene. We used this system to analyze 48 fixed, paraffin-embedded tissue sections (41 specimens from 33 cervical carcinomas, four normal cervical tissues, and several control tissues) for the presence of HPV DNA. HPV sequences were detected in all carcinoma samples and none of the control samples. Hybridization analyses showed that the results obtained with the two amplification schemes concurred completely. This approach allowed rapid confirmation of typing results and may improve the likelihood of detecting a wide variety of HPV sequences, including those of novel HPVs.
Collapse
Affiliation(s)
- R M Resnick
- Department of Infectious Diseases, Cetus Corporation, Emeryville, CA 94608
| | | | | | | | | | | | | |
Collapse
|
7
|
Cornelissen MT, Smits HL, Briët MA, van den Tweel JG, Struyk AP, van der Noordaa J, ter Schegget J. Uniformity of the splicing pattern of the E6/E7 transcripts in human papillomavirus type 16-transformed human fibroblasts, human cervical premalignant lesions and carcinomas. J Gen Virol 1990; 71 ( Pt 5):1243-6. [PMID: 2161056 DOI: 10.1099/0022-1317-71-5-1243] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We utilized the RNA polymerase chain reaction (PCR) to analyse the transcripts of the E6/E7 open reading frames of human papillomavirus type 16 (HPV-16). Total RNA was isolated from 14 cervical squamous carcinomas, nine cervical intraepithelial neoplasias and from human fibroblasts transformed with different HPV-16 constructs. In all specimens two spliced transcripts were detected. Sequence analysis of the cloned PCR products showed that both transcripts were generated by splicing out an intron in E6, from nucleotides (nt) 226 to 409 in one transcript and from nt 226 to 526 in the other. The major transcript present in all RNA specimens had the smallest intron in E6. The RNA PCR described here is the method of choice for analysing splice and donor sites in tissue specimens where a limited amount of RNA is available. Results obtained with transformed cells revealed no difference in splicing whether HPV-16 was controlled by its homologous promoter or by a heterologous promoter, the Rous sarcoma virus long terminal repeat.
Collapse
Affiliation(s)
- M T Cornelissen
- Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
8
|
Van Eys GJ, Gravekamp C, Gerritsen MJ, Quint W, Cornelissen MT, Schegget JT, Terpstra WJ. Detection of leptospires in urine by polymerase chain reaction. J Clin Microbiol 1989; 27:2258-62. [PMID: 2584377 PMCID: PMC267006 DOI: 10.1128/jcm.27.10.2258-2262.1989] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Primers for polymerase chain reaction (PCR) were synthesized from clones derived from a Leptospira hardjo (type hardjobovis) library. One pair of synthetic oligonucleotide primers was selected for further analysis. Under experimental conditions an amplification was obtained with DNA of Leptospira interrogans of some serovars belonging to serogroup sejroe. However, very little or no amplification was observed with DNA from other serovars of this group. No amplification was observed with DNA from other serogroups, other bacteria, or eucaryotic organisms. Cattle urine, seeded with hardjobovis, was processed in several ways and subsequently subjected to PCR. Boiling of the samples or treatment with detergents appeared to be most effective. Urine samples containing fewer than 10 leptospires gave a positive result in the PCR assay. Twenty urine samples obtained from a slaughterhouse or farm cows were investigated using the PCR assay, culture isolation, dot and quick blot hybridization, and serological tests. This comparative study suggests that amplification by PCR may be a valuable method for the detection of leptospires in cattle urine.
Collapse
Affiliation(s)
- G J Van Eys
- N. H. Swellengrebel Laboratory for Tropical Hygiene, Royal Tropical Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
9
|
Cornelissen MT, van den Tweel JG, Struyk AP, Jebbink MF, Briët M, van der Noordaa J, ter Schegget JT. Localization of human papillomavirus type 16 DNA using the polymerase chain reaction in the cervix uteri of women with cervical intraepithelial neoplasia. J Gen Virol 1989; 70 ( Pt 10):2555-62. [PMID: 2552002 DOI: 10.1099/0022-1317-70-10-2555] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The localization of human papillomavirus type 16 (HPV-16) DNA throughout the cervix uteri of women with cervical intraepithelial neoplasia (CIN) was studied by utilizing the polymerase chain reaction technique directly on histologically defined sections of paraffin-embedded cervical tissue obtained by conizations. HPV-16 DNA was detected only in the sections that contained CIN lesions and/or koilocytes. No HPV-16 DNA was detected in sections that contained only normal epithelium. This is in accordance with HPV-16 playing a role in the development of CIN lesions.
Collapse
Affiliation(s)
- M T Cornelissen
- Department of Medical Microbiology, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
10
|
Cornelissen MT, van der Velden KJ, Walboomers JM, Briët MA, Smits HL, van der Noordaa J, ter Schegget J. Evaluation of different DNA-DNA hybridisation techniques in detection of HPV 16 DNA in cervical smears and biopsies. J Med Virol 1988; 25:105-14. [PMID: 2842441 DOI: 10.1002/jmv.1890250114] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The sensitivities of dot blot hybridisation and in situ filter hybridisation for the detection of HPV DNA were compared. Dot blot hybridisation was 10-50 times more sensitive than in situ filter hybridisation in detecting HPV 16 DNA in the cervical cancer cell lines SiHa and CaSki. Cervical smears collected from 51 women with a history of one or more abnormal cervical smears were tested by both hybridisation techniques for the presence of HPV 16 DNA; 11 were positive in the in situ filter hybridisation, 35 in the dot blot hybridisation. Thirty-five cervical biopsies available from this group of 51 women were processed for dot blot hybridisation. In 30 of the 35 cases the results of this hybridisation corresponded with the results of the dot blot hybridisation on the smears.
Collapse
Affiliation(s)
- M T Cornelissen
- Department of Virology, University of Amsterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
11
|
Leer RJ, van Raamsdonk-Duin MM, Schoppink PJ, Cornelissen MT, Cohen LH, Mager WH, Planta RJ. Yeast ribosomal protein S33 is encoded by an unsplit gene. Nucleic Acids Res 1983; 11:7759-68. [PMID: 6196722 PMCID: PMC326528 DOI: 10.1093/nar/11.22.7759] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The structure of the gene coding for ribosomal protein S33, - a protein which escapes the coordinate control of ribosomal protein synthesis in rna 2 mutant cells -, was determined by sequence analysis. The gene comprises an uninterrupted coding region of 204 nucleotides encoding a protein of 8.9 kD. Like for other yeast ribosomal protein genes that have been sequenced so far, a relatively strong codon bias was observed. By S1 nuclease mapping the 5' end of the S33 mRNA was shown to be located at 11 to 15 nucleotides upstream from the initiation codon.
Collapse
|