Biomedical subjects

Marc Van Ranst

Publications and source records attributed to Marc Van Ranst.

At least 37 records · Page 2Linked to original sources

PubMed2005

Circulation of genetically distinct contemporary human coronavirus OC43 strains.

In this study, we report the complete genome sequence of two contemporary human coronavirus OC43 (HCoV-OC43) strains detected in 2003 and 2004, respectively. Comparative genetic analyses of the circulating strains and the prototype HCoV-OC43 strain (ATCC VR759) were performed. Remarkably, a lower than expected similarity is found between the complete genomes and more in particular between the spike genes of the BE03 and BE04 strains. This finding suggests the existence of two genetically distinct HCoV-OC43 strains, circulating in Belgium in 2003 and 2004. Spike gene sequencing of three additional 2003 and two additional 2004 HCoV-OC43 strains, and subsequent phylogenetic analysis confirm this assumption. Compared to the ATCC prototype HCoV-OC43 strain, an important amino acid substitution is present in the potential cleavage site sequence of the spike protein of all contemporary strains, restoring the N-RRXRR-C motif, associated with increased spike protein cleavability in bovine coronaviruses. We here describe specific characteristics associated with circulating HCoV-OC43 strains, and we provide substantial evidence for the genetic variability of HCoV-OC43.

Coronavirus Infections↗

PubMed2005

Progressive multifocal leukoencephalopathy after natalizumab therapy for Crohn's disease.

The prior diagnosis of fatal astrocytoma in a 60-year-old man with Crohn's disease treated with natalizumab, a monoclonal antibody against alpha4 integrins, was reclassified as JC virus-related progressive multifocal leukoencephalopathy (PML). Analysis of frozen serum samples showed that JC virus DNA had appeared in the serum three months after the initiation of open-label natalizumab monotherapy and two months before the appearance of symptomatic PML. There was staining of the brain lesion for polyomavirus. This case report, along with two others, suggests that anti-alpha4-integrin therapy can result in JC virus-induced PML.

Antibodies, Monoclonal↗

PubMed2005

Growth kinetics of SARS-coronavirus in Vero E6 cells.

Vero E6 cells are commonly used for in vitro studies of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and for antiviral evaluation purposes. A better understanding of the SARS-CoV growth kinetics in Vero E6 cells is crucial to help elucidate the mechanism of antiviral activity of selective antiviral agents. In this study, the growth kinetics of SARS-CoV in Vero E6 cells were studied by quantitation of intra- and extracellular viral RNA load as well as extracellular virus yield at different time points post-infection. At 12h post-infection, the intracellular viral RNA load was 3x10(2)-fold higher than at the time of infection, and the extracellular viral RNA load was increased with a factor of 2 x 10(3). Intracellular viral RNA levels started to rise at 6h post-infection. One hour later (at 7h post-infection), the levels of extracellular SARS-CoV RNA also began to rise. This was corroborated by the fact that infectious progeny SARS-CoV also first appeared in the supernatant between 6 and 7h post-infection. At 12h post-infection, SARS-CoV reached titers in the supernatant of 5.2 x 10(3) CCID(50)/ml.

Animals↗

PubMed2005

Typing of human rotaviruses: nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure.

BACKGROUND: Rotavirus genotyping is performed by using reverse transcription PCR with type-specific-primers. Because the high rotavirus mutation rate generates an extensive genomic variation, different G-type-specific primer sets are applied in different geographical locations. In Bangladesh, a significant proportion (36.9%) of the rotavirus strains isolated in 2002 could not be G-typed using the routinely used primer set. To investigate the reason why the strains were untypeable, nucleotide sequencing of the VP7 genes was performed. RESULTS: Four nucleotide substitutions at the G1 primer-binding site of the VP7 gene of Bangladeshi G1 rotaviruses rendered a major proportion of circulating strains untypeable using the routine primer set. Using an alternative primer set, we could identify G1 rotaviruses as the most prevalent genotype (44.8%), followed by G9 (21.7%), G2 (15.0%) and G4 (13.8%). CONCLUSION: Because of the natural variation in the rotaviral gene sequences, close monitoring of rotavirus genotyping methods is important.

Antigens, Viral↗

PubMed2005

Chromatography paper strip sampling of enteric adenoviruses type 40 and 41 positive stool specimens.

BACKGROUND: The enteric subgroup F adenoviruses type 40 (Ad40) and 41 (Ad41) are the second most important cause of acute infantile gastroenteritis after rotaviruses. Repeated community outbreaks have been associated with antigenic changes among the Ad40 and Ad41 strains due to host immune pressure. Therefore large field epidemiological surveys and studies on the genetic variations in different isolates of Ad40 and Ad41 are important for disease control programs, the design of efficient diagnostic kits and vaccines against subgroup F adenoviruses. A novel method using sodium dodecyl sulphate SDS/EDTA-pretreated chromatography paper strips was evaluated for the collection, storage and shipping of Ad40/41 contaminated stool samples. RESULTS: This study shows that adenoviral DNA can be successfully detected in the filter strips by PCR after four months storage at -20 degrees C, 4 degrees C, room temperature (20-25 degrees C) and 37 degrees C. Furthermore no adenoviral infectivity was observed upon contact with the SDS/EDTA-pretreated strips. CONCLUSIONS: Collecting, storing and transporting adenovirus type 40 and 41 positive stool samples on SDS/EDTA-pretreated chromatography filter strips is a convenient, biosafe and cost effective method for studying new genome variants and monitoring spread of enteric adenovirus strains during outbreaks.

Adenoviridae↗

PubMed2005

A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium.

BACKGROUND: Four human coronaviruses are currently known to infect the respiratory tract: human coronaviruses OC43 (HCoV-OC43) and 229E (HCoV-229E), SARS associated coronavirus (SARS-CoV) and the recently identified human coronavirus NL63 (HCoV-NL63). In this study we explored the incidence of HCoV-NL63 infection in children diagnosed with respiratory tract infections in Belgium. METHODS: Samples from children hospitalized with respiratory diseases during the winter seasons of 2003 and 2004 were evaluated for the presence of HCoV-NL63 using a optimized pancoronavirus RT-PCR assay. RESULTS: Seven HCoV-NL63 positive samples were identified, six were collected during January/February 2003 and one at the end of February 2004. CONCLUSIONS: Our results support the notation that HCoV-NL63 can cause serious respiratory symptoms in children. Sequence analysis of the S gene showed that our isolates could be classified into two subtypes corresponding to the two prototype HCoV-NL63 sequences isolated in The Netherlands in 1988 and 2003, indicating that these two subtypes may currently be cocirculating.

Adolescent↗

PubMed2005

Isolation and cloning of a papillomavirus from a North American porcupine by using multiply primed rolling-circle amplification: the Erethizon dorsatum papillomavirus type 1.

The complete genome of a novel papillomavirus was isolated from a cutaneous papillomatous lesion of a North American porcupine (Erethizon dorsatum) using multiply primed rolling-circle amplification (RCA). The nucleotide sequence, genome organization, and phylogenetic position of the Erethizon dorsatum papillomavirus type 1 (EdPV-1) were determined. EdPV-1 is only distantly related to other benign cutaneous papillomavirus sequences and is the first member of the novel Sigma papillomavirus genus.

Animals↗

PubMed2005

Predominance of rotavirus G9 genotype in children hospitalized for rotavirus gastroenteritis in Belgium during 1999-2003.

BACKGROUND: Group A rotavirus genotypes G1, G2, G3 and G4 are the main etiological agents of infantile diarrhea. The G9 rotavirus has recently emerged as a fifth important genotype all over the world. OBJECTIVE: To characterize the VP7 gene of group A rotaviruses from gastroenteritis patients admitted to the Gasthuisberg University Hospital, Leuven, Belgium, during 1999-2003. STUDY DESIGN: Rotavirus antigen was detected in stool specimens using an enzyme immunoassay. G-typing was performed by reverse transcriptase polymerase chain reaction (RT-PCR) amplification and sequencing of the complete VP7 gene. RESULTS: The genotype distribution varied markedly over the four rotavirus years in Belgium. In the 1999-2000 rotavirus year, G1 was the predominating type (72%), and G9 was present in 5% of the rotavirus-positive patients. In the 2000-2001 and 2002-2003 years, G9 appeared as the dominating strain (45% and 53%, respectively). In the 2001-2002 year, between two G9 epidemic years, G1 was dominating (66%) but G9 was still present in 24%. All the G9 isolates were combined with P[8] and shared a high gene sequence similarity (<3% sequence divergence on the nucleotide and amino acid level). Phylogenetic analysis of the VP7 genes revealed that our Belgian G9 strains clustered together with recent G9 strains from all over the world, distinct from the prototype G9 strains isolated in the 1980s. CONCLUSION: Our study indicates that although the first introduction of G9 isolates in the Belgian population was recorded in 1997, G9 strains were able to establish themselves quickly as the predominant genotype. The emergence of G9 as an important pathogen in both developing as industrialized countries necessitates the urgent consideration of the G9 moiety in rotavirus vaccines.

Antigens, Viral↗

PubMed2005

A genotypic resistance assay for the detection of drug resistance in the human immunodeficiency virus type 1 envelope gene.

Since it is not clear yet whether enfuvirtide resistance is restricted to gp41, it was decided to develop a genotypic assay for the detection of drug resistance in the entire human immunodeficiency virus type 1 (HIV-1) env gene. Given the increasing prevalence of HIV-1 non-B subtypes in Europe, it is important to evaluate the performance of the assay on a panel of genetically divergent samples. A panel of 1 laboratory and 10 clinical isolates from 10 patients was tested, all enfuvirtide naive and chosen according to the subtype as determined in the pol region (A, B, C, H, CRF01-AE, CRF02-AG, CRF05-DF, CRF11-cpx and U), while their env sequences belonged to subtypes A, B, C, H, A/G recombinant, B/H recombinant, CRF01-AE, CRF02-AG, CRF05-DF and CRF11-cpx. The detection limits of the gp120 and the gp41 PCRs ranged between 500 and 5000 RNA copies/ml plasma. The highest sensitivity was obtained for the laboratory strain, whereas the detection limit for all patient samples, except for the subtype C sample, was 1000 RNA copies/ml. The numerous insertions and deletions in the gp120 gene, that were often present as quasi-species, necessitated the sequencing of cloned PCR products. The gp41 gene displayed less diversity and less insertions/deletions. Especially, the heptad repeat 1 was highly conserved and none of the enfuvirtide naive samples contained any of the already known enfuvirtide resistance mutations at amino acid positions 36-45. This study demonstrates that the assay is able to genotype genetically diverse HIV-1 strains with a good sensitivity.

Drug Resistance, Viral↗

PubMed2005

Frequency of the CCR5-Delta32 mutant allele is not increased in Belgian hepatitis C virus-infected patients.

A 32-base pair deletion in the CC-chemokine receptor 5 gene (CCR5), associated with resistance to human immunodeficiency virus type 1 (HIV-1) infection, has recently been suggested to act as an adverse host factor in hepatitis C virus (HCV) infection. To examine this hypothesis, we determined the CCR5-Delta32 allele frequency by polymerase chain reaction in a Belgian cohort of 163 HCV-infected patients and 310 healthy control subjects. The resulting CCR5-Delta32 allele frequencies were 0.080 and 0.119 for the patient group and control group, respectively. In contrast with a previous study, we could not show a statistically significant difference between the CCR5-Delta32 allele frequencies in HCV patients and controls. Moreover, genotype distributions in both populations were in agreement with Hardy-Weinberg equilibrium. Our results do not support the hypothesis that the CCR5-Delta32 mutant allele is a risk factor for hepatitis C virus infection.

Belgium↗

PubMed2005

Crohn's disease and month of birth.

BACKGROUND: Environmental factors trigger the onset of inflammatory bowel disease (IBD) in genetically predisposed individuals. Exposure to seasonal external factors during the maturation of the immune system is suspected to be an inducing factor for IBD. Some studies suggested an association between the month of birth and the later development of IBD. We studied this putative relationship in a large cohort of Belgian patients with Crohn's disease (CD). METHODS: Data from 1025 patients born between 1935 and 1990 were collected. Diagnosis of CD was based on generally accepted clinical, endoscopic, and histologic criteria. As a control group, a cohort of 5125 non-IBD patients seen at the same hospital and matched for birth year and sex was used. Odds ratios were calculated using multivariate unconditional logistic regression including the matching variables and allowing for cyclic variation in risk with month of birth. RESULTS: A cyclic pattern described by a 4-month periodic function was observed with peaks in April and August. Moreover, being born in June significantly reduced the risk of developing CD later in life (P = 0.012). CONCLUSION: In this Belgian cohort, a significant association was found between the month of birth and later development of IBD; a significant reduced risk to develop CD was observed for people born in June. Moreover, environmental yearly reoccurring factors during pregnancy or postpartum might be associated with the occurrence of CD later in life.

Adolescent↗

PubMed2005

Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primers.

Partial sequences of a novel papillomavirus were amplified from a cutaneous lesion biopsy of a raccoon (Procyon lotor), by using PCR with degenerate papillomavirus-specific primers. The Procyon lotor papillomavirus type 1 (PlPV-1) DNA was amplified with long template PCR in two overlapping fragments, together encompassing the entire genome, and the complete PlPV-1 genomic sequence was determined. The PlPV-1 genome consists of 8170 bp, and contains the typical papillomaviral open reading frames, encoding five early proteins and two late capsid proteins. Besides the classical non-coding region (NCR1) between the end of L1 and the start of E6, PlPV-1 contains an additional non-coding region (NCR2) of 1065 bp between the early and late protein region, which has previously also been described for the canine oral papillomavirus (COPV) and the Felis domesticus papillomavirus (FdPV-1). Phylogenetic analysis places PlPV-1 together with COPV and FdPV-1 in a monophyletic branch which encompasses the Lambda papillomavirus genus.

Animals↗

PubMed2005

Development of one-step, real-time, quantitative reverse transcriptase PCR assays for absolute quantitation of human coronaviruses OC43 and 229E.

The clinical significance of human coronaviruses in more severe respiratory illnesses has recently been shown to be higher than was previously assumed. Rapid and reliable diagnosis of human coronavirus infections therefore becomes indispensable in a routine clinical setting. In this study, we present a very sensitive and specific TaqMan-based, real-time quantitative reverse transcriptase PCR (qRT-PCR) for the rapid detection and quantitation of human coronaviruses (HCoVs) OC43 and 229E. Absolute viral load measurement in clinical samples was achieved through the construction of in-house HCoV OC43 and 229E cRNA standards for the generation of a standard curve. The HCoV OC43 assay allows quantitation over a range from 20 to 2 x 10(8) RNA copies per reaction mixture (5 microl RNA extract). When this is extrapolated to clinical samples, this corresponds to a detection range of 10(3) to 10(10) viral genome equivalents per ml. By using the HCoV 229E qRT-PCR assay, viral RNA copies ranging from 200 to 2 x 10(9) per reaction mixture can be detected, which corresponds to 10(4) to 10(11) viral genome equivalents per ml sample. A total of 100 respiratory samples screened for the presence of HCoVs OC43 and 229E by using conventional RT-PCR were assessed in parallel by the qRT-PCR assays. By use of the real-time qRT-PCR techniques, the detection rate of HCoVs OC43 and 229E increased from 2.0% to 3.1% and from 0.3% to 2.5%, respectively. The real-time qRT-PCR assays described here allow the rapid, specific, and sensitive laboratory detection and quantitation of human coronaviruses OC43 and 229E.

Child↗

PubMed2005

Use of a commercially available line probe assay for genotyping of hepatitis C virus 5a strains.

To validate a commercially available line probe assay for samples containing the infrequently found hepatitis C virus (HCV) genotype 5a, we sequenced a 511-nucleotide fragment of the NS4b region of Belgian and South African HCV genotype 5a samples. Phylogenetic analysis of the sequence data was performed. For the 77 HCV genotype 5a samples collected, there was 100% concordance between the genotype assignment by the line probe assay and the genotyping based on nucleotide sequencing, despite sequence heterogeneity in the probe binding sites of some samples.

5' Untranslated Regions↗

PubMed2005

Characterization of a novel P[25],G11 human group a rotavirus.

A novel rotavirus strain (Dhaka6) isolated from a 21-year-old Bangladeshi male patient was characterized by sequence analysis of its VP7 and VP4 gene segments. Phylogenetic analysis of the VP7 gene of the Dhaka6 strain revealed a common evolutionary lineage with porcine G11 rotavirus strains. This isolate is the first reported G11 rotavirus strain infecting a human host. Comparison of the VP4 gene sequences with all currently recognized 24 different P genotypes revealed only low nucleotide (54 to 71%) and amino acid (52 to 76%) sequence identities. This lack of high sequence similarity in the VP4 gene indicates that the Dhaka6 isolate represents a new group A rotavirus P genotype, to which we propose assignment of the designation P[25].

Adult↗

PubMed2005

Detection and characterization of human group C rotaviruses in Bangladesh.

Group C rotaviruses were detected by reverse transcription-PCR in 14 (2.3%) of 611 group A rotavirus-negative stool specimens from the patients admitted to the International Centre for Diarrhoeal Disease Research, Bangladesh hospital, Dhaka, Bangladesh, during July to December 2003. The low rate of detection suggested that infection with group C rotaviruses was an uncommon cause of hospitalization due to gastroenteritis. In addition, coinfections with pathogenic enteric bacteria were frequently observed in group C rotavirus-infected patients. Nucleotide sequence comparison of the VP4, VP6, and VP7 genes revealed that the Bangladeshi group C rotaviruses were most similar to Nigerian group C rotavirus strains. Phylogenetic analysis suggested that all human group C rotaviruses, including the strains isolated in our study, clustered in a monophyletic branch, which was distantly related to the branch comprised of animal group C rotaviruses.

Adolescent↗

PubMed2005

Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G protein.

Human respiratory syncytial virus (HRSV) is the most important cause of acute respiratory disease in infants. Two major subgroups (A and B) have been identified based on antigenic differences in the attachment G protein. Antigenic variation between and within the subgroups may contribute to reinfections with these viruses by evading the host immune responses. To investigate the circulation patterns and mechanisms by which HRSV-B viruses evolve, we analyzed the G protein genetic variability of subgroup B sequences isolated over a 45-year period, including 196 Belgian strains obtained over 22 epidemic seasons (1982 to 2004). Our study revealed that the HRSV-B evolutionary rate (1.95 x 10(-3) nucleotide substitutions/site/year) is similar to that previously estimated for HRSV-A (1.83 x 10(-3) nucleotide substitutions/site/year). However, natural HRSV-B isolates appear to accommodate more drastic changes in their attachment G proteins. The most recent common ancestor of the currently circulating subgroup B strains was estimated to date back to around the year 1949. The divergence between the two major subgroups was calculated to have occurred approximately 350 years ago. Furthermore, we have identified 12 positively selected sites in the G protein ectodomain, suggesting that immune-driven selective pressure operates in certain codon positions. HRSV-A and -B strains have similar phylodynamic patterns: both subgroups are characterized by global spatiotemporal strain dynamics, where the high infectiousness of HRSV permits the rapid geographic spread of novel strain variants.

Amino Acid Sequence↗

PubMed2005

Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event.

Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR759). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 x 10(-4) nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak.

Animals↗