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1.
J Appl Microbiol ; 130(1): 292-301, 2021 Jan.
Article in English | MEDLINE | ID: mdl-32639660

ABSTRACT

AIMS: The aim of the present study was to develop a colorimetric LAMP assay for the detection of enteroviruses belonging to species A-D targeting the 5' untranslated region (5' UTR) of enteroviruses genome. METHODS AND RESULTS: The RNA was converted to cDNA by the reverse transcriptase and then amplified via LAMP by the WarmStart®Bst DNA polymerase, simultaneously in a single reaction tube, so we shortened the reaction time to 50 min. The sensitivity of the assay regarding Enterovirus B, C and D was determined to be 0·30 CCID50 assay-1 while the sensitivity for Enterovirus A was 3·00 CCID50 assay-1 . The assay demonstrated high specificity and sensitivity for the detection of 45 reference strains of Enteroviruses A-D and validated on 20 clinical isolates. CONCLUSIONS: This assay can be used as a diagnostic tool for the rapid, sensitive and specific detection of enteroviruses, easily implemented in small clinical and research laboratories since LAMP amplicons were visualized by colour changes eliminating the requirement for post-amplification processing steps. SIGNIFICANCE AND IMPACT OF THE STUDY: We developed a colorimetric assay ideal for field situations for the detection of enteroviruses, by targeting the 5' UTR. This assay demonstrated high specificity and sensitivity, based on its performance on 45 EV A-D reference strains, on 20 EV B clinical isolates and on three non-enteroviral RNA viruses.


Subject(s)
5' Untranslated Regions/genetics , Colorimetry , Enterovirus/isolation & purification , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , Enterovirus/genetics , Enterovirus Infections/virology , Genome, Viral/genetics , Humans , RNA Viruses/genetics , RNA Viruses/isolation & purification , Reproducibility of Results , Sensitivity and Specificity
2.
J Med Microbiol ; 67(11): 1638-1644, 2018 Nov.
Article in English | MEDLINE | ID: mdl-30303478

ABSTRACT

PURPOSE: The tumour suppressor protein RB plays a decisive role in negative control of the cell cycle, inhibiting tumour development. The present analysis investigated the prevalence of the nucleotide polymorphism A153104G, which is located at intron 18 of the RB1 gene, and investigated the impact of the polymorphic variability in the exon 19 and its flanking intronic sequences on the severity of cervical disease in HPV16-positive Greek women. METHODOLOGY: The nucleotide polymorphism A153104G was detected by PCR-RFLP assay, while the amplicons were further subjected to cloning and sequencing. Moreover, molecular evolutionary analysis was performed using the maximum-likelihood (ML) and empirical Bayesian (EB) methods in order to evaluate the selective pressure acting on exon 19 of the RB1 gene.Results/Key findings. The A153104G nucleotide polymorphism was only detected in one control case. Moreover, sequence analysis of the amplicons revealed that the polymorphic variability in the RB1 gene increased with the severity of the cervical dysplasia. The link between the observed polymorphic variability and the progress of cervical disease was reflected in the molecular evolutionary analysis that was performed on the exon 19 of the RB1 gene, since negative selective pressure was acting upon exon 19 in the control and low-grade squamous intraepithelial lesion (LSIL) cervical samples, while positive selective pressure was acting upon exon 19 in the high-grade squamous intraepithelial lesion (HSIL) specimens. CONCLUSIONS: The A153104G nucleotide polymorphism did not emerge as a potential biomarker for the development of precancerous lesions in the Greek patients, while the accumulation of sequence variations in RB1 gene might influence patients' susceptibility towards the progression of cervical neoplasia.


Subject(s)
Human papillomavirus 16/isolation & purification , Polymorphism, Genetic , Precancerous Conditions , Retinoblastoma Binding Proteins/genetics , Ubiquitin-Protein Ligases/genetics , Uterine Cervical Dysplasia/genetics , Uterine Cervical Neoplasms/genetics , Bayes Theorem , Biomarkers, Tumor/genetics , Case-Control Studies , DNA, Viral/genetics , Evolution, Molecular , Exons/genetics , Female , Genotype , Greece/epidemiology , Human papillomavirus 16/genetics , Humans , Introns/genetics , Papillomavirus Infections/epidemiology , Papillomavirus Infections/virology , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , Precancerous Conditions/genetics , Prospective Studies , Torticollis/genetics , Uterine Cervical Neoplasms/ethnology , Uterine Cervical Neoplasms/virology , Uterine Cervical Dysplasia/ethnology , Uterine Cervical Dysplasia/virology
3.
Lett Appl Microbiol ; 65(3): 234-240, 2017 Sep.
Article in English | MEDLINE | ID: mdl-28631392

ABSTRACT

In this report a strand specific RT-PCR was established for the detection of the replicative negative RNA strand of poliovirus sabin 1 (Sabin1) and Echovirus 19 (E19) strains. The key for the successful conduction of the assay was the use of a specific reverse transcription primer targeting the 5'-UTR of enteroviruses that consisted of a stem-loop structure at the 5'-end and an enteroviral-specific sequence at the 3'-end. The stem loop RT-PCR was found to be an accurate and sensitive method, detecting even 10-2 CCID50 of poliovirus sabin 1 (Sabin1) and E19 strains 6 h postinfection (p.i.), while CPE appeared 3 days later. This assay was also validated in SiHa and Caski cell lines that are not used for the detection of enteroviruses. The negative RNA strand was detected 6 h and 12 h p.i. in SiHa and Caski cells, when these cell lines were inoculated with 105 and 1 CCID50 respectively, whereas CPE was observed 5 days p.i for SiHa cells and 8 days p.i for Caski cells and that only at 105 CCID50 . The results show that this approach may be used for replacing the time-consuming cell cultures in order to detect the active replication of enteroviruses. SIGNIFICANCE AND IMPACT OF THE STUDY: Enteroviruses are positive stranded RNA viruses that may cause severe diseases. The conventional method for detection of active viral replication involves virus isolation in sensitive cell cultures followed by titration and seroneutralization. In this report, we describe the use of a stem-loop secondary structured oligonucleotide in RT-PCR assay for the detection of the replicative negative strand of the positive-stranded RNA of poliovirus sabin 1 and E19 strains. This approach proved to be a useful tool that may be used for replacing the time-consuming cell culture assays in order to detect the active replication of enteroviruses.


Subject(s)
Enterovirus B, Human/genetics , Enterovirus Infections/virology , Poliomyelitis/virology , Poliovirus/genetics , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , Cell Line , DNA Primers/genetics , Enterovirus B, Human/isolation & purification , Humans , Poliovirus/isolation & purification , Reverse Transcription
4.
Virus Genes ; 52(4): 453-62, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27098645

ABSTRACT

Polioviruses (PVs) are the causal agents of acute paralytic poliomyelitis. Since the 1960s, poliomyelitis has been effectively controlled by the use of two vaccines containing all three serotypes of PVs, the inactivated poliovirus vaccine and the live attenuated oral poliovirus vaccine (OPV). Despite the success of OPV in polio eradication programme, a significant disadvantage was revealed: the emergence of vaccine-associated paralytic poliomyelitis (VAPP). VAPP is the result of accumulated mutations and putative recombination events located at the genome of attenuated vaccine Sabin strains. In the present study, ten Sabin isolates derived from OPV vaccinees and environmental samples were studied in order to identify recombination types located from VP1 to 3D genomic regions of virus genome. The experimental procedure that was followed was virus RNA extraction, reverse transcription to convert the virus genome into cDNA, PCR and multiplex-PCR using specific designed primers able to localize and identify each recombination following agarose gel electrophoresis. This multiplex RT-PCR assay allows for the immediate detection and identification of multiple recombination types located at the viral genome of OPV derivatives. After the eradication of wild PVs, the remaining sources of poliovirus infection worldwide would be the OPV derivatives. As a consequence, the immediate detection and molecular characterization of recombinant derivatives are important to avoid epidemics due to the circulation of neurovirulent viral strains.


Subject(s)
Multiplex Polymerase Chain Reaction/methods , Poliovirus/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , DNA Primers/genetics , Genome, Viral/genetics , Humans , Poliomyelitis/immunology , Poliomyelitis/virology , Poliovirus/immunology , Poliovirus Vaccine, Oral/immunology , RNA, Viral/genetics , Recombination, Genetic/genetics
5.
Mol Cell Probes ; 30(1): 6-12, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26627739

ABSTRACT

Integration of HPV16 DNA into the host chromosome is considered to be a crucial step towards genomic instability and cervical cancer development. Aim of the present study was to investigate the presence of HPV16 rearranged intra-viral sequences in HPV16-positive normal, precancerous and cervical cancer samples using the method of Restriction Site-PCR (RS-PCR). Sequence analysis of HPV16 integrants revealed for the first time in clinical samples two distinct rearranged intra-viral sequences, concerning the conjunction of E2 and L1 genes and the conjunction of E1 and L1 genes with inverted orientation. Furthermore mapping analysis of the E1 and E2 genes in cervical samples with rearranged intra-viral sequences of HPV16 genome was conducted in order to determine the integrity of viral genes. The identification of intra-viral rearrangements provides valuable information regarding the HPV16 DNA integration, and may be a significant biomarker for the presence of chromosomal instability and DNA damages in clinical samples.


Subject(s)
DNA, Viral/genetics , Human papillomavirus 16/genetics , Papillomavirus Infections/virology , Precancerous Conditions/virology , Uterine Cervical Dysplasia/virology , Uterine Cervical Neoplasms/virology , Base Sequence , Cell Line, Tumor , DNA, Viral/chemistry , Female , Gene Rearrangement , Genes, Viral/genetics , Humans , Polymerase Chain Reaction , Sequence Analysis, DNA/methods
6.
J Med Virol ; 87(11): 1973-80, 2015 Nov.
Article in English | MEDLINE | ID: mdl-25959607

ABSTRACT

Integration of HPV16 DNA into the host chromosome usually disrupts the E1 and/or E2 genes. The present study investigated the disruption of E1, E2 genes in a total of eighty four HPV16-positive precancerous and cervical cancer specimens derived from Greek women (seventeen paraffin-embedded cervical biopsies and sixty seven Thin Prep samples). Complete E2 and E1 genes were amplified using three and nine overlapping primer sets respectively, in order to define the sites of disruption. Extensive mapping analysis revealed that disruption/deletion events within E2 gene occurred in high grade and cervical cancer samples (x(2) test, P < 0.01), while no evidence of E2 gene disruption was documented among low grade cervical intraepithelial neoplasias. In addition, disruptions within the E1 gene occur both in high and low grade cervical intraepithelial neoplasia. This leads to the assumption that in low grade cervical intraepithelial neoplasias only E1 gene disruption was involved (Fisher's exact test, P < 0.05), while in high grade malignancies and cervical cancer cases deletions in both E1 and E2 genes occurred. Furthermore, the most prevalent site of disruption of E1 gene was located between nucleotides 1059 and 1323, while the most prevalent deleted region of the E2 gene was located between nucleotides 3172 and 3649 (E2 hinge region). Therefore, it is proposed that each population has its own profile of frequencies and sites of disruptions and extensive mapping analysis of E1 and E2 genes is mandatory in order to determine suitable markers for HPV16 DNA integration analysis in distinct populations.


Subject(s)
DNA-Binding Proteins/genetics , Human papillomavirus 16/physiology , Oncogene Proteins, Viral/genetics , Uterine Cervical Dysplasia/pathology , Uterine Cervical Neoplasms/pathology , Virus Integration , Female , Greece , Human papillomavirus 16/genetics , Humans , Sequence Deletion , Uterine Cervical Neoplasms/virology , Uterine Cervical Dysplasia/virology
7.
Mol Cell Probes ; 29(1): 13-8, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25281890

ABSTRACT

Long-term infection with high-risk HPV genotypes is the leading cause of cervical cancer. In the present study a Duplex Real-time PCR assay was developed in order to identify HPV types 16, 18, 31, 35, 51 and 66 in three reactions, through SYBR green I melting curve analysis. The method utilizes type-specific primer sets that allowed the amplification of highly conserved regions of L1 gene. Reconstitution experiments were conducted by using HPV DNA plasmids in order to determine the sensitivity of the assay. The newly designed assay has a limit of detection of 10 copies per reaction. The most prevalent HPV genotype in single and in multiple HPV infections was HPV16 followed by HPV18, HPV51, HPV31, HPV35 and HPV66. The proposed method is a simple, specific, sensitive and cost-effective assay that can be easily incorporated in small and medium size laboratories for the rapid identification of the most clinically important HPV genotypes.


Subject(s)
Multiplex Polymerase Chain Reaction/methods , Papillomaviridae/classification , Papillomaviridae/isolation & purification , Papillomavirus Infections/diagnosis , DNA, Viral/analysis , Female , Genotype , Humans , Multiplex Polymerase Chain Reaction/economics , Papillomaviridae/genetics , Papillomavirus Infections/virology , Sensitivity and Specificity , Transition Temperature
8.
Arch Virol ; 160(1): 207-14, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25344303

ABSTRACT

The causal association between persistent human papillomavirus (HPV) infection and cervical cancer has lead to the development of a variety of molecular assays for HPV detection. The present study focused on the development of a simple, sensitive and cost-effective HPV genotyping method based on multiplex PCR methodology that could be easily performed in small laboratories. Three multiplex PCR assays were developed to identify the HPV genotypes 16, 18, 45, 35, 66, 33, 51, 58, and 31 together with an internal control. The method was established by designing nine type-specific primer sets that target conserved regions of the L1 gene. The assay was applied using HPV-positive cervical specimens, and cloning and sequencing of all of the amplicons that were generated were performed to examine the specificity of the newly designed primers. Moreover, an experimental cutoff value was determined through reconstitution experiments using HPV DNA plasmids. Amplicons of expected size were obtained, while cloning and sequencing of PCR products confirmed the genomic specificity of the amplicons. The sensitivity of this method was determined to be 10 copies of each individual HPV genotype per test. Multiple and single HPV infections were documented in 42.2 % and 57.8 % of cervical specimens, respectively. The most prevalent HPV genotype was HPV16, followed by HPV18, HPV66 and HPV51. The present multiplex PCR assay is a simple method with high specificity and sensitivity that can be applied in clinical or epidemiological analyses for rapid identification of the most clinically important HPV genotypes present in cervical intraepithelial neoplasias.


Subject(s)
Genotype , Multiplex Polymerase Chain Reaction/methods , Papillomaviridae/genetics , Papillomaviridae/isolation & purification , DNA, Viral/genetics , Humans , Plasmids , Sensitivity and Specificity
9.
Mol Cell Probes ; 28(4): 204-10, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24751495

ABSTRACT

Noroviruses (NoVs) are a major causative agent of acute gastroenteritis in humans. They are members of the Caliciviridae family and based on the genetic analysis of the RdRp and capsid regions, human NoVs are divided into three genogroups (Gs), GI, GII, and GIV. The three genogroups further segregate into distinct lineages called genotypes. The NoV genus is genetically diverse and recombination of viral RNA is known to depend upon various immunological and intracellular constraints that may allow the emergence of viable recombinants. In this study, three Noroviral strains detected in clinical samples revealed two hitherto unobserved recombination events between GII.9/GII.4 and GII.9/GI.7 genogroups. To our knowledge, these intergenotype and intergenogroup recombination events of GII.9/GII.4 and GII.9/GI.7, in ORF1 and ORF2 genes respectively are reported for the first time and highlight the ongoing evolution of noroviruses.


Subject(s)
Caliciviridae Infections/virology , Gastroenteritis/virology , Norovirus/genetics , Norovirus/isolation & purification , Reassortant Viruses/genetics , Adolescent , Base Sequence , Female , Genotype , Greece , Humans , Male , Molecular Sequence Data , Norovirus/classification , Open Reading Frames , Phylogeny , RNA, Viral/genetics
10.
J Med Virol ; 86(5): 778-84, 2014 May.
Article in English | MEDLINE | ID: mdl-24519452

ABSTRACT

Recent studies have focused on sequence variation of the HPV16 E1 gene. The present study investigates the prevalence of E1-1374^63nt duplication in the Greek population, and the sequence variation at the 5' end of the E1 and E6 genes from samples that harbored this genetic alteration. Fifty HPV16 positive cervical samples, derived from Greek patients were investigated. The 5' end of the E1 gene was amplified through PCR and the variant amplicons were cloned, sequenced, and bioinformatically analyzed for selective pressure. The E1-1374^63nt duplication was identified in 24% of the examined samples, with the same prevalence in both high and low-grade cervical malignancies. The E1-1374^63nt duplication was linked to the European variant lineage (x² = 5.076, P < 0.024) and it was significantly associated with the nucleotide variation A1053C (x² = 23.102, P < 0.0001). Molecular evolution analyses anticipate that the E1-1374^63nt duplication induces functional constraints on the 5' end of E1 gene, and it is proposed that this duplication might not affect negatively the function or structure of the E1 protein. The E1-1374^63nt duplication is prevalent in the Greek population, whereas the A1053C variation might constitute a significant marker for the characterization of the E1-1374^63nt variant in the Greek population, thus providing significant information about viral pathogenicity.


Subject(s)
Human papillomavirus 16/classification , Human papillomavirus 16/isolation & purification , Oncogene Proteins, Viral/genetics , Papillomavirus Infections/epidemiology , Papillomavirus Infections/virology , Cluster Analysis , DNA, Viral/chemistry , DNA, Viral/genetics , Female , Genotype , Greece/epidemiology , Human papillomavirus 16/genetics , Humans , Molecular Epidemiology , Molecular Sequence Data , Mutation , Phylogeny , Polymerase Chain Reaction , Prevalence , Sequence Analysis, DNA
11.
Mol Cell Probes ; 28(4): 107-12, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24315968

ABSTRACT

Poliomyelitis has been effectively controlled by the use of inactivated poliovirus vaccine (IPV) or trivalent live attenuated oral poliovirus vaccine (OPV). Since 1964, the use of OPV in mass vaccinations has resulted in drastic reductions of the number of poliomyelitis cases caused by wild-type polioviruses. However, the characterization of OPV derivatives with increased neurovirulence, constituted a real problem with respect to OPV safety. Mutations at attenuating sites of the genome and recombination events between Sabin strains of the trivalent OPV vaccine have been correlated with the loss of the attenuated phenotype of OPV strains and the acquisition of traits characteristic of wild polioviruses. In consequence, early detection and characterization of recombinant evolved derivatives of vaccine strains is highly important. In this report, ten PCR assays are described which allow for the identification of rare recombination events located in VP1, 2A, 2C, 3A, 3C and 3D genomic regions and predominant recombination events located in 2C and 3D genomic regions of OPV derivatives. These assays could be readily implemented in diagnostics laboratories lacking sequencing facilities as a first approach for the early detection and characterization of recombinant OPV derivatives.


Subject(s)
Poliovirus Vaccine, Oral/genetics , Recombination, Genetic , Reverse Transcriptase Polymerase Chain Reaction/methods , Genome, Viral , Humans , Poliomyelitis/prevention & control , Poliovirus Vaccine, Oral/classification , Poliovirus Vaccine, Oral/isolation & purification , RNA, Viral/analysis
12.
Arch Virol ; 159(1): 51-63, 2014 Jan.
Article in English | MEDLINE | ID: mdl-23881083

ABSTRACT

The E1 ORF is one of the most conserved regions in the human papillomavirus (HPV) genome. The complete E1 gene of the HPV16 genome was amplified with four overlapping primer sets in 16 high-grade (CIN II, III) and 13 low-grade cervical (CIN I) intraepithelial neoplasias as well as in one cervical cancer case. Sequence analysis of the E6 and E7 genes was also carried out in the same cervical samples in order to confirm the association between nucleotide sequence variations in the HPV16 E1 ORF and HPV16 variant lineages. Analysis of the E1 ORF revealed 27 nucleotide changes, and these changes were correlated with those found in HPV16 Asian American and African type II variants. Of these nucleotide variations, A1668G, G2073A, T2169C, T2189C, A2453T, C2454T, A2587T and G2650A were identified only in high-grade dysplasia cases. A phylogenetic tree of the E1 ORF and nucleotide sequence analysis of the E1, E6 and E7 genes revealed that intratypic nucleotide sequence polymorphisms located in the E1 ORF can be used to identify the major phylogenetic branch to which a HPV16 genome belongs. Moreover, amplification of the E1 ORF revealed a disruption between nucleotides 878 and 1523 in five high- and two low-grade cervical cases, indicating that integration of HPV DNA occurs at an early stage of viral infection.


Subject(s)
Human papillomavirus 16/genetics , Oncogene Proteins, Viral/genetics , Polymorphism, Single Nucleotide , Uterine Cervical Dysplasia/virology , Uterine Cervical Neoplasms/virology , Adult , Base Sequence , Female , Human papillomavirus 16/classification , Human papillomavirus 16/isolation & purification , Humans , Middle Aged , Molecular Sequence Data , Open Reading Frames , Papillomavirus Infections/virology , Phylogeny
13.
Virus Genes ; 48(1): 23-31, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24142407

ABSTRACT

Noroviruses (NoVs) are members of the Caliciviridae family and are recognized as a worldwide cause of acute nonbacterial gastroenteritis. Based on the genetic analysis of the RdRp and capsid regions, human NoVs are divided into three genogroups (Gs), GI, GII, and GIV, which further segregate into distinct lineages called genotypes. In this study, in an attempt to discern the circulation of an intergenotypic recombinant GII.9/GII.6, which was previously reported by our group in central Greece, we investigated NoVs in raw sewages from 2006 to 2011 and compared the results with the viruses detected from clinical samples in the same area and in the same time period. Two specific primer pairs for NoVs were designed which amplified in a single PCR fragment from polymerase to capsid gene covering the widespread recombination point in ORF1/ORF2 junction. Based on the genetic analysis, recombinant NoV strains GII.9/GII.6 were identified. Fourteen out of 15 environmental and eight out of ten clinical samples that were used in the present study were positive, with both primer pairs, confirming that the intergenotypic recombinant GII.9/GII.6 was circulating in the population of central Greece from 2006 to 2011. The crossover point was identified to be within the overlapping region of ORF1/ORF2 (GII.9/GII.6, respectively) and was determined by Simplot at nucleotide position 5,032 bp.


Subject(s)
Caliciviridae Infections/epidemiology , Genetic Variation , Norovirus/classification , Norovirus/genetics , Sewage/virology , Caliciviridae Infections/virology , Child , Child, Preschool , Cluster Analysis , Genotype , Greece/epidemiology , Humans , Molecular Epidemiology , Molecular Sequence Data , Norovirus/isolation & purification , Phylogeny , RNA, Viral/genetics , Recombination, Genetic , Sequence Analysis, DNA
14.
J Med Microbiol ; 62(Pt 11): 1688-1696, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23946477

ABSTRACT

Human papillomavirus type 16 (HPV16) non-European variants have been associated with persistent infection and cervical cancer development, while the L83V variant of the E6 gene has been correlated with the progression of cervical malignancy. The present study investigated the presence of the HPV16 L83V variant in Greek women. Molecular evolutionary analysis of the HPV16 E6 and E7 oncogenes was conducted in order to estimate the evolution of the HPV16 genome in the Greek population. The E6 L83V variant was found in 78.2 % of high- and 64.28 % of low-grade specimens. Moreover, the prototype and E6 L83V variants were both prevalent in high- and low-grade malignancies in Greek women. Selective pressure analysis of the individual amino acid residues of HPV16 sequences from the Greek population indicates that codon 83 of the E6 protein, as well as codon 85 of the E7 protein, are undergoing positive selection. Novel sequence variations were recorded within the E6 and E7 genes in cervical samples, characterized as (T350G) European variants. However, no signal of intratypic recombination event was identified within the E6-E7 region. Molecular and evolutionary analyses of HPV16 genomes from distinct geographical locations might provide valuable information about viral evolution and oncogenecity.


Subject(s)
Human papillomavirus 16/genetics , Human papillomavirus 16/isolation & purification , Oncogene Proteins, Viral/genetics , Papillomavirus E7 Proteins/genetics , Papillomavirus Infections/virology , Polymorphism, Genetic , Repressor Proteins/genetics , Adult , DNA, Viral/chemistry , DNA, Viral/genetics , Female , Genotype , Greece , Human papillomavirus 16/classification , Humans , Middle Aged , Molecular Epidemiology , Molecular Sequence Data , Papillomavirus Infections/epidemiology , Phylogeography , Sequence Analysis, DNA
15.
Arch Virol ; 158(4): 821-8, 2013 Apr.
Article in English | MEDLINE | ID: mdl-23208280

ABSTRACT

The rate of evolution of the human papillomavirus 16 (HPV16) genome is low. However, the ability of the E6 oncoprotein to interact with distinct p53 variants causes selective pressure on the E6 gene. In addition, intratypic recombination events in the HPV16 E6 and E7 genes have been characterized as extraordinary phenomena during the evolutionary history of virus. In the present study, we identified two new sequence variants through nucleotide analysis of the E6-E7 region of the HPV16 genome. Maximum-likelihood and empirical Bayesian methods were used in order to identify positive selection at particular residues of the E6 and E7 genes. Using the single recombination breakpoint (SBP) method, we found evidence of recombination events in the E6 ORF. Nucleotide sequence analysis showed that the new sequence variants are phylogenetically distant from the other members of the population. Our results indicate that new evolutionary intermediates of HPV16 might be formed either though positive selective pressure or through recombination events by multiple infections with distinct HPV16 variants.


Subject(s)
Genetic Variation , Human papillomavirus 16/genetics , Oncogene Proteins, Viral/genetics , Papillomavirus E7 Proteins/genetics , Papillomavirus Infections/virology , Repressor Proteins/genetics , Base Sequence , Bayes Theorem , Cervix Uteri/virology , Cloning, Molecular , Evolution, Molecular , Female , Genome, Viral , Greece/epidemiology , Humans , Likelihood Functions , Oncogene Proteins, Viral/chemistry , Papillomavirus E7 Proteins/chemistry , Papillomavirus Infections/epidemiology , Phylogeny , Repressor Proteins/chemistry
16.
Arch Virol ; 157(9): 1729-39, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22684534

ABSTRACT

The HPV16 E1(∧)E4 protein is thought to contribute to the release of newly formed viral particles from infected epithelia. In order to investigate amino acid mutations in the HPV16 E1(∧)E4 protein, the complete E4 ORF was amplified by PCR in 27 HPV16-positive cervical samples, and the amplicons were cloned. Fifteen nucleic acid variations were identified in the E4 ORF, including seven silent nucleic acid mutations. In addition, nine amino acid mutations (A7V, A7P, L16I, D45E, L59I, L59T, Q66P, S72F, H75Q) were detected in the E1(∧)E4 protein, and these were associated with the severity of cervical malignancy. A maximum-likelihood phylogenetic tree was constructed based on the E4 ORF, and nucleotide sequence analysis of the E4, E6 and E7 genes from the same samples was conducted in order to determine the phylogenetic origin of the cloned sequences from the amplified HPV16 E4. Based on the nucleotide sequence and phylogenetic analysis it was revealed that even though E4 ORF constitutes a small polymorphic portion of the viral genome (288 bp), it could provide valuable information about the origins of the HPV16 genome. In addition, molecular evolutionary analysis of the E4 coding region revealed that neutral selection is dominant in the overlapping region of the E4 and E2 ORFs.


Subject(s)
Human papillomavirus 16/classification , Human papillomavirus 16/genetics , Oncogene Proteins, Viral/genetics , Papillomavirus Infections/epidemiology , Papillomavirus Infections/virology , Amino Acid Substitution , Cluster Analysis , DNA, Viral/chemistry , DNA, Viral/genetics , Female , Genotype , Greece/epidemiology , Human papillomavirus 16/isolation & purification , Humans , Molecular Epidemiology , Molecular Sequence Data , Mutation, Missense , Phylogeny , Sequence Analysis, DNA
17.
Arch Virol ; 157(5): 825-32, 2012 May.
Article in English | MEDLINE | ID: mdl-22294445

ABSTRACT

The E2 gene of human papilloma virus is expressed at the early stage of the viral life cycle, encoding the E2 transcription factor, and regulates the expression of E6 and E7 oncogenes. Disruption of E2 gene due to viral integration inhibits the transcriptional suppression of the HPV oncogenes, inducing cell proliferation. In the present study, a total of 22 HPV16-positive cytological specimens derived from high- and low-grade cervical intraepithelial lesions were investigated in order to identify sequence variations in the HPV16 E2 ORF. The E2 gene was amplified by PCR using external and internal overlapping sets of primers. Amplicons were cloned and sequenced. Disruption sites were detected in cervical samples diagnosed as high-grade cervical intraepithelial lesions. Moreover, sequence variations were identified in the E2 ORF and specific variations were associated with non-European variants such as African type I, African type II and Asian American. A total of three new sequence variations were identified at positions 2791, 2823 (transactivation domain) and 3361 (hinge region). Distinct phylogenetic branches were formed according to E2 analysis that characterized the different HPV16 variants. It was ascertained that non-European variants are circulating in the Greek population.


Subject(s)
DNA-Binding Proteins/genetics , Genetic Variation , Human papillomavirus 16/genetics , Oncogene Proteins, Viral/genetics , Papillomavirus Infections/virology , Uterine Cervical Dysplasia/virology , Base Sequence , DNA-Binding Proteins/chemistry , Female , Greece , Human papillomavirus 16/chemistry , Human papillomavirus 16/classification , Human papillomavirus 16/isolation & purification , Humans , Molecular Sequence Data , Oncogene Proteins, Viral/chemistry , Phylogeny , Protein Structure, Tertiary
18.
Virus Genes ; 44(2): 237-43, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22173981

ABSTRACT

Human noroviruses (NoVs) of the Caliciviridae family are a major cause of epidemic gastroenteritis. The NoV genus is genetically diverse and recombination of viral RNA is known to depend upon various immunological and intracellular constraints that may allow the emergence of viable recombinants. In the present study, we report the development of a broadly reactive RT-PCR assay, which allowed the characterization of strain A6 at molecular level, established its genetic relationship at the sub-genogroup level and classified A6 strain at the sub-genotype level. The detection was carried out initially by enzyme-linked immunosorbent assay (ELISA) and the subsequent detection and molecular characterization of NoV strain was achieved by reverse transcription-PCR and sequencing. Based on the sequence analysis, A6 strain was revealed to belong to the GII genogroup of NoVs. Partial ORF1 gene sequencing analysis and complete ORF2 gene sequencing revealed that ORF1 and ORF2 belonged to two distinct genotypes GII/9 and GII/6, respectively, making obvious that A6 strain is a rare intergenotypic recombinant within the genogroup GII between GII.9 and GII.6 genotypes. A6 strain represents the first human NoV from Greece, whose genome has been partially (ORF1&ORF3) and completed (ORF2) sequenced. To our knowledge the recombination event GII.9/GII.6 in RdRp and capsid gene, respectively, that was revealed in the present study is reported for the first time.


Subject(s)
Caliciviridae Infections/virology , Norovirus/genetics , Norovirus/isolation & purification , RNA, Viral/genetics , Recombination, Genetic , Cluster Analysis , Enzyme-Linked Immunosorbent Assay , Gastroenteritis/virology , Genotype , Greece , Humans , Molecular Sequence Data , Norovirus/classification , Open Reading Frames , Reverse Transcriptase Polymerase Chain Reaction/methods , Sequence Analysis, DNA
19.
Clin Microbiol Infect ; 17(8): 1170-3, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21489045

ABSTRACT

The molecular characterization of two enterovirus strains (LR51A5 and LR61G3) isolated from the sewage treatment plant unit in Larissa, Greece, in May and June 2006 and the investigation of their relationship with enteroviruses of the same serotype isolated in Greece in 2001 and 2007 were performed by complete VP1 sequence analysis of the isolates. The close phylogenetic relationship and the high nucleotide similarity (98%) led to the conclusion that the virus isolated from sewage in 2006 was associated with that isolated from an aseptic meningitis outbreak 1 year later. Bootscan analysis of the VP1 genomic region revealed that intraserotypic multi-recombination events might have been involved in the evolutionary past history of the LR51A5 and LR61G3 isolates.


Subject(s)
Capsid Proteins/genetics , Disease Outbreaks , Echovirus 6, Human/genetics , Echovirus Infections/epidemiology , Meningitis, Aseptic/epidemiology , Sewage/virology , Base Sequence , Capsid Proteins/chemistry , Echovirus 6, Human/classification , Echovirus 6, Human/isolation & purification , Echovirus Infections/virology , Greece/epidemiology , Humans , Meningitis, Aseptic/virology , Molecular Epidemiology , Phylogeny , Recombination, Genetic , Sequence Analysis, DNA
20.
Clin Microbiol Infect ; 17(10): 1554-62, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21375661

ABSTRACT

The live oral poliovirus vaccine (OPV) strains are genetically unstable, causing, in rare cases, vaccine-associated paralytic poliomyelitis. Reversions of the known attenuating mutations in OPV strains and intertypic recombination have been identified as the underlying causes of the increased neurovirulence of poliovirus isolates. In this study, three OPV isolates (one non-recombinant and two recombinants) were tested in order to correlate phenotypic traits such as temperature sensitivity (Rct test) and growth kinetics (one-step growth curve test) with mutations and recombination events of the viral genome. Moreover, the immunity level of the western Greek population aged 1-40 years was evaluated against OPV isolates and Sabin vaccine strains, with a microneutralization assay. Members of the 1-40-year age group (both pooled and individual sera) showed no significant differences in neutralization test (NT) titres against OPV isolates in comparison with the Sabin vaccine strains. However, all three OPV isolates showed reverted phenotypic traits in Rct or one-step growth curve assays. The results of our study revealed a significant decrease in immunity level from the 1-10-year age group to the 21-30-year age group (pooled sera) for both poliovirus types 1 and 3. For both poliovirus types, the highest NT titres were observed in the 1-10-year age group, and the lowest NT titre was observed in the 21-30-year age group, towards poliovirus type 3. Our study underlines the need for immunological studies in all age groups, in order to allow reconsideration of the current vaccination policies and to avoid epidemics caused by the circulation of highly evolved OPV derivatives.


Subject(s)
Capsid Proteins/genetics , Genome, Viral , Poliovirus Vaccine, Oral/immunology , Poliovirus/genetics , Adolescent , Adult , Cell Line , Child , Child, Preschool , Computers, Molecular , Environmental Microbiology , Feces/virology , Genotype , Greece , Humans , Infant , Mutation , Neutralization Tests , Phenotype , Poliovirus/growth & development , Poliovirus/immunology , Poliovirus/isolation & purification , Poliovirus Vaccine, Oral/administration & dosage , RNA, Untranslated/genetics , Recombination, Genetic , Sequence Alignment , Sequence Analysis, Protein , Serum/immunology , Temperature , Virus Shedding , Young Adult
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