G Magiorkinis

Publications (11)32.23 Total impact

• Article: Quantitative detection of the M204V hepatitis B virus minor variants by amplification refractory mutation system real-time PCR combined with molecular beacon technology.

  F Ntziora, D Paraskevis, C Haida, E Magiorkinis, E Manesis, G Papatheodoridis, S Manolakopoulos, A Beloukas, S Chryssoy, G Magiorkinis, V Sypsa, A Hatzakis
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  ABSTRACT: Mutations in the highly conserved tyrosine-methionine-aspartate-aspartate (YMDD) motif are frequently associated with resistance to antivirals and represent a major concern in the treatment of hepatitis B virus (HBV) infection. Conventional methods fail to detect minority populations of drug-resistant viral quasispecies if they represent less than 25% of the total sample virus population. The amplification refractory mutation system real-time PCR (ARMS RT-PCR) was combined with molecular beacon technology using the LightCycler system. The samples from HBV patients selected for assay evaluation included (i) 57 samples from treatment-naïve patients for biological discriminatory ability (cutoff) estimation, (ii) 12 samples from patients with treatment failure that were M204V positive by sequencing, and (iii) 13 samples from patients with treatment failure that were negative for mutation at codon 204 by sequencing. The discriminatory ability of the assay was 0.25% when tested with laboratory-synthesized DNA target sequences. The median mutant-to-wild-type ratio for samples from naive patients tested positive for the wild type and for mutant variants was 0.01% (5th and 95th percentiles = 0.0001 and 0.04%, respectively). A value of 0.04% was selected as the biological cutoff of the assay of clinical samples. In all samples M204V positive by sequencing (12/12), the mutant variant was detected as the predominant population (range, 82.76 to 99.43%). Interestingly, in 5 (38%) of 13 samples negative by sequencing, the M204V variant was detected at a ratio above the biological cutoff (0.05 to 28%). The assay represents an efficient technique for the early detection and quantification of M204V variants before mutant strains emerge to dominate the population.
  Journal of clinical microbiology 07/2009; 47(8):2544-50. · 4.16 Impact Factor
• Article: The phylogenetic information profile of HIV-1 and the degradation effect of recombination.

  G Magiorkinis, D Paraskevis, H A Schmidt, A Hatzakis
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  ABSTRACT: HIV-1, while known to recombine frequently and evolve rapidly, is one of the most sequenced organisms. The availability of many and long sequences (almost full-length) renders HIV-1 as a good model for studying theoretical predictions linked to evolution and phylogenetic inferences. Here we study the effects of rapid and through-recombination evolution on phylogenetic information in order to confirm theoretical predictions of the characteristics of phylogenetic information on a real dataset. Firstly we study the fluctuation of the phylogenetic information along the HIV-1 genome showing that genomic regions such as the first part and the last part of the pol gene contain less phylogenetic information, while the vpr, vpu and the first exon of the tat gene contain more phylogenetic information compared to the rest of the genome. Moreover, we provide evidence that phylogenetic information is correlated to the sequence similarity of the dataset used and is degraded by the effect of recombination.
  Infection Genetics and Evolution 04/2008; 8(2):139-45. · 3.13 Impact Factor
• Article: Analysing the evolutionary history of HCV: puzzle of ancient phylogenetic discordance.

  G Magiorkinis, F Ntziora, D Paraskevis, E Magiorkinis, A Hatzakis
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  ABSTRACT: Though recombination is an important evolutionary strategy in RNA viruses, only two cases of HCV recombinant strains have been reported. Our objective was to analyze the evolutionary history of the HCV genotypes aiming to obtain evidence of significant phylogenetic discordance due to either recombination or selective forces leading to convergent/divergent evolution. The data support an evolutionary preservation of the interferon-resistance related genomic region (ISDR) for the genotypes 1 and 4. On the other hand, there was no evidence that recombination has occurred in the past with the possible exception of genotype 4. Moreover, it is evidenced that genotypes 3 and 10 split more recently than genotypes 6-9 and 11. This analysis reverberates a commonly found pattern in rapidly evolving viruses, that is the strongly disturbed evolutionary history which deforms the uniform distribution of the phylogenetic relationships across the genome, and introduces a conservative inference framework for approaching this kind of data.
  Infection Genetics and Evolution 07/2007; 7(3):354-60. · 3.13 Impact Factor
• Source

  Available from: Antigoni Katsoulidou

  Article: Molecular epidemiology of hepatitis C virus (HCV) in Greece: temporal trends in HCV genotype-specific incidence and molecular characterization of genotype 4 isolates.

  A Katsoulidou, V Sypsa, N C Tassopoulos, J Boletis, A Karafoulidou, I Ketikoglou, D Tsantoulas, I Vafiadi, G Hatzis, A Skoutelis, E Akriviadis, T Vasiliadis, G Kitis, G Magiorkinis, A Hatzakis
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  ABSTRACT: This study aimed to estimate the overall HCV genotype distribution and to reconstruct the HCV genotype-specific incidence in Greece during the recent decades. It also focused at the identification of genotype 4 subtype variability in Greek isolates. A total of 1686 chronically infected HCV patients with detectable serum HCV RNA by RT-PCR, belonging to different risk groups were studied. Amplified products from the 5'-noncoding region were typed using a commercially available assay based on the reverse hybridization principle. The HCV genotype-specific incidence was estimated using a previously described back calculation method. HCV genotype 1 was the most prevalent (46.9%) followed by genotype 3 (28.1%), 4 (13.2%), 2 (6.9%) and 5 (0.4%). A high prevalence of genotype 1 (66.3%) in haemophilia patients was recorded whereas HCV genotype 3 was found mainly among patients infected by I.V. drug use (58.2%). Data on the temporal patterns of HCV genotype-specific incidence in Greece revealed a moderate increase (1.3-1.6 times) for genotypes 1 and 4, and a decrease (1.5 times) for genotype 2 from 1970 to 1990, whereas there was a sharp (13-fold) increase for genotype 3. The molecular characterization of 41 genotype 4 HCV isolates belonging to various risk groups revealed that, subtype 4a was the most frequently detected (78%). Phylogenetic comparison of the Greek 4a isolates with all HCV-4a isolates reported worldwide so far revealed a topology which does not discriminate Greek isolates from the others. HCV-4 does not represent a recent introduction in Greece.
  Journal of Viral Hepatitis 02/2006; 13(1):19-27. · 4.09 Impact Factor
• Source

  Available from: Dimitrios Paraskevis

  Chapter: Web Service-Enabled Grid-Based Platform for Drug Resistance Management

  P. Gouvas, G. Magiorkinis, A. Bouras, D. Paraskevis, D. Alexandrou, A. Hatzakis, G. Mentzas
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  ABSTRACT: HIV Drug Resistance testing has been established as a routine test in several cases. Estimation of genotypic resistance is a laborious task consisting of experimental procedure and complicated algorithmic interpretation of mutational pattern (sequence data). Since the sequencing procedure is not error free, it is often necessary to proceed into quality checking and manual editing of the raw data (chromatograms). This paper presents the design and development of a grid-based platform that assists the storage and analysis of HIV nucleotide sequences both for clinical practice and research purposes. Modular software components were implemented for sequence uploading, quality verification, mutation identification, genotypic resistance interpretation, phylogenetic analysis, multiple-sequence alignment and sophisticated mutation querying. Moreover these services have been exported as web services in order to provide a high layer of abstraction and enhanced collaboration among researchers. The platform has been validated and tested with more than 500 HIV sequences.
  10/2005: pages 469-479;
• Article: SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.

  D Paraskevis, K Deforche, P Lemey, G Magiorkinis, A Hatzakis, A-M Vandamme
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  ABSTRACT: We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. Sliding-Bayes provides a powerful approach for detecting potential recombination, especially between highly divergent sequences and complex HIV-1 recombinants for which simpler methods like neighbor joining (NJ) may be less powerful. SlidingBayes guides Markov Chain Monte Carlo (MCMC) sampling performed by MrBayes in a sliding window across the alignment (Bayesian scanning). The tool can be used for nucleotide and amino acid sequences and combines all the modeling possibilities of MrBayes with the ability to plot the posterior probability support for clustering of various combinations of taxa.
  Bioinformatics 05/2005; 21(7):1274-5. · 5.47 Impact Factor
• Source

  Available from: Dimitrios Paraskevis

  Article: Re-analysis of 34 full-length HIV-1 intersubtype recombinant sequences.

  G Magiorkinis, D Paraskevis, E Magiorkinis, A-M Vandamme, A Hatzakis
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  ABSTRACT: One of the main characteristics of the HIV-1 is its extensive genetic heterogeneity. Intersubtype recombination was first described in 1995 and since then a significant proportion of the HIV-1 isolates was found to comprise mosaic sequences. Re-analysis of 34 full-length HIV-1 intersubtype recombinants, including all "pure" HIV-1 subtypes revealed that 19 of the 34 analyzed mosaics consist of a more complex mosaic pattern than initially described. These findings indicate that the complexity of the HIV-1 recombinants is much greater than previously estimated.
  Infection Genetics and Evolution 05/2005; 5(3):225-9. · 3.13 Impact Factor
• Source

  Available from: Dimitrios Paraskevis

  Article: Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.

  G Magiorkinis, E Magiorkinis, D Paraskevis, A M Vandamme, M Van Ranst, V Moulton, A Hatzakis
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  ABSTRACT: The origin of the severe acute respiratory syndrome-coronavirus (SARS-CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS-CoV, for the largest part of the genome ( approximately 80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. There is discordant phylogenetic clustering of SARS-CoV and coronaviruses sequences, throughout the genome, compatible with either ancient recombination events or altered evolutionary rates in different lineages, or a combination of both.
  Journal of Medical Virology 12/2004; 74(3):369-72. · 2.82 Impact Factor
• Article: Mutations associated with genotypic resistance to antiretroviral therapy in treatment naïve HIV-1 infected patients in Greece.

  E Magiorkinis, D Paraskevis, G Magiorkinis, S Chryssou, M Chini, M Lazanas, V Paparizos, G Saroglou, A Antoniadou, E Giamarellou, A Karafoulidou, A Hatzakis
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  ABSTRACT: The widespread use of antiviral drugs against HIV has increased the prevalence of HIV-1 resistant strains among naïve individuals due to transmission of resistant strains. The purpose of this study was to investigate the presence of HIV-1 strains harboring resistance mutations in naïve patients in Greece. Blood samples were collected from 25 individuals. The DNA sequence of protease and partial reverse transcriptase regions (codons 41-223) were obtained by direct sequencing. Our results showed the absence of any primary resistance mutations in the study population. However, we were able to identify high prevalence of sequence polymorphisms at positions in reverse transcriptase region associated mainly with resistance to NNRTIs. Moreover, in protease region several secondary mutations were detected, suggesting the higher genetic variability of this region. The clinical significance of the polymorphisms associated with reduced susceptibility to NNRTIs remains to be clarified.
  Virus Research 05/2002; 85(1):109-15. · 2.94 Impact Factor
• Article: Molecular characterization of a complex, recombinant human immunodeficiency virus type 1 (HIV-1) isolate (A/G/J/K/?): evidence to support the existence of a novel HIV-1 subtype.

  D Paraskevis, E Magiorkinis, G Magiorkinis, C Anastassopoulou, M Lazanas, G Chrysos, A M Vandamme, A Hatzakis
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  ABSTRACT: Recombination is one of several factors that contribute to the great genetic diversity of human immunodeficiency virus type 1 (HIV-1). In the current study, analysis of the full-length genome of a novel complex mosaic HIV-1 isolate (99GR303) from a Greek sailor who was possibly infected in Sierra Leone, Africa is presented. The 99GR303 isolate was found to comprise genomic regions belonging to subtypes A, G, J and K as well as of regions of a subtype that remains unclassified. For a partial region of env as well as vpr, no apparent similarity to the known HIV-1 subtypes or to any of the circulating recombinant forms was found. In fact, in the partial env gene, including the C2-V3 region, the 99GR303 isolate formed a new clade, suggesting the existence of an additional HIV-1 subtype. Thus, novel recombinants embody partial genomic regions which may have originated either from subtypes that existed in the past and became extinct or from contemporary subtypes that are extremely rare.
  Journal of General Virology 11/2001; 82(Pt 10):2509-14. · 3.36 Impact Factor
• Article: Mutations associated with genotypic resistance to antiretroviral therapy in treatment naı̈ve HIV-1 infected patients in Greece

  E. Magiorkinis, D. Paraskevis, G. Magiorkinis, S. Chryssou, M. Chini, M. Lazanas, V. Paparizos, G. Saroglou, A. Antoniadou, E. Giamarellou, A. Karafoulidou, A. Hatzakis
  [show abstract] [hide abstract]
  ABSTRACT: The widespread use of antiviral drugs against HIV has increased the prevalence of HIV-1 resistant strains among naı̈ve individuals due to transmission of resistant strains. The purpose of this study was to investigate the presence of HIV-1 strains harboring resistance mutations in naı̈ve patients in Greece. Blood samples were collected from 25 individuals. The DNA sequence of protease and partial reverse transcriptase regions (codons 41–223) were obtained by direct sequencing. Our results showed the absence of any primary resistance mutations in the study population. However, we were able to identify high prevalence of sequence polymorphisms at positions in reverse transcriptase region associated mainly with resistance to NNRTIs. Moreover, in protease region several secondary mutations were detected, suggesting the higher genetic variability of this region. The clinical significance of the polymorphisms associated with reduced susceptibility to NNRTIs remains to be clarified.
  Virus Research.