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Petala M, Kostoglou M, Karapantsios T, Dovas CI, Lytras T, Paraskevis D, Roilides E, Koutsolioutsou-Benaki A, Panagiotakopoulos G, Sypsa V, Metallidis S, Papa A, Stylianidis E, Papadopoulos A, Tsiodras S, Papaioannou N. Relating SARS-CoV-2 shedding rate in wastewater to daily positive tests data: A consistent model based approach. Sci Total Environ 2022; 807:150838. [PMID: 34627900 PMCID: PMC8497956 DOI: 10.1016/j.scitotenv.2021.150838] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/15/2021] [Accepted: 10/02/2021] [Indexed: 05/13/2023]
Abstract
During the COVID-19 pandemic, wastewater-based epidemiology (WBE) has been engaged to complement medical surveillance and in some cases to also act as an early diagnosis indicator of viral spreading in the community. Most efforts worldwide by the scientific community and commercial companies focus on the formulation of protocols for SARS-CoV-2 analysis in wastewater and approaches addressing the quantitative relationship between WBE and medical surveillance are lacking. In the present study, a mathematical model is developed which uses as input the number of daily positive medical tests together with the highly non-linear shedding rate curve of individuals to estimate the evolution of global virus shedding rate in wastewater along calendar days. A comprehensive parametric study by the model using as input actual medical surveillance and WBE data for the city of Thessaloniki (~700,000 inhabitants, North Greece) during the outbreak of November 2020 reveals the conditions under which WBE can be used as an early warning tool for predicting pandemic outbreaks. It is shown that early warning capacity is different along the days of an outbreak and depends strongly on the number of days apart between the day of maximum shedding rate of infected individuals in their disease cycle and the day of their medical testing. The present data indicate for Thessaloniki an average early warning capacity of around 2 days. Moreover, the data imply that there exists a proportion between unreported cases (asymptomatic persons with mild symptoms that do not seek medical advice) and reported cases. The proportion increases with the number of reported cases. The early detection capacity of WBE improves substantially in the presence of an increasing number of unreported cases. For Thessaloniki at the peak of the pandemic in mid-November 2020, the number of unreported cases reached a maximum around 4 times the number of reported cases.
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Affiliation(s)
- M Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
| | - M Kostoglou
- Laboratory of Chemical and Environmental Technology, Dept. of Chemistry, Aristotle University of Thessaloniki, 54 124, Thessaloniki 54124, Greece
| | - Th Karapantsios
- Laboratory of Chemical and Environmental Technology, Dept. of Chemistry, Aristotle University of Thessaloniki, 54 124, Thessaloniki 54124, Greece.
| | - C I Dovas
- Faculty of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Th Lytras
- National Public Health Organization, Athens, Greece; European University Cyprus, Nicosia, Cyprus
| | - D Paraskevis
- National and Kapodistrian University of Athens, Athens, Greece
| | - E Roilides
- Infectious Diseases Unit and 3rd Department of Pediatrics, Aristotle University School of Health Sciences, Hippokration Hospital, Thessaloniki 54642, Greece
| | - A Koutsolioutsou-Benaki
- Department of Environmental Health, Directory of Epidemiology and Prevention of Non Communicable Diseases and Injuries, National Public Health Organization, Athens, Greece
| | | | - V Sypsa
- National and Kapodistrian University of Athens, Athens, Greece
| | - S Metallidis
- Department of Haematology, First Department of Internal Medicine, Faculty of Medicine, AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki 54636, Greece
| | - A Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - E Stylianidis
- School of Spatial Planning and Development, Faculty of Engineering, Aristotle University of Thessaloniki, 54124, Greece
| | - A Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., Thessaloniki 54636, Greece
| | - S Tsiodras
- National and Kapodistrian University of Athens, Athens, Greece
| | - N Papaioannou
- Faculty of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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Paraskevis D, Kostaki EG, Magiorkinis G, Panayiotakopoulos G, Sourvinos G, Tsiodras S. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infect Genet Evol 2020; 79:104212. [PMID: 32004758 PMCID: PMC7106301 DOI: 10.1016/j.meegid.2020.104212] [Citation(s) in RCA: 396] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus. METHODS Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods. RESULTS Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5'-part spanning the first 11,498 nucleotides and the last 3'-part spanning 24,341-30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3'-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch. CONCLUSIONS The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - E G Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - G Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - G Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece
| | - S Tsiodras
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Williams LD, Korobchuk A, Pavlitina E, Nikolopoulos GK, Skaathun B, Schneider J, Kostaki EG, Smyrnov P, Vasylyeva TI, Psichogiou M, Paraskevis D, Morgan E, Hadjikou A, Downing MJ, Hatzakis A, Friedman SR. Experiences of Stigma and Support Reported by Participants in a Network Intervention to Reduce HIV Transmission in Athens, Greece; Odessa, Ukraine; and Chicago, Illinois. AIDS Behav 2019; 23:1210-1224. [PMID: 30680540 PMCID: PMC6511315 DOI: 10.1007/s10461-019-02402-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A growing body of evidence suggests that network-based interventions to reduce HIV transmission and/or improve HIV-related health outcomes have an important place in public health efforts to move towards 90-90-90 goals. However, the social processes involved in network-based recruitment may pose a risk to participants of increasing HIV-related stigma if network recruitment causes HIV status to be assumed, inferred, or disclosed. On the other hand, the social processes involved in network-based recruitment to HIV testing may also encourage HIV-related social support. Yet despite the relevance of these processes to both network-based interventions and to other more common interventions (e.g., partner services), there is a dearth of literature that directly examines them among participants of such interventions. Furthermore, both HIV-related stigma and social support may influence participants' willingness and ability to recruit their network members to the study. This paper examines (1) the extent to which stigma and support were experienced by participants in the Transmission Reduction Intervention Project (TRIP), a risk network-tracing intervention aimed at locating recently HIV-infected and/or undiagnosed HIV-infected people and linking them to care in Athens, Greece; Odessa, Ukraine; and Chicago, Illinois; and (2) whether stigma and support predicted participant engagement in the intervention. Overall, experiences of stigma were infrequent and experiences of support frequent, with significant variation between study sites. Experiences and perceptions of HIV-related stigma did not change significantly between baseline and six-month follow-up for the full TRIP sample, and significantly decreased during the course of the study at the Chicago site. Experiences of HIV-related support significantly increased among recently-HIV-infected participants at all sites, and among all participants at the Odessa site. Both stigma and support were found to predict participants' recruitment of network members to the study at the Athens site, and to predict participants' interviewer-rated enthusiasm for naming and recruiting their network members at both the Athens and Odessa sites. These findings suggest that network-based interventions like TRIP which aim to reduce HIV transmission likely do not increase stigma-related risks to participants, and may even encourage increased social support among network members. However, the present study is limited by its associational design and by some variation in implementation by study site. Future research should directly assess contextual differences to improve understanding of the implications of site-level variation in stigma and support for the implementation of network-based interventions, given the finding that these constructs predict participants' recruitment of network members and engagement in the intervention, and thereby could limit network-based interventions' abilities to reach those most in need of HIV testing and care.
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Affiliation(s)
- Leslie D Williams
- Institute for Infectious Disease Research, National Development and Research Institutes, 71 West 23rd Street, Fourth Floor, New York, NY, 10010, USA.
| | - A Korobchuk
- The Alliance for Public Health, Kiev, Ukraine
| | - E Pavlitina
- Transmission Reduction Intervention Project, Athens, Greece
| | | | - B Skaathun
- University of California San Diego, San Diego, USA
| | - J Schneider
- Medical School, University of Chicago, Chicago, USA
| | - E-G Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - P Smyrnov
- The Alliance for Public Health, Kiev, Ukraine
| | - T I Vasylyeva
- Department of Zoology, University of Oxford, Oxford, UK
| | - M Psichogiou
- First Department of Internal Medicine, Laiko General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - D Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - E Morgan
- Institute for Sexual and Gender Minority Health and Wellbeing, Northwestern University, Chicago, IL, USA
| | - A Hadjikou
- Medical School, University of Cyprus, Nicosia, Cyprus
| | - M J Downing
- Institute for Infectious Disease Research, National Development and Research Institutes, 71 West 23rd Street, Fourth Floor, New York, NY, 10010, USA
- Department of Psychology, Lehman College, Bronx, NY, USA
| | - A Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - S R Friedman
- Institute for Infectious Disease Research, National Development and Research Institutes, 71 West 23rd Street, Fourth Floor, New York, NY, 10010, USA
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Paraskevis D, Kostaki E, Magiorkinis G, Gargalianos P, Xylomenos G, Magiorkinis E, Lazanas M, Chini M, Nikolopoulos G, Skoutelis A, Papastamopoulos V, Antoniadou A, Papadopoulos A, Psichogiou M, Daikos GL, Oikonomopoulou M, Zavitsanou A, Chrysos G, Paparizos V, Kourkounti S, Sambatakou H, Sipsas NV, Lada M, Panagopoulos P, Maltezos E, Drimis S, Hatzakis A. Prevalence of drug resistance among HIV-1 treatment-naive patients in Greece during 2003-2015: Transmitted drug resistance is due to onward transmissions. Infect Genet Evol 2017; 54:183-191. [PMID: 28688977 DOI: 10.1016/j.meegid.2017.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND The prevalence of HIV-1 drug resistance among treatment-naïve patients ranges between 8.3% and 15% in Europe and North America. Previous studies showed that subtypes A and B were the most prevalent in the Greek HIV-1 epidemic. Our aim was to estimate the prevalence of resistance among drug naïve patients in Greece and to investigate the levels of transmission networking among those carrying resistant strains. METHODS HIV-1 sequences were determined from 3428 drug naïve HIV-1 patients, in Greece sampled during 01/01/2003-30/6/2015. Transmission clusters were estimated by means of phylogenetic analysis including as references sequences from patients failing antiretroviral treatment in Greece and sequences sampled globally. RESULTS The proportion of sequences with SDRMs was 5.98% (n=205). The most prevalent SDRMs were found for NNRTIs (3.76%), followed by N(t)RTIs (2.28%) and PIs (1.02%). The resistance prevalence was 22.2% based on all mutations associated with resistance estimated using the HIVdb resistance interpretation algorithm. Resistance to NNRTIs was the most common (16.9%) followed by PIs (4.9%) and N(t)RTIs (2.8%). The most frequently observed NNRTI resistant mutations were E138A (7.7%), E138Q (4.0%), K103N (2.3%) and V179D (1.3%). The majority of subtype A sequences (89.7%; 245 out of 273) with the dominant NNRTI resistance mutations (E138A, K103N, E138Q, V179D) were found to belong to monophyletic clusters suggesting regional dispersal. For subtype B, 68.1% (139 out of 204) of resistant strains (E138A, K103N, E138Q V179D) belonged to clusters. For N(t)RTI-resistance, evidence for regional dispersal was found for 27.3% and 21.6% of subtype A and B sequences, respectively. CONCLUSIONS The TDR rate based on the prevalence of SDRM is lower than the average rate in Europe. However, the prevalence of NNRTI resistance estimated using the HIVdb approach, is high in Greece and it is mostly due to onward transmissions among drug-naïve patients.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece.
| | - E Kostaki
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - G Magiorkinis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - P Gargalianos
- 1st Department of Internal Medicine, G. Genimatas GH, Athens, Greece
| | - G Xylomenos
- 1st Department of Internal Medicine, G. Genimatas GH, Athens, Greece
| | - E Magiorkinis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - M Lazanas
- 3rd Internal Medicine Department-Infectious Diseases, Red Cross Hospital, Athens, Greece
| | - M Chini
- 3rd Internal Medicine Department-Infectious Diseases, Red Cross Hospital, Athens, Greece
| | | | - A Skoutelis
- 5th Department of Medicine and Infectious Diseases, Evaggelismos GH, Athens, Greece
| | - V Papastamopoulos
- 5th Department of Medicine and Infectious Diseases, Evaggelismos GH, Athens, Greece
| | - A Antoniadou
- 4th Department of Medicine, Attikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Papadopoulos
- 4th Department of Medicine, Attikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Psichogiou
- 1st Department of Medicine, Laikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - G L Daikos
- 1st Department of Medicine, Laikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Oikonomopoulou
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - A Zavitsanou
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - G Chrysos
- Department of Internal Medicine, Tzaneio GH, Piraeus, Greece
| | - V Paparizos
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, Athens, Greece
| | - S Kourkounti
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, Athens, Greece
| | - H Sambatakou
- HIV Unit, 2nd Department of Internal Medicine, Hippokration GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - N V Sipsas
- 1st Department of Pathophysiology, Laikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Lada
- 2nd Department of Internal Medicine, Sismanogleion GH, Athens, Greece
| | - P Panagopoulos
- Department of Internal Medicine, University GH, Democritus University of Thrace, Alexandroupolis, Greece
| | - E Maltezos
- Department of Internal Medicine, University GH, Democritus University of Thrace, Alexandroupolis, Greece
| | - S Drimis
- Department of Internal Medicine, Tzaneio GH, Piraeus, Greece
| | - A Hatzakis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
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Ayouba A, Paraskevis D, Peeters M. Erratum to "Editorial for special issue on Evolution of HIV" [Infect. Genet. Evol., Vol. 46, December 2016, pp. 149]. Infect Genet Evol 2017; 48:164. [PMID: 28219520 DOI: 10.1016/j.meegid.2017.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- A Ayouba
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France.
| | - D Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - M Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France.
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Paraskevis D, Ayouba A, Peeters M. Editorial. Infect Genet Evol 2016; 46:149. [PMID: 27914559 DOI: 10.1016/j.meegid.2016.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- D Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Ayouba
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - M Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
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Paraskevis D, Nikolopoulos GK, Magiorkinis G, Hodges-Mameletzis I, Hatzakis A. The application of HIV molecular epidemiology to public health. Infect Genet Evol 2016; 46:159-168. [PMID: 27312102 DOI: 10.1016/j.meegid.2016.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 02/02/2023]
Abstract
HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - G K Nikolopoulos
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
| | - G Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, United Kingdom
| | | | - A Hatzakis
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
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Oikonomopoulou M, Demetriou V, Kostrikis L, Paraskevis D. Re-analysis of unassigned hepatitis C virus (HCV) strain CYHCV025: evidence of a highly divergent lineage within genotype 1. J Virus Erad 2016. [DOI: 10.1016/s2055-6640(20)31203-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, Van de Vijver DAMC, Åsjö B, Beshkov D, Coughlan S, Descamps D, Griskevicius A, Hamouda O, Horban A, Van Kasteren M, Kolupajeva T, Kostrikis LG, Liitsola K, Linka M, Mor O, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Staneková D, Stanojevic M, Van Laethem K, Zazzi M, Zidovec Lepej S, Boucher CAB, Schmit JC, Wensing AMJ, Puchhammer-Stockl E, Sarcletti M, Schmied B, Geit M, Balluch G, Vandamme AM, Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Vandekerckhove LPR, Van den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Van Laethem K, Beshkov D, Alexiev I, Lepej SZ, Begovac J, Kostrikis L, Demetriades I, Kousiappa I, Demetriou V, Hezka J, Linka M, Maly M, Machala L, Nielsen C, Jørgensen LB, Gerstoft J, Mathiesen L, Pedersen C, Nielsen H, Laursen A, Kvinesdal B, Liitsola K, Ristola M, Suni J, Sutinen J, Descamps D, Assoumou L, Castor G, Grude M, Flandre P, Storto A, Hamouda O, Kücherer C, Berg T, Braun P, Poggensee G, Däumer M, Eberle J, Heiken H, Kaiser R, Knechten H, Korn K, Müller H, Neifer S, Schmidt B, Walter H, Gunsenheimer-Bartmeyer B, Harrer T, Paraskevis D, Hatzakis A, Zavitsanou A, Vassilakis A, Lazanas M, Chini M, Lioni A, Sakka V, Kourkounti S, Paparizos V, Antoniadou A, Papadopoulos A, Poulakou G, Katsarolis I, Protopapas K, Chryssos G, Drimis S, Gargalianos P, Xylomenos G, Lourida G, Psichogiou M, Daikos GL, Sipsas NV, Kontos A, Gamaletsou MN, Koratzanis G, Sambatakou H, Mariolis H, Skoutelis A, Papastamopoulos V, Georgiou O, Panagopoulos P, Maltezos E, Coughlan S, De Gascun C, Byrne C, Duffy M, Bergin C, Reidy D, Farrell G, Lambert J, O'Connor E, Rochford A, Low J, Coakely P, O'Dea S, Hall W, Mor O, Levi I, Chemtob D, Grossman Z, Zazzi M, de Luca A, Balotta C, Riva C, Mussini C, Caramma I, Capetti A, Colombo MC, Rossi C, Prati F, Tramuto F, Vitale F, Ciccozzi M, Angarano G, Rezza G, Kolupajeva T, Vasins O, Griskevicius A, Lipnickiene V, Schmit JC, Struck D, Sauvageot N, Hemmer R, Arendt V, Michaux C, Staub T, Sequin-Devaux C, Wensing AMJ, Boucher CAB, van de Vijver DAMC, van Kessel A, van Bentum PHM, Brinkman K, Connell BJ, van der Ende ME, Hoepelman IM, van Kasteren M, Kuipers M, Langebeek N, Richter C, Santegoets RMWJ, Schrijnders-Gudde L, Schuurman R, van de Ven BJM, Åsjö B, Kran AMB, Ormaasen V, Aavitsland P, Horban A, Stanczak JJ, Stanczak GP, Firlag-Burkacka E, Wiercinska-Drapalo A, Jablonowska E, Maolepsza E, Leszczyszyn-Pynka M, Szata W, Camacho R, Palma C, Borges F, Paixão T, Duque V, Araújo F, Otelea D, Paraschiv S, Tudor AM, Cernat R, Chiriac C, Dumitrescu F, Prisecariu LJ, Stanojevic M, Jevtovic D, Salemovic D, Stanekova D, Habekova M, Chabadová Z, Drobkova T, Bukovinova P, Shunnar A, Truska P, Poljak M, Lunar M, Babic D, Tomazic J, Vidmar L, Vovko T, Karner P, Garcia F, Paredes R, Monge S, Moreno S, Del Amo J, Asensi V, Sirvent JL, de Mendoza C, Delgado R, Gutiérrez F, Berenguer J, Garcia-Bujalance S, Stella N, de Los Santos I, Blanco JR, Dalmau D, Rivero M, Segura F, Elías MJP, Alvarez M, Chueca N, Rodríguez-Martín C, Vidal C, Palomares JC, Viciana I, Viciana P, Cordoba J, Aguilera A, Domingo P, Galindo MJ, Miralles C, Del Pozo MA, Ribera E, Iribarren JA, Ruiz L, de la Torre J, Vidal F, Clotet B, Albert J, Heidarian A, Aperia-Peipke K, Axelsson M, Mild M, Karlsson A, Sönnerborg A, Thalme A, Navér L, Bratt G, Karlsson A, Blaxhult A, Gisslén M, Svennerholm B, Bergbrant I, Björkman P, Säll C, Mellgren Å, Lindholm A, Kuylenstierna N, Montelius R, Azimi F, Johansson B, Carlsson M, Johansson E, Ljungberg B, Ekvall H, Strand A, Mäkitalo S, Öberg S, Holmblad P, Höfer M, Holmberg H, Josefson P, Ryding U. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis 2015; 62:655-663. [PMID: 26620652 PMCID: PMC4741360 DOI: 10.1093/cid/civ963] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors. Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.
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Affiliation(s)
- L Marije Hofstra
- Luxembourg Institute of Health, Luxembourg.,Department of Virology, University Medical Center Utrecht, The Netherlands
| | | | - Jan Albert
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Federico Garcia
- Complejo Hospitalario Universitario de Granada, Instituto de Investigación IBS Granada; on behalf of Cohorte de Adultos de la Red de Investigación en SIDA, Spain
| | | | | | | | - Danail Beshkov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Diane Descamps
- AP-HP Groupe hospitalier Bichat-Claude Bernard, IAME INSERM UMR 1137, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | | | | | | | | | | | | | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - Orna Mor
- National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. dr. Matei Bals", Bucharest, Romania
| | | | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia
| | | | - Anders Sönnerborg
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
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Casadellà M, van Ham PM, Noguera-Julian M, van Kessel A, Pou C, Hofstra LM, Santos JR, Garcia F, Struck D, Alexiev I, Bakken Kran AM, Hoepelman AI, Kostrikis LG, Somogyi S, Liitsola K, Linka M, Nielsen C, Otelea D, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Staneková D, Stanojevic M, Van Laethem K, Zidovec Lepej S, Clotet B, Boucher CAB, Paredes R, Wensing AMJ. Primary resistance to integrase strand-transfer inhibitors in Europe. J Antimicrob Chemother 2015; 70:2885-8. [PMID: 26188038 DOI: 10.1093/jac/dkv202] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/16/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. METHODS This was a multicentre, cross-sectional study within the European SPREAD HIV resistance surveillance programme. A representative set of 300 samples was selected from 1950 naive HIV-positive subjects newly diagnosed in 2006-07. The prevalence of InSTI resistance was evaluated using quality-controlled baseline population sequencing of integrase. Signature raltegravir, elvitegravir and dolutegravir resistance mutations were defined according to the IAS-USA 2014 list. In addition, all integrase substitutions relative to HXB2 were identified, including those with a Stanford HIVdb score ≥ 10 to at least one InSTI. To rule out circulation of minority InSTI-resistant HIV, 65 samples were selected for 454 integrase sequencing. RESULTS For the population sequencing analysis, 278 samples were retrieved and successfully analysed. No signature resistance mutations to any of the InSTIs were detected. Eleven (4%) subjects had mutations at resistance-associated positions with an HIVdb score ≥ 10. Of the 56 samples successfully analysed with 454 sequencing, no InSTI signature mutations were detected, whereas integrase substitutions with an HIVdb score ≥ 10 were found in 8 (14.3%) individuals. CONCLUSIONS No signature InSTI-resistant variants were circulating in Europe before the introduction of InSTIs. However, polymorphisms contributing to InSTI resistance were not rare. As InSTI use becomes more widespread, continuous surveillance of primary InSTI resistance is warranted. These data will be key to modelling the kinetics of InSTI resistance transmission in Europe in the coming years.
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Affiliation(s)
- M Casadellà
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - P M van Ham
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | - M Noguera-Julian
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - A van Kessel
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | - C Pou
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - L M Hofstra
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - J R Santos
- HIV Unit, Hospital Universitari Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - F Garcia
- Complejo Hospitalario Univeristario de Granada, Instituto de Investigación IBS, Granada, Cohorte de Adultos de la Red de Investigación en SIDA (CoRIS) Spain
| | - D Struck
- Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - I Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - A I Hoepelman
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | | | - S Somogyi
- Robert Koch-Institute, Berlin, Germany
| | - K Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - M Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - C Nielsen
- Statens Serum Institut, Copenhagen, Denmark
| | - D Otelea
- National Institute for Infectious Diseases 'Prof. Dr. Matei Bals', Bucharest, Romania
| | - D Paraskevis
- National Retrovirus Reference Center, University of Athens, Athens, Greece
| | - M Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | - D Staneková
- Slovak Medical University, Bratislava, Slovakia
| | - M Stanojevic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - K Van Laethem
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium
| | - S Zidovec Lepej
- University Hospital for Infectious Diseases 'Dr. Fran Mihaljevic', Zagreb, Croatia
| | - B Clotet
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - C A B Boucher
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - R Paredes
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - A M J Wensing
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
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11
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Panagopoulos P, Paraskevis D, Katsarolis I, Sypsa V, Detsika M, Protopapas K, Antoniadou A, Papadopoulos A, Petrikkos G, Hatzakis A. High prevalence of the UGT1A1*28 variant in HIV-infected individuals in Greece. Int J STD AIDS 2014; 25:860-5. [DOI: 10.1177/0956462414523259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hyperbilirubinaemia with or without jaundice is one of the side effects of atazanavir boosted with low-dose ritonavir (ATV/rit) related to the drug plasma levels, as a result of its metabolism by UGT1A1 – uridine diphosphate-glucuronosyl transferase. Genotyping for UGT1A1*28 before initiation of antiretroviral therapy containing atazanavir may aid in identifying individuals at risk of hyperbilirubinaemia. Our objective was to estimate the prevalence of the UGTA1A1*28 polymorphism in HIV-infected individuals in Greece and to determine its potential association with hyperbilirubinaemia in patients receiving ATV/rit. The prevalence of the UGTA1A1*28 variant was estimated in 79 HIV-infected patients prior to the administration of the first-line treatment. The UGTA1A1*28 variant was detected in 46 out of 79 individuals (58.2%). Antiretroviral therapy was administered to 64/79 patients (81%). Among them, 26/64 (40.6%) received ATV/rit. Of the ATV/rit-treated patients, 14 were found to be carriers of the UGT1A1*28 variant (54%), and maximum serum bilirubin levels were significantly higher in the carrier population (4.71 vs. 2.69 mg/dL, p = 0.026). In 50% of the population, maximum levels were recorded in the first month of follow-up. Although carriage of UGT1A1 is linked with the development of hyperbilirubinaemia, the implementation of a pharmacogenomic approach in clinical practice cannot yet be recommended as a standard of care.
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Affiliation(s)
- P Panagopoulos
- 4th Department of Internal Medicine, ATTIKON University General Hospital, Haidari Athens, Greece
- 2nd Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - D Paraskevis
- Hygiene and Epidemiology Department, Medical School, University of Athens, Greece
| | - I Katsarolis
- 4th Department of Internal Medicine, ATTIKON University General Hospital, Haidari Athens, Greece
| | - V Sypsa
- Hygiene and Epidemiology Department, Medical School, University of Athens, Greece
| | - M Detsika
- Hygiene and Epidemiology Department, Medical School, University of Athens, Greece
| | - K Protopapas
- 4th Department of Internal Medicine, ATTIKON University General Hospital, Haidari Athens, Greece
| | - A Antoniadou
- 4th Department of Internal Medicine, ATTIKON University General Hospital, Haidari Athens, Greece
| | - A Papadopoulos
- 4th Department of Internal Medicine, ATTIKON University General Hospital, Haidari Athens, Greece
| | - G Petrikkos
- 4th Department of Internal Medicine, ATTIKON University General Hospital, Haidari Athens, Greece
| | - A Hatzakis
- Hygiene and Epidemiology Department, Medical School, University of Athens, Greece
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Magiorkinis E, Paraskevis D, Pavlopoulou I, Kantzanou M, Haida C, Hatzakis A, Boletis I. Renal transplantation from hepatitis B surface antigen (HBsAg)-positive donors to HBsAg-negative recipients: a case of post-transplant fulminant hepatitis associated with an extensively mutated hepatitis B virus strain and review of the current literature. Transpl Infect Dis 2013; 15:393-9. [DOI: 10.1111/tid.12094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 11/25/2012] [Accepted: 12/08/2012] [Indexed: 02/06/2023]
Affiliation(s)
- E. Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics; Athens University Medical School; Athens; Greece
| | - D. Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics; Athens University Medical School; Athens; Greece
| | - I.D. Pavlopoulou
- Pediatric Research Laboratory; Faculty of Nursing; University of Athens; Athens; Greece
| | - M. Kantzanou
- Department of Hygiene, Epidemiology and Medical Statistics; Athens University Medical School; Athens; Greece
| | - C. Haida
- Department of Hygiene, Epidemiology and Medical Statistics; Athens University Medical School; Athens; Greece
| | - A. Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics; Athens University Medical School; Athens; Greece
| | - I.N. Boletis
- Department of Nephrology and Renal Transplantation Unit; “Laikon” Hospital; Athens University Medical School; Athens; Greece
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Hatzakis A, Paraskevis D, Kremastinou J, Malliori M. Authors’ reply: HIV-1 outbreak among injecting drug users in Greece, 2011: a preliminary report. Euro Surveill 2011. [DOI: 10.2807/ese.16.41.19987-en] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- A Hatzakis
- National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece
| | - D Paraskevis
- National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece
| | - J Kremastinou
- Hellenic Center for Diseases Control and Prevention, Athens, Greece
| | - M Malliori
- Organization Against Drugs (OKANA), Athens, Greece
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Paraskevis D, Nikolopoulos G, Tsiara C, Paraskeva D, Antoniadou A, Lazanas M, Gargalianos P, Psychogiou M, Malliori M, Kremastinou J, Hatzakis A. HIV-1 outbreak among injecting drug users in Greece, 2011: a preliminary report. ACTA ACUST UNITED AC 2011; 16. [PMID: 21924120 DOI: 10.2807/ese.16.36.19962-en] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A significant increase (more than 10-fold) in the number of newly diagnosed HIV-1 infections among injecting drug users (IDUs) was observed in Greece during the first seven months of 2011. Molecular epidemiology results revealed that a large proportion (96%) of HIV-1 sequences from IDUs sampled in 2011 fall within phylogenetic clusters suggesting high levels of transmission networking. Cases originated from diverse places outside Greece supporting the potential role of immigrant IDUs in the initiation of this outbreak.
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Affiliation(s)
- D Paraskevis
- National Retrovirus Reference Center, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece
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15
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Nikolopoulos GK, Paraskevis D, Hatzitheodorou E, Moschidis Z, Sypsa V, Zavitsanos X, Kalapothaki V, Hatzakis A. HIV/HBV co-infection and rate of antiretroviral treatment change after highly active antiretroviral treatment initiation in a cohort of HIV-infected patients in Greece. Int J STD AIDS 2011; 21:702-7. [PMID: 21139149 DOI: 10.1258/ijsa.2010.010112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The current study investigated the impact of human immunodeficiency virus (HIV)/hepatitis B virus (HBV) co-infection on the rate of change of antiretroviral drugs after the initiation of highly active antiretroviral treatment (HAART). The data on 1425 HIV-positive patients with recorded serology for hepatitis B surface antigen (HBsAg) were retrospectively analysed. The estimated rate of treatment change was slightly higher in the HBsAg-positive group (0.57 per year) compared with the HBsAg-negative group (0.50 per year). Although this difference was insignificant in multivariable modelling, the confidence intervals of the estimates barely included unity. Antiretroviral drug family, calendar period, prior exposure to antiretrovirals and the diagnosis of acquired immunodeficiency syndrome were independently associated with the number of drug alterations. A slight impact of co-infection on the frequency of treatment change after the beginning of HAART cannot be excluded. However, the paucity of studies on this issue necessitates the conduct of further research.
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Affiliation(s)
- G K Nikolopoulos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece
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16
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van de Vijver DAMC, Wensing AMJ, Åsjö B, Bruckova M, Jorgensen LB, Camacho R, Horban A, Linka M, Lazanas M, Loveday C, MacRae E, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Ruiz L, Schmit JC, Stanczak G, Stanojevic M, Vandamme AM, Vercauteren J, Zazzi M, Bacheler L, Lecocq P, Villacian J, Boucher CAB. HIV-1 drug-resistance patterns among patients on failing treatment in a large number of European countries. Acta Dermatovenerol Alp Pannonica Adriat 2010; 19:3-9. [PMID: 21390473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
BACKGROUND Information about patterns of HIV-1 drug resistance among treatment-exposed patients is crucial for the development of novel effective drugs. Currently no system exists that monitors patterns of resistance in patients failing therapy. METHODS The study included 1,988 HIV-1 sequences from patients experiencing therapy failure collected between 2000 and 2004 in 15 European countries. Genotypic resistance was interpreted using the ANRS algorithm. Phenotypic resistance was predicted using the Virco geno- to phenotype system. RESULTS 80.7% of the sequences included at least one drug-resistance mutation. Mutations were found for NRTIs (73.5%), NNRTIs (48.5%), and protease inhibitors (35.8%). Ninety percent of sequences with genotypic resistance harbored M184V, M41L, K103N, D67N, and/or T215Y. Among NRTIs, resistance was most frequently predicted for lamivudine. About half of all sequences had reduced susceptibility for NNRTIs. Resistance to most boosted protease inhibitors was found in < 25%. No sequence had resistance to all currently available drugs. CONCLUSION Levels of resistance among patients with therapy failure were high. The patterns of resistance reflect resistance to drugs available for a longer time. Fully suppressive regimens can be designed even for the most mutated HIV because boosted protease inhibitors have remained active against most circulating viruses and new drug classes have become available.
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Affiliation(s)
- D A M C van de Vijver
- Dept. of Virology, Erasmus MC, Rotterdam University Medical Centre, Rotterdam, the Netherlands.
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17
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Panagopoulos P, Paraskevis D, Sypsa V, Detsika M, Protopapas K, Sakka V, Poulakou G, Papadopoulos A, Petrikkos G, Hatzakis A. High prevalence of the UGT1A1*28 variant in HIV-infected individuals in Greece. J Int AIDS Soc 2010. [PMCID: PMC3112923 DOI: 10.1186/1758-2652-13-s4-p146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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18
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Abstract
Greece has experienced early the effect of HIV/AIDS on morbidity and mortality. The era of highly active antiretroviral therapy has alleviated many of the consequences of the epidemic, however, HIV infection remains an issue of utmost significance. Men who have sex with men are the driving force of the HIV epidemic in Greece followed by heterosexually-infected individuals, while infections among injecting drug users remain at low levels. HIV-1 molecular epidemiology studies reveal a high genetic heterogeneity amongst the circulating strains in Greece. The epidemic began with subtype B, as in most of the European countries, however, subtype A was detected at a high prevalence among the newly diagnosed HIV-1-infected individuals in recent years. HIV requires an effective and sustained response meeting the needs of vulnerable subpopulations.
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Affiliation(s)
- G Nikolopoulos
- National Retrovirus Reference Center, Department of Hygiene Epidemiology & Medical Statistics, Medical School, University of Athens, Greece.
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19
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Paraskevis D, Magiorkinis E, Magiorkinis G, Paparizos V, Lazanas MC, Chini M, Sambatakou H, Karafoulidou A, Hatzakis A. Therapeutic options in heavily pretreated HIV-1 patients based on the genotypic resistance patterns. J Int AIDS Soc 2008. [DOI: 10.1186/1758-2652-11-s1-p47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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20
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Magiorkinis G, Paraskevis D, Schmidt HA, Hatzakis A. The phylogenetic information profile of HIV-1 and the degradation effect of recombination. Infect Genet Evol 2007; 8:139-45. [PMID: 18093883 DOI: 10.1016/j.meegid.2007.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 10/31/2007] [Accepted: 11/08/2007] [Indexed: 11/20/2022]
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.
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Affiliation(s)
- G Magiorkinis
- Medical School, National and Kapodistrian University of Athens, Greece.
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21
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Magiorkinis G, Ntziora F, Paraskevis D, Magiorkinis E, Hatzakis A. Analysing the evolutionary history of HCV: puzzle of ancient phylogenetic discordance. Infect Genet Evol 2006; 7:354-60. [PMID: 16720108 DOI: 10.1016/j.meegid.2006.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 04/04/2006] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
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.
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Affiliation(s)
- G Magiorkinis
- National Retrovirus Reference Center Department of Hygiene and Epidemiology University of Athens, School of Medicine Alexandroupoleos 25, 11527 Goudi, Athens, Greece
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22
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Paraskevis D, Magiorkinis E, Katsoulidou A, Hatzitheodorou E, Antoniadou A, Papadopoulos A, Poulakou G, Paparizos V, Botsi C, Stavrianeas N, Lelekis M, Chini M, Gargalianos P, Magafas N, Lazanas M, Chryssos G, Petrikkos G, Panos G, Kordossis T, Theodoridou M, Sypsa V, Hatzakis A. Prevalence of resistance-associated mutations in newly diagnosed HIV-1 patients in Greece. Virus Res 2005; 112:115-22. [PMID: 16022906 DOI: 10.1016/j.virusres.2005.03.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Revised: 02/23/2005] [Accepted: 03/10/2005] [Indexed: 10/25/2022]
Abstract
The prevalence of HIV-1 drug resistance mutations in naïve patients has been previously shown to differ greatly with the geographic origin. The purpose of this study was to prospectively estimate the prevalence of HIV-1 drug resistance in Greece by analyzing a representative sample of newly HIV-1 diagnosed patients, as part of the SPREAD collaborative study. Protease (PR) and partial reverse transcriptase (RT) sequences were determined from 101 newly diagnosed HIV-1 patients, in Greece, during the period September 2002--August 2003, representing one-third of the total newly diagnosed HIV-1 patients in the same time period. The prevalence of HIV-1 drug resistance was estimated according to the IAS-USA mutation table taking into account all mutations in RT and only major mutations in PR region. The overall prevalence of resistance was 9% [95% confidence interval (CI): 4.2--16.2%]. The prevalence of mutations associated with resistance to NRTIs was 5% (95% CI: 1.6--11.2%), for NNRTIs was 4% (95% CI: 1.1--9.8%), while no major resistance mutations were found in PR. No multi-class resistance was detected in the study population. The prevalence of resistant mutations in the recent seroconverters was 22%. For two individuals, there was clear evidence for transmitted resistance based on epidemiological information for a known source of HIV-1 transmission. The prevalence of the HIV-1 non-B subtypes and recombinants was 52%.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene and Epidemiology, Athens University Medical School, Mikras Asias 75, GR-11527 Athens, Greece.
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23
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Abecasis A, Paraskevis D, Epalanga M, Fonseca M, Burity F, Bartolomeu J, Carvalho AP, Gomes P, Vandamme AM, Camacho R. HIV-1 genetic variants circulation in the North of Angola. Infection, Genetics and Evolution 2005; 5:231-7. [PMID: 15737914 DOI: 10.1016/j.meegid.2004.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 07/07/2004] [Indexed: 11/23/2022]
Abstract
Few molecular epidemiological data on HIV-1 in Angola are available. In this study, we analysed 37 pol sequences from patients originated from Luanda and Cabinda in Angola. It was our objective to investigate the circulation of different HIV-1 subtypes in this country. We found a high HIV-1 genetic diversity. The predominant subtypes were C and F, while subtypes A, D, G and H were also detected. Three sequences were untypable and may possibly belong to new subtypes or recombinants of unknown subtypes. Moreover, 13 recombinant sequences were found, most of them with very complex patterns including untypable fragments.
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Affiliation(s)
- A Abecasis
- Laboratório de Virologia, Serviço de Imuno-hemoterapia, Hospital de Egas Moniz, Rua da Junqueira, 126, 1349-019 Lisboa, Portugal.
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24
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Paraskevis D, Deforche K, Abecasis A, Camacho R, Vandamme AM. Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method. Infect Genet Evol 2005; 5:219-24. [PMID: 15737912 DOI: 10.1016/j.meegid.2004.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 07/01/2004] [Indexed: 11/26/2022]
Abstract
The increased complexity of HIV-1 genetic heterogeneity raises the issue for reliable classification and analysis of these sequences. Until now, bootscanning analysis has been the main method used for the analysis of potential HIV-1 intersubtype recombinants. We show evidence that in some cases of complex recombinants, where three or more segments with discordant phylogenetic signal may exist in protease (PR) and partial reverse transcriptase (RT) region, Bayesian scanning provides a clearer picture than bootscanning plots about the boundaries of potential recombination. Thus, a recently developed Bayesian scanning tool can facilitate the analysis and classification of HIV-1 mosaic sequences.
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Affiliation(s)
- D Paraskevis
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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25
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Magiorkinis G, Paraskevis D, Magiorkinis E, Vandamme AM, Hatzakis A. Re-analysis of 34 full-length HIV-1 intersubtype recombinant sequences. Infect Genet Evol 2004; 5:225-9. [PMID: 15737913 DOI: 10.1016/j.meegid.2004.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 05/11/2004] [Indexed: 11/17/2022]
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.
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Affiliation(s)
- G Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Mikras Asias 75, 11527 Athens, Greece
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26
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Paraskevis D, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM. SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinformatics 2004; 21:1274-5. [PMID: 15546940 DOI: 10.1093/bioinformatics/bti139] [Citation(s) in RCA: 17] [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: 11/12/2022] Open
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.
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Affiliation(s)
- D Paraskevis
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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27
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Magiorkinis G, Magiorkinis E, Paraskevis D, Vandamme A, Van Ranst M, Moulton V, Hatzakis A. Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions. J Med Virol 2004; 74:369-72. [PMID: 15368527 PMCID: PMC7166499 DOI: 10.1002/jmv.20187] [Citation(s) in RCA: 20] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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.
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Affiliation(s)
- G. Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
| | - E. Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
| | - D. Paraskevis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute and University Hospitals, Leuven, Belgium
| | - A.M. Vandamme
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute and University Hospitals, Leuven, Belgium
| | - M. Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute and University Hospitals, Leuven, Belgium
| | - V. Moulton
- The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
| | - A. Hatzakis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
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28
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Paraskevis D, Lemey P, Salemi M, Suchard M, Van De Peer Y, Vandamme AM. Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using bayesian inference: implications for the origin of HIV-1. Mol Biol Evol 2003; 20:1986-96. [PMID: 12949143 DOI: 10.1093/molbev/msg207] [Citation(s) in RCA: 19] [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: 11/14/2022] Open
Abstract
The most plausible origin of HIV-1 group M is an SIV lineage currently represented by SIVcpz isolated from the chimpanzee subspecies Pan troglodytes troglodytes. The origin of HIV-1 group O is less clear. Putative recombination between any of the HIV-1 and SIVcpz sequences was tested using bootscanning and Bayesian-scanning plots, as well as a new method using a Bayesian multiple change-point (BMCP) model to infer parental sequences and crossing-over points. We found that in the case of highly divergent sequences, such as HIV-1/SIVcpz, Bayesian scanning and BMCP methods are more appropriate than bootscanning analysis to investigate spatial phylogenetic variation, including estimating the boundaries of the regions with discordant evolutionary relationships and the levels of support of the phylogenetic clusters under study. According to the Bayesian scanning plots and BMCP method, there was strong evidence for discordant phylogenetic clustering throughout the genome: (1) HIV-1 group O clustered with SIVcpzANT/TAN in middle pol, and partial vif/env; (2) SIVcpzGab1 clustered with SIVcpzANT/TAN in 3'pol/vif, and middle env; (3) HIV-1 group O grouped with SIVcpzCamUS and SIVcpzGab1 in p17/p24; (4) HIV-1 group M was more closely related to SIVcpzCamUS in 3'gag/pol and in middle pol, whereas in partial gp120 group M clustered with group O. Conditionally independent phylogenetic analysis inferred by maximum likelihood (ML) and Bayesian methods further confirmed these findings. The discordant phylogenetic relationships between the HIV-1/SIVcpz sequences may have been caused by ancient recombination events, but they are also due, at least in part, to altered rates of evolution between parental SIVcpz lineages.
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Affiliation(s)
- D Paraskevis
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
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29
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Paraskevis D, Haida C, Tassopoulos N, Raptopoulou M, Tsantoulas D, Papachristou H, Sypsa V, Hatzakis A. Development and assessment of a novel real-time PCR assay for quantitation of HBV DNA. J Virol Methods 2002; 103:201-12. [PMID: 12008014 DOI: 10.1016/s0166-0934(02)00033-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [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]
Abstract
HBV DNA quantitation is used extensively for the monitoring of treatment of hepatitis B virus (HBV) infection. The aim of this study was to develop a highly sensitive and reproducible real-time PCR (RTD-PCR) assay for the quantitation of HBV DNA using the LightCycler system. The performance of this assay was assessed by analyzing serial dilutions of HBV genomic DNA of known concentration and the lower limit of detection was found to be 1 DNA copy/reaction. By using serial dilutions of plasmid standard, RTD-PCR was determined to quantify HBV DNA in a 10-log10 dynamic range. RTD-PCR was found to be more sensitive than the commercially available tests such as the Quantiplex HBV DNA and the AMPLICOR HBV MONITOR assays. The median coefficient of variation of interexperimental variability was 3.2%. The HBV DNA values obtained with RTD-PCR were highly correlated with assays available commercially. These findings suggest that our RTD-PCR assay combines high sensitivity and reproducibility for HBV DNA quantitation in an incomparable high dynamic range of quantitation.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene and Epidemiology, Athens University Medical School, Greece
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30
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Magiorkinis E, Paraskevis D, Magiorkinis G, Chryssou S, Chini M, Lazanas M, Paparizos V, Saroglou G, Antoniadou A, Giamarellou E, Karafoulidou A, Hatzakis A. Mutations associated with genotypic resistance to antiretroviral therapy in treatment naïve HIV-1 infected patients in Greece. Virus Res 2002; 85:109-15. [PMID: 11955643 DOI: 10.1016/s0168-1702(02)00022-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [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: 10/27/2022]
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.
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Affiliation(s)
- E Magiorkinis
- Department of Hygiene and Epidemiology, National Retrovirus Reference Center, Athens School of Medicine, University of Athens, Alexanfroupoles 25, GR-115 27, Greece
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Hatzakis A, Gargalianos P, Kiosses V, Lazanas M, Sypsa V, Anastassopoulou C, Vigklis V, Sambatakou H, Botsi C, Paraskevis D, Stalgis C. Low-dose IFN-alpha monotherapy in treatment-naive individuals with HIV-1 infection: evidence of potent suppression of viral replication. J Interferon Cytokine Res 2001; 21:861-9. [PMID: 11710999 DOI: 10.1089/107999001753238114] [Citation(s) in RCA: 39] [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: 11/13/2022] Open
Abstract
To evaluate the safety and antiviral action of interferon-alpha (IFN-alpha) in HIV-1 infection, we undertook a proof of concept study in 27 treatment-naive patients. Eligible patients comprised two groups: the IFN-alphaT group (n = 17), which received 5 MIU IFN-alpha s.c. daily for 32 consecutive days, and the IFN-alphaNT group (n = 10), which did not receive IFN-alpha prior to highly active antiretroviral therapy (HAART), which was commenced on day 28 in both groups. IFN-alphaTreatment was well tolerated in 14 of the 17 patients of the IFN-alphaT group who completed the study. The mean HIV RNA reduction in the IFN-alphaT group on day 14 was 1.1 log(10). Viral load suppression was inversely associated with baseline viral load (p = 0.031). Four weeks after initiation of HAART, IFN-alphaT and IFN-alphaNT group patients had 2.40 and 1.82 log(10) HIV RNA reduction from baseline, respectively (p < 0.001). There was no evidence of cross-resistance with existing antiretrovirals in patients with HIV-RNA rebound after initial plasma viral load decline > or = 1 log(10) during IFN-alpha monotherapy. Thus, low daily IFN-alpha exhibits potent anti-HIV-1 activity in vivo without serious adverse effects. These properties render IFN-alpha an attractive candidate for further assessment as a constituent of HAART.
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Affiliation(s)
- A Hatzakis
- Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece.
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32
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Paraskevis D, Magiorkinis E, Magiorkinis G, Anastassopoulou C, Lazanas M, Chrysos G, Vandamme AM, Hatzakis A. 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. J Gen Virol 2001; 82:2509-2514. [PMID: 11562543 DOI: 10.1099/0022-1317-82-10-2509] [Citation(s) in RCA: 9] [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: 11/18/2022] Open
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.
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Affiliation(s)
- D Paraskevis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | - E Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | - G Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | - C Anastassopoulou
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | | | - G Chrysos
- Tzanio General Hospital, Piraeus, Greece3
| | - A M Vandamme
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Belgium4
| | - A Hatzakis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
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33
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Katsoulidou A, Paraskevis D, Anastassopoulou CG, Chryssou SE, Sypsa V, Boletis J, Malliori M, Karafoulidou A, Tassopoulos NC, Hatzakis A. Prevalence and genotypic distribution of TT virus in Athens, Greece. J Med Virol 2001; 65:423-9. [PMID: 11536255 DOI: 10.1002/jmv.2052] [Citation(s) in RCA: 10] [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: 12/24/2022]
Abstract
The prevalence of TT virus (TTV) infection in various population groups from Athens, Greece, was assessed by the polymerase chain reaction (PCR) using two primer sets from distinct regions of the genome: the conventional set derived from the open reading frame-1 (ORF-1) and the new, highly sensitive set targeting the region that includes the TATA signal localized upstream of ORF-2. Based on both primer sets, TTV DNA was detected in 42/50 (84.0%) healthy individuals, 42/50 (84.0%) chronic hepatitis C patients, 31/39 (79.5%) acute non-A-E hepatitis patients (group I), 14/16 (87.5%) renal failure patients with acute non-A-E hepatitis (group II), 47/50 (94.0%) intravenous drug users (IVDU), 36/50 (72.0%) hemophiliacs, and 21/31 (67.7%) hemodialysis patients. The presence of TTV was not associated with any particular risk group, and no differences were observed in relation to demographic, biochemical and virological characteristics between TTV DNA-positive and -negative patients. TTV did not seem to have a profound effect on the course of chronic C or acute non-A-E hepatitis either. Phylogenetic analysis revealed that TTV strains circulating in the greater metropolitan area of Athens belong not only to the G1 and G2 genotypes that are encountered worldwide, but also to G3 and to G5 that are found mainly in Europe and Asia, respectively. Further studies will shed light on the role of this highly prevalent virus.
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Affiliation(s)
- A Katsoulidou
- Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
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Paraskevis D, Magiorkinis M, Vandamme AM, Kostrikis LG, Hatzakis A. Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated 'subtype I', reveals a unique complex A/G/H/K/? mosaic pattern. J Gen Virol 2001; 82:575-580. [PMID: 11172098 DOI: 10.1099/0022-1317-82-3-575] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) has been classified into three main groups and 11 distinct subtypes. Moreover, several circulating recombinant forms (CRFs) of HIV-1 have been recently documented to have spread widely causing extensive HIV-1 epidemics. A subtype, initially designated I (CRF04_cpx), was documented in Cyprus and Greece and was found to comprise regions of sequence derived from subtypes A and G as well as regions of unclassified sequence. Re-analysis of the three full-length CRF04_cpx sequences that were available revealed a mosaic genomic organization of unique complexity comprising regions of sequence from at least five distinct subtypes, A, G, H, K and unclassified regions. These strains account for approximately 2% of the total HIV-1-infected population in Greece, thus providing evidence of the great capability of HIV-1 to recombine and produce highly divergent strains which can be spread successfully through different infection routes.
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Affiliation(s)
- D Paraskevis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, M. Asias 75, Athens 115 27, Greece1
| | - M Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, M. Asias 75, Athens 115 27, Greece1
| | - A M Vandamme
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Belgium2
| | - L G Kostrikis
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York 10016, USA3
| | - A Hatzakis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, M. Asias 75, Athens 115 27, Greece1
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Anastassopoulou CG, Touloumi G, Katsoulidou A, Hatzitheodorou H, Pappa M, Paraskevis D, Lazanas M, Gargalianos P, Hatzakis A. Comparative evaluation of the QUANTIPLEX HIV-1 RNA 2.0 and 3.0 (bDNA) assays and the AMPLICOR HIV-1 MONITOR v1.5 test for the quantitation of human immunodeficiency virus type 1 RNA in plasma. J Virol Methods 2001; 91:67-74. [PMID: 11164487 DOI: 10.1016/s0166-0934(00)00245-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [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: 10/17/2022]
Abstract
HIV-1 RNA measurements from 84 plasma specimens obtained with the QUANTIPLEX HIV-1 RNA 2.0 and 3.0 (bDNA) assays (Chiron Diagnostics, Emeryville, CA) and with the AMPLICOR HIV-1 MONITOR Test, version 1.5 with ultra-sensitive specimen preparation (Roche Diagnostic Systems, Inc., Branchburg, NJ) were compared. The absolute RNA values of tested specimens differed significantly between bDNA 2.0 and bDNA 3.0 or Monitor v1.5 measurements (Wilcoxon signed-rank test P<0.001). Results generated with bDNA 3.0 or with Monitor v1.5 were approximately twofold greater than those generated with bDNA 2.0, with smaller differences at higher HIV-1 RNA levels and greater differences at RNA levels below 1000 copies per ml. Although highly correlated (r=0.92 and 0.86, respectively), viral load data generated with bDNA 2.0 and either bDNA 3.0 or Monitor v1.5 were in poor agreement. Concordant results (difference in log(10) copies per ml <0.5) were found at frequencies of 80% for bDNA 2.0 and bDNA 3.0 and only at 58.5% for bDNA 2.0 and Monitor v1.5. In contrast, bDNA 3.0 and Monitor v1.5 measurements were highly correlated (r=0.96) and in good agreement (92.7%).
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Affiliation(s)
- C G Anastassopoulou
- Department of Hygiene and Epidemiology, National Retrovirus Reference Center, Athens University Medical School, 75 Mikras Asias Street, GR-11527 (Goudi), Athens, Greece
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Abstract
The relevance of GB virus C/hepatitis G virus (GBV-C/HGV) infections in liver pathology remains unclear. To investigate the epidemiology of GBV-C/HGV in Athens, Greece, sera from 512 subjects were screened for present and past markers of GBV-C/HGV infection using a reverse transcription-polymerase chain reaction (RT-PCR) and a serological assay, respectively. GBV-C/HGV RNA was detected in 18/56 (32.1%), 12/42 (28.6%), and 16/55 (29.1%) patients with acute hepatitis B, C, or non-A-E, and in 5/58 (8.6%) and 18/68 (26.5%) patients with chronic hepatitis B or C, respectively, as well as in 50/133 (37.6%) hemodialysis patients and 10/100 (10%) healthy individuals. The data indicated that GBV-C/HGV seroprevalence is age-dependent; thus, GBV-C/HGV RNA and anti-E2 positivity were shown to be associated with younger age [odds ratio 0.98, 95% confidence interval (CI) 0. 97-1.00, P = 0.017] and older age (odds ratio 1.03, 95% CI 1.01-1.05, P = 0.002), respectively. No significant associations were identified between GBV-C/HGV RNA status and alanine aminotransferase (ALT) levels in either hepatitis or hemodialysis patients. Nevertheless, GBV-C/HGV RNA-positive acute non-A-E hepatitis patients were more likely to manifest a more severe clinical form of acute hepatitis (P = 0.024). Phylogenetic analysis of partial 5'-untranslated region sequences isolated from 18 viremic individuals showed that most GBV-C/HGV strains circulating in the greater metropolitan area of Athens belong to the 2a subgroup. A genetically diverse type 2 sequence that may represent a novel subtype within group 2 was also characterized.
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Affiliation(s)
- C G Anastassopoulou
- Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
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Paraskevis D, Magiorkinis M, Paparizos V, Pavlakis GN, Hatzakis A. Molecular characterization of a recombinant HIV type 1 isolate (A/G/E/?): unidentified regions may be derived from parental subtype E sequences. AIDS Res Hum Retroviruses 2000; 16:845-55. [PMID: 10875610 DOI: 10.1089/08892220050042783] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [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: 11/13/2022] Open
Abstract
Recombination is one of several factors contributing to the genetic diversity of HIV-1, which is divided into group M (itself comprising 11 subtypes, A-K) and two other groups named O and N. In the present study, the full-length genome of an HIV-1 isolate obtained from a Greek subject (GR17) infected in the Democratic Republic of the Congo (formerly Zaire) was analyzed to reveal a novel mosaic sequence composed of subtypes A, G, and E and regions of indeterminate classification. In particular, most of pol and tat/vpu, as well as the region encoding intracellular domain of gp41, did not cluster with any of the previously characterized HIV-1 subtypes. The clustering of the LTR of GR17 with subtype E was suggestive of a subtype E origin of the unclassified regions. However, the identification of distinct characteristics in the LTR, such as two functional NF-kappaB sites and a distinct TAR element, compared with those of circulating (A/E) recombinants, suggests that the partial subtype E sequences found in GR17 and the mosaic viruses (A/E) have not derived from each other. These results provide evidence that parental subtype E may have existed in the geographic area of Central Africa.
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Affiliation(s)
- D Paraskevis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Greece
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Paraskevis D, Magiorkinis E, Theodoridou M, Mostrou G, Papaevangelou V, Kiosses VG, Hatzakis A, Matsaniotis N. Molecular epidemiology of vertical human immunodeficiency virus type 1 transmission in Greece: evidence of non-B subtypes. J Hum Virol 1999; 2:339-43. [PMID: 10774550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
OBJECTIVES To investigate the subtype classification of the circulating virus strains among human immunodeficiency virus type 1 (HIV-1)-infected children in Greece. STUDY DESIGN/METHODS Since the beginning of the acquired immunodeficiency syndrome (AIDS) epidemic in Greece in 1982, 23 children have been reported to be vertically infected with HIV-1. Blood samples were available for 19 of these children, and the C2-C4 env region was successfully amplified by nested polymerase chain reaction (PCR) for 16 subjects. HIV-1 subtype was established by the heteroduplex mobility assay (HMA) in 16 subjects and confirmed by DNA sequencing and phylogenetic analysis in 8 subjects. RESULTS Most subjects (9; 56%) fell into subtype B. However, a substantial proportion (44%) were classified as subtypes A (3; 19%), C (1; 6%), D (1; 6%), and I (2; 12%). According to epidemiologic information, 5 of 7 children infected with non-B HIV-1 subtypes were born to Greek parents. CONCLUSION These findings clearly suggest that non-B strains have been introduced into Greece, providing evidence that HIV epidemic in this country will probably change profile over time. In addition, subtype I was identified in 2 HIV-1-infected children, both of whom were born to Greek parents.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene and Epidemiology, Athens University Medical School, Greece
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Magiorkinis E, Paraskevis D, Lazanas M, Kiosses VG, Gargalianos P, Hatzakis A. Identification of reverse transcriptase mutations associated with HIV-1 drug resistance mainly against non-nucleoside reverse transcriptase inhibitors in treatment-naive patients. AIDS 1999; 13:1276-8. [PMID: 10416535 DOI: 10.1097/00002030-199907090-00020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nasioulas G, Paraskevis D, Magiorkinis E, Theodoridou M, Hatzakis A. Molecular analysis of the full-length genome of HIV type 1 subtype I: evidence of A/G/I recombination. AIDS Res Hum Retroviruses 1999; 15:745-58. [PMID: 10357470 DOI: 10.1089/088922299310836] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [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: 11/12/2022] Open
Abstract
Phylogenetic analysis of partial env sequences of HIV-1 isolates from Cyprus and Greece suggested the existence of a distinct subtype of the virus, designated as I. We examined whether this subtype represents a distinct group, or a mosaic consisting of previously characterized subtypes. The full-length sequences under consideration were recovered from serum samples of "subtype I" obtained from two nonepidemiologically linked HIV-1-infected subjects in Greece. The first subject was an intravenous drug user (IDU), while the second was a vertically infected child born in 1984 whose parents were both IDUs. A variety of methods, such as diversity plots as well as phylogenetic and informative site analyses, were used to classify the DNA sequences. Subsequent detailed analysis revealed a unique genomic organization composed of alternating portions of subtypes A, G, and I. The two Greek isolates formed a distinct group in most of the pol, gp120, and gp41 regions, and in the vif/vpr, vpu, LTR, and 5' terminus of nef. In contrast, different parts of env and gag as well as the 3' pol region, and the first exons of tat and rev, appeared to have arisen from subtypes A and G. Our results indicate that subtype I, which was probably circulating in Greece in the early 1980s, is a triple mosaic consisting of A, G, and I sequences.
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MESH Headings
- Adolescent
- Cyprus
- DNA, Viral/genetics
- Genes, env
- Genes, gag
- Genes, nef
- Genes, pol
- Genes, vpr
- Genes, vpu
- Genome, Viral
- Greece
- HIV Infections/complications
- HIV Infections/transmission
- HIV Infections/virology
- HIV Long Terminal Repeat/genetics
- HIV-1/classification
- HIV-1/genetics
- Humans
- Infectious Disease Transmission, Vertical
- Phylogeny
- Polymerase Chain Reaction
- Recombination, Genetic
- Sequence Analysis, DNA
- Substance Abuse, Intravenous/complications
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Affiliation(s)
- G Nasioulas
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Greece
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Katsoulidou A, Paraskevis D, Kalapothaki V, Arvanitis D, Karayiannis P, Hadjiconstantiou V, Hatzakis A. Molecular epidemiology of a hepatitis C virus outbreak in a haemodialysis unit. Multicentre Haemodialysis Cohort Study on Viral Hepatitis. Nephrol Dial Transplant 1999; 14:1188-94. [PMID: 10344360 DOI: 10.1093/ndt/14.5.1188] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [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: 12/26/2022] Open
Abstract
BACKGROUND Haemodialysis patients are at high risk of infection by hepatitis C virus. The aim of this study was to investigate a hepatitis C virus outbreak which occurred in a haemodialysis unit, using epidemiological and molecular methods. METHODS Five seroconversions to hepatitis C virus antibody (anti-HCV) were observed over a 6 month period and these were added to the four previously recorded anti-HCV-positive patients. All nine patients involved in the outbreak were tested for HCV RNA by reverse transcription-polymerase chain reaction and hepatitis C genotype determination was accomplished by a reverse hybridization assay. Furthermore, part of the NS5 region of hepatitis C genome (nucleotide positions 7904-8304) was amplified and sequenced in all HCV RNA-positive patients. Then, phylogenetic analysis of the nucleotide sequences obtained was carried out in order to investigate any possible epidemiological linkage among patients. Detailed epidemiological records were also available for all haemodialysis patients. RESULTS Samples from all five incident cases and three out of four prevalent HCV infections were found positive for HCV RNA. HCV genotyping studies revealed that all incident cases were classified as 4c/d, whereas one and two prevalent cases were 1a and 4c/d respectively. Sequence comparisons and phylogenetic tree analysis revealed that six of the patients harboured very similar strains and clustered together, including all incident and one prevalent case, which was implicated as index case. Further epidemiological analysis was consistent with patient to patient transmission. CONCLUSIONS Molecular and epidemiological analysis suggested that horizontal nosocomial patient to patient transmission was the most likely explanation for the virus spread within the haemodialysis unit under study.
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Affiliation(s)
- A Katsoulidou
- Department of Hygiene and Epidemiology, Athens University Medical School, Greece
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Anastassopoulou CG, Paraskevis D, Sypsa V, Psichogiou M, Katsoulidou A, Tassopoulos N, Skoutelis A, Malliori M, Hatzakis A. Prevalence patterns and genotypes of GB virus C/hepatitis G virus among imprisoned intravenous drug users. J Med Virol 1998. [PMID: 9783693 DOI: 10.1002/(sici)1096-9071(199811)56:3<246::aid-jmv12>3.0.co;2-c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An RT-PCR assay using primers from the 5'-UTR of the GBV-C/HGV genome was used to detect viremia, and a serological assay was used to detect past exposure to GBV-C/HGV, in sera from 106 imprisoned Greek intravenous drug users. High seroprevalence rates indicative of the parenteral route of transmission of the virus were found (32.1% for GBV-C RNA and 46.2% for anti-GBV-C E2). These rates were nonetheless lower in comparison to the corresponding rates of HCV infection markers (64.2% for HCV RNA and 77.4% for anti-HCV). Statistically significant univariate associations were observed between GBV-C-RNA positivity and younger age (P=0.006) and HCV-RNA positivity (P=0.024), as well as with higher serum alanine aminotransferase levels (P< 0.001); this latter association was shown to be independent of coinfection with HCV and of age by a multiple logistic regression model. Apparently, GBV-C/HGV had spread readily by needle-sharing in prison, while causing acute subclinical hepatitis in infected inmates. Phylogenetic analysis of the partial 5'-UTR of the GBV-C/HGV genome from 16 seropositive individuals, which delineated their grouping within genotype 2, also revealed a close genetic relationship between two sets of sequences from 4 drug addicts, 3 of whom admitted to sharing needles while imprisoned.
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Affiliation(s)
- C G Anastassopoulou
- Department of Hygiene and Epidemiology, Athens University Medical School, Goudi, Greece
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Nasioulas G, Paraskevis D, Paparizos V, Lazanas M, Karafoulidou A, Hatzakis A. Genotypic characterization of human immunodeficiency virus type 1 in Greece. Multicentre Study on HIV-1 Heterogeneity. AIDS Res Hum Retroviruses 1998; 14:685-90. [PMID: 9618080 DOI: 10.1089/aid.1998.14.685] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 subtype distribution in 83 HIV-1-seropositive individuals living in Greece was investigated by using the heteroduplex mobility assay (HMA), DNA sequencing, and phylogenetic analysis. The results revealed that partial HIV-1 gp120 sequences from 71 (86%) patients were subtype B, 5 (6%) were subtype A, 4 were subtype D (5%), 2 (2%) were subtype C, and 1 (1%) was subtype I. The subtype I isolate was documented in an intravenous drug user. A high prevalence (90-100%) of B isolates among intravenous drug users, hemophiliacs, and homosexual men was observed, in contrast to heterosexuals, among whom non-B subtypes seemed to be common (42.9%, p < 0.001). Among the Greek population subtype B is the most frequent (94%), in contrast to the high prevalence (57%) of non-B isolates found in emigrants living in Greece (p < 0.001). A heterosexual transmission case of subtype D in a Greek individual not traveling abroad was also documented. The broad HIV-1 diversity in Greece may be explained by population movements, such as migration and traveling.
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Affiliation(s)
- G Nasioulas
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Greece
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Nasioulas G, Dean M, Koumbarelis E, Paraskevis D, Gialeraki A, Karafoulidou A, Mandalaki T, Hatzakis A. Allele frequency of the CCR5 mutant chemokine receptor in Greek Caucasians. J Acquir Immune Defic Syndr Hum Retrovirol 1998; 17:181-2. [PMID: 9473023 DOI: 10.1097/00042560-199802010-00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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