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Pérez-Parra S, Álvarez M, Fernandez-Caballero JA, Pérez AB, Santos J, Bisbal O, Aguilera A, Rivero M, García-Fraile L, García F. Continued propagation of the CRF19_cpx variant among HIV-positive MSM patients in Spain. J Antimicrob Chemother 2019; 73:1031-1038. [PMID: 29325134 DOI: 10.1093/jac/dkx474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/15/2017] [Indexed: 01/15/2023] Open
Abstract
Objectives The HIV-1 CRF19_cpx genetic form has been recently associated with greater pathogenicity. We used CoRIS, a national cohort of 31 reference hospitals in Spain, to investigate the current epidemiological situation of this variant in Spain. Patients and methods We analysed 4734 naive HIV-1-positive patients diagnosed during the 2007-15 period with an available pol gene sequence in the CoRIS resistance database. HIV-1 CRF19_cpx was ascribed through REGA3.0 and confirmed by a phylogenetic analysis. We analysed the presence of the transmission clusters of HIV-1 CRF19_cpx by maximum likelihood [with the randomized accelerated maximum likelihood (RAxML) program] and the time to the most recent common ancestor using Bayesian inference (BEAST, v. 1.7.5). Results Nineteen patients were infected with CRF19_cpx: all were male, they had a mean age of 42.9 years (95% CI: 36.4-52.5 years), the majority were MSM [n = 18 (95%)] and of Spanish nationality [n = 16 (84.2%)] and they had high CD4+ T cell counts (∼415 cells/mm3). Fifteen patients were grouped into four different transmission clusters: two clusters (two patients each) grouped the patients from Valencia and another cluster grouped one patient from Madrid and another from Seville. We found a larger cluster that grouped nine patients from southern Spain (Malaga and Seville), of which six presented mutation G190A. We estimated the origin of all the transmission clusters to take place between 2009 and 2010. Conclusions We demonstrate that this variant has spread in Spain in recent years among young HIV-positive MSM and we note a recent expansion in southern Spain in patients who carry mutation G190A. We alert healthcare managers to enhance preventive measures to prevent the continuous spread of HIV-1 CRF19_cpx.
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Affiliation(s)
- S Pérez-Parra
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - M Álvarez
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - J A Fernandez-Caballero
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - A B Pérez
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - J Santos
- Infectious Diseases Unit, Hospital Universitario Virgen de la Victoria, Malaga, Spain
| | - O Bisbal
- Infectious Diseases Unit, Hospital 12 de Octubre, Madrid, Spain
| | - A Aguilera
- Clinical Microbiology Dept, Complexo Hospitalario Santiago de Compostela, Spain
| | - M Rivero
- Infectious Diseases Unit, Hospital de Navarra, Pamplona, Spain
| | - L García-Fraile
- Infectious Diseases Unit, Hospital de la Princesa, Madrid, Spain
| | - F García
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
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Pérez-Parra S, Chueca N, Álvarez M, Pasquau J, Omar M, Collado A, Vinuesa D, Lozano AB, Yebra G, García F. Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain. PLoS One 2016; 11:e0168099. [PMID: 28002469 PMCID: PMC5176287 DOI: 10.1371/journal.pone.0168099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/23/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Since 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain. PATIENTS & METHODS We studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6. RESULTS Of the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987), with an evolutionary rate of 2.4 (95%CI: 1.7-3.1) x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations. CONCLUSIONS We provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.
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Affiliation(s)
- Santiago Pérez-Parra
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Marta Álvarez
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Juan Pasquau
- Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain
| | - Mohamed Omar
- Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain
| | - Antonio Collado
- Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain
| | - David Vinuesa
- Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain
| | - Ana B. Lozano
- Servicio de Infecciosas, Hospital de Poniente, Almería, Spain
| | - Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Federico García
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
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3
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Sagnelli C, Ciccozzi M, Coppola N, Minichini C, Lo Presti A, Starace M, Alessio L, Macera M, Cella E, Gualdieri L, Caprio N, Pasquale G, Sagnelli E. Molecular diversity in irregular or refugee immigrant patients with HBV-genotype-E infection living in the metropolitan area of Naples. J Med Virol 2016; 89:1015-1024. [PMID: 27805272 DOI: 10.1002/jmv.24724] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2016] [Indexed: 12/12/2022]
Abstract
In a recent testing in the metropolitan area of Naples, Italy, on 945 irregular immigrants or refugees, 87 HBsAg chronic carriers were identified, 53 of whom were infected by HBV-genotype E. The aim of the present study was to identify the genetic diversity of HBV-genotype E in these 53 immigrants. The 53 immigrant patients with HBV-genotype-E infection were born in Africa, central or eastern Asia, eastern Europe or Latin America. These patients had been seen for a clinical consultation at one of the four first-level units from January 2012 to 2013. The first dataset contained 53 HBV-S gene isolates plus 128 genotype/subgenotype specific reference sequences downloaded from the National Center for Biotechnology Information. The second dataset, comprising the 53 HBV-S gene isolates, previously classified as HBV-genotype E, was used to perform the time-scaled phylogeny reconstruction using a Bayesian approach. Phylogenetic analysis showed that all 53 HBV-S isolates belonged to HBV-genotype E. Bayes factor analysis showed that the relaxed clock exponential growth model fitted the data significantly better than the other models. The time-scaled Bayesian phylogenetic tree of the second dataset showed that the root of the tree dated back to the year 1990 (95% HPD:1984-2000). Four statistically supported clusters were identified. Cluster A dated back to 2012 (95% HPD:1997-2012); cluster B dated back to 2008 (95% HPD:2001-2015); cluster C to 2006 (95% HPD:1999-2013); cluster D to 2004 (95% HPD:1998-2011). This study disclosed the genetic evolution and phylogenesis in a group of HBV-genotype-E-infected immigrants. J. Med. Virol. 89:1015-1024, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Caterina Sagnelli
- Department of Clinical and Experimental Medicine and Surgery, Second University of Naples, Naples, Italy.,Medical Center, Centro Sociale ex Canapificio, Caserta, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy.,University of Biomedical Campus, Rome, Italy
| | - Nicola Coppola
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Carmine Minichini
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Alessandra Lo Presti
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Mario Starace
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Loredana Alessio
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Margherita Macera
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Eleonora Cella
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy.,Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Luciano Gualdieri
- Medical Center, Centro per la Tutela della Salute degli Immigrati, Naples, Italy
| | - Nunzio Caprio
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy.,Medical center, Centro Suore Missionarie della Carità, Naples, Italy
| | - Giuseppe Pasquale
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
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4
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Angeletti S, Lo Presti A, Cella E, Ciccozzi M. Molecular epidemiology and phylogeny of Nipah virus infection: A mini review. ASIAN PAC J TROP MED 2016; 9:630-4. [PMID: 27393089 PMCID: PMC7105010 DOI: 10.1016/j.apjtm.2016.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 12/22/2022] Open
Abstract
Nipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia. It is classified as a Biosafety Level-4 (BSL-4) agent. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Phylogenetic and evolutionary analyses can be used to help in understanding the epidemiology and the temporal origin of this virus. This review provides an overview of evolutionary studies performed on Nipah viruses circulating in different countries. Thirty phylogenetic studies have been published from 2000 to 2015 years, searching on pub-med using the key words 'Nipah virus AND phylogeny' and twenty-eight molecular epidemiological studies from 2006 to 2015 have been performed, typing the key words 'Nipah virus AND molecular epidemiology'. Overall data from the published study demonstrated as phylogenetic and evolutionary analysis represent promising tools to evidence NiV epidemics, to study their origin and evolution and finally to act with effective preventive measure.
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Affiliation(s)
- Silvia Angeletti
- Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy
| | - Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
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5
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Lo Presti A, Cella E, Angeletti S, Ciccozzi M. Molecular epidemiology, evolution and phylogeny of Chikungunya virus: An updating review. INFECTION GENETICS AND EVOLUTION 2016; 41:270-278. [PMID: 27085290 DOI: 10.1016/j.meegid.2016.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/08/2023]
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus belonging to the Togaviridae family, causing a febrile illness associated with severe arthralgia and rash. In this review, we summarized a series of articles published from 2013 to 2016 concerning CHIKV epidemiology, phylogeny, vaccine and therapies, to give an update of our most recent article written in 2014 (Lo Presti et al.,2014). CHIKV infection was first reported in 1952 from Makonde plateaus and since this time caused many outbreaks worldwide, involving the Indian Ocean region, African countries, American continent and Italy. CHIKV infection is still underestimated and it is normally associated with clinical symptoms overlapping with dengue virus, recurring epidemics and mutations within the viral genome. These characteristics promote the geographical spread and the inability to control vector-mediated transmission of the virus. For these reasons, the majority of studies were aimed to describe outbreaks and to enhance knowledge on CHIKV biology, pathogenesis, infection treatment, and prevention. In this review, 16 studies on CHIKV phylogenetic and phylodinamics were considered, during the years 2013-2016. Phylogenetic and phylodinamic analysis are useful tools to investigate how the genealogy of a pathogen population is influenced by pathogen's demographic history, host immunological milieu and environmental/ecological factors. Phylogenetic tools were revealed important to reconstruct the geographic spread of CHIKV during the epidemics wave and to have information on the circulating strains of the virus, that are important for the prediction and control of the epidemics, as well as for vaccines and antiviral drugs development. In conclusion, this updating review can give a critical appraisal of the epidemiology, therapeutic and phylogenesis of CHIKV, reinforcing the need to monitor the geographic spread of virus and vectors.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Rome, Italy.
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6
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Giovanetti M, Milano T, Alcantara LC, Carcangiu L, Cella E, Lai A, Lo Presti A, Pascarella S, Zehender G, Angeletti S, Ciccozzi M. Zika Virus spreading in South America: Evolutionary analysis of emerging neutralizing resistant Phe279Ser strains. ASIAN PAC J TROP MED 2016; 9:445-52. [PMID: 27261852 DOI: 10.1016/j.apjtm.2016.03.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/16/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE To investigate the genetic diversity of Zika Virus (ZIKV) and the relationships existing among these circulating viruses worldwide. To evaluate the genetic polymorphisms harbored from ZIKV that can have an influence on the virus circulation. METHODS Three different ZIKV dataset were built. The first dataset included 63 E gene sequences, the second one 22 NS3 sequences and the third dataset was composed of 108 NS5 gene sequences. Phylogenetic and selective pressure analysis was performed. The edited nucleic acid alignment from the Envelope dataset was used to generate a conceptual translation to the corresponding peptide sequences through UGene software. RESULTS The phylogeographic reconstruction was able to discriminate unambiguously that the Brazilian strains are belonged to the Asian lineage. The structural analysis reveals instead the presence of the Ser residue in the Brazilian sequences (however already observed in other previously reported ZIKV infections) that could suggest the presence of a neutralization-resistant population of viruses. CONCLUSIONS Phylogenetic, evolutionary and selective pressure analysis contributed to improve the knowledge on the circulation of ZIKV.
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Affiliation(s)
- Marta Giovanetti
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Department of Biology, University of Rome 'Tor Vergata', Rome, Italy; Laboratory of Hematology, Genetic and Computational Biology, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB/CPqGM/FIOCRUZ), Salvador, Bahia, Brazil
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Università La Sapienza, 00185 Roma, Italy
| | - Luiz Carlos Alcantara
- Laboratory of Hematology, Genetic and Computational Biology, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB/CPqGM/FIOCRUZ), Salvador, Bahia, Brazil
| | - Laura Carcangiu
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy
| | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Alessia Lai
- Laboratory of Infectious Diseases and Tropical Medicine, University of Milan, Italy
| | - Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Università La Sapienza, 00185 Roma, Italy
| | | | - Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; University Campus Bio-Medico, Rome, Italy.
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Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and Bayesian phylogenetic analysis to characterize Candida clinical isolates. J Microbiol Methods 2015; 119:214-22. [PMID: 26551247 DOI: 10.1016/j.mimet.2015.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/01/2015] [Accepted: 11/05/2015] [Indexed: 11/23/2022]
Abstract
Clinical Candida isolates from two different hospitals in Rome were identified and clustered by MALDI-TOF MS system and their origin and evolution estimated by Bayesian phylogenetic analysis. The different species of Candida were correctly identified and clustered separately, confirming the ability of these techniques to discriminate between different Candida species. Focusing MALDI-TOF analysis on a single Candida species, Candida albicans and Candida parapsilosis strains clustered differently for hospital setting as well as for period of isolation than Candida glabrata and Candida tropicalis isolates. The evolutionary rates of C. albicans and C. parapsilosis (1.93×10(-2) and 1.17×10(-2)substitutions/site/year, respectively) were in agreement with a higher rate of mutation of these species, even in a narrow period, than what was observed in C. glabrata and C. tropicalis strains (6.99×10(-4) and 7.52×10(-3)substitutions/site/year, respectively). C. albicans resulted as the species with the highest between and within clades genetic distance values in agreement with the temporal-related clustering found by MALDI-TOF and the high evolutionary rate 1.93×10(-2)substitutions/site/year.
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8
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Lo Presti A, Cella E, Giovanetti M, Lai A, Angeletti S, Zehender G, Ciccozzi M. Origin and evolution of Nipah virus. J Med Virol 2015; 88:380-8. [PMID: 26252523 DOI: 10.1002/jmv.24345] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2015] [Indexed: 01/22/2023]
Abstract
Nipah virus, member of the Paramyxoviridae family, is classified as a Biosafety Level-4 agent and category C priority pathogen. Nipah virus disease is endemic in south Asia and outbreaks have been reported in Malaysia, Singapore, India, and Bangladesh. Bats of the genus Pteropus appear to be the natural reservoir of this virus. The aim of this study was to investigate the genetic diversity of Nipah virus, to estimate the date of origin and the spread of the infection. The mean value of Nipah virus N gene evolutionary rate, was 6.5 × 10(-4) substitution/site/year (95% HPD: 2.3 × 10(-4)-1.18 × 10(-3)). The time-scaled phylogenetic analysis showed that the root of the tree originated in 1947 (95% HPD: 1888-1988) as the virus entered in south eastern Asiatic regions. The segregation of sequences in two main clades (I and II) indicating that Nipah virus had two different introductions: one in 1995 (95% HPD: 1985-2002) which correspond to clade I, and the other in 1985 (95% HPD: 1971-1996) which correspond to clade II. The phylogeographic reconstruction indicated that the epidemic followed two different routes spreading to the other locations. The trade of infected pigs may have played a role in the spread of the virus. Bats of the Pteropus genus, that are able to travel to long distances, may have contributed to the spread of the infection. Negatively selected sites, statistically supported, could reflect the stability of the viral N protein.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Marta Giovanetti
- Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Section of Infectious Diseases and Immonupathology, University of Milan, Milan, Italy
| | - Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Section of Infectious Diseases and Immonupathology, University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,University Hospital Campus Bio-Medico, Rome, Italy
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9
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Lunar MM, Vandamme AM, Tomažič J, Karner P, Vovko TD, Pečavar B, Volčanšek G, Poljak M, Abecasis AB. Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe. BMC Infect Dis 2015; 15:65. [PMID: 25887543 PMCID: PMC4345027 DOI: 10.1186/s12879-015-0802-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 02/04/2015] [Indexed: 11/19/2022] Open
Abstract
Background The HIV-1 epidemic in Slovenia, a small Central European country, has some characteristics that make it an ideal model to study HIV-1 transmission. The epidemic is predominantly affecting men who have sex with men infected with subtype B (89% of all patients), has a low prevalence (less than 1/1000) and is growing slowly. The aim of the present study was to analyze in detail the evolutionary history and the determinants of transmission. Methods A total of 223 partial pol gene sequences from therapy naïve individuals were included, representing 52% of all patients newly diagnosed in 13 years (2000–2012) and analyzed together with genetically similar worldwide sequences, selected in a BLAST search. Results Combined analysis (maximum likelihood and Bayesian) of HIV-1 transmission chains revealed 8 major clusters (n ≥ 10 patients), 1 group of 4 patients, 2 trios and 12 transmission pairs, thus leaving only 43 (19.3%) Slovenian patients infected with subtype B without a local epidemiological link, indicating a predominance of local transmission of HIV-1 infection. Bayesian analysis performed on a full set of sequences estimated several introductions of HIV-1 into Slovenia, with the most recent common ancestor (tMRCA) of the earliest Slovenian cluster dated to the late 1980s, although tMRCAs obtained from separate independent analysis of each cluster showed considerably more recent estimates. These findings indicate inconsistencies in molecular clock estimation, which we further explored. We hypothesize that these inconsistent dating estimates across the tree could be caused by an evolutionary rate acceleration of HIV-1 after entering the Slovenia epidemic that is not taken into account by the molecular clock model. It could be caused by a lower transmission rate in this setting, as demonstrated by the low epidemic growth rate estimated by Bayesian skyline plot analysis. Conclusions HIV-1 subtype B was introduced into Slovenia at several time points from the late 80s onward. The majority of patients had a local transmission link, indicating a closed HIV community. The observed slower epidemic rate suggests that individuals with a long-lasting infection are the driving force of the epidemic in this region.
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Affiliation(s)
- Maja M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Anne-Mieke Vandamme
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, B-3000, Leuven, Belgium. .,Unidade de Microbiologia e Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.
| | - Janez Tomažič
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia.
| | - Primož Karner
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia.
| | - Tomaž D Vovko
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia.
| | - Blaž Pečavar
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia.
| | - Gabriele Volčanšek
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia.
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Ana B Abecasis
- Unidade de Saúde Pública Internacional e Bioestatística e Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.
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Ciccozzi M, Lo Presti A, Andreotti M, Mancinelli S, Ceffa S, Galluzzo CM, Buonomo E, Luhanga R, Jere H, Cella E, Scarcella P, Mirra M, Marazzi MC, Vella S, Palombi L, Giuliano M. Viral sequence analysis of HIV-positive women and their infected children: insight on the timing of infection and on the transmission network. AIDS Res Hum Retroviruses 2014; 30:1010-5. [PMID: 25103792 DOI: 10.1089/aid.2014.0143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We used high-resolution phylogenetic methods in the context of mother-to-child transmission to obtain information on the timing of the infection and on the transmission network. A total of 33 pol sequences (from maternal peripheral blood, from breast milk, and from plasma of children) belonging to five cases of HIV infant transmission were studied. Using time-scaled phylogeny we were able to estimate that in two cases the transmission occurred after the recommended duration of breastfeeding, supporting a longer, not reported, duration of breastfeeding as a significant factor associated with HIV infant acquisition in this cohort. Among the postnatal infections we were also able to demonstrate that the cell-free virus in breast milk was the most likely population associated with the event of transmission. Our study showed that a coalescent-based model within a Bayesian statistical framework can provide important information that can contribute to optimizing preventive strategies.
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Affiliation(s)
- Massimo Ciccozzi
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM), Istituto Superiore di Sanità, Rome, Italy
- University Hospital Campus Bio-Medico, Rome, Italy
| | - Alessandra Lo Presti
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM), Istituto Superiore di Sanità, Rome, Italy
| | - Mauro Andreotti
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Sandro Mancinelli
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | | | - Clementina Maria Galluzzo
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Ersilia Buonomo
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | | | - Haswell Jere
- DREAM Program, Community of S. Egidio, Blantyre, Malawi
| | - Eleonora Cella
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM), Istituto Superiore di Sanità, Rome, Italy
| | - Paola Scarcella
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Marco Mirra
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | | | - Stefano Vella
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Leonardo Palombi
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Marina Giuliano
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
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11
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Siljic M, Salemovic D, Jevtovic D, Pesic-Pavlovic I, Zerjav S, Nikolic V, Ranin J, Stanojevic M. Molecular typing of the local HIV-1 epidemic in Serbia. INFECTION GENETICS AND EVOLUTION 2013; 19:378-85. [PMID: 23797143 DOI: 10.1016/j.meegid.2013.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/05/2013] [Accepted: 06/12/2013] [Indexed: 01/08/2023]
Abstract
Worldwide HIV-1 pandemic is becoming increasingly complex, with growing heterogeneity of subtypes and recombinant viruses. Previous studies have documented HIV-1 subtype B as the predominant one in Serbia, with limited presence and genetic diversity of non B subtypes. In recent years, MSM transmission has become the most frequently reported risk for HIV infection among newly diagnosed patients in Serbia, but very little is known of the network structure and dynamics of viral transmission in this and other risk groups. To gain insight about the HIV-1 subtypes distribution pattern as well as characteristics of HIV-1 transmission clusters in Serbia, we analyzed the genetic diversity of the pol gene segment in 221 HIV-1-infected patients sampled during 2002-2011. Subtype B was found to still be the most prevalent one in Serbia, accounting for over 90% of samples, while greater diversity of other subtypes was found than previously reported, including subtypes G, C, A, F, CRF01 and CRF02. In total, 41.3% of analyzed subtype B sequences were found associated in transmission clusters/network, that are highly related with MSM transmission route.
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Affiliation(s)
- Marina Siljic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
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12
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Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. AIDS 2013; 27:1045-57. [PMID: 23902920 DOI: 10.1097/qad.0b013e32835cffd9] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Ivanov IA, Beshkov D, Shankar A, Hanson DL, Paraskevis D, Georgieva V, Karamacheva L, Taskov H, Varleva T, Elenkov I, Stoicheva M, Nikolova D, Switzer WM. Detailed molecular epidemiologic characterization of HIV-1 infection in Bulgaria reveals broad diversity and evolving phylodynamics. PLoS One 2013; 8:e59666. [PMID: 23527245 PMCID: PMC3602066 DOI: 10.1371/journal.pone.0059666] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 02/20/2013] [Indexed: 11/19/2022] Open
Abstract
Limited information is available to describe the molecular epidemiology of HIV-1 in Bulgaria. To better understand the genetic diversity and the epidemiologic dynamics of HIV-1 we analyzed 125 new polymerase (pol) sequences from Bulgarians diagnosed through 2009 and 77 pol sequences available from our previous study from persons infected prior to 2007. Epidemiologic and demographic information was obtained from each participant and phylogenetic analysis was used to infer HIV-1 evolutionary histories. 120 (59.5%) persons were infected with one of five different HIV-1 subtypes (A1, B, C, F1 and H) and 63 (31.2%) persons were infected with one of six different circulating recombinant forms (CRFs; 01_AE, 02_AG, 04_cpx, 05_DF, 14_BG, and 36_cpx). We also for the first time identified infection with two different clusters of unique A-like and F-like sub-subtype variants in 12 persons (5.9%) and seven unique recombinant forms (3.5%), including a novel J/C recombinant. While subtype B was the major genotype identified and was more prevalent in MSM and increased between 2000–2005, most non-B subtypes were present in persons ≥45 years old. CRF01_AE was the most common non-B subtype and was higher in women and IDUs relative to other risk groups combined. Our results show that HIV-1 infection in Bulgaria reflects the shifting distribution of genotypes coincident with the changing epidemiology of the HIV-1 epidemic among different risk groups. Our data support increased public health interventions targeting IDUs and MSM. Furthermore, the substantial and increasing HIV-1 genetic heterogeneity, combined with fluctuating infection dynamics, highlights the importance of sustained and expanded surveillance to prevent and control HIV-1 infection in Bulgaria.
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Affiliation(s)
- Ivailo Alexiev Ivanov
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria.
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14
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Ciccozzi M, Madeddu G, Lo Presti A, Cella E, Giovanetti M, Budroni C, Babudieri S, Mura MS, Zehender G, Salemi M. HIV type 1 origin and transmission dynamics among different risk groups in sardinia: molecular epidemiology within the close boundaries of an Italian island. AIDS Res Hum Retroviruses 2013; 29:404-10. [PMID: 22985362 DOI: 10.1089/aid.2012.0209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Italy, the HIV-1 epidemic is still mainly sustained by the subtype B genetic form, although other and novel subtypes and circulating recombinant forms (CRFs) have been reported. A total of 215 HIV-1 pol gene sequences were collected between 1992 and 2010. Multiple alignments spanning subtype-specific HIV-1 B pol sequences were analyzed by Bayesian phylogenetic methods. Subtype B represented 90.7% (n=195) of the sequences. Three main clusters were detected. The root of the tree dated to 1987. Most of the observed viral gene flow events occurred from heterosexual to intravenous drug users (IDUs). Phylogenetic and molecular clock analysis showed an early HIV-1 subtype B introduction in the mid-1980s and dissemination within local risk-specific clusters. This is the first study to describe in detail the HIV-1 molecular epidemiology in one of the largest islands in the European basin. The future potential of the Sardinian epidemic as a hub between Southern and Northern Europe has to been considered.
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Affiliation(s)
- Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Giordano Madeddu
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Alessandra Lo Presti
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Eleonora Cella
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Marta Giovanetti
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Carla Budroni
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Sergio Babudieri
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Maria Stella Mura
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Gianguglielmo Zehender
- Department of Clinical Sciences, L. Sacco Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
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Ciccozzi M, Lo Presti A, Ciccaglione AR, Zehender G, Ciotti M. Phylogeny and phylodinamic of Hepatitis C in Italy. BMC Infect Dis 2012; 12 Suppl 2:S5. [PMID: 23173700 PMCID: PMC3495630 DOI: 10.1186/1471-2334-12-s2-s5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus infection (HCV) is one of the most pressing health emergencies in the world with a global prevalence of about 170 million people chronically infected worldwide. In Europe, Italy has the highest HCV prevalence (3 - 4.4%) with peaks of 12.6 - 26% in Southern regions and the major islands. In Italy HCV genotype 1b prevails, and genotype 4 is mainly found in the south of the country where the prevalence is particularly high in regions such as Calabria. Phylogenetics analysis is a molecular tool widely used to study rapidly-evolving RNA viruses that establish chronic infections such as HCV. Searching the scientific literature, it was found that thirty-nine genetic studies on HCV genotypes have been carried out in Italy between 1997 to 2012 years. However, phylogenetic analysis was performed only in fourteen out of thirty-nine HCV studies (36%) considered. Monitoring the genetic evolution of HCV is an essential step to control the local as well as global HCV epidemic and to develop efficient preventive and therapeutic strategies.
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Affiliation(s)
- Massimo Ciccozzi
- Department of Infectious, Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy.
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