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Neukam K, Ridruejo E, Pérez P, Campos RH, Martínez AP, Di Lello FA. Prevalence of hepatitis C virus infection according to the year of birth: identification of risk groups. Eur J Clin Microbiol Infect Dis 2017; 37:247-254. [PMID: 29076048 DOI: 10.1007/s10096-017-3123-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/12/2017] [Indexed: 12/18/2022]
Abstract
Hepatitis C virus (HCV) screening according to the year of birth is recommended is some countries based on epidemiological data. The aim of this study was to analyze anti-HCV prevalence among people born between 1905 and 2015 in Argentina. Patients attending a tertiary care hospital in Buenos Aires, Argentina, from 2001 to 2015, who had a determination of anti-HCV, were included. Of 22,079 patients analyzed, 1,152 (5.2%; 95% confidence interval [CI]: 4.9%-5.5%) patients showed positive anti-HCV and 729 (3.3%; 95% CI: 3.1%-3.5%) patients showed detectable viremia. Three risk groups were identified (HCV prevalence): low-risk group-outpatient clinics/emergencies (2.8%); intermediate-risk group-in-patients (8%); and high-risk group-dialysis/transplants (27.2%). In the low-risk group, being born in 1973 or before was identified as a cut-off value for the risk of anti-HCV acquisition (area under the receiver-operator characteristic curve: 75.1 [95% asymptotic CI: 0.732-0.770; p < 0.001]). Ninety-one patients born after 1973 (0.8%) showed positive anti-HCV versus 457 individuals born in 1973 or before (5.8%), p < 0.001. In this group, positive anti-HCV was observed in 252 females (2.1%) and 296 males (4.1%), p < 0.001. In a multivariate analysis adjusted for gender, alanine-aminotransferase levels and HIV coinfection, being born in 1973 or before was independently identified as a risk for positive anti-HCV (adjusted odds ratio: 14.234 [95% CI: 9.993-20.277]; p < 0.001). People born in 1973 or before without other risk factors should be included in screening programs to link the highest possible number of HCV-infected patients to appropriate care and treatment.
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Affiliation(s)
- K Neukam
- Cátedra de Virología, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Junín 956, 4° piso, 1113, Ciudad de Buenos Aires, Argentina. .,Unit of Infectious Diseases, Microbiology and Preventive Medicine, Instituto de Biomedicina de Sevilla/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda Manuel Siurot s/n, 41013, Seville, Spain.
| | - E Ridruejo
- Hepatology Section, Department of Medicine, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - P Pérez
- Cátedra de Virología, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Junín 956, 4° piso, 1113, Ciudad de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - R H Campos
- Cátedra de Virología, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Junín 956, 4° piso, 1113, Ciudad de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - A P Martínez
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Buenos Aires, Argentina
| | - F A Di Lello
- Cátedra de Virología, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Junín 956, 4° piso, 1113, Ciudad de Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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2
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Rajhi M, Ghedira K, Chouikha A, Djebbi A, Cheikh I, Ben Yahia A, Sadraoui A, Hammami W, Azouz M, Ben Mami N, Triki H. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa. PLoS One 2016; 11:e0153761. [PMID: 27100294 PMCID: PMC4839596 DOI: 10.1371/journal.pone.0153761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/04/2016] [Indexed: 01/06/2023] Open
Abstract
HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization.
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Affiliation(s)
- Mouna Rajhi
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
- University of Carthage, Faculty of Sciences, Bizerte, Tunisia
- * E-mail:
| | - Kais Ghedira
- Pasteur Institute, Tunis, Tunisia; Laboratory of Bioinformatics, Mathematics and Statistics, Tunis, Tunisia
- University of Tunis El Manar, Tunis, 1036, Tunisia
| | - Anissa Chouikha
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Ahlem Djebbi
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Imed Cheikh
- Department of Gastroenterology, Regional Hospital of Bizerte, Bizerte, Tunisia
| | - Ahlem Ben Yahia
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Amel Sadraoui
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Walid Hammami
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Msaddek Azouz
- Department of Gastroenterology, Regional Hospital of Nabeul, Nabeul, Tunisia
| | - Nabil Ben Mami
- Department of Gastroenterology, La Rabta Hospital, Tunis, Tunisia
| | - Henda Triki
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
- University of Tunis El Manar, Tunis, 1036, Tunisia
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Lu L, An Y, Zou J, Gu L, Zhao Z, Zhang X, Li C, Kurihara C, Hokari R, Itakura J, Kurosaki M, Izumi N, Fu Y, Nakano T, Kato T, Negro F, Chen G. The evolutionary patterns of hepatitis C virus subtype 2a and 6a isolates linked to an outbreak in China in 2012. Virology 2015; 485:431-8. [PMID: 26343863 DOI: 10.1016/j.virol.2015.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/29/2015] [Accepted: 08/10/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED An HCV outbreak occurred in 2012 in China, affecting hundreds of patients. We characterized HCV subtype 2a and 6a sequences from 60 and 102 patients, respectively, and co-analyzed them with 82 local controls and 103 calibrating references. The close grouping of the patients׳ sequences contrasted sharply with the diversity of local controls. Scaled by the calibrating references, the emergence of patients׳ isolates was estimated at 2-5 years before sampling. In contrast, the controls intermingled with the calibrating references that were much older. For both subtypes, the major and minor clusters could be defined, with the closeness to indicate linked transmission. CONCLUSION HCV sequences from the study patients grouped into three subtype 2a and two subtype 6a clusters, in addition to three 6a solitary branches, representing descendants of eight earlier strains that were distinct and otherwise sporadic. Due to iatrogenic transmission through reusing needles, five strains were highly selected and preferentially spread.
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Affiliation(s)
- Ling Lu
- Laboratory for Hepatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; The Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America.
| | - Yuling An
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ji Zou
- Laboratory for Hepatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lin Gu
- Laboratory for Hepatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhixin Zhao
- Laboratory for Hepatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaohong Zhang
- Laboratory for Hepatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chunhua Li
- The Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Chie Kurihara
- Department of Internal Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Ryota Hokari
- Department of Internal Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Jun Itakura
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino, Tokyo, Japan
| | - Masayuki Kurosaki
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino, Tokyo, Japan
| | - Namiki Izumi
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Musashino, Tokyo, Japan
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Tatsunori Nakano
- Department of Internal Medicine, Fujita Health University, Nanakuri Sanatorium, Tsu, Mie, Japan
| | - Takanobu Kato
- Department of Virology II, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan
| | - Francesco Negro
- Divisions of Gastroenterology and Hepatology and of Clinical pathology, University, Hospitals, Geneva, Switzerland
| | - Guihua Chen
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
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Epidemic history of major genotypes of hepatitis C virus in Uruguay. INFECTION GENETICS AND EVOLUTION 2015; 32:231-8. [PMID: 25801607 DOI: 10.1016/j.meegid.2015.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 12/23/2022]
Abstract
Worldwide, more than 170 million people are chronically infected with the hepatitis C virus (HCV) and every year die more than 350,000 people from HCV-related liver diseases. Recently, HCV was reclassified into seven major genotypes and 67 subtypes. Some subtypes as 1a, 1b and 3a, have become epidemic as a result of the new parenteral transmission routes and are responsible for most HCV infections in Western countries. HCV 1a subtype have been sub-categorized into two separate sub clades. Recent studies based on the analysis of NS5B genome region, reveal that HCV epidemics in Argentina and Brazil are characterized by multiple introductions events of subtypes 1a, 1b and 3a, followed by subsequent local dispersion. There is no data about HCV genotypes circulating in Uruguay and their evolutionary and demographic history. To this end, a total of 153 HCV NS5B gene sequences were obtained from Uruguayan patients between 2005 and 2011. 86 (56%) sequences grouped with subtype 1a, 40 (26%) with subtype 3a and 27 (18%) with subtype 1b. Furthermore, subtype 1a sequences were distributed among both clades, 1 (n=62, 72%) and 2 (n=24, 28%). Four local HCV clades were found: UY-1a(I), UY-1a(II), UY-1a(III) and UY-3a; comprising a 39% of all HCV viruses analyzed in this study. HCV epidemic in Uruguay has been driving by multiple introductions of subtypes 1a, 1b and 3a and by local dissemination of a few country-specific strains. The evolutionary and demographic history of the major Uruguayan HCV clade UY-1a(I) was reconstructed under two different molecular clock rate models and displayed an epidemic history characterized by an initial phase of rapid expansion followed by a more recent reduction of growth rate since 2000-2005. This is the first comprehensive study about the molecular epidemiology and epidemic history of HCV in Uruguay.
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Di Lello FA, Farias AA, Culasso ACA, Pérez PS, Pisano MB, Contigiani MS, Campos RH, Ré VE. Changing epidemiology of hepatitis C virus genotypes in the central region of Argentina. Arch Virol 2015; 160:909-15. [PMID: 25762309 DOI: 10.1007/s00705-015-2390-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/28/2015] [Indexed: 01/19/2023]
Abstract
The aim of this study was to analyze the prevalence of hepatitis C virus (HCV) genotypes in Córdoba province, Argentina, over a 12-year period and to study the changes at the molecular level. The HCV genotype was determined in 357 HCV-infected patients, and the phylogeny and demographic reconstruction for HCV-1 was assessed. A significant reduction in HCV-2 prevalence with respect to HCV-1 in Córdoba after 2003 was observed. These findings are consistent with the epidemiological changes observed in South America. Nevertheless, the consequences of these changes remain to be elucidated.
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Affiliation(s)
- Federico Alejandro Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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Marascio N, Torti C, Liberto M, Focà A. Update on different aspects of HCV variability: focus on NS5B polymerase. BMC Infect Dis 2014; 14 Suppl 5:S1. [PMID: 25234810 PMCID: PMC4160895 DOI: 10.1186/1471-2334-14-s5-s1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The study of hepatitis C virus (HCV) genotypes/subtypes, quasispecies and recombinants obtained by virus genome sequencing are important for epidemiological studies, to trace the source of infection, for development of new direct acting antivirals (DAAs) therapy and for understanding antiviral selection pressures. The HCV NS5B gene encodes a polymerase, which is responsible for virus replication and is a potential target for the development of antiviral agents. Many studies for classification of HCV use a particular segment of the NS5B gene, in addition to other specific regions, and phylogenetic analysis. Actually, some nucleoside/nucleotide analogues and non-nucleoside inhibitors target NS5B protein. This review focuses on HCV variability, phylogenetic analysis and the role of NS5B in the virus-host interactions.
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Spreading of hepatitis C virus subtypes 1a and 1b through the central region of Argentina. INFECTION GENETICS AND EVOLUTION 2014; 26:32-40. [DOI: 10.1016/j.meegid.2014.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 12/16/2022]
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Back to the origin of HCV 2c subtype and spreading to the Calabria region (Southern Italy) over the last two centuries: a phylogenetic study. INFECTION GENETICS AND EVOLUTION 2014; 26:352-8. [PMID: 24973737 DOI: 10.1016/j.meegid.2014.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/23/2014] [Accepted: 06/09/2014] [Indexed: 12/12/2022]
Abstract
Circulation of HCV genotype 2 has been described in European Countries where numerous subtypes and unclassified HCV 2 lineages have been reported. In Italy, subtype 1b is the most prevalent, followed by genotype 2. In the present study, phylogeny of HCV 2c was investigated. The phylogeny of HCV 2c isolated from 54 Italian patients in the Calabria region (Southern Italy) was investigated by analyzing a fragment of the NS5B gene. Patients came from 5 metropolitan areas and a small village (Sersale). These areas were geographically dispersed throughout the entire region. A Bayesian coalescent-based framework was used to estimate origin and spreading of HCV 2c in this region. Phylogenetic analysis showed that 28 Italian sequences were intermixed with foreign HCV 2c reference sequences and grouped into 3 major clades: A, B, and C. Nineteen inter-clade sequences were associated uniquely with surgery as risk factor for HCV acquisition. By contrast, a sub-cluster within clade B was associated with blood transfusion. Moreover, sequences from Sersale village grouped in the Italian sub-cluster and were intermixed with 10 sequences from metropolitan areas. The three isolates with the longest branch came from Sersale and belonged to patients who had glass syringes as risk factor. HCV 2c isolates from the Calabria region shared a common ancestor whose origin was traced back to 1889. Our results suggest that, after its introduction - possibly as a result of population movements between Italy and African Countries during Italian colonialism - HCV 2c spread through multiple risk factors, not including intravenous drug use. So, transmission chains followed a pathway different from other European Countries. Although HCV incidence is decreasing, these ways are still ongoing, possibly justifying stability in the relative prevalence of HCV 2c.
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Kühnert D, Stadler T, Vaughan TG, Drummond AJ. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model. J R Soc Interface 2014; 11:20131106. [PMID: 24573331 PMCID: PMC3973358 DOI: 10.1098/rsif.2013.1106] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible–infected–removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth–death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970.
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Affiliation(s)
- Denise Kühnert
- Department of Computer Science, University of Auckland, , Auckland, New Zealand
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10
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Golemba MD, Culasso ACA, Villamil FG, Bare P, Gadano A, Ridruejo E, Martinez A, Di Lello FA, Campos RH. Hepatitis C virus diversification in Argentina: comparative analysis between the large city of Buenos Aires and the small rural town of O'Brien. PLoS One 2013; 8:e84007. [PMID: 24386322 PMCID: PMC3875501 DOI: 10.1371/journal.pone.0084007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/11/2013] [Indexed: 01/19/2023] Open
Abstract
Background The estimated prevalence of HCV infection in Argentina is around 2%. However, higher rates of infection have been described in population studies of small urban and rural communities. The aim of this work was to compare the origin and diversification of HCV-1b in samples from two different epidemiological scenarios: Buenos Aires, a large cosmopolitan city, and O'Brien, a small rural town with a high prevalence of HCV infection. Patients and Methods The E1/E2 and NS5B regions of the viral genome from 83 patients infected with HCV-1b were sequenced. Phylogenetic analysis and Bayesian Coalescent methods were used to study the origin and diversification of HCV-1b in both patient populations. Results Samples from Buenos Aires showed a polyphyletic behavior with a tMRCA around 1887–1900 and a time of spread of infection approximately 60 years ago. In contrast, samples from ÓBrien showed a monophyletic behavior with a tMRCA around 1950–1960 and a time of spread of infection more recent than in Buenos Aires, around 20–30 years ago. Conclusion Phylogenetic and coalescence analysis revealed a different behavior in the epidemiological histories of Buenos Aires and ÓBrien. HCV infection in Buenos Aires shows a polyphyletic behavior and an exponential growth in two phases, whereas that in O'Brien shows a monophyletic cluster and an exponential growth in one single step with a more recent tMRCA. The polyphyletic origin and the probability of encountering susceptible individuals in a large cosmopolitan city like Buenos Aires are in agreement with a longer period of expansion. In contrast, in less populated areas such as O'Brien, the chances of HCV transmission are strongly restricted. Furthermore, the monophyletic character and the most recent time of emergence suggest that different HCV-1b ancestors (variants) that were in expansion in Buenos Aires had the opportunity to colonize and expand in O’Brien.
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Affiliation(s)
- Marcelo D. Golemba
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrés C. A. Culasso
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico G. Villamil
- Unidad de Trasplante Hepático, Hospital Británico de Buenos Aires, Argentina y Unidad de Trasplante Hepático, Hospital El Cruce, Buenos Aires, Argentina
| | - Patricia Bare
- Sección Virología, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Adrián Gadano
- Hepatology Unit, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Ezequiel Ridruejo
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno, CEMIC, Buenos Aires, Argentina
| | - Alfredo Martinez
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno, CEMIC, Buenos Aires, Argentina
| | - Federico A. Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rodolfo H. Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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11
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Gededzha MP, Selabe SG, Blackard JT, Kyaw T, Mphahlele MJ. Near full-length genome analysis of HCV genotype 5 strains from South Africa. INFECTION GENETICS AND EVOLUTION 2013; 21:118-23. [PMID: 24220189 DOI: 10.1016/j.meegid.2013.10.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/25/2013] [Accepted: 10/27/2013] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) genotype 5 is the predominant genotype in South Africa. However, to date, only 2 full-length genotype 5 genomes have been sequenced and only one is from South Africa. This study characterized HCV genotype 5 sequences from South Africa, including six near full-length genomes, as well as the E1 region from an additional 12 genotype 5 samples. Phylogenetic analysis of these near full-length genome sequences revealed that all genotype 5 sequences formed a close cluster with high bootstrap support. Bayesian analysis of the E1 region was used to estimate the time of the most recent common ancestor (tMRCA). The tMRCA for HCV genotype 5a was estimated at 114-134 years before the last sampling date. In conclusion, this study provides six near full-length genotype 5 nucleotide sequences for use as references to design efficient vaccines and for the development of new antiviral agents, and provides further insight into the diversity of HCV genotypes circulating in South Africa.
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Affiliation(s)
- Maemu P Gededzha
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
| | - Selokela G Selabe
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
| | - Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Thanda Kyaw
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
| | - M Jeffrey Mphahlele
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
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Dearlove B, Wilson DJ. Coalescent inference for infectious disease: meta-analysis of hepatitis C. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120314. [PMID: 23382432 PMCID: PMC3678333 DOI: 10.1098/rstb.2012.0314] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Genetic analysis of pathogen genomes is a powerful approach to investigating the population dynamics and epidemic history of infectious diseases. However, the theoretical underpinnings of the most widely used, coalescent methods have been questioned, casting doubt on their interpretation. The aim of this study is to develop robust population genetic inference for compartmental models in epidemiology. Using a general approach based on the theory of metapopulations, we derive coalescent models under susceptible–infectious (SI), susceptible–infectious–susceptible (SIS) and susceptible–infectious–recovered (SIR) dynamics. We show that exponential and logistic growth models are equivalent to SI and SIS models, respectively, when co-infection is negligible. Implementing SI, SIS and SIR models in BEAST, we conduct a meta-analysis of hepatitis C epidemics, and show that we can directly estimate the basic reproductive number (R0) and prevalence under SIR dynamics. We find that differences in genetic diversity between epidemics can be explained by differences in underlying epidemiology (age of the epidemic and local population density) and viral subtype. Model comparison reveals SIR dynamics in three globally restricted epidemics, but most are better fit by the simpler SI dynamics. In summary, metapopulation models provide a general and practical framework for integrating epidemiology and population genetics for the purposes of joint inference.
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Affiliation(s)
- Bethany Dearlove
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
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Ye Y, Yan YS, Chen G, Yan PP, Zheng WX, Deng YQ, Yang XH, Wu SL, Zhang ZS. Molecular epidemiology of hepatitis C virus among different groups of people in the province of Fujian, China. Arch Virol 2012; 158:611-8. [PMID: 23132411 DOI: 10.1007/s00705-012-1513-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/10/2012] [Indexed: 12/19/2022]
Abstract
Genotyping of hepatitis C virus (HCV) can provide valuable information for prognosis and treatment duration prediction. To explore the genetic diversity of HCV in Fujian Province, China, 112, 104 and 48 anti-HCV-positive serum samples were collected from volunteer blood donors, IDUs and patients, respectively, from Jan 2008 to Dec 2008 and were genotyped through sequence analysis, followed by phylogenetic analysis in the C/E1 and NS5B regions. Genotypes could be determined for 85.61 and 84.85 % of samples in the C/E1 and NS5B region, respectively. 6a was the most prevalent subtype, which accounted for 42.04 and 43.75 % in the C/E1 and NS5B region, respectively. Mixed infection and potential recombination were detected in this study. Kappa tests indicated that similar results were obtained by two genotyping methods targeting the C/E1 and NS5B regions. The differences in the main prevalent subtype between the three target groups suggest diversity of HCV prevalence in different populations.
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Affiliation(s)
- Ying Ye
- Department of Pathogenic Biology, School of Basic Medical, Fujian Medical University, No. 88, Jiaotong Road, Fuzhou, 350004 Fujian, People's Republic of China
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Culasso ACA, Elizalde M, Campos RH, Barbini L. Molecular survey of hepatitis C virus in the touristic city of Mar del Plata, Argentina. PLoS One 2012; 7:e44757. [PMID: 23028605 PMCID: PMC3454412 DOI: 10.1371/journal.pone.0044757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 08/06/2012] [Indexed: 12/13/2022] Open
Abstract
The global epidemiology of Hepatitis C Virus (HCV) may be roughly described by two groups of genotypes: the worldwide distributed ones (subtypes 1a, 1b, 2a and 3a, among others) and the endemic ones (subtypes 4a, 5a, 6a, among others). Epidemiological and population dynamic studies of the worldwide distributed genotypes have shown that subtypes 1a and 3a are common among intravenous drug users (IDUs) and that they are also in expansion in some countries. The molecular survey of HCV provides some clues about the epidemiological status of the infections in a local scale and the phylogenetic and demographic reconstruction analyses complement this study by inferring whether the infections of certain subtypes are in a steady state or expanding. Here, a molecular survey of the HCV variants that circulate in the touristic city of Mar del Plata (Buenos Aires, Argentina) was performed in samples obtained from 42 patients. The subtypes detected were 1a (32 patients), 3a (8 patients) and 1b (2 patients). The demographic history of subtype 1a inferred using the sequence data showed an exponential growth in the 1990′s. The period of viral expansion was delayed compared with that observed for the same genotype in other countries where the transmission was associated with IDUs. Also, the phylogeographic analysis of HCV-1a showed a statistically significant association between the location of the samples and the phylogeny, which may be the result of the local transmission of HCV in the city. The molecular analysis helped in the description of the complex epidemiological context of a touristic city, and pointed out that some sanitary measures should be taken in order to reduce the transmission of HCV (and maybe of HIV) among IDUs.
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Affiliation(s)
- Andrés C. A. Culasso
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mercedes Elizalde
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rodolfo H. Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
| | - Luciana Barbini
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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