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Mazzucco W, Chiara di Maio V, Bronte F, Fabeni L, Pipitone RM, Grimaudo S, Ferraro D, Marotta C, Aragri M, Macaluso M, Vitale F, Di Raimondo F, Ceccherini-Silberstein F, Di Marco V. Phylogenetic analysis in the clinical risk management of an outbreak of hepatitis C virus infection among transfused thalassaemia patients in Italy. J Hosp Infect 2021; 115:51-58. [PMID: 34171407 DOI: 10.1016/j.jhin.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Occurrence of hepatitis C virus (HCV) infection is reduced by effective risk management procedures, but patient-to-patient transmission continues to be reported in healthcare settings. AIM To report the use of phylogenetic analysis in the clinical risk management of an HCV outbreak among 128 thalassaemia outpatients followed at a thalassaemia centre of an Italian hospital. METHODS Epidemiological investigation and root-cause analysis were performed. All patients with acute hepatitis and known chronic infection were tested for HCV RNA, HCV genotyping, and NS3, NS5A, and NS5B HCV genomic region sequencing. To identify transmission clusters, phylogenetic trees were built for each gene employing Bayesian methods. FINDINGS All patients with acute hepatitis were infected with HCV genotype 1b. Root-cause analysis, including a lookback procedure, excluded blood donors as the source of HCV transmission. The phylogenetic analysis, conducted on seven patients with acute infection and eight patients with chronic infection, highlighted four transmission clusters including at least one patient with chronic and one patient with acute HCV infection. All patients in the same cluster received a blood transfusion during the same day. Two patients with acute hepatitis spontaneously cleared HCV within four weeks and nine patients received ledipasvir plus sofosbuvir for six weeks, all achieving a sustained virological response. CONCLUSION Combined use of root-cause analysis and molecular epidemiology was effective in ascertaining the origin of the HCV outbreak. Antiviral therapy avoided the chronic progression of the infection and further spread in care units and in the family environment.
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Affiliation(s)
- W Mazzucco
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, Palermo, Italy; Clinical Epidemiology and Cancer Registry Unit, COVID-19 Western Sicilian Regional Reference Laboratory, Palermo University Hospital (AOUP) 'P. Giaccone', Palermo, Italy; Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital, Cincinnati, OH, USA.
| | - V Chiara di Maio
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - F Bronte
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, Palermo, Italy
| | - L Fabeni
- Laboratory of Virology, 'Lazzaro Spallanzani' National Institute for Infectious Diseases, IRCCS, Rome, Italy
| | - R M Pipitone
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, Palermo, Italy
| | - S Grimaudo
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, Palermo, Italy
| | - D Ferraro
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, Palermo, Italy
| | - C Marotta
- General Directorate of Health Prevention, Ministry of Health, Rome, Italy
| | - M Aragri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - M Macaluso
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - F Vitale
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, Palermo, Italy; Clinical Epidemiology and Cancer Registry Unit, COVID-19 Western Sicilian Regional Reference Laboratory, Palermo University Hospital (AOUP) 'P. Giaccone', Palermo, Italy
| | - F Di Raimondo
- Division of Hematology, Azienda Ospedaliero-Universitaria Policlinico, Department of Surgery and Medical Specialties, University of Catania, Catania, Italy
| | | | - V Di Marco
- Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, Palermo, Italy
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2
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Colomba GME, Urone N, Marco VD, Ferraro D. Phylodynamic Analysis and Implication of HCV Genotype 4 Variability on Antiviral Drug Response and T-Cell Recognition. Viruses 2020; 12:E1363. [PMID: 33260596 PMCID: PMC7761199 DOI: 10.3390/v12121363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Therapies for HCV care could change the prevalence and the geographic distribution of genotypes due to differences in Sustained Virologic Response (SVR). In this scenario, uncommon genotypes/subtypes, such as genotype 4, could spread from high-risk groups, replacing genotypes eradicated by antiviral drugs. Genotype eradication is also strongly influenced by the CD8+ T cell response. In this study, the genetic variability in HCV genotype 4 strains obtained from a cohort of 67 patients naïve to DAA therapy was evaluated. We found that the presence of resistance-associated substitutions (RAS) was able to affect drug responses. Next, using a prediction tool, viral mutations were identified by their ability, or lack thereof, to reduce the binding affinity with HLA, which affects T cell recognition. The Bayesian coalescent analysis suggested two different circulation clusters, one in risk groups (IDUs and MSM) and the other due to migration flows, dated to 1940 and 1915, respectively. Most of the RAS overlapped with HLA and a lack of binding mutations was observed in 96% of strains. This study describes the introduction of HCV genotype 4 in a region of the Mediterranean basin and evaluates how HCV genotype 4's genetic variability could affect the response of antiviral drugs and CD8+ T cell recognition.
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Affiliation(s)
| | | | | | - Donatella Ferraro
- Dipartimento di Scienze per la Promozione della Salute, Materno-Infantile di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, 90133 Palermo, Italy; (G.M.E.C.); (N.U.); (V.d.M.)
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3
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Khedhiri M, Ghedira K, Chouikha A, Touzi H, Sadraoui A, Hammemi W, Triki H. Tracing the epidemic history of hepatitis C virus genotype 1b in Tunisia and in the world, using a Bayesian coalescent approach. INFECTION GENETICS AND EVOLUTION 2019; 75:103944. [PMID: 31260787 DOI: 10.1016/j.meegid.2019.103944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Marwa Khedhiri
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Research Laboratory: "Transmission Controle et Immunobiologie des Infections" (LR11-IPT02), Pasteur Institute of Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Anissa Chouikha
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Research Laboratory: "Transmission Controle et Immunobiologie des Infections" (LR11-IPT02), Pasteur Institute of Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Henda Touzi
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Research Laboratory: "Transmission Controle et Immunobiologie des Infections" (LR11-IPT02), Pasteur Institute of Tunis, Tunisia; Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia; Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia.
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4
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Temporal dynamics of hepatitis C genotypes in a five-year hospital-based surveillance in Northern Italy. Arch Virol 2016; 161:2727-37. [DOI: 10.1007/s00705-016-2975-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 07/06/2016] [Indexed: 02/06/2023]
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5
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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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Ferraro D, Urone N, Di Marco V, Craxì A. HCV-1b intra-subtype variability: Impact on genetic barrier to protease inhibitors. INFECTION GENETICS AND EVOLUTION 2014; 23:80-5. [PMID: 24508244 DOI: 10.1016/j.meegid.2014.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/23/2014] [Accepted: 01/26/2014] [Indexed: 12/28/2022]
Abstract
Due to error-prone RNA polymerase and the lack of proofreading mechanisms, to the spread worldwide and probable long-term presence in human population, HCV showed a high degree of inter- and intra-subtype genetic variability. Protease inhibitors (PIs), a new class of drugs, have been designed specifically on the HCV genotype 1 NS3 protease three-dimensional structure. The viral genetic barrier limits the efficacy of PIs, and fourteen loci in the HCV NS3 gene are involved in resistance to PIs. A sensitive method (15UI/ml) for study the HCV genetic profile of 125 strains from patients naïve to PIs, was developed through the use of new degenerate primers for subtype 1b. We observed the presence of naturally resistance-associated variants in 14% of the HCV strains (V36L, F43S, T54S, I153V, R155Q, D168A/G). T54S was the most common mutation (4%) detected. We investigated, through minimal score (m.s.) calculating, how the HCV intra-subtype 1b variability modifies the genetic barrier to PIs. For >60% of strains a single transition (m.s. of 1) was required for selection of low to medium resistance mutations, while more than one transition/transversion (m.s. ⩾2.5) or one transition plus one transversion (m.s. ⩾3.5) was necessary for most of the high level PI-resistant-associated mutations, except for A156V, for which a single transition was sufficient (m.s. of 1). However, the presence at locus 36 of the amino acid polymorphism S36 in one case and the wild type V36 in 6 isolates, encoded by unusual GTA or GTG codons, might determined a higher probability of V36L/M mutations because of the reduction of the genetic barrier. Instead, the presence of the CGA and CGT codons in the 155(th) position increases the genetic barrier for R155M or R155Q/M. The large intra-subtype variability, suggests that a routine baseline resistance test must be used before PIs-treatment.
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Affiliation(s)
- Donatella Ferraro
- Sezione di Microbiologia, Dipartimento di Scienze per la Promozione della Salute ''G. D'Alessandro'', Università degli Studi di Palermo, Palermo, Italy.
| | - Noemi Urone
- Sezione di Microbiologia, Dipartimento di Scienze per la Promozione della Salute ''G. D'Alessandro'', Università degli Studi di Palermo, Palermo, Italy
| | - Vito Di Marco
- Sezione di Gastroenterologia, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S.), Università degli Studi di Palermo, Palermo, Italy
| | - Antonio Craxì
- Sezione di Gastroenterologia, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S.), Università degli Studi di Palermo, Palermo, Italy
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7
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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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8
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The current hepatitis C virus prevalence in China may have resulted mainly from an officially encouraged plasma campaign in the 1990s: a coalescence inference with genetic sequences. J Virol 2013; 87:12041-50. [PMID: 23986603 DOI: 10.1128/jvi.01773-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In this study, we investigated hepatitis C virus (HCV) molecular epidemiology and evolutionary dynamics. Both E1 and NS5B sequences were characterized in 379 of 433 patients in southern China and classified into five major subtypes: 1b in 256 patients, 6a in 67 patients, 2a in 29 patients, 3a in 14 patients, and 3b in 13 patients. Using the E1 sequences obtained, along with those from other studies using samples from China, we inferred the HCV epidemic history by means of coalescence strategies. Five Bayesian skyline plots (BSPs) were estimated for the five subtypes. They concurrently highlighted the rapid growth in the HCV-infected population size from 1993 to 2000, followed by an abrupt slowing. Although flanked on both sides by variable population sizes, the plots showed distinct patterns of rapid HCV growth. Coincidently, 1993 to 2000 was a period when contaminated blood transfusions were common in China due to a procedural error in an officially encouraged plasma campaign. The abrupt slowing in 1998 to 2000 corresponded to the central government outlawing paid blood donations in 1998. Using a parametric model, the HCV population growth rates were estimated during 1993 to 2000. It was revealed that the 6a rate was the highest, followed by those of 1b, 2a, 3b, and 3a. Because these rates differed significantly (P < 1e-9) from each other, they may help explain why 6a is increasingly prevalent in southern China and 1b is predominant nationwide. These rates are approximately 10-fold higher than those reported elsewhere. These findings suggested that during the plasma campaign, certain barriers to efficient viral transmission were removed, allowing wide HCV dissemination.
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9
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Yuan M, Lu T, Li C, Lu L. The evolutionary rates of HCV estimated with subtype 1a and 1b sequences over the ORF length and in different genomic regions. PLoS One 2013; 8:e64698. [PMID: 23762247 PMCID: PMC3675120 DOI: 10.1371/journal.pone.0064698] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 04/17/2013] [Indexed: 01/06/2023] Open
Abstract
Background Considerable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance. Methods/Results 176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10−3 substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure. Conclusion Among the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.
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Affiliation(s)
- Manqiong Yuan
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Teng Lu
- University of Southern California, Los Angeles, California, United States of America
| | - Chunhua Li
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Ling Lu
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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10
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Hahné SJM, Veldhuijzen IK, Wiessing L, Lim TA, Salminen M, Laar MVD. Infection with hepatitis B and C virus in Europe: a systematic review of prevalence and cost-effectiveness of screening. BMC Infect Dis 2013; 13:181. [PMID: 23597411 PMCID: PMC3716892 DOI: 10.1186/1471-2334-13-181] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 03/21/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Treatment for chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infection is improving but not benefiting individuals unaware to be infected. To inform screening policies we assessed (1) the hepatitis B surface antigen (HBsAg) and anti-hepatitis C virus antibody (anti-HCV-Ab) prevalence for 34 European countries; and (2) the cost-effectiveness of screening for chronic HBV and HCV infection. METHODS We searched peer-reviewed literature for data on HBsAg and anti-HCV-Ab prevalence and cost-effectiveness of screening of the general population and five subgroups, and used data for people who inject drugs (PWID) and blood donors from two European organizations. Of 1759 and 468 papers found in the prevalence and cost-effectiveness searches respectively, we included 124 and 29 papers after assessing their quality. We used decision rules to calculate weighted prevalence estimates by country. RESULTS The HBsAg and anti-HCV-Ab prevalence in the general population ranged from 0.1%-5.6% and 0.4%-5.2% respectively, by country. For PWID, men who have sex with men and migrants, the prevalence of HBsAg and anti-HCV-Ab was higher than the prevalence in the general population in all but 3 countries. There is evidence that HCV screening of PWID and HBsAg screening of pregnant women and migrants is cost-effective. CONCLUSION The prevalence of chronic HBV and HCV infection varies widely between European countries. Anti-HCV-Ab screening of PWID and HBsAg screening of pregnant women and migrants have European public health priority. Cost-effectiveness analyses may need to take effect of antiviral treatment on preventing HBV and HCV transmission into account.
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Affiliation(s)
- Susan J M Hahné
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), PO Box 1, Bilthoven, 3720 BA, The Netherlands.
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11
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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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12
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Forbi JC, Purdy MA, Campo DS, Vaughan G, Dimitrova ZE, Ganova-Raeva LM, Xia GL, Khudyakov YE. Epidemic history of hepatitis C virus infection in two remote communities in Nigeria, West Africa. J Gen Virol 2012; 93:1410-1421. [PMID: 22456613 DOI: 10.1099/vir.0.042184-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We investigated the molecular epidemiology and population dynamics of HCV infection among indigenes of two semi-isolated communities in North-Central Nigeria. Despite remoteness and isolation, ~15% of the population had serological or molecular markers of hepatitis C virus (HCV) infection. Phylogenetic analysis of the NS5b sequences obtained from 60 HCV-infected residents showed that HCV variants belonged to genotype 1 (n=51; 85%) and genotype 2 (n=9; 15%). All sequences were unique and intermixed in the phylogenetic tree with HCV sequences from people infected from other West African countries. The high-throughput 454 pyrosequencing of the HCV hypervariable region 1 and an empirical threshold error correction algorithm were used to evaluate intra-host heterogeneity of HCV strains of genotype 1 (n=43) and genotype 2 (n=6) from residents of the communities. Analysis revealed a rare detectable intermixing of HCV intra-host variants among residents. Identification of genetically close HCV variants among all known groups of relatives suggests a common intra-familial HCV transmission in the communities. Applying Bayesian coalescent analysis to the NS5b sequences, the most recent common ancestors for genotype 1 and 2 variants were estimated to have existed 675 and 286 years ago, respectively. Bayesian skyline plots suggest that HCV lineages of both genotypes identified in the Nigerian communities experienced epidemic growth for 200-300 years until the mid-20th century. The data suggest a massive introduction of numerous HCV variants to the communities during the 20th century in the background of a dynamic evolutionary history of the hepatitis C epidemic in Nigeria over the past three centuries.
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MESH Headings
- Adult
- Africa, Western/epidemiology
- Cluster Analysis
- Epidemics/history
- Female
- Genotype
- Hepacivirus/classification
- Hepacivirus/genetics
- Hepacivirus/isolation & purification
- Hepatitis C/epidemiology
- Hepatitis C/history
- Hepatitis C/virology
- High-Throughput Nucleotide Sequencing
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- Humans
- Male
- Molecular Epidemiology
- Molecular Sequence Data
- Nigeria/epidemiology
- Phylogeny
- Polymorphism, Genetic
- Population Groups
- Prevalence
- RNA, Viral/genetics
- Viral Nonstructural Proteins/genetics
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Affiliation(s)
- Joseph C Forbi
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Michael A Purdy
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - David S Campo
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Gilberto Vaughan
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Zoya E Dimitrova
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lilia M Ganova-Raeva
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Guo-Liang Xia
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Yury E Khudyakov
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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13
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Mora MVA, Romano CM, Gomes-Gouvêa MS, Gutiérrez MF, Carrilho FJ, Pinho JRR. Molecular characterization, distribution, and dynamics of hepatitis C virus genotypes in blood donors in Colombia. J Med Virol 2011; 82:1889-98. [PMID: 20872715 DOI: 10.1002/jmv.21908] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hepatitis C virus (HCV) is a frequent cause of acute and chronic hepatitis and a leading cause for cirrhosis of the liver and hepatocellular carcinoma. HCV is classified in six major genotypes and more than 70 subtypes. In Colombian blood banks, serum samples were tested for anti-HCV antibodies using a third-generation ELISA. The aim of this study was to characterize the viral sequences in plasma of 184 volunteer blood donors who attended the "Banco Nacional de Sangre de la Cruz Roja Colombiana," Bogotá, Colombia. Three different HCV genomic regions were amplified by nested PCR. The first of these was a segment of 180 bp of the 5'UTR region to confirm the previous diagnosis by ELISA. From those that were positive to the 5'UTR region, two further segments were amplified for genotyping and subtyping by phylogenetic analysis: a segment of 380 bp from the NS5B region; and a segment of 391 bp from the E1 region. The distribution of HCV subtypes was: 1b (82.8%), 1a (5.7%), 2a (5.7%), 2b (2.8%), and 3a (2.8%). By applying Bayesian Markov chain Monte Carlo simulation, it was estimated that HCV-1b was introduced into Bogotá around 1950. Also, this subtype spread at an exponential rate between about 1970 to about 1990, after which transmission of HCV was reduced by anti-HCV testing of this population. Among Colombian blood donors, HCV genotype 1b is the most frequent genotype, especially in large urban conglomerates such as Bogotá, as is the case in other South American countries.
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Affiliation(s)
- Mónica Viviana Alvarado Mora
- Laboratory of Gastroenterology and Hepatology, Department of Gastroenterology, School of Medicine, São Paulo Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
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14
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Lampe E, Espirito-Santo MP, Martins RM, Bello G. Epidemic history of Hepatitis C virus in Brazil. INFECTION GENETICS AND EVOLUTION 2010; 10:886-95. [DOI: 10.1016/j.meegid.2010.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/15/2010] [Accepted: 05/18/2010] [Indexed: 02/07/2023]
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15
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Mariano A, Scalia Tomba G, Tosti ME, Spada E, Mele A. Estimating the incidence, prevalence and clinical burden of hepatitis C over time in Italy. ACTA ACUST UNITED AC 2010; 41:689-99. [PMID: 19579149 DOI: 10.1080/00365540903095358] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Our objective was to estimate HCV clinical burden over time in Italy. A national age-specific HCV prevalence in 1995 was obtained from studies conducted in general population samples and intravenous drug users. Age profile of new HCV infections and trend of incidence since 1985 were derived from a database of reported acute HCV infections. These incidence and prevalence data were used to estimate HCV burden from 1950 to 2030 by mathematical modelling. Different rates of HCV related liver disease progression were tested to assess the robustness of estimates. It is estimated that HCV had a major spread in Italy in 1945-1969. HCV RNA-positive subjects peaked around 1970; their prevalence in 2005 was 3.2%, 58% of them being >65 y of age. The number of individuals with HCV related cirrhosis and that of HCV liver related deaths peaked in 1980-1985. In 2005, they were approximately 230,000 (range 150,000-240,000, according to lower or higher disease progression rates) and approximately 7,000 (range 2200-12,300), respectively: both will be halved by 2025. In conclusion, unlike other industrialized countries, the burden of clinically relevant HCV-positive cases in Italy is already on the decline and will further reduce in the future. This is due to differences in the age-specific prevalence, most of HCV-positive Italians currently being >65 y of age.
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Affiliation(s)
- Andrea Mariano
- Reparto di Epidemiologia Clinica e Linee Guida, Istituto Superiore di Sanità, Rome, Italy.
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16
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Holmberg SD. Molecular epidemiology of health care-associated transmission of hepatitis B and C viruses. Clin Liver Dis 2010; 14:37-48; vii-viii. [PMID: 20123438 DOI: 10.1016/j.cld.2009.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The term "molecular epidemiology" has been ascribed to a host of different activities that involve gene-sequence analysis. Some examples of molecular epidemiology include modeling exercises of phylogenetic trees to reconstruct epidemics; studies of the evolution of hepatitis C virus (HCV); rates of nucleotide substitution in the hepatitis B virus (HBV) surface (S) gene; variations in the core promoter/pre-core/core region of HBV genotype C from different sources; analysis of HBV surface antigen mutations; molecular clock analyses of the short-term evolution of HCV; and analyses of clades and surface antigen polymorphisms of HBV. However, for most epidemiologists molecular epidemiology of viral hepatitis usually refers to studies of gene-sequence homology in HBV or HCV recovered from people in the community or an institution that allows better characterization and assignment of related clusters of infection.
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Affiliation(s)
- Scott D Holmberg
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, TB, and STD Prevention, Centers for Disease Control and Prevention, CDC Mailstop G-37; 1600 Clifton Road, Atlanta, GA 30333, USA.
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17
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Golemba MD, Di Lello FA, Bessone F, Fay F, Benetti S, Jones LR, Campos RH. High prevalence of hepatitis C virus genotype 1b infection in a small town of Argentina. Phylogenetic and Bayesian coalescent analysis. PLoS One 2010; 5:e8751. [PMID: 20090919 PMCID: PMC2807465 DOI: 10.1371/journal.pone.0008751] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 12/23/2009] [Indexed: 12/11/2022] Open
Abstract
Previous studies in Argentina have documented a general prevalence of Hepatitis C Virus (HCV) infection close to 2%. In addition, a high prevalence of HCV has been recently reported in different Argentinean small rural communities. In this work, we performed a study aimed at analyzing the origins and diversification patterns of an HCV outbreak in Wheelwright, a small rural town located in Santa Fe province (Argentina).A total of 89 out of 1814 blood samples collected from people living in Wheelwright, were positive for HCV infection. The highest prevalence (4.9%) was observed in people older than 50 years, with the highest level for the group aged between 70-79 years (22%). The RFLP analyses showed that 91% of the positive samples belonged to the HCV-1b genotype. The E1/E2 and NS5B genes were sequenced, and their phylogenetic analysis showed that the HCV-1b sequences from Wheelwright were monophyletic. Bayesian coalescent-based methods were used to estimate substitution rates and time of the most recent common ancestor (tMRCA). The mean estimated substitution rates and the tMRCA for E1/E2 with and without HVR1 and NS5B were 7.41E-03 s/s/y and 61 years, 5.05E-03 s/s/y and 58 years and 3.24E-03 s/s/y and 53 years, respectively. In summary, the tMRCA values, the demographic model with constant population size, and the fact that the highest prevalence of infection was observed in elder people support the hypothesis that the HCV-1b introduction in Wheelwright initially occurred at least five decades ago and that the early epidemic was characterized by a fast rate of virus transmission. The epidemic seems to have been controlled later on down to the standard transmission rates observed elsewhere.
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Affiliation(s)
- Marcelo D. Golemba
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico A. Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fernando Bessone
- Hospital Provincial del Centenario, Servicio de Gastroenterología y Hepatología, Universidad Nacional de Rosario, Rosario, Argentina
| | - Fabian Fay
- Laboratorio Cibic-Rosario, Rosario, Argentina
| | | | - Leandro R. Jones
- Division of Molecular Biology, Estación de Fotobiología Playa Unión, CC 15, (9103) Rawson, Chubut, Argentina
| | - Rodolfo H. Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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18
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Amodio E, Di Benedetto MA, Gennaro L, Maida CM, Romano N. Knowledge, attitudes and risk of HIV, HBV and HCV infections in hairdressers of Palermo city (South Italy). Eur J Public Health 2009; 20:433-7. [PMID: 19892853 DOI: 10.1093/eurpub/ckp178] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Emanuele Amodio
- Department of Sciences for Health Promotion G. D'Alessandro, University of Palermo, Palermo, Italy.
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19
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Pizzillo P, Almasio PL, Ferraro D, Craxì A, Di Stefano R. HCV genotypes in Sicily: Is there any evidence of a shift? J Med Virol 2009; 81:1040-6. [DOI: 10.1002/jmv.21498] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Argentini C, Genovese D, Dettori S, Rapicetta M. HCV genetic variability: from quasispecies evolution to genotype classification. Future Microbiol 2009; 4:359-73. [PMID: 19327119 DOI: 10.2217/fmb.09.8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
HCV is a ssRNA virus belonging to the Flaviviruses and is found worldwide worldwide in humans. Following primary infection, persistent infection develops in more than 85% of cases, which in up to 30% of cases, may progress to liver disease, cirrhosis and hepatocellular carcinoma. The virus presents a high degree of genetic variability owing to the combination of a lack of proofreading by the RNA-dependent RNA polymerase and a high level of viral replication. This genetic variability allows the classification of genotypes, subtypes, isolates and quasispecies to which epidemiological and pathogenetic significance may be associated. The features and biological implications of HCV variability and of quasispecies dynamics in infection transmission, mechanisms of chronicity and resistance to antiviral therapy are discussed.
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Affiliation(s)
- Claudio Argentini
- Viral Hepatitis Unit, Department of Infectious, Parasitic & Immune-Mediated Disease, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy.
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