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Ebranati E, Mancon A, Airoldi M, Renica S, Shkjezi R, Dragusha P, Della Ventura C, Ciccaglione AR, Ciccozzi M, Bino S, Tanzi E, Micheli V, Riva E, Galli M, Zehender G. Time and Mode of Epidemic HCV-2 Subtypes Spreading in Europe: Phylodynamics in Italy and Albania. Diagnostics (Basel) 2021; 11:diagnostics11020327. [PMID: 33671355 PMCID: PMC7922790 DOI: 10.3390/diagnostics11020327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 01/21/2023] Open
Abstract
Hepatitis C virus (HCV) genotype 2 causes about 10% of global infections and has the most variable circulation profile in Europe. The history of “endemic” HCV-2 subtypes has been satisfactorily reconstructed, instead there is little information about the recent spread of the “epidemic” subtypes, including HCV-2c. To investigate the origin and dispersion pathways of HCV-2c, 245 newly characterized Italian and Albanian HCV-2 NS5B sequences were aligned with 247 publicly available sequences and included in phylogeographic and phylodynamic analyses using the Bayesian framework. Our findings show that HCV-2c was the most prevalent subtype in Italy and Albania. The phylogeographic analysis suggested an African origin of HCV-2c before it reached Italy about in the 1940s. Phylodynamic analysis revealed an exponential increase in the effective number of infections and Re in Italy between the 1940s and 1960s, and in Albania between the 1990s and the early 2000s. It seems very likely that HCV-2c reached Italy from Africa at the time of the second Italian colonization but did not reach Albania until the period of dramatic migration to Italy in the 1990s. This study contributes to reconstructing the history of the spread of epidemic HCV-2 subtypes to Europe.
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Affiliation(s)
- Erika Ebranati
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (E.E.); (M.A.); (S.R.); (C.D.V.); (M.G.)
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, 20122 Milan, Italy
| | - Alessandro Mancon
- Unit of Microbiology, Hospital Sacco of Milan, 20157 Milan, Italy; (A.M.); (V.M.)
| | - Martina Airoldi
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (E.E.); (M.A.); (S.R.); (C.D.V.); (M.G.)
| | - Silvia Renica
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (E.E.); (M.A.); (S.R.); (C.D.V.); (M.G.)
| | - Renata Shkjezi
- Faculty of Medicine and Surgery, Catholic University “Our Lady of the Good Counsel”, 1001 Tirana, Albania; (R.S.); (P.D.)
| | - Pranvera Dragusha
- Faculty of Medicine and Surgery, Catholic University “Our Lady of the Good Counsel”, 1001 Tirana, Albania; (R.S.); (P.D.)
| | - Carla Della Ventura
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (E.E.); (M.A.); (S.R.); (C.D.V.); (M.G.)
| | - Anna Rita Ciccaglione
- Viral Hepatitis Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Roma, Italy;
| | - Silvia Bino
- National Institute of Health, 1001 Tirana, Albania;
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for the Health, University of Milan, 20133 Milan, Italy;
| | - Valeria Micheli
- Unit of Microbiology, Hospital Sacco of Milan, 20157 Milan, Italy; (A.M.); (V.M.)
| | - Elisabetta Riva
- Laboratory of Virology, Campus Bio-Medico University, 00128 Rome, Italy;
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (E.E.); (M.A.); (S.R.); (C.D.V.); (M.G.)
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, 20122 Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (E.E.); (M.A.); (S.R.); (C.D.V.); (M.G.)
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, 20122 Milan, Italy
- Correspondence: ; Tel.: +39-02-503-19770
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Sanarico N, D’Amato S, Bruni R, Rovetto C, Salvi E, Di Zeo P, Chionne P, Madonna E, Pisani G, Costantino A, Equestre M, Tosti ME, Cenci A, Maggiorella MT, Sernicola L, Pontali E, Pansera A, Quattrocchi R, Carbonara S, Signorile F, Surace LA, Federzoni G, Garlassi E, Starnini G, Monarca R, Babudieri S, Rapicetta M, Pompa MG, Caraglia A, Ensoli B, Ciccaglione AR, Buttò S. Correlates of infection and molecular characterization of blood-borne HIV, HCV, and HBV infections in HIV-1 infected inmates in Italy: An observational cross-sectional study. Medicine (Baltimore) 2016; 95:e5257. [PMID: 27858889 PMCID: PMC5591137 DOI: 10.1097/md.0000000000005257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coinfection of blood-borne hepatitis B and hepatitis C viruses (HBV and HCV, respectively) in human immunodeficiency virus type 1 (HIV-1)-positive individuals frequently occurs in inmate population and peculiar viral strains and patterns of virological markers may be observed.Plasma from 69 HIV-1-positive inmates was obtained from 7 clinical centers connected with correctional centers in different towns in Italy. HIV, HBV, and HCV markers were tested by commercial assays. Virus genotyping was carried out by sequencing the protease and reverse transcriptase-encoding region (PR-RT region) for HIV and a region encompassing the NS5B gene for HCV and subsequent phylogenetic analysis.Twelve over 14 HIV-subtyped inmates were infected with HIV-1 subtype B strains. The 2 non-B strains belonged to subtype G and CRF02_AG, in an Italian and a Gambian patient, respectively. Variants carrying the K103N and Y181C resistance mutations to non-nucleoside reverse transcriptase inhibitors (NNRTIs) were found in 2 out of 9 patients naive for combined antiretroviral therapy (cART) (22.2%). Most HIV-positive patients (92.8%) showed evidence of past or present HBV and/or HCV infection. Prevalence of HBV and HCV was 81.2% for both viruses, whereas prevalence of HBV/HCV coinfection was 69.6%. A significantly higher presence of HCV infection was found in Italians [odds ratio (OR) 11.0; interval 1.7-80.9] and in drug users (OR 27.8; interval 4.9-186.0). HCV subtypes were determined in 42 HCV or HBV/HCV-coinfected individuals. HCV subtypes 1a, 3a, 4d, and 1b were found in 42.9%, 40.5%, 14.3%, and 2.4% of inmates, respectively. Low titers of HBV DNA in HBV DNA positive subjects precluded HBV subtyping.The high prevalence of HBV and HCV coinfections in HIV-infected inmates, as well as the heterogeneity of HIV and HCV subtypes suggest the need to adopt systematic controls in prisons to monitor both the burden and the genetic forms of blood-borne viral infections, in order to apply targeted therapeutic interventions.
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Affiliation(s)
| | | | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | - Emanuela Salvi
- National AIDS Center, Istituto Superiore di Sanità, Rome
| | | | - Paola Chionne
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | - Giulio Pisani
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | - Angela Costantino
- National AIDS Center, Istituto Superiore di Sanità, Rome
- Italian Ministry of Health, Rome
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | - Michele Equestre
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | - Maria E. Tosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | | | | | - Emanuele Pontali
- ASL 3 Genovese and Department of Infectious Diseases, Galliera Hospital, Genova
| | | | | | | | | | - Lorenzo Antonio Surace
- Centro Medicina del Viaggiatore e delle Migrazioni, Presidio Ospedaliero di Lamezia Terme, Giovanni Paolo II Hospital, Lamezia Terme
| | | | | | | | | | | | - Maria Rapicetta
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome
| | | | | | - Barbara Ensoli
- National AIDS Center, Istituto Superiore di Sanità, Rome
| | | | - Stefano Buttò
- National AIDS Center, Istituto Superiore di Sanità, Rome
- Correspondence: Stefano Buttò, National AIDS Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy (e-mail: )
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Construction of infectious cDNA clone derived from a classical swine fever virus field isolate in BAC vector using in vitro overlap extension PCR and recombination. J Virol Methods 2015; 226:60-6. [DOI: 10.1016/j.jviromet.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/26/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022]
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Zhang EZ, Bartels DJ, Frantz JD, Seepersaud S, Lippke JA, Shames B, Zhou Y, Lin C, Kwong A, Kieffer TL. Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples. Virol J 2013; 10:53. [PMID: 23402332 PMCID: PMC3575352 DOI: 10.1186/1743-422x-10-53] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 02/07/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Direct-acting antiviral (DAAs) agents for hepatitis C virus (HCV) span a variety of targets, including proteins encoded by the NS3/4A, NS4B, NS5A, and NS5B genes. Treatment with DAAs has been shown to select variants with sequence changes in the HCV genome encoding amino acids that may confer resistance to the treatment. In order to assess these effects in patients, a Reverse Transcription Polymerase Chain Reaction (RT-PCR) method was developed to sequence these regions of HCV from patient plasma. METHODS A method was developed to amplify and sequence genotype 1 HCV RNA from patient plasma. Optimization of HCV RNA isolation, cDNA synthesis, and nested PCR steps were performed. The optimization of HCV RNA isolation, design of RT-PCR primers, optimization of RT-PCR amplification conditions and reagents, and the evaluation of the RT-PCR method performance is described. RESULTS The optimized method is able to successfully, accurately, and reproducibly amplify near full-length genotype 1 HCV RNA containing a wide range of concentrations (103 to 108 IU/mL) with a success rate of 97%. The lower limit of detection was determined to be 1000 IU/mL HCV RNA. CONCLUSIONS This assay allows viral sequencing of all regions targeted by the most common DAAs currently in development, as well as the possibility to determine linkage between variants conferring resistance to multiple DAAs used in combination therapy.
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Affiliation(s)
- Eileen Z Zhang
- Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139-4242, USA
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Abstract
A long reverse transcription polymerase chain reaction (LRP) protocol is described for the amplification of large RNA sequences. The amplification of near full-length hepatitis C virus (HCV) genome from serum samples is used as an example to detail each step in LRP procedure, including primer design, RNA extraction, reverse transcription, and PCR. The protocol for efficient cloning of such large amplicons is also presented. Since HCV represents a difficult template in terms of its near full-length amplification due to extensive secondary structures and low titers in clinical samples, methods described in this chapter should be applicable for other RNA viruses and cellular RNA templates.
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Affiliation(s)
- Xiaofeng Fan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
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6
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Lwin AA, Shinji T, Khin M, Win N, Obika M, Okada S, Koide N. Hepatitis C virus genotype distribution in Myanmar: Predominance of genotype 6 and existence of new genotype 6 subtype. Hepatol Res 2007; 37:337-45. [PMID: 17441806 DOI: 10.1111/j.1872-034x.2007.00053.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AIM This study was performed to determine the prevalence and distribution of hepatitis C virus (HCV) genotypes in Myanmar. METHODS A total of 1333 peripheral blood samples were collected from four different border cities of Myanmar. The anti-HCV antibody-positive serum samples were identified. HCV was genotyped by reverse transcriptase polymerase chain reaction, direct DNA sequencing and phylogenetic analysis on the partial core genome. RESULTS The overall prevalence of HCV infection was 11.6% (154/1333). Regionally, it was 13.5% (47/349) in the north-eastern city, 12.8% (64/501) in the north-western city, 4.2% (16/380) in the southern city and 26.2% (27/103) in the western city. HCV was genotyped in 145/154 (94.2%) samples. Genotype 6 was the most prevalent genotype in this study (71/145, 49%), followed by genotype 3 (57/145, 39.3%), genotype 1 (16/145, 11%), and genotype 2 (1/145, 0.7%). Genotype 6 was mostly found in the northern cities and genotype 3 in the southern and western cities of Myanmar. Multiple HCV genotypes/subtypes were successfully characterized as 1a, 1b, 2a, 3a, 3b, 6m, 6n, and a new 6 subtype. Among them, subtype 6n was the most predominant subtype (38.6%), followed by subtype 3b (29.7%), 3a (9.6%), 6m (9%), 1b (6.9%), 1a (4.1%), new 6 subtype (1.4%) and 2a (0.7%). Subtype 6n was more widely distributed in the northern cities whereas subtype 3b was more common in the western city. The newly discovered genotype 6 subtype was from the northern cities. CONCLUSIONS The results indicate there are regional differences of HCV genotype distribution in Myanmar. There is a distinct geographic variation from other South-East Asian countries in terms of the existence of the new genotype 6 subtype.
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Affiliation(s)
- Aye Aye Lwin
- Department of Laboratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan, and Department of Medical Research (Lower Myanmar), Yangon, Myanmar
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Li C, Fu Y, Lu L, Ji W, Yu J, Hagedorn CH, Zhang L. Complete genomic sequences for hepatitis C virus subtypes 6e and 6g isolated from Chinese patients with injection drug use and HIV-1 co-infection. J Med Virol 2006; 78:1061-9. [PMID: 16789024 DOI: 10.1002/jmv.20663] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In one of our recent studies, two HCV genotype 6 variants were identified in patients from Hong Kong and Guangxi in southern China, with injection drug use and HIV-1 co-infection. We report the complete genomic sequences for these two variants: GX004 and HK6554. Their entire genome lengths were 9,468 and 9,462 nt; the 5' UTRs were 338 nt followed by single ORFs of 9,069 nt; the 3' UTRs were 61 and 55 nt including 29 and 23 nt poly(U) tracks. Phylogenetic analysis using a maximum likelihood method showed that HK6554 was classified into subtype 6g and GX004 represented the first complete genome sequence for subtype 6e. Further analysis with reference sequences in three different genomic regions revealed that GX004 closely clustered with a group of subtype 6e variants, which were previously exclusively found in Vietnam and recently increasingly identified in injection drug users from the Guangxi province in southern China that borders Vietnam. This suggests that subtype 6e could become epidemic in southern China by network transmission among injection drug users.
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Affiliation(s)
- Chunhua Li
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA.
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Fan X, Xu Y, Di Bisceglie AM. Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun 2006; 346:1163-72. [PMID: 16793008 PMCID: PMC7092855 DOI: 10.1016/j.bbrc.2006.06.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 06/02/2006] [Indexed: 11/27/2022]
Abstract
Long RT-PCR (LRP) amplification of RNA templates is sometimes difficult compared to long PCR of DNA templates. Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. The only source for viral genome amplification is clinical samples in which HCV is usually present at low titers. We have created a comprehensive optimization protocol that allows robust amplification of a 9.1 kb fragment of HCV, followed by efficient cloning into a novel vector. Detailed analyses indicate the lack of potential LRP-mediated recombination and the preservation of viral diversity. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics.
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Affiliation(s)
- Xiaofeng Fan
- Division of Gastroenterology and Hepatology, Saint Louis University Liver Center, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63110, USA.
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Bracho MA, Carrillo-Cruz FY, Ortega E, Moya A, González-Candelas F. A new subtype of hepatitis C virus genotype 1: complete genome and phylogenetic relationships of an Equatorial Guinea isolate. J Gen Virol 2006; 87:1697-1702. [PMID: 16690936 DOI: 10.1099/vir.0.81666-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) is the leading cause of chronic liver disease and is associated with hepatocellular carcinoma. However, there have been few studies on the distribution and genetic diversity of HCV isolates in non-developed countries. Here, the complete genome sequence of an HCV genotype 1 isolate from Equatorial Guinea is reported, the first complete HCV-1 genome of African origin. Phylogenetic analysis revealed that this sequence always grouped with sequences of genotype 1, but did not group clearly with any subtype described so far. An analysis of partial NS5B gene sequences with additional sequences of African origin also failed to find close similarities between the new sequence and any previously known isolate. Genetic divergence of the coding region of this new sequence with respect to the recognized subtypes of HCV-1 ranged from 20 to 22%. It is proposed that this isolate is a representative of a new, distinct variant of HCV subtype 1.
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Affiliation(s)
- Maria Alma Bracho
- Institut 'Cavanilles' de Biodiversitat i Biologia Evolutiva, Universitat de València, 46070 València, Spain
| | | | - Enrique Ortega
- Hospital General Universitari, Avinguda Tres Creus s/n, 46014 València, Spain
| | - Andrés Moya
- Institut 'Cavanilles' de Biodiversitat i Biologia Evolutiva, Universitat de València, 46070 València, Spain
| | - Fernando González-Candelas
- Institut 'Cavanilles' de Biodiversitat i Biologia Evolutiva, Universitat de València, 46070 València, Spain
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Jones LR, Zandomeni RO, Weber EL. A long distance RT-PCR able to amplify the Pestivirus genome. J Virol Methods 2006; 134:197-204. [PMID: 16497393 PMCID: PMC7112918 DOI: 10.1016/j.jviromet.2006.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 01/03/2006] [Accepted: 01/10/2006] [Indexed: 01/08/2023]
Abstract
A method to amplify long genomic regions (up to approximately 12.3 kb) from pestiviruses in one RT-PCR is described. The difficulty in designing conserved Pestivirus primers for the amplification of genomes from highly divergent isolates simply by means of overlapping segments is demonstrated using new bioinformatic tools. An alternative procedure consisting of optimizing the length of the genomic cDNA fragments and their subsequent amplification by polymerase chain reaction (PCR) using a limited set of specific primers is described. The amplification of long DNA fragments from a variety of sources, including genomic, mitochondrial, and viral DNAs as well as cDNA produced by reverse transcription (RT) has been achieved using this methodology, known as long distance PCR. In the case of viruses, it is necessary to obtain viral particles from infected cells prior to RT procedures. This work provides improvements in four steps of long distance RT-PCR (L-RT-PCR): (i) preparation of a viral stock, (ii) preparation of template RNA, (iii) reverse transcription and (iv) amplification of the cDNA by LD-PCR. The usefulness of L-RT-PCR is discussed in the light of current knowledge on pestivirus diversity. The genomic sequence of Singer_Arg reference strain obtained using this method is presented and characterized.
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Affiliation(s)
- Leandro R. Jones
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
| | - Rubén O. Zandomeni
- Instituto de Microbiología y Zoología Agrícola, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
| | - E. Laura Weber
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
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Lu L, Nakano T, Li C, Fu Y, Miller S, Kuiken C, Robertson BH, Hagedorn CH. Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6. J Gen Virol 2006; 87:629-634. [PMID: 16476984 DOI: 10.1099/vir.0.81400-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Here, the complete genome sequences for three hepatitis C virus (HCV) variants identified from China and belonging to genotype 6 are reported: km41, km42 and gz52557. Their entire genome lengths were 9430, 9441 and 9448 nt, respectively; the 5' untranslated regions (UTRs) contained 341, 342 and 339 nt, followed by single open reading frames of 9045, 9045 and 9057 nt, respectively; the 3' UTRs, up to the poly(U) tracts, were 41, 51 and 52 nt, respectively. Phylogenetic analyses showed that km41 is classified into subtype 6k and km42 into subtype 6n. Although gz52557 clustered distantly with subtype 6g, it appeared to belong to a distinct subtype. Analysis with 53 and 105 partial core and NS5B region sequences, respectively, representing 17 subtypes from 6a to 6q and three unassigned isolates of genotype 6 in co-analyses demonstrated that gz52557 was equidistant from all of these isolates, indicating that it belongs to a novel subtype. However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype.
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Affiliation(s)
- Ling Lu
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
| | - Tatsunori Nakano
- Department of Internal Medicine, Ichinomiya Nishi Hospital, Ichinomiya, Aichi, Japan
| | - Chunhua Li
- Graduate School of the Chinese Academy of Sciences, Beijing, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou City, Guangdong Province, China
| | - Steve Miller
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
| | - Carla Kuiken
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Betty H Robertson
- National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Curt H Hagedorn
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
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