Full-length genomes of 16 hepatitis C virus genotype 1 isolates representing subtypes 1c, 1d, 1e, 1g, 1h, 1i, 1j and 1k, and two new subtypes 1m and 1n, and four unclassified variants reveal ancestral relationships among subtypes

Journal of General Virology

Volumn 95, Issue PART 7, 2014, Pages 1479-1487

  Lu, Ling ^a   Li, Chunhua ^a   Xu, Yan ^a   Murphy, Donald G ^b  

^a UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

^b Institut National Desanté Publique du Québec   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EVOLUTION; GENETIC VARIABILITY; GENOME ANALYSIS; GEOGRAPHIC ORIGIN; HAITI; HEPATITIS C VIRUS GENOTYPE 1; HEPATITIS C VIRUS SUBTYPE 1C; HEPATITIS C VIRUS SUBTYPE 1D; HEPATITIS C VIRUS SUBTYPE 1E; HEPATITIS C VIRUS SUBTYPE 1G; HEPATITIS C VIRUS SUBTYPE 1H; HEPATITIS C VIRUS SUBTYPE 1I; HEPATITIS C VIRUS SUBTYPE 1J; HEPATITIS C VIRUS SUBTYPE 1K; HEPATITIS C VIRUS SUBTYPE 1M; HEPATITIS C VIRUS SUBTYPE 1N; IMMIGRANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PLESIOMORPHY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; VIRUS GENOME; VIRUS NOMENCLATURE;

CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENOME, VIRAL; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, VIRAL; SEQUENCE ANALYSIS, DNA;

EID: 84902669925     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.064980-0     Document Type: Article

References (22)

1. Alter, M. J. (2007). Epidemiology of hepatitis C virus infection. World J Gastroenterol 13, 2436-2441.
2. Andernach, I. E., Nolte, C., Pape, J. W. & Muller, C. P. (2009). Slave trade and hepatitis B virus genotypes and subgenotypes in Haiti and Africa. Emerg Infect Dis 15, 1222-1228.
3. Bracho, M. A., Saludes, V., Martró, E., Bargalló, A., González-Candelas, F. & Ausina, V. (2008). Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses. Virol J 5, 72.
4. CDC (1998). Recommendations for prevention and control of hepatitis C virus (HCV) infection and HCV-related chronic disease. MMWR Recomm Rep 47 (RR-19), 1-39.
5. CIA (2008) World Factbook [accessed 11 May 2103]. https://www.cia. gov/library/publications/download/download-2008.
6. Demetriou, V. L. & Kostrikis, L. G. (2011). Near-full genome characterization of unclassified hepatitis C virus strains relating to genotypes 1 and 4. J Med Virol 83, 2119-2127.
7. Drummond, A. J. & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7, 214.
8. Geggus, D. (2000). La traite des esclaves aux Antilles francaises à la fin du 18me siècle: quelques aspects du marchélocal. In Négoce, ports et océans, XVIe-XXe siècles, pp. 235-245. Edited by S. Marzagalli & H. Bonin. Bordeaux: Presses Universitaires de Bordeaux.
9. Geggus, D. (2001). The French slave trade: an overview. William Mary Q 58, 119-138.
10. Jeannel, D., Fretz, C., Traore, Y., Kohdjo, N., Bigot, A., Pê Gamy, E., Jourdan, G., Kourouma, K., Maertens, G. & other authors (1998). Evidence for high genetic diversity and long-termendemicity of hepatitis C virus genotypes 1 and 2 in West Africa. J Med Virol 55, 92-97.
11. Kuiken, C., Yusim, K., Boykin, L. & Richardson, R. (2005). The Los Alamos hepatitis C sequence database. Bioinformatics 21, 379-384.
12. Li, C., Njouom, R., Pépin, J., Nakano, T., Bennett, P., Pybus, O. G. & Lu, L. (2013). Characterization of full-length hepatitis C virus sequences for subtypes 1e, 1h and 1l, and a novel variant revealed Cameroon as an area in origin for genotype 1. J Gen Virol 94, 1780-1790.
13. Morgan, P. D. (1998). Slave trade: transatlantic. In Macmillan Encyclopedia of World Slavery, pp. 837-844. Edited by P. Finkelman & J. C. Miller. New York: Macmillan Reference.
14. Murphy, D. G., Willems, B., Deschênes, M., Hilzenrat, N., Mousseau, R. & Sabbah, S. (2007). Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E1 and 59 untranslated region sequences. J Clin Microbiol 45, 1102-1112.
15. Pybus, O. G., Markov, P. V., Wu, A. & Tatem, A. J. (2007). Investigating the endemic transmission of the hepatitis C virus. Int J Parasitol 37, 839-849.
16. Sepinwall, A. G. (2012). Haitian History: New Perspectives. New York: Routledge.
17. Simmonds, P. (2004). Genetic diversity and evolution of hepatitis C virus-15 years on. J Gen Virol 85, 3173-3188.
18. Simmonds, P., Bukh, J., Combet, C., Deléage, G., Enomoto, N., Feinstone, S., Halfon, P., Inchauspé, G., Kuiken, C. & other authors (2005). Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42, 962-973.
19. Smith, D. B., Bukh, J., Kuiken, C., Muerhoff, A. S., Rice, C. M., Stapleton, J. T. & Simmonds, P. (2014). Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 59, 318-327.
20. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739.
21. WHO (1997). Hepatitis C. Wkly Epidemiol Rec 72, 65-69.
22. Yuan, M., Lu, T., Li, C. & Lu, L. (2013). The evolutionary rates of HCV estimated with subtype 1a and 1b sequences over the ORF length and in different genomic regions. PLoS ONE 8, e64698.