Origin of hepatitis C virus genotype 3 in Africa as estimated through an evolutionary analysis of the full-length genomes of nine subtypes, including the newly sequenced 3d and 3e

被引:18
作者
Li, Chunhua [1 ]
Lu, Ling [1 ]
Murphy, Donald G. [2 ]
Negro, Francesco [3 ,4 ]
Okamoto, Hiroaki [5 ]
机构
[1] Univ Kansas, Med Ctr, Dept Pathol & Lab Med, Ctr Viral Oncol, Kansas City, KS 66103 USA
[2] Inst Natl Sante Publ Quebec, Lab Sante Publ Quebec, Ste Anne De Bellevue, PQ, Canada
[3] Univ Hosp, Div Gastroenterol & Hepatol, Geneva, Switzerland
[4] Univ Hosp, Div Clin Pathol, Geneva, Switzerland
[5] Jichi Med Univ, Sch Med, Dept Infect & Immun, Div Virol, Shimotsuke, Tochigi 3290498, Japan
关键词
TRANSCRIPTASE PCR ASSAY; LINE PROBE ASSAY; MOLECULAR EPIDEMIOLOGY; NS5B REGION; CLASSIFICATION; IDENTIFICATION; VARIANTS; CORE; INFECTION; LIVER;
D O I
10.1099/vir.0.065128-0
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
We characterized the full-length genomes of nine hepatitis C virus genotype 3 (HCV-3) isolates: QC7, QC8, QC9, QC10, QC34, QC88, NE145, NE274 and 811. To the best of our knowledge, NE274 and NE145 were the first full-length genomes for confirming the provisionally assigned subtypes 3d and 3e, respectively, whereas 811 represented the first HCV-3 isolate that had its extreme 3' UTR terminus sequenced. Based on these full-length genomes, together with 42 references representing eight assigned subtypes and an unclassified variant of HCV-3, and 10 sequences of six other genotypes, a timescaled phylogenetic tree was reconstructed after an evolutionary analysis using a coalescent Bayesian procedure. The results indicated that subtypes 3a, 3d and 3e formed a subset with a common ancestor dated to similar to 202.89 [95 % highest posterior density (HPD): 160.11, 264.6] years ago. The analysis of all of the HCV-3 sequences as a single lineage resulted in the dating of the divergence time to similar to 457.81 (95% HPD: 350.62, 587.53) years ago, whereas the common ancestor of all of the seven HCV genotypes dated to similar to 780.86 (95 % HPD: 592.15, 1021.34) years ago. As subtype 3h and the unclassified variant were relatives, and represented the oldest HCV-3 lineages with origins in Africa and the Middle East, these findings may indicate the ancestral origin of HCV-3 in Africa. We speculate that the ancestral HCV-3 strains may have been brought to South Asia from Africa by land and/or across the sea to result in its indigenous circulation in that region. The spread was estimated to have occurred in the era after Vasco da Gama had completed his expeditions by sailing along the eastern coast of Africa to India. However, before this era, Arabians had practised slave trading from Africa to the Middle East and South Asia for centuries, which may have mediated the earliest spread of HCV-3.
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收藏
页码:1677 / 1688
页数:12
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