Genotype-Specific Evolution of Hepatitis E Virus

被引:32
作者
Brayne, Adam B. [1 ]
Dearlove, Bethany L. [1 ]
Lester, James S. [1 ]
Pond, Sergei L. Kosakovsky [2 ]
Frost, Simon D. W. [1 ]
机构
[1] Univ Cambridge, Cambridge, England
[2] Temple Univ, Philadelphia, PA 19122 USA
基金
英国医学研究理事会; 美国国家卫生研究院;
关键词
evolution; evolutionary biology; genotypic identification; hepatitis E virus; positive selection; ORF3; PROTEIN; PHYLOGENETIC ANALYSIS; IGG SEROPREVALENCE; MOLECULAR-CLONING; NATURAL-SELECTION; MOSAIC STRUCTURE; RECOMBINATION; INFECTION; SEQUENCE; INTERACTS;
D O I
10.1128/JVI.02241-16
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilize this natural case-control study for investigating the evolution of zoonotic viruses compared to single-host viruses, using 244 near-full-length HEV genomes. Genome-wide estimates of the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS ratio) located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype-specific evolution of these regions may reflect their fitness. Bayesian inference of evolutionary rates shows that genotypes 3 and 4 have significantly higher rates than genotype 1 across all ORFs. Reconstruction of the phylogenies of zoonotic genotypes demonstrates significant intermingling of isolates between hosts. We speculate that the genotype-specific differences may result from cyclical adaptation to different hosts in genotypes 3 and 4. IMPORTANCE Hepatitis E virus (HEV) is increasingly recognized as a pathogen that affects both the developing and the developed world. While most often clinically mild, HEV can be severe or fatal in certain demographics, such as expectant mothers. Like many other viral pathogens, HEV has been classified into several distinct genotypes. We show that most of the HEV genome is evolutionarily constrained. One locus of positive selection is unusual in that it encodes two distinct protein products. We are the first to detect positive selection in this overlap region. Genotype 1, which infects humans only, appears to be evolving differently from genotypes 3 and 4, which infect multiple species, possibly because genotypes 3 and 4 are unable to achieve the same fitness due to repeated host jumps.
引用
收藏
页数:16
相关论文
共 95 条
[1]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[2]  
[Anonymous], SCIENCE
[3]  
[Anonymous], 2005, VIRUS TAXONOMY
[4]   Human and porcine hepatitis E virus strains, United Kingdom [J].
Banks, M ;
Bendall, R ;
Grierson, S ;
Heath, G ;
Mitchell, J ;
Dalton, H .
EMERGING INFECTIOUS DISEASES, 2004, 10 (05) :953-955
[5]   A Comparison of Two Commercially Available Anti-HEV IgG Kits and a Re-Evaluation of Anti-HEY IgG Seroprevalence Data in Developed Countries [J].
Bendall, Richard ;
Ellis, Vic ;
Ijaz, Samreen ;
Ali, Rachel ;
Dalton, Harry .
JOURNAL OF MEDICAL VIROLOGY, 2010, 82 (05) :799-805
[6]  
Benson DA, 2010, NUCLEIC ACIDS RES, V38, pD46, DOI [10.1093/nar/gkp1024, 10.1093/nar/gkx1094, 10.1093/nar/gkl986, 10.1093/nar/gkw1070, 10.1093/nar/gks1195, 10.1093/nar/gkn723, 10.1093/nar/gkg057, 10.1093/nar/gkr1202, 10.1093/nar/gkq1079]
[7]   Hepatitis E Virus in Pork Food Chain, United Kingdom, 2009-2010 [J].
Berto, Alessandra ;
Martelli, Francesca ;
Grierson, Sylvia ;
Banks, Malcolm .
EMERGING INFECTIOUS DISEASES, 2012, 18 (08) :1358-1360
[8]   An exact nonparametric method for inferring mosaic structure in sequence triplets [J].
Boni, Maciej F. ;
Posada, David ;
Feldman, Marcus W. .
GENETICS, 2007, 176 (02) :1035-1047
[9]   HLA DNA Sequence Variation among Human Populations: Molecular Signatures of Demographic and Selective Events [J].
Buhler, Stephane ;
Sanchez-Mazas, Alicia .
PLOS ONE, 2011, 6 (02)
[10]   BLAST plus : architecture and applications [J].
Camacho, Christiam ;
Coulouris, George ;
Avagyan, Vahram ;
Ma, Ning ;
Papadopoulos, Jason ;
Bealer, Kevin ;
Madden, Thomas L. .
BMC BIOINFORMATICS, 2009, 10