FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Front Microbiol / Evolutionary Analysis Provides Insight Into the Origin and A...
Frontiers in microbiology2018; 9; 854; doi: 10.3389/fmicb.2018.00854

Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV.

Abstract: Hepatitis C virus (HCV) belongs to the genus and is genetically heterogeneous, with seven major genotypes further divided into several recognized subtypes. HCV origin was previously dated in a range between ∼200 and 1000 years ago. Hepaciviruses have been identified in several domestic and wild mammals, the largest viral diversity being observed in bats and rodents. The closest relatives of HCV were found in horses/donkeys (equine hepaciviruses, EHV). However, the origin of HCV as a human pathogen is still an unsolved puzzle. Using a selection-informed evolutionary model, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago (CI: 3192-5221 years ago), with the oldest genotypes being endemic to Asia. EHV originated around 1100 CE (CI: 291-1640 CE). These time estimates exclude that EHV transmission was mainly sustained by widespread veterinary practices and suggest that HCV originated from a single zoonotic event with subsequent diversification in human populations. We also describe a number of biologically important sites in the major HCV genotypes that have been positively selected and indicate that drug resistance-associated variants are significantly enriched at positively selected sites. HCV exploits several cell-surface molecules for cell entry, but only two of these (CD81 and OCLN) determine the species-specificity of infection. Herein evolutionary analyses do not support a long-standing association between primates and hepaciviruses, and signals of positive selection at CD81 were only observed in Chiroptera. No evidence of selection was detected for OCLN in any mammalian order. These results shed light on the origin of HCV and provide a catalog of candidate genetic modulators of HCV phenotypic diversity.
Get Full Text
Publication Date: 2018-05-01 PubMed ID: 29765366PubMed Central: PMC5938362DOI: 10.3389/fmicb.2018.00854Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research is focusing on the origin and adaptation of Hepatitis C virus (HCV) through an evolutionary analysis model. The scientists found that the common ancestor of present HCV genotypes existed at least 3000 years ago, mainly in Asia, and identified numerous sites in the virus’s genotypes that have been positively selected for drug resistance.

Overview of Hepatitis C Virus (HCV)

  • The study is based on Hepatitis C virus (HCV), a genetically diverse virus found in the Hepaciviruses genus. The virus has seven major genotypes, and within these genotypes, there are numerous subtypes.
  • While hepaciviruses are found in several domestic and wild mammals, they are most diverse in bats and rodents. Horses and donkeys (equine hepaciviruses or EHV) are known to carry the closest relatives to HCV.

Origins and Evolutionary Analysis of HCV

  • Using a new model of evolutionary research that incorporates selection, the researchers estimate the common ancestor of all current HCV genotypes existed around 3000 years ago. This contradicts previous research that dated the origin of HCV between 200 and 1000 years ago.
  • The oldest HCV genotypes are believed to be endemic to Asia, while EHV is thought to have originated around the year 1100.
  • Based on these timeframes, the researchers argue that HCV probably originated from a single event where the virus passed from animals to humans (zoonotic event). It then diversified within human populations.

HCV Drug Resistance and Genetic Variants

  • The researchers identified key sites within the primary HCV genotypes that have been positively selected, meaning these genetic variants have proven advantageous for the survival of the virus.
  • These positively selected sites are significantly enriched with genetic variants associated with drug resistance, making them important areas for ongoing research and development of HCV treatments.

HCV Cell Entry and Infection Specifics

  • HCV uses a number of cell-surface molecules to enter cells, but only two of these, CD81 and OCLN, determine the specific species that the virus can infect.
  • The evolutionary analysis found no indication of long-standing association between primates and hepaciviruses, and positive selection for CD81 was only observed in bats. No signs of selection were detected for OCLN in any mammalian species.
  • This aspect of the research provides insight into how the virus may have adapted over time and the specifics of its infection process.

This research thus provides a better understanding of the origins and evolution of HCV and contributes to a knowledge base that may ultimately assist in the development of more effective medications and treatments for hepatitis C.

Cite This Article

APA
Forni D, Cagliani R, Pontremoli C, Pozzoli U, Vertemara J, De Gioia L, Clerici M, Sironi M. (2018). Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV. Front Microbiol, 9, 854. https://doi.org/10.3389/fmicb.2018.00854

Publication

Frontiers in microbiology
ISSN: 1664-302X
NlmUniqueID: 101548977
Country: Switzerland
Language: English
Volume: 9
Pages: 854
PII: 854

Researcher Affiliations

Forni, Diego
  • Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy.
Cagliani, Rachele
  • Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy.
Pontremoli, Chiara
  • Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy.
Pozzoli, Uberto
  • Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy.
Vertemara, Jacopo
  • Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy.
De Gioia, Luca
  • Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy.
Clerici, Mario
  • Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.
  • Don C. Gnocchi Foundation Onlus, IRCCS, Milan, Italy.
Sironi, Manuela
  • Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy.

References

This article includes 119 references
  1. Aiewsakun P, Katzourakis A. Time-Dependent Rate Phenomenon in Viruses.. J Virol 2016 Aug 15;90(16):7184-95.
    doi: 10.1128/JVI.00593-16pmc: PMC4984659pubmed: 27252529google scholar: lookup
  2. Akamatsu S, Hayes CN, Ochi H, Uchida T, Kan H, Murakami E, Abe H, Tsuge M, Miki D, Akiyama R, Hiraga N, Imamura M, Aikata H, Kawaoka T, Kawakami Y, Chayama K. Association between variants in the interferon lambda 4 locus and substitutions in the hepatitis C virus non-structural protein 5A.. J Hepatol 2015 Sep;63(3):554-63.
    doi: 10.1016/j.jhep.2015.03.033pubmed: 25849245google scholar: lookup
  3. Anisimova M, Bielawski JP, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.. Mol Biol Evol 2001 Aug;18(8):1585-92.
    doi: 10.1093/oxfordjournals.molbev.a003945pubmed: 11470850google scholar: lookup
  4. Anisimova M, Bielawski JP, Yang Z. Accuracy and power of bayes prediction of amino acid sites under positive selection.. Mol Biol Evol 2002 Jun;19(6):950-8.
    doi: 10.1093/oxfordjournals.molbev.a004152pubmed: 12032251google scholar: lookup
  5. Ansari MA, Pedergnana V, L C Ip C, Magri A, Von Delft A, Bonsall D, Chaturvedi N, Bartha I, Smith D, Nicholson G, McVean G, Trebes A, Piazza P, Fellay J, Cooke G, Foster GR, Hudson E, McLauchlan J, Simmonds P, Bowden R, Klenerman P, Barnes E, Spencer CCA. Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus.. Nat Genet 2017 May;49(5):666-673.
    doi: 10.1038/ng.3835pmc: PMC5873514pubmed: 28394351google scholar: lookup
  6. Bartenschlager R, Lohmann V, Penin F. The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection.. Nat Rev Microbiol 2013 Jul;11(7):482-96.
    doi: 10.1038/nrmicro3046pubmed: 23748342google scholar: lookup
  7. Bay RA, Bielawski JP. Recombination detection under evolutionary scenarios relevant to functional divergence.. J Mol Evol 2011 Dec;73(5-6):273-86.
    doi: 10.1007/s00239-011-9473-0pubmed: 22210457google scholar: lookup
  8. Bertaux C, Dragic T. Different domains of CD81 mediate distinct stages of hepatitis C virus pseudoparticle entry.. J Virol 2006 May;80(10):4940-8.
    doi: 10.1128/JVI.80.10.4940-4948.2006pmc: PMC1472091pubmed: 16641285google scholar: lookup
  9. Bitzegeio J, Bankwitz D, Hueging K, Haid S, Brohm C, Zeisel MB, Herrmann E, Iken M, Ott M, Baumert TF, Pietschmann T. Adaptation of hepatitis C virus to mouse CD81 permits infection of mouse cells in the absence of human entry factors.. PLoS Pathog 2010 Jul 1;6(7):e1000978.
    doi: 10.1371/journal.ppat.1000978pmc: PMC2895659pubmed: 20617177google scholar: lookup
  10. Burbelo PD, Dubovi EJ, Simmonds P, Medina JL, Henriquez JA, Mishra N, Wagner J, Tokarz R, Cullen JM, Iadarola MJ, Rice CM, Lipkin WI, Kapoor A. Serology-enabled discovery of genetically diverse hepaciviruses in a new host.. J Virol 2012 Jun;86(11):6171-8.
    doi: 10.1128/JVI.00250-12pmc: PMC3372197pubmed: 22491452google scholar: lookup
  11. Cannalire R, Barreca ML, Manfroni G, Cecchetti V. A Journey around the Medicinal Chemistry of Hepatitis C Virus Inhibitors Targeting NS4B: From Target to Preclinical Drug Candidates.. J Med Chem 2016 Jan 14;59(1):16-41.
    doi: 10.1021/acs.jmedchem.5b00825pubmed: 26241789google scholar: lookup
  12. Catanese MT, Loureiro J, Jones CT, Dorner M, von Hahn T, Rice CM. Different requirements for scavenger receptor class B type I in hepatitis C virus cell-free versus cell-to-cell transmission.. J Virol 2013 Aug;87(15):8282-93.
    doi: 10.1128/JVI.01102-13pmc: PMC3719822pubmed: 23698298google scholar: lookup
  13. Chan DP, Sun HY, Wong HT, Lee SS, Hung CC. Sexually acquired hepatitis C virus infection: a review.. Int J Infect Dis 2016 Aug;49:47-58.
    doi: 10.1016/j.ijid.2016.05.030pubmed: 27270138google scholar: lookup
  14. Chen ZW, Li H, Ren H, Hu P. Global prevalence of pre-existing HCV variants resistant to direct-acting antiviral agents (DAAs): mining the GenBank HCV genome data.. Sci Rep 2016 Feb 4;6:20310.
    doi: 10.1038/srep20310pmc: PMC4740856pubmed: 26842909google scholar: lookup
  15. Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking.. Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W96-9.
    doi: 10.1093/nar/gkh354pmc: PMC441492pubmed: 15215358google scholar: lookup
  16. Corman VM, Grundhoff A, Baechlein C, Fischer N, Gmyl A, Wollny R, Dei D, Ritz D, Binger T, Adankwah E, Marfo KS, Annison L, Annan A, Adu-Sarkodie Y, Oppong S, Becher P, Drosten C, Drexler JF. Highly divergent hepaciviruses from African cattle.. J Virol 2015 Jun;89(11):5876-82.
    doi: 10.1128/JVI.00393-15pmc: PMC4442428pubmed: 25787289google scholar: lookup
  17. de S Leal E, Holmes EC, Zanotto PM. Distinct patterns of natural selection in the reverse transcriptase gene of HIV-1 in the presence and absence of antiretroviral therapy.. Virology 2004 Aug 1;325(2):181-91.
    doi: 10.1016/j.virol.2004.04.004pubmed: 15246258google scholar: lookup
  18. Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Kosakovsky Pond SL. CodonTest: modeling amino acid substitution preferences in coding sequences.. PLoS Comput Biol 2010 Aug 19;6(8).
    doi: 10.1371/journal.pcbi.1000885pmc: PMC2924240pubmed: 20808876google scholar: lookup
  19. Ding Q, von Schaewen M, Ploss A. The impact of hepatitis C virus entry on viral tropism.. Cell Host Microbe 2014 Nov 12;16(5):562-8.
    doi: 10.1016/j.chom.2014.10.009pmc: PMC4272444pubmed: 25525789google scholar: lookup
  20. Dobson AP, Carper ER. Infectious diseased and human population history. Bioscience 46 115–126.
    doi: 10.2307/1312814google scholar: lookup
  21. Donovan J, Dufner M, Korennykh A. Structural basis for cytosolic double-stranded RNA surveillance by human oligoadenylate synthetase 1.. Proc Natl Acad Sci U S A 2013 Jan 29;110(5):1652-7.
    doi: 10.1073/pnas.1218528110pmc: PMC3562804pubmed: 23319625google scholar: lookup
  22. Drexler JF, Corman VM, Müller MA, Lukashev AN, Gmyl A, Coutard B, Adam A, Ritz D, Leijten LM, van Riel D, Kallies R, Klose SM, Gloza-Rausch F, Binger T, Annan A, Adu-Sarkodie Y, Oppong S, Bourgarel M, Rupp D, Hoffmann B, Schlegel M, Kümmerer BM, Krüger DH, Schmidt-Chanasit J, Setién AA, Cottontail VM, Hemachudha T, Wacharapluesadee S, Osterrieder K, Bartenschlager R, Matthee S, Beer M, Kuiken T, Reusken C, Leroy EM, Ulrich RG, Drosten C. Evidence for novel hepaciviruses in rodents.. PLoS Pathog 2013;9(6):e1003438.
    doi: 10.1371/journal.ppat.1003438pmc: PMC3688547pubmed: 23818848google scholar: lookup
  23. Drummer HE, Boo I, Poumbourios P. Mutagenesis of a conserved fusion peptide-like motif and membrane-proximal heptad-repeat region of hepatitis C virus glycoprotein E1.. J Gen Virol 2007 Apr;88(Pt 4):1144-1148.
    doi: 10.1099/vir.0.82567-0pubmed: 17374757google scholar: lookup
  24. Drummer HE, Wilson KA, Poumbourios P. Identification of the hepatitis C virus E2 glycoprotein binding site on the large extracellular loop of CD81.. J Virol 2002 Nov;76(21):11143-7.
    doi: 10.1128/JVI.76.21.11143-11147.2002pmc: PMC136624pubmed: 12368358google scholar: lookup
  25. Duchêne S, Duchêne D, Holmes EC, Ho SY. The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data.. Mol Biol Evol 2015 Jul;32(7):1895-906.
    doi: 10.1093/molbev/msv056pubmed: 25771196google scholar: lookup
  26. Duchêne S, Holmes EC, Ho SY. Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates.. Proc Biol Sci 2014 Jul 7;281(1786).
    doi: 10.1098/rspb.2014.0732pmc: PMC4046420pubmed: 24850916google scholar: lookup
  27. Flint M, von Hahn T, Zhang J, Farquhar M, Jones CT, Balfe P, Rice CM, McKeating JA. Diverse CD81 proteins support hepatitis C virus infection.. J Virol 2006 Nov;80(22):11331-42.
    doi: 10.1128/JVI.00104-06pmc: PMC1642177pubmed: 16943299google scholar: lookup
  28. Forni D, Cagliani R, Clerici M, Sironi M. Molecular Evolution of Human Coronavirus Genomes.. Trends Microbiol 2017 Jan;25(1):35-48.
    doi: 10.1016/j.tim.2016.09.001pmc: PMC7111218pubmed: 27743750google scholar: lookup
  29. Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.. J Med Chem 2006 Oct 19;49(21):6177-96.
    pubmed: 17034125doi: 10.1021/jm051256ogoogle scholar: lookup
  30. Gale M Jr, Blakely CM, Kwieciszewski B, Tan SL, Dossett M, Tang NM, Korth MJ, Polyak SJ, Gretch DR, Katze MG. Control of PKR protein kinase by hepatitis C virus nonstructural 5A protein: molecular mechanisms of kinase regulation.. Mol Cell Biol 1998 Sep;18(9):5208-18.
    doi: 10.1128/MCB.18.9.5208pmc: PMC109106pubmed: 9710605google scholar: lookup
  31. Gouttenoire J, Castet V, Montserret R, Arora N, Raussens V, Ruysschaert JM, Diesis E, Blum HE, Penin F, Moradpour D. Identification of a novel determinant for membrane association in hepatitis C virus nonstructural protein 4B.. J Virol 2009 Jun;83(12):6257-68.
    doi: 10.1128/JVI.02663-08pmc: PMC2687391pubmed: 19357161google scholar: lookup
  32. Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML.. Methods Mol Biol 2009;537:113-37.
    doi: 10.1007/978-1-59745-251-9_6pubmed: 19378142google scholar: lookup
  33. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.. Syst Biol 2010 May;59(3):307-21.
    doi: 10.1093/sysbio/syq010pubmed: 20525638google scholar: lookup
  34. Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.. J Chem Theory Comput 2016 Jan 12;12(1):281-96.
    doi: 10.1021/acs.jctc.5b00864pubmed: 26584231google scholar: lookup
  35. He J, Sun E, Bujny MV, Kim D, Davidson MW, Zhuang X. Dual function of CD81 in influenza virus uncoating and budding.. PLoS Pathog 2013;9(10):e1003701.
    doi: 10.1371/journal.ppat.1003701pmc: PMC3795033pubmed: 24130495google scholar: lookup
  36. Ho SY, Duchêne S, Molak M, Shapiro B. Time-dependent estimates of molecular evolutionary rates: evidence and causes.. Mol Ecol 2015 Dec;24(24):6007-12.
    doi: 10.1111/mec.13450pubmed: 26769402google scholar: lookup
  37. Hung H, Nguyen KD, Bellwood P, Carson MT. Coastal connectivity: long-term trading networks across the South China Sea. J. Island Coast. Archaeol. 8 384–404.
    doi: 10.1080/15564894.2013.781085google scholar: lookup
  38. Jackowiak P, Kuls K, Budzko L, Mania A, Figlerowicz M, Figlerowicz M. Phylogeny and molecular evolution of the hepatitis C virus.. Infect Genet Evol 2014 Jan;21:67-82.
    doi: 10.1016/j.meegid.2013.10.021pubmed: 24200590google scholar: lookup
  39. Kapoor A, Simmonds P, Gerold G, Qaisar N, Jain K, Henriquez JA, Firth C, Hirschberg DL, Rice CM, Shields S, Lipkin WI. Characterization of a canine homolog of hepatitis C virus.. Proc Natl Acad Sci U S A 2011 Jul 12;108(28):11608-13.
    doi: 10.1073/pnas.1101794108pmc: PMC3136326pubmed: 21610165google scholar: lookup
  40. Kapoor A, Simmonds P, Scheel TK, Hjelle B, Cullen JM, Burbelo PD, Chauhan LV, Duraisamy R, Sanchez Leon M, Jain K, Vandegrift KJ, Calisher CH, Rice CM, Lipkin WI. Identification of rodent homologs of hepatitis C virus and pegiviruses.. mBio 2013 Apr 9;4(2):e00216-13.
    doi: 10.1128/mBio.00216-13pmc: PMC3622934pubmed: 23572554google scholar: lookup
  41. Kosakovsky Pond SL, Frost SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection.. Mol Biol Evol 2005 May;22(5):1208-22.
    doi: 10.1093/molbev/msi105pubmed: 15703242google scholar: lookup
  42. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. Automated phylogenetic detection of recombination using a genetic algorithm.. Mol Biol Evol 2006 Oct;23(10):1891-901.
    doi: 10.1093/molbev/msl051pubmed: 16818476google scholar: lookup
  43. Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking.. Nat Protoc 2017 Feb;12(2):255-278.
    doi: 10.1038/nprot.2016.169pmc: PMC5540229pubmed: 28079879google scholar: lookup
  44. Lange CM, Bellecave P, Dao Thi VL, Tran HT, Penin F, Moradpour D, Gouttenoire J. Determinants for membrane association of the hepatitis C virus NS2 protease domain.. J Virol 2014 Jun;88(11):6519-23.
    doi: 10.1128/JVI.00224-14pmc: PMC4093864pubmed: 24648458google scholar: lookup
  45. Lavie M, Sarrazin S, Montserret R, Descamps V, Baumert TF, Duverlie G, Séron K, Penin F, Dubuisson J. Identification of conserved residues in hepatitis C virus envelope glycoprotein E2 that modulate virus dependence on CD81 and SRB1 entry factors.. J Virol 2014 Sep;88(18):10584-97.
    doi: 10.1128/JVI.01402-14pmc: PMC4178871pubmed: 24990994google scholar: lookup
  46. Lawler A. Sailing Sinbad's seas.. Science 2014 Jun 27;344(6191):1440-5.
    doi: 10.1126/science.344.6191.1440pubmed: 24970060google scholar: lookup
  47. Li C, Lu L, Murphy DG, Negro F, Okamoto H. 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.. J Gen Virol 2014 Aug;95(Pt 8):1677-1688.
    doi: 10.1099/vir.0.065128-0pmc: PMC4103067pubmed: 24795446google scholar: lookup
  48. Li HF, Huang CH, Ai LS, Chuang CK, Chen SS. Mutagenesis of the fusion peptide-like domain of hepatitis C virus E1 glycoprotein: involvement in cell fusion and virus entry.. J Biomed Sci 2009 Sep 24;16(1):89.
    doi: 10.1186/1423-0127-16-89pmc: PMC2759930pubmed: 19778418google scholar: lookup
  49. Lindenbach BD, Rice CM. The ins and outs of hepatitis C virus entry and assembly.. Nat Rev Microbiol 2013 Oct;11(10):688-700.
    doi: 10.1038/nrmicro3098pmc: PMC3897199pubmed: 24018384google scholar: lookup
  50. Longdon B, Brockhurst MA, Russell CA, Welch JJ, Jiggins FM. The evolution and genetics of virus host shifts.. PLoS Pathog 2014 Nov;10(11):e1004395.
    doi: 10.1371/journal.ppat.1004395pmc: PMC4223060pubmed: 25375777google scholar: lookup
  51. Lontok E, Harrington P, Howe A, Kieffer T, Lennerstrand J, Lenz O, McPhee F, Mo H, Parkin N, Pilot-Matias T, Miller V. Hepatitis C virus drug resistance-associated substitutions: State of the art summary.. Hepatology 2015 Nov;62(5):1623-32.
    doi: 10.1002/hep.27934pubmed: 26095927google scholar: lookup
  52. Löytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions.. Proc Natl Acad Sci U S A 2005 Jul 26;102(30):10557-62.
    doi: 10.1073/pnas.0409137102pmc: PMC1180752pubmed: 16000407google scholar: lookup
  53. Lu L, Li C, Xu Y, Murphy DG. 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.. J Gen Virol 2014 Jul;95(Pt 7):1479-1487.
    doi: 10.1099/vir.0.064980-0pmc: PMC4059268pubmed: 24718832google scholar: lookup
  54. Mark S. Alexander the Great, seafaring, and the spread of leprosy.. J Hist Med Allied Sci 2002 Jul;57(3):285-311.
    doi: 10.1093/jhmas/57.3.285pubmed: 12211973google scholar: lookup
  55. Martin D, Rybicki E. RDP: detection of recombination amongst aligned sequences.. Bioinformatics 2000 Jun;16(6):562-3.
    doi: 10.1093/bioinformatics/16.6.562pubmed: 10980155google scholar: lookup
  56. Martin DP, Murrell B, Khoosal A, Muhire B. Detecting and Analyzing Genetic Recombination Using RDP4.. Methods Mol Biol 2017;1525:433-460.
    doi: 10.1007/978-1-4939-6622-6_17pubmed: 27896731google scholar: lookup
  57. Messina JP, Humphreys I, Flaxman A, Brown A, Cooke GS, Pybus OG, Barnes E. Global distribution and prevalence of hepatitis C virus genotypes.. Hepatology 2015 Jan;61(1):77-87.
    doi: 10.1002/hep.27259pmc: PMC4303918pubmed: 25069599google scholar: lookup
  58. Mohd Hanafiah K, Groeger J, Flaxman AD, Wiersma ST. Global epidemiology of hepatitis C virus infection: new estimates of age-specific antibody to HCV seroprevalence.. Hepatology 2013 Apr;57(4):1333-42.
    doi: 10.1002/hep.26141pubmed: 23172780google scholar: lookup
  59. Murray GG, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ. The effect of genetic structure on molecular dating and tests for temporal signal.. Methods Ecol Evol 2016 Jan;7(1):80-89.
    doi: 10.1111/2041-210X.12466pmc: PMC4832290pubmed: 27110344google scholar: lookup
  60. Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. Gene-wide identification of episodic selection.. Mol Biol Evol 2015 May;32(5):1365-71.
    doi: 10.1093/molbev/msv035pmc: PMC4408417pubmed: 25701167google scholar: lookup
  61. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. Detecting individual sites subject to episodic diversifying selection.. PLoS Genet 2012;8(7):e1002764.
    doi: 10.1371/journal.pgen.1002764pmc: PMC3395634pubmed: 22807683google scholar: lookup
  62. Muse SV, Gaut BS. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.. Mol Biol Evol 1994 Sep;11(5):715-24.
    pubmed: 7968485doi: 10.1093/oxfordjournals.molbev.a040152google scholar: lookup
  63. Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E. Tracing the peopling of the world through genomics.. Nature 2017 Jan 18;541(7637):302-310.
    doi: 10.1038/nature21347pmc: PMC5772775pubmed: 28102248google scholar: lookup
  64. O'Brien TR, Prokunina-Olsson L, Donnelly RP. IFN-λ4: the paradoxical new member of the interferon lambda family.. J Interferon Cytokine Res 2014 Nov;34(11):829-38.
    doi: 10.1089/jir.2013.0136pmc: PMC4217005pubmed: 24786669google scholar: lookup
  65. Outram AK, Stear NA, Bendrey R, Olsen S, Kasparov A, Zaibert V, Thorpe N, Evershed RP. The earliest horse harnessing and milking.. Science 2009 Mar 6;323(5919):1332-5.
    doi: 10.1126/science.1168594pubmed: 19265018google scholar: lookup
  66. Patiño-Galindo JÁ, González-Candelas F. Comparative analysis of variation and selection in the HCV genome.. Infect Genet Evol 2017 Apr;49:104-110.
    doi: 10.1016/j.meegid.2017.01.010pubmed: 28087495google scholar: lookup
  67. Patiño-Galindo JÁ, Salvatierra K, González-Candelas F, López-Labrador FX. Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6.. Antimicrob Agents Chemother 2016 Apr;60(4):2402-16.
    doi: 10.1128/AAC.02776-15pmc: PMC4808155pubmed: 26856832google scholar: lookup
  68. Pavio N, Romano PR, Graczyk TM, Feinstone SM, Taylor DR. Protein synthesis and endoplasmic reticulum stress can be modulated by the hepatitis C virus envelope protein E2 through the eukaryotic initiation factor 2alpha kinase PERK.. J Virol 2003 Mar;77(6):3578-85.
    doi: 10.1128/JVI.77.6.3578-3585.2003pmc: PMC149509pubmed: 12610133google scholar: lookup
  69. Pearson M. Trade, Circulation, and Flow in the Indian Ocean World. .
  70. Pedergnana V, Smith D, Klenerman P, Barnes E, Spencer CC, Ansari MA. Interferon lambda 4 variant rs12979860 is not associated with RAV NS5A Y93H in hepatitis C virus genotype 3a.. Hepatology 2016 Oct;64(4):1377-8.
    doi: 10.1002/hep.28533pmc: PMC5042047pubmed: 26945900google scholar: lookup
  71. Peiffer KH, Sommer L, Susser S, Vermehren J, Herrmann E, Döring M, Dietz J, Perner D, Berkowski C, Zeuzem S, Sarrazin C. Interferon lambda 4 genotypes and resistance-associated variants in patients infected with hepatitis C virus genotypes 1 and 3.. Hepatology 2016 Jan;63(1):63-73.
    doi: 10.1002/hep.28255pubmed: 26406534google scholar: lookup
  72. Perales C, Beach NM, Gallego I, Soria ME, Quer J, Esteban JI, Rice C, Domingo E, Sheldon J. Response of hepatitis C virus to long-term passage in the presence of alpha interferon: multiple mutations and a common phenotype.. J Virol 2013 Jul;87(13):7593-607.
    doi: 10.1128/JVI.02824-12pmc: PMC3700284pubmed: 23637397google scholar: lookup
  73. Pfaender S, Brown RJ, Pietschmann T, Steinmann E. Natural reservoirs for homologs of hepatitis C virus.. Emerg Microbes Infect 2014 Mar;3(3):e21.
    doi: 10.1038/emi.2014.19pmc: PMC3974340pubmed: 26038514google scholar: lookup
  74. Pflugheber J, Fredericksen B, Sumpter R Jr, Wang C, Ware F, Sodora DL, Gale M Jr. Regulation of PKR and IRF-1 during hepatitis C virus RNA replication.. Proc Natl Acad Sci U S A 2002 Apr 2;99(7):4650-5.
    doi: 10.1073/pnas.062055699pmc: PMC123702pubmed: 11904369google scholar: lookup
  75. Posada D, Crandall KA. Evaluation of methods for detecting recombination from DNA sequences: computer simulations.. Proc Natl Acad Sci U S A 2001 Nov 20;98(24):13757-62.
    doi: 10.1073/pnas.241370698pmc: PMC61114pubmed: 11717435google scholar: lookup
  76. Privman E, Penn O, Pupko T. Improving the performance of positive selection inference by filtering unreliable alignment regions.. Mol Biol Evol 2012 Jan;29(1):1-5.
    doi: 10.1093/molbev/msr177pubmed: 21772063google scholar: lookup
  77. Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, Harvey PH. The epidemic behavior of the hepatitis C virus.. Science 2001 Jun 22;292(5525):2323-5.
    doi: 10.1126/science.1058321pubmed: 11423661google scholar: lookup
  78. Pybus OG, Gray RR. Virology: The virus whose family expanded.. Nature 2013 Jun 20;498(7454):310-1.
    doi: 10.1038/498310bpmc: PMC7095075pubmed: 23783626google scholar: lookup
  79. Pybus OG, Markov PV, Wu A, Tatem AJ. Investigating the endemic transmission of the hepatitis C virus.. Int J Parasitol 2007 Jul;37(8-9):839-49.
    doi: 10.1016/j.ijpara.2007.04.009pubmed: 17521655google scholar: lookup
  80. Pybus OG, Thézé J. Hepacivirus cross-species transmission and the origins of the hepatitis C virus.. Curr Opin Virol 2016 Feb;16:1-7.
    doi: 10.1016/j.coviro.2015.10.002pubmed: 26517843google scholar: lookup
  81. Quan PL, Firth C, Conte JM, Williams SH, Zambrana-Torrelio CM, Anthony SJ, Ellison JA, Gilbert AT, Kuzmin IV, Niezgoda M, Osinubi MO, Recuenco S, Markotter W, Breiman RF, Kalemba L, Malekani J, Lindblade KA, Rostal MK, Ojeda-Flores R, Suzan G, Davis LB, Blau DM, Ogunkoya AB, Alvarez Castillo DA, Moran D, Ngam S, Akaibe D, Agwanda B, Briese T, Epstein JH, Daszak P, Rupprecht CE, Holmes EC, Lipkin WI. Bats are a major natural reservoir for hepaciviruses and pegiviruses.. Proc Natl Acad Sci U S A 2013 May 14;110(20):8194-9.
    doi: 10.1073/pnas.1303037110pmc: PMC3657805pubmed: 23610427google scholar: lookup
  82. Rai R, Deval J. New opportunities in anti-hepatitis C virus drug discovery: targeting NS4B.. Antiviral Res 2011 May;90(2):93-101.
    pubmed: 21295075doi: 10.1016/j.antiviral.2011.01.009google scholar: lookup
  83. Richens J. Donovanosis (granuloma inguinale).. Sex Transm Infect 2006 Dec;82 Suppl 4(Suppl 4):iv21-2.
    doi: 10.1136/sti.2006.023135pmc: PMC2563899pubmed: 17151047google scholar: lookup
  84. Russell RS, Kawaguchi K, Meunier JC, Takikawa S, Faulk K, Bukh J, Purcell RH, Emerson SU. Mutational analysis of the hepatitis C virus E1 glycoprotein in retroviral pseudoparticles and cell-culture-derived H77/JFH1 chimeric infectious virus particles.. J Viral Hepat 2009 Sep;16(9):621-32.
    doi: 10.1111/j.1365-2893.2009.01111.xpmc: PMC2770242pubmed: 19302336google scholar: lookup
  85. Sakamoto H, Okamoto K, Aoki M, Kato H, Katsume A, Ohta A, Tsukuda T, Shimma N, Aoki Y, Arisawa M, Kohara M, Sudoh M. Host sphingolipid biosynthesis as a target for hepatitis C virus therapy.. Nat Chem Biol 2005 Nov;1(6):333-7.
    doi: 10.1038/nchembio742pubmed: 16408072google scholar: lookup
  86. Samper JC, Tibary A. Disease transmission in horses.. Theriogenology 2006 Aug;66(3):551-9.
    doi: 10.1016/j.theriogenology.2006.04.019pubmed: 16837034google scholar: lookup
  87. Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock.. Bioinformatics 2003 Jan 22;19(2):301-2.
    doi: 10.1093/bioinformatics/19.2.301pubmed: 12538260google scholar: lookup
  88. Sawyer S. Statistical tests for detecting gene conversion.. Mol Biol Evol 1989 Sep;6(5):526-38.
    pubmed: 2677599doi: 10.1093/oxfordjournals.molbev.a040567google scholar: lookup
  89. Schaer J, Perkins SL, Decher J, Leendertz FH, Fahr J, Weber N, Matuschewski K. High diversity of West African bat malaria parasites and a tight link with rodent Plasmodium taxa.. Proc Natl Acad Sci U S A 2013 Oct 22;110(43):17415-9.
    doi: 10.1073/pnas.1311016110pmc: PMC3808598pubmed: 24101466google scholar: lookup
  90. Scheel TK, Simmonds P, Kapoor A. Surveying the global virome: identification and characterization of HCV-related animal hepaciviruses.. Antiviral Res 2015 Mar;115:83-93.
    doi: 10.1016/j.antiviral.2014.12.014pmc: PMC5081135pubmed: 25545071google scholar: lookup
  91. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking.. Nucleic Acids Res 2005 Jul 1;33(Web Server issue):W363-7.
    doi: 10.1093/nar/gki481pmc: PMC1160241pubmed: 15980490google scholar: lookup
  92. Sela I, Ashkenazy H, Katoh K, Pupko T. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.. Nucleic Acids Res 2015 Jul 1;43(W1):W7-14.
    doi: 10.1093/nar/gkv318pmc: PMC4489236pubmed: 25883146google scholar: lookup
  93. Shepard CW, Finelli L, Alter MJ. Global epidemiology of hepatitis C virus infection.. Lancet Infect Dis 2005 Sep;5(9):558-67.
    doi: 10.1016/S1473-3099(05)70216-4pubmed: 16122679google scholar: lookup
  94. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects.. J Med Chem 2006 Jan 26;49(2):534-53.
    doi: 10.1021/jm050540cpubmed: 16420040google scholar: lookup
  95. Silvie O, Rubinstein E, Franetich JF, Prenant M, Belnoue E, Rénia L, Hannoun L, Eling W, Levy S, Boucheix C, Mazier D. Hepatocyte CD81 is required for Plasmodium falciparum and Plasmodium yoelii sporozoite infectivity.. Nat Med 2003 Jan;9(1):93-6.
    doi: 10.1038/nm808pubmed: 12483205google scholar: lookup
  96. Simmonds P. The origin of hepatitis C virus.. Curr Top Microbiol Immunol 2013;369:1-15.
    doi: 10.1007/978-3-642-27340-7_1pubmed: 23463195google scholar: lookup
  97. Sironi M, Cagliani R, Forni D, Clerici M. Evolutionary insights into host-pathogen interactions from mammalian sequence data.. Nat Rev Genet 2015 Apr;16(4):224-36.
    doi: 10.1038/nrg3905pmc: PMC7096838pubmed: 25783448google scholar: lookup
  98. Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, Simmonds P. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource.. Hepatology 2014 Jan;59(1):318-27.
    doi: 10.1002/hep.26744pmc: PMC4063340pubmed: 24115039google scholar: lookup
  99. Smith DB, Pathirana S, Davidson F, Lawlor E, Power J, Yap PL, Simmonds P. The origin of hepatitis C virus genotypes.. J Gen Virol 1997 Feb;78 ( Pt 2):321-8.
    doi: 10.1099/0022-1317-78-2-321pubmed: 9018053google scholar: lookup
  100. Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection.. Mol Biol Evol 2015 May;32(5):1342-53.
    doi: 10.1093/molbev/msv022pmc: PMC4408413pubmed: 25697341google scholar: lookup
  101. Sumpter R Jr, Wang C, Foy E, Loo YM, Gale M Jr. Viral evolution and interferon resistance of hepatitis C virus RNA replication in a cell culture model.. J Virol 2004 Nov;78(21):11591-604.
    doi: 10.1128/JVI.78.21.11591-11604.2004pmc: PMC523295pubmed: 15479800google scholar: lookup
  102. Taguchi T, Nagano-Fujii M, Akutsu M, Kadoya H, Ohgimoto S, Ishido S, Hotta H. Hepatitis C virus NS5A protein interacts with 2',5'-oligoadenylate synthetase and inhibits antiviral activity of IFN in an IFN sensitivity-determining region-independent manner.. J Gen Virol 2004 Apr;85(Pt 4):959-969.
    doi: 10.1099/vir.0.19513-0pubmed: 15039538google scholar: lookup
  103. Tanaka T, Kuroda K, Ikeda M, Wakita T, Kato N, Makishima M. Hepatitis C virus NS4B targets lipid droplets through hydrophobic residues in the amphipathic helices.. J Lipid Res 2013 Apr;54(4):881-92.
    doi: 10.1194/jlr.M026443pmc: PMC3605996pubmed: 23315449google scholar: lookup
  104. Taylor DR, Shi ST, Romano PR, Barber GN, Lai MM. Inhibition of the interferon-inducible protein kinase PKR by HCV E2 protein.. Science 1999 Jul 2;285(5424):107-10.
    doi: 10.1126/science.285.5424.107pubmed: 10390359google scholar: lookup
  105. Tellinghuisen TL, Marcotrigiano J, Rice CM. Structure of the zinc-binding domain of an essential component of the hepatitis C virus replicase.. Nature 2005 May 19;435(7040):374-9.
    doi: 10.1038/nature03580pmc: PMC1440517pubmed: 15902263google scholar: lookup
  106. Van Nguyen D, Van Nguyen C, Bonsall D, Ngo TT, Carrique-Mas J, Pham AH, Bryant JE, Thwaites G, Baker S, Woolhouse M, Simmonds P. Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam.. Viruses 2018 Feb 28;10(3).
    doi: 10.3390/v10030102pmc: PMC5869495pubmed: 29495551google scholar: lookup
  107. Walter S, Rasche A, Moreira-Soto A, Pfaender S, Bletsa M, Corman VM, Aguilar-Setien A, García-Lacy F, Hans A, Todt D, Schuler G, Shnaiderman-Torban A, Steinman A, Roncoroni C, Veneziano V, Rusenova N, Sandev N, Rusenov A, Zapryanova D, García-Bocanegra I, Jores J, Carluccio A, Veronesi MC, Cavalleri JMV, Drosten C, Lemey P, Steinmann E, Drexler JF. Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys.. J Virol 2017 Jan 1;91(1).
    pmc: PMC5165184pubmed: 27795428doi: 10.1128/jvi.01711-16google scholar: lookup
  108. Weng L, Hirata Y, Arai M, Kohara M, Wakita T, Watashi K, Shimotohno K, He Y, Zhong J, Toyoda T. Sphingomyelin activates hepatitis C virus RNA polymerase in a genotype-specific manner.. J Virol 2010 Nov;84(22):11761-70.
    doi: 10.1128/JVI.00638-10pmc: PMC2977884pubmed: 20844041google scholar: lookup
  109. Wernersson R, Pedersen AG. RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences.. Nucleic Acids Res 2003 Jul 1;31(13):3537-9.
    doi: 10.1093/nar/gkg609pmc: PMC169015pubmed: 12824361google scholar: lookup
  110. Wertheim JO, Chu DK, Peiris JS, Kosakovsky Pond SL, Poon LL. A case for the ancient origin of coronaviruses.. J Virol 2013 Jun;87(12):7039-45.
    doi: 10.1128/JVI.03273-12pmc: PMC3676139pubmed: 23596293google scholar: lookup
  111. Wertheim JO, Kosakovsky Pond SL. Purifying selection can obscure the ancient age of viral lineages.. Mol Biol Evol 2011 Dec;28(12):3355-65.
    doi: 10.1093/molbev/msr170pmc: PMC3247791pubmed: 21705379google scholar: lookup
  112. Wertheim JO, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL. Evolutionary origins of human herpes simplex viruses 1 and 2.. Mol Biol Evol 2014 Sep;31(9):2356-64.
    doi: 10.1093/molbev/msu185pmc: PMC4137711pubmed: 24916030google scholar: lookup
  113. White JA. Manifestations and management of lymphogranuloma venereum.. Curr Opin Infect Dis 2009 Feb;22(1):57-66.
    doi: 10.1097/QCO.0b013e328320a8aepubmed: 19532081google scholar: lookup
  114. Xu Z, Choi J, Yen TS, Lu W, Strohecker A, Govindarajan S, Chien D, Selby MJ, Ou J. Synthesis of a novel hepatitis C virus protein by ribosomal frameshift.. EMBO J 2001 Jul 16;20(14):3840-8.
    doi: 10.1093/emboj/20.14.3840pmc: PMC125543pubmed: 11447125google scholar: lookup
  115. Yalaoui S, Zougbédé S, Charrin S, Silvie O, Arduise C, Farhati K, Boucheix C, Mazier D, Rubinstein E, Froissard P. Hepatocyte permissiveness to Plasmodium infection is conveyed by a short and structurally conserved region of the CD81 large extracellular domain.. PLoS Pathog 2008 Feb 29;4(2):e1000010.
    doi: 10.1371/journal.ppat.1000010pmc: PMC2279262pubmed: 18389082google scholar: lookup
  116. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood.. Mol Biol Evol 2007 Aug;24(8):1586-91.
    doi: 10.1093/molbev/msm088pubmed: 17483113google scholar: lookup
  117. Yang Z, Wong WS, Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection.. Mol Biol Evol 2005 Apr;22(4):1107-18.
    doi: 10.1093/molbev/msi097pubmed: 15689528google scholar: lookup
  118. Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.. Mol Biol Evol 2005 Dec;22(12):2472-9.
    doi: 10.1093/molbev/msi237pubmed: 16107592google scholar: lookup
  119. Zuiani A, Chen K, Schwarz MC, White JP, Luca VC, Fremont DH, Wang D, Evans MJ, Diamond MS. A Library of Infectious Hepatitis C Viruses with Engineered Mutations in the E2 Gene Reveals Growth-Adaptive Mutations That Modulate Interactions with Scavenger Receptor Class B Type I.. J Virol 2016 Dec 1;90(23):10499-10512.
    doi: 10.1128/JVI.01011-16pmc: PMC5110168pubmed: 27630236google scholar: lookup

Citations

This article has been cited 12 times.
  1. Cocker ATH, Liu F, Djaoud Z, Guethlein LA, Parham P. CD56-negative NK cells: Frequency in peripheral blood, expansion during HIV-1 infection, functional capacity, and KIR expression. Front Immunol 2022;13:992723.
    doi: 10.3389/fimmu.2022.992723pubmed: 36211403google scholar: lookup
  2. Cole TL, Zhou C, Fang M, Pan H, Ksepka DT, Fiddaman SR, Emerling CA, Thomas DB, Bi X, Fang Q, Ellegaard MR, Feng S, Smith AL, Heath TA, Tennyson AJD, Borboroglu PG, Wood JR, Hadden PW, Grosser S, Bost CA, Cherel Y, Mattern T, Hart T, Sinding MS, Shepherd LD, Phillips RA, Quillfeldt P, Masello JF, Bouzat JL, Ryan PG, Thompson DR, Ellenberg U, Dann P, Miller G, Dee Boersma P, Zhao R, Gilbert MTP, Yang H, Zhang DX, Zhang G. Genomic insights into the secondary aquatic transition of penguins. Nat Commun 2022 Jul 19;13(1):3912.
    doi: 10.1038/s41467-022-31508-9pubmed: 35853876google scholar: lookup
  3. Bulankina AV, Richter RM, Welsch C. Regulatory Role of Phospholipids in Hepatitis C Virus Replication and Protein Function. Pathogens 2022 Jan 15;11(1).
    doi: 10.3390/pathogens11010102pubmed: 35056049google scholar: lookup
  4. Palor M, Stejskal L, Mandal P, Lenman A, Alberione MP, Kirui J, Moeller R, Ebner S, Meissner F, Gerold G, Shepherd AJ, Grove J. Cholesterol sensing by CD81 is important for hepatitis C virus entry. J Biol Chem 2020 Dec 11;295(50):16931-16948.
    doi: 10.1074/jbc.RA120.014761pubmed: 32900848google scholar: lookup
  5. Moreira-Soto A, Arroyo-Murillo F, Sander AL, Rasche A, Corman V, Tegtmeyer B, Steinmann E, Corrales-Aguilar E, Wieseke N, Avey-Arroyo J, Drexler JF. Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths. Virus Evol 2020 Jul;6(2):veaa033.
    doi: 10.1093/ve/veaa033pubmed: 32704383google scholar: lookup
  6. Cagliani R, Forni D, Sironi M. Mode and tempo of human hepatitis virus evolution. Comput Struct Biotechnol J 2019;17:1384-1395.
    doi: 10.1016/j.csbj.2019.09.007pubmed: 31768229google scholar: lookup
  7. Theys K, Lemey P, Vandamme AM, Baele G. Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases. Front Public Health 2019;7:208.
    doi: 10.3389/fpubh.2019.00208pubmed: 31428595google scholar: lookup
  8. Rasche A, Sander AL, Corman VM, Drexler JF. Evolutionary biology of human hepatitis viruses. J Hepatol 2019 Mar;70(3):501-520.
    doi: 10.1016/j.jhep.2018.11.010pubmed: 30472320google scholar: lookup
  9. Săndulescu O, Matičič M, Garcia F, Blomé MA, Mondelli MU, Irving W, Zidovec-Lepej S, Widell A, Şahin GÖ. Evolving insights into viral hepatitis: Advances, evidence, and expert perspectives from the ESCMID Study Group for Viral Hepatitis (ESGVH) - Part 2: hepatitis B, C, and delta. Germs 2025 Sep;15(3):263-273.
    doi: 10.18683/germs.2025.1473pubmed: 41334128google scholar: lookup
  10. Sallam M, Khalil R. Contemporary Insights into Hepatitis C Virus: A Comprehensive Review. Microorganisms 2024 May 21;12(6).
    doi: 10.3390/microorganisms12061035pubmed: 38930417google scholar: lookup
  11. Wyżewski Z, Stępkowska J, Kobylińska AM, Mielcarska A, Mielcarska MB. Mcl-1 Protein and Viral Infections: A Narrative Review. Int J Mol Sci 2024 Jan 17;25(2).
    doi: 10.3390/ijms25021138pubmed: 38256213google scholar: lookup
  12. Jose-Abrego A, Roman S, Laguna-Meraz S, Panduro A. Host and HBV Interactions and Their Potential Impact on Clinical Outcomes. Pathogens 2023 Sep 8;12(9).
    doi: 10.3390/pathogens12091146pubmed: 37764954google scholar: lookup
Subscribe to our newsletter
Join 99,357 horse owners like you who receive our email updates on horse health and nutrition.