title: Viral phylodynamics.
abstract: Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viralphylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light on how these dynamics impact viral genetic variation. Transmission dynamics can be considered at the level of cells within an infected host, individual hosts within a population, or entire populations of hosts. Many viruses, especially RNA viruses, rapidly accumulate genetic variation because of short generation times and high mutation rates. Patterns of viral genetic variation are therefore heavily influenced by how quickly transmission occurs and by which entities transmit to one another. Patterns of viral genetic variation will also be affected by selection acting on viral phenotypes. Although viruses can differ with respect to many phenotypes, phylodynamic studies have to date tended to focus on a limited number of viral phenotypes. These include virulence phenotypes, phenotypes associated with viral transmissibility, cell or tissue tropism phenotypes, and antigenic phenotypes that can facilitate escape from host immunity. Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread[2], spatio-temporal dynamics including metapopulation dynamics[3], zoonotic transmission, tissue tropism[4], and antigenic drift[5]. The quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics.
authors.affiliation: Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America. erikvolz@umich.edu
authors.forename: Erik M
authors.initials: EM
authors.lastname: Volz
authors.forename: Katia
authors.initials: K
authors.lastname: Koelle
authors.forename: Trevor
authors.initials: T
authors.lastname: Bedford
mesh_terms: D000220:Adaptation, Biological; D019295:Computational Biology; D019143:Evolution, Molecular; D006801:Humans; D008954:Models, Biological; D010802:Phylogeny; D014777:Virus Diseases / Q000821:virology*; D018406:Virus Physiological Phenomena; D014780:Viruses / Q000235:genetics*
references.citation: Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17209-14
references.pmid: 12481034
references.citation: Nature. 2005 Nov 17;438(7066):355-9
references.pmid: 16292310
references.citation: Mol Biol Evol. 2010 Aug;27(8):1877-85
references.pmid: 20203288
references.citation: PLoS One. 2009 Jun 17;4(6):e5950
references.pmid: 19536329
references.citation: N Engl J Med. 2011 May 19;364(20):1943-54
references.pmid: 21591946
references.citation: Proc Natl Acad Sci U S A. 2007 May 8;104(19):7993-8
references.pmid: 17470818
references.citation: Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19359-64
references.pmid: 22084096
references.citation: Philos Trans R Soc Lond B Biol Sci. 2010 Jun 27;365(1548):1879-90
references.pmid: 20478883
references.citation: J Infect Dis. 2010 May 15;201(10):1488-97
references.pmid: 20384495
references.citation: Nature. 2008 Oct 2;455(7213):661-4
references.pmid: 18833279
references.citation: Nature. 2003 Mar 27;422(6930):428-33
references.pmid: 12660783
references.citation: J R Soc Interface. 2012 Apr 7;9(69):648-56
references.pmid: 21865253
references.citation: J Gen Virol. 1996 Apr;77 ( Pt 4):661-71
references.pmid: 8627254
references.citation: PLoS Comput Biol. 2011 Oct;7(10):e1002185
references.pmid: 22022243
references.citation: Infect Genet Evol. 2005 Apr;5(3):199-208
references.pmid: 15737910
references.citation: Infect Genet Evol. 2011 Dec;11(8):1825-41
references.pmid: 21906695
references.citation: J Virol. 2003 Jun;77(11):6359-66
references.pmid: 12743293
references.citation: AIDS. 1997 Jul 15;11(9):1089-94
references.pmid: 9233454
references.citation: PLoS Pathog. 2010 May 27;6(5):e1000918
references.pmid: 20523898
references.citation: Science. 2008 Apr 18;320(5874):340-6
references.pmid: 18420927
references.citation: Nature. 2008 May 29;453(7195):615-9
references.pmid: 18418375
references.citation: Virology. 2009 Jan 5;383(1):156-61
references.pmid: 19000628
references.citation: Science. 2006 Dec 22;314(5807):1898-903
references.pmid: 17185596
references.citation: Science. 2001 Jun 22;292(5525):2323-5
references.pmid: 11423661
references.citation: Curr HIV Res. 2003 Jan;1(1):69-86
references.pmid: 15043213
references.citation: Science. 2004 Jul 16;305(5682):371-6
references.pmid: 15218094
references.citation: PLoS Comput Biol. 2012;8(3):e1002413
references.pmid: 22412361
references.citation: AIDS Rev. 2006 Jul-Sep;8(3):125-40
references.pmid: 17078483
references.citation: Science. 2009 Jun 19;324(5934):1557-61
references.pmid: 19433588
references.citation: PLoS Pathog. 2012;8(5):e1002656
references.pmid: 22570609
references.citation: PLoS Comput Biol. 2012;8(6):e1002552
references.pmid: 22761556
references.citation: Biol Direct. 2006 Oct 26;1:34
references.pmid: 17067369
references.citation: Mol Biol Evol. 1999 Nov;16(11):1457-65
references.pmid: 10555276
references.citation: J Acquir Immune Defic Syndr. 2002 Feb 1;29(2):184-90
references.pmid: 11832690
references.citation: Science. 2010 Jun 4;328(5983):1272-5
references.pmid: 20522774
references.citation: Science. 2004 Jan 16;303(5656):327-32
references.pmid: 14726583
references.citation: Mol Biol Evol. 2006 Dec;23(12):2336-41
references.pmid: 16945980
references.citation: Annu Rev Genet. 1995;29:401-21
references.pmid: 8825481
references.citation: J R Soc Interface. 2007 Feb 22;4(12):137-42
references.pmid: 17015285
references.citation: J R Soc Interface. 2012 May 7;9(70):997-1007
references.pmid: 21920961
references.citation: BMC Biol. 2012 Apr 30;10:38
references.pmid: 22546494
references.citation: Science. 2010 Aug 6;329(5992):676-9
references.pmid: 20689015
references.citation: Mol Biol Evol. 2001 Jul;18(7):1365-71
references.pmid: 11420374
references.citation: Genetics. 1999 Feb;151(2):427-38
references.pmid: 9927440
references.citation: Genetics. 2004 Jul;167(3):1059-68
references.pmid: 15280223
references.citation: Genetics. 2002 Jul;161(3):1307-20
references.pmid: 12136032
references.citation: J R Soc Interface. 2010 Sep 6;7(50):1257-74
references.pmid: 20335193
references.citation: Influenza Other Respir Viruses. 2012 Nov;6(6):404-16
references.pmid: 22260278
references.citation: Genetics. 2009 Dec;183(4):1421-30
references.pmid: 19797047
references.citation: Philos Trans R Soc Lond B Biol Sci. 2001 Jun 29;356(1410):855-66
references.pmid: 11405933
references.citation: PLoS One. 2011;6(11):e27489
references.pmid: 22132104
references.citation: Microbiol Rev. 1992 Mar;56(1):152-79
references.pmid: 1579108
references.citation: Genetics. 2012 Nov;192(3):1027-47
references.pmid: 22960215
references.citation: PLoS Comput Biol. 2007 Feb 16;3(2):e29
references.pmid: 17305421
references.citation: J Gen Virol. 1992 Oct;73 ( Pt 10):2737-42
references.pmid: 1402807
references.citation: Proc Natl Acad Sci U S A. 1993 May 1;90(9):4171-5
references.pmid: 8387212
references.citation: Curr Opin HIV AIDS. 2010 Jul;5(4):327-34
references.pmid: 20543609
references.citation: PLoS One. 2007 Dec 12;2(12):e1296
references.pmid: 18074020
references.citation: Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14711-5
references.pmid: 19706556
references.citation: J Gen Virol. 1994 Mar;75 ( Pt 3):513-27
references.pmid: 8126449
references.citation: Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7160-4
references.pmid: 1831267
references.citation: Mol Biol Evol. 2011 Sep;28(9):2443-51
references.pmid: 21415025
references.citation: Mol Biol Evol. 2005 May;22(5):1185-92
references.pmid: 15703244
references.citation: J Clin Microbiol. 1999 Sep;37(9):3005-9
references.pmid: 10449491
references.citation: J Virol. 2007 Apr;81(8):4315-22
references.pmid: 17287258
references.citation: Genetics. 2012 Jan;190(1):187-201
references.pmid: 22042576
references.citation: PLoS Pathog. 2010 May 06;6(5):e1000876
references.pmid: 20463808
references.citation: Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7712-8
references.pmid: 9223253
references.citation: BMC Evol Biol. 2011 Jul 25;11:220
references.pmid: 21787390
references.citation: Am J Epidemiol. 2009 Dec 15;170(12):1455-63
references.pmid: 19910379
references.citation: J R Soc Interface. 2010 Jul 6;7(48):1119-27
references.pmid: 20147314
references.citation: Science. 2009 Oct 30;326(5953):726-8
references.pmid: 19900931
references.citation: PLoS Med. 2008 Mar 18;5(3):e50
references.pmid: 18351795
references.citation: Am J Epidemiol. 2009 Dec 15;170(12):1464-6; discussion 1467-8
references.pmid: 19910381
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1760-5
references.pmid: 17264216
references.citation: PLoS Comput Biol. 2009 Sep;5(9):e1000520
references.pmid: 19779555
references.citation: Nat Rev Genet. 2004 Jan;5(1):52-61
references.pmid: 14708016
references.citation: Mol Biol Evol. 2001 Dec;18(12):2298-305
references.pmid: 11719579
references.citation: N Engl J Med. 2008 Oct 30;359(18):1965-6
references.pmid: 18971501
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 30;104(44):17441-6
references.pmid: 17954909
references.citation: J Theor Biol. 2010 Dec 7;267(3):396-404
references.pmid: 20851708