Coronavirus as a possible cause of severe acute respiratory syndrome.[Lancet. 2003]

Peiris JS, Lai ST, Poon LL, Guan Y, Yam LY, Lim W, Nicholls J, Yee WK, Yan WW, Cheung MT, Cheng VC, Chan KH, Tsang DN, Yung RW, Ng TK, Yuen KY, SARS study group.

Lancet. 2003 Apr 19; 361(9366):1319-25.
Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage.[J Mol Biol. 2003]

Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, Guan Y, Rozanov M, Spaan WJ, Gorbalenya AE

J Mol Biol. 2003 Aug 29; 331(5):991-1004.
Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia.[N Engl J Med. 2012]

Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA

N Engl J Med. 2012 Nov 8; 367(19):1814-20.
Avian coronavirus in wild aquatic birds.[J Virol. 2011]

Chu DK, Leung CY, Gilbert M, Joyner PH, Ng EM, Tse TM, Guan Y, Peiris JS, Poon LL

J Virol. 2011 Dec; 85(23):12815-20.
Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.[J Virol. 2012]

Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY

J Virol. 2012 Apr; 86(7):3995-4008.
Evolutionary insights into the ecology of coronaviruses.[J Virol. 2007]

Vijaykrishna D, Smith GJ, Zhang JX, Peiris JS, Chen H, Guan Y

J Virol. 2007 Apr; 81(8):4012-20.
Recent transmission of a novel alphacoronavirus, bat coronavirus HKU10, from Leschenault's rousettes to pomona leaf-nosed bats: first evidence of interspecies transmission of coronavirus between bats of different suborders.[J Virol. 2012]

Lau SK, Li KS, Tsang AK, Shek CT, Wang M, Choi GK, Guo R, Wong BH, Poon RW, Lam CS, Wang SY, Fan RY, Chan KH, Zheng BJ, Woo PC, Yuen KY

J Virol. 2012 Nov; 86(21):11906-18.

Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.[J Virol. 2012]

Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY

J Virol. 2012 Apr; 86(7):3995-4008.
Review Nidovirales: evolving the largest RNA virus genome.[Virus Res. 2006]

Gorbalenya AE, Enjuanes L, Ziebuhr J, Snijder EJ

Virus Res. 2006 Apr; 117(1):17-37.
Evolutionary insights into the ecology of coronaviruses.[J Virol. 2007]

Vijaykrishna D, Smith GJ, Zhang JX, Peiris JS, Chen H, Guan Y

J Virol. 2007 Apr; 81(8):4012-20.
Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage.[J Mol Biol. 2003]

Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, Guan Y, Rozanov M, Spaan WJ, Gorbalenya AE

J Mol Biol. 2003 Aug 29; 331(5):991-1004.
Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA synthesis.[Proc Natl Acad Sci U S A. 2006]

Minskaia E, Hertzig T, Gorbalenya AE, Campanacci V, Cambillau C, Canard B, Ziebuhr J

Proc Natl Acad Sci U S A. 2006 Mar 28; 103(13):5108-13.
Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing.[PLoS Pathog. 2010]

Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, Spiro DJ, Denison MR

PLoS Pathog. 2010 May 6; 6(5):e1000896.
Review Rates of evolutionary change in viruses: patterns and determinants.[Nat Rev Genet. 2008]

Duffy S, Shackelton LA, Holmes EC

Nat Rev Genet. 2008 Apr; 9(4):267-76.

Purifying selection can obscure the ancient age of viral lineages.[Mol Biol Evol. 2011]

Wertheim JO, Kosakovsky Pond SL

Mol Biol Evol. 2011 Dec; 28(12):3355-65.

The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond.[J Biol Chem. 2001]

Ziebuhr J, Thiel V, Gorbalenya AE

J Biol Chem. 2001 Aug 31; 276(35):33220-32.
MUSCLE: multiple sequence alignment with high accuracy and high throughput.[Nucleic Acids Res. 2004]

Edgar RC

Nucleic Acids Res. 2004; 32(5):1792-7.
Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats.[J Gen Virol. 2008]

Chu DKW, Peiris JSM, Chen H, Guan Y, Poon LLM

J Gen Virol. 2008 May; 89(Pt 5):1282-1287.

GARD: a genetic algorithm for recombination detection.[Bioinformatics. 2006]

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD

Bioinformatics. 2006 Dec 15; 22(24):3096-8.
Estimating maximum likelihood phylogenies with PhyML.[Methods Mol Biol. 2009]

Guindon S, Delsuc F, Dufayard JF, Gascuel O

Methods Mol Biol. 2009; 537():113-37.
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.[Mol Biol Evol. 2010]

Gouy M, Guindon S, Gascuel O

Mol Biol Evol. 2010 Feb; 27(2):221-4.

HyPhy: hypothesis testing using phylogenies.[Bioinformatics. 2005]

Pond SL, Frost SD, Muse SV

Bioinformatics. 2005 Mar 1; 21(5):676-9.
A random effects branch-site model for detecting episodic diversifying selection.[Mol Biol Evol. 2011]

Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K

Mol Biol Evol. 2011 Nov; 28(11):3033-43.

Evolutionary fingerprinting of genes.[Mol Biol Evol. 2010]

Pond SL, Scheffler K, Gravenor MB, Poon AF, Frost SD

Mol Biol Evol. 2010 Mar; 27(3):520-36.

GARD: a genetic algorithm for recombination detection.[Bioinformatics. 2006]

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD

Bioinformatics. 2006 Dec 15; 22(24):3096-8.
CONFIDENCE LIMITS ON THE MAXIMUM-LIKELIHOOD ESTIMATE OF THE HOMINOID TREE FROM MITOCHONDRIAL-DNA SEQUENCES.[Evolution. 1989]

Hasegawa M, Kishino H

Evolution. 1989 May; 43(3):672-677.
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea.[J Mol Evol. 1989]

Kishino H, Hasegawa M

J Mol Evol. 1989 Aug; 29(2):170-9.

A random effects branch-site model for detecting episodic diversifying selection.[Mol Biol Evol. 2011]

Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K

Mol Biol Evol. 2011 Nov; 28(11):3033-43.

Not so different after all: a comparison of methods for detecting amino acid sites under selection.[Mol Biol Evol. 2005]

Kosakovsky Pond SL, Frost SD

Mol Biol Evol. 2005 May; 22(5):1208-22.

Not so different after all: a comparison of methods for detecting amino acid sites under selection.[Mol Biol Evol. 2005]

Kosakovsky Pond SL, Frost SD

Mol Biol Evol. 2005 May; 22(5):1208-22.

HyPhy: hypothesis testing using phylogenies.[Bioinformatics. 2005]

Pond SL, Frost SD, Muse SV

Bioinformatics. 2005 Mar 1; 21(5):676-9.
Site-to-site variation of synonymous substitution rates.[Mol Biol Evol. 2005]

Pond SK, Muse SV

Mol Biol Evol. 2005 Dec; 22(12):2375-85.

Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.[J Virol. 2012]

Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY

J Virol. 2012 Apr; 86(7):3995-4008.
Distant relatives of severe acute respiratory syndrome coronavirus and close relatives of human coronavirus 229E in bats, Ghana.[Emerg Infect Dis. 2009]

Pfefferle S, Oppong S, Drexler JF, Gloza-Rausch F, Ipsen A, Seebens A, Müller MA, Annan A, Vallo P, Adu-Sarkodie Y, Kruppa TF, Drosten C

Emerg Infect Dis. 2009 Sep; 15(9):1377-84.
Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2.[PLoS Comput Biol. 2009]

Wertheim JO, Worobey M

PLoS Comput Biol. 2009 May; 5(5):e1000377.
Island biogeography reveals the deep history of SIV.[Science. 2010]

Worobey M, Telfer P, Souquière S, Hunter M, Coleman CA, Metzger MJ, Reed P, Makuwa M, Hearn G, Honarvar S, Roques P, Apetrei C, Kazanji M, Marx PA

Science. 2010 Sep 17; 329(5998):1487.
Purifying selection can obscure the ancient age of viral lineages.[Mol Biol Evol. 2011]

Wertheim JO, Kosakovsky Pond SL

Mol Biol Evol. 2011 Dec; 28(12):3355-65.
Hitchhiking and the population genetic structure of avian influenza virus.[J Mol Evol. 2010]

Chen R, Holmes EC

J Mol Evol. 2010 Jan; 70(1):98-105.

Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.[J Virol. 2012]

Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY

J Virol. 2012 Apr; 86(7):3995-4008.

Molecular phylogeny of the alphaherpesvirinae subfamily and a proposed evolutionary timescale.[J Mol Biol. 1994]

McGeoch DJ, Cook S

J Mol Biol. 1994 Apr 22; 238(1):9-22.
Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses.[J Mol Biol. 1995]

McGeoch DJ, Cook S, Dolan A, Jamieson FE, Telford EA

J Mol Biol. 1995 Mar 31; 247(3):443-58.
A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution.[Proc Natl Acad Sci U S A. 2008]

Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW

Proc Natl Acad Sci U S A. 2008 Dec 23; 105(51):20362-7.
Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.[PLoS Pathog. 2010]

Belyi VA, Levine AJ, Skalka AM

PLoS Pathog. 2010 Jul 29; 6(7):e1001030.
Filoviruses are ancient and integrated into mammalian genomes.[BMC Evol Biol. 2010]

Taylor DJ, Leach RW, Bruenn J

BMC Evol Biol. 2010 Jun 22; 10():193.
An endogenous foamy-like viral element in the coelacanth genome.[PLoS Pathog. 2012]

Han GZ, Worobey M

PLoS Pathog. 2012; 8(6):e1002790.
Macroevolution of complex retroviruses.[Science. 2009]

Katzourakis A, Gifford RJ, Tristem M, Gilbert MT, Pybus OG

Science. 2009 Sep 18; 325(5947):1512.
Purifying selection can obscure the ancient age of viral lineages.[Mol Biol Evol. 2011]

Wertheim JO, Kosakovsky Pond SL

Mol Biol Evol. 2011 Dec; 28(12):3355-65.

Molecular phylogeny and divergence times of deuterostome animals.[Mol Biol Evol. 2005]

Blair JE, Hedges SB

Mol Biol Evol. 2005 Nov; 22(11):2275-84.
Purifying selection can obscure the ancient age of viral lineages.[Mol Biol Evol. 2011]

Wertheim JO, Kosakovsky Pond SL

Mol Biol Evol. 2011 Dec; 28(12):3355-65.

Evolutionary insights into the ecology of coronaviruses.[J Virol. 2007]

Vijaykrishna D, Smith GJ, Zhang JX, Peiris JS, Chen H, Guan Y

J Virol. 2007 Apr; 81(8):4012-20.
Recent transmission of a novel alphacoronavirus, bat coronavirus HKU10, from Leschenault's rousettes to pomona leaf-nosed bats: first evidence of interspecies transmission of coronavirus between bats of different suborders.[J Virol. 2012]

Lau SK, Li KS, Tsang AK, Shek CT, Wang M, Choi GK, Guo R, Wong BH, Poon RW, Lam CS, Wang SY, Fan RY, Chan KH, Zheng BJ, Woo PC, Yuen KY

J Virol. 2012 Nov; 86(21):11906-18.
Avian coronavirus in wild aquatic birds.[J Virol. 2011]

Chu DK, Leung CY, Gilbert M, Joyner PH, Ng EM, Tse TM, Guan Y, Peiris JS, Poon LL

J Virol. 2011 Dec; 85(23):12815-20.
Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus.[J Virol. 2012]

Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY

J Virol. 2012 Apr; 86(7):3995-4008.

Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.[J Virol. 2008]

Hon CC, Lam TY, Shi ZL, Drummond AJ, Yip CW, Zeng F, Lam PY, Leung FC

J Virol. 2008 Feb; 82(4):1819-26.
Distortions in genealogies due to purifying selection.[Mol Biol Evol. 2012]

Nicolaisen LE, Desai MM

Mol Biol Evol. 2012 Nov; 29(11):3589-600.
Review Time-dependent rates of molecular evolution.[Mol Ecol. 2011]

Ho SY, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A

Mol Ecol. 2011 Aug; 20(15):3087-101.
Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing.[PLoS Pathog. 2010]

Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, Spiro DJ, Denison MR

PLoS Pathog. 2010 May 6; 6(5):e1000896.

Purifying selection can obscure the ancient age of viral lineages.[Mol Biol Evol. 2011]

Wertheim JO, Kosakovsky Pond SL

Mol Biol Evol. 2011 Dec; 28(12):3355-65.
A random effects branch-site model for detecting episodic diversifying selection.[Mol Biol Evol. 2011]

Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K

Mol Biol Evol. 2011 Nov; 28(11):3033-43.
Site-to-site variation of synonymous substitution rates.[Mol Biol Evol. 2005]

Pond SK, Muse SV

Mol Biol Evol. 2005 Dec; 22(12):2375-85.

Review Mass extinctions, biodiversity and mitochondrial function: are bats 'special' as reservoirs for emerging viruses?[Curr Opin Virol. 2011]

Wang LF, Walker PJ, Poon LL

Curr Opin Virol. 2011 Dec; 1(6):649-57.
Comparative analysis of bat genomes provides insight into the evolution of flight and immunity.[Science. 2013]

Zhang G, Cowled C, Shi Z, Huang Z, Bishop-Lilly KA, Fang X, Wynne JW, Xiong Z, Baker ML, Zhao W, Tachedjian M, Zhu Y, Zhou P, Jiang X, Ng J, Yang L, Wu L, Xiao J, Feng Y, Chen Y, Sun X, Zhang Y, Marsh GA, Crameri G, Broder CC, Frey KG, Wang LF, Wang J

Science. 2013 Jan 25; 339(6118):456-60.

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