Phylodynamic Datasets - Links


Databases

NameInformation
GenBankNCBI Public database for all sequences
Influenza Virus ResourceNCBI public database for influenza sequences (useful interface to GenBank)
RNA Virus DatabaseDatabase of RNA viruses, reference alignments and trees
Foot-and-Mouth DiseaseFMD Database at Pirbright
Disease BioPortalFMD Portal for real time surveillance by University of California, Davis

Software

NameInformation
BioEditViewing and aligning sequences (Windows)
MEGA 5Generating trees, viewing and aligning sequences
Path-o-genTest for molecular clock signal (e.g. before running BEAST)
BEAST 1Generating time resolved bayesian tree sets with complex models
BEAST 2Generating time resolved bayesian tree sets with complex models
TracerAnalysing BEAST log file outputs, including mutation rate and other model paramter estimates
FigTreeViewing and colouring phylogenetic trees

Other resources

Institute of Veterinary Virology, University of Bern, useful BVDV website BVD-info.ch

Institute of Virology, Hannover, Community Reference Laboratory for Classical Swine Fever Virus http://viro08.tiho-hannover.de/eg/index.html

Scientific Papers

ASFV

de Villier et al (2010) "Phylogenomic analysis of 11 complete African swine fever virus genome sequences" Virology 400:128-136
http://dx.doi.org/10.1016/j.virol.2010.01.019

Lubisi et al (2005) "Molecular epidemiology of African swine fever in East Africa" Archives of Virology 150:2439-2452
http://link.springer.com/article/10.1007%2Fs00705-005-0602-1

Boshof et al (2007) "Genetic characterisation of African swine fever viruses from outbreaks in southern Africa (1973-1999)" Veterniary Microbiology 121:45-55
http://dx.doi.org/10.1016/j.vetmic.2006.11.007

Avian Influenza

Lu L, Lycett SJ, Leigh Brown AJ (2014) "Reassortment patterns of avian influenza virus internal segments among different subtypes" BMC Evolutionary Biology 14:16. doi:10.1186/1471-2148-14-16 - Data on Dryad

Lam et al (2013) "The genesis and source of the H7N9 influenza viruses causing human infections in China" Nature 502:241244 doi:10.1038/nature12515

Ward MJ, Lycett SJ, Avila D, Bollback J, Leigh Brown AJ (2013) "Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza" BMC Evol Biol 2013 13:222 doi:10.1186/1471-2148-13-222

Lycett SJ et al (2012) "Estimating reassortment rates in co-circulating Eurasian swine influenza viruses" J Gen Virol 9311:2326-2336 doi:10.1099/vir.0.044503-0

Worobey M, Han G-Z, Rambaut A (2014) "A synchronized global sweep of the internal genes of modern avian influenza virus" Nature 508:254-257 doi:10.1038/nature13016

BVDV

Richard E Booth, Carole J Thomas, Laila MR El-Attar, George Gunn and Joe Brownlie
"A phylogenetic analysis of Bovine Viral Diarrhoea Virus (BVDV) isolates from six different regions of the UK and links to animal movement data"
Veterinary Research 2013, 44:43 Open access paper

Chernick A, Godson DL, van der Meer F (2014) "Metadata beyond the sequence enables the phylodynamic inference of bovine viral diarrhea virus type 1a isolates from Western Canada"
Infect Genet Evolpii: S1567-1348(14)00006-9. doi: 10.1016/j.meegid.2014.01.003 http://dx.doi.org/10.1016/j.meegid.2014.01.003

CSFV

Postel et al (2012) "Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences"
Vet Res. 2012 Jun 7;43:50 doi: 10.1186/1297-9716-43-50

FMDV

Carrillo et al (2005) "Comparative Genomics of Foot-and-Mouth Disease Virus" J. Virol.May 2005 79(10):6487-6504 doi: 10.1128/JVI.79.10.6487-6504.2005

Cottam et al (2006) "Molecular Epidemiology of the Foot-and-Mouth Disease Virus Outbreak in the United Kingdom in 2001" J. Virol. November 2006 80(22):11274-11282 doi: 10.1128/JVI.01236-06

Cottam et al (2008) "Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus" Proc. R. Soc. B 22 April 2008 275(1637):887-895 doi:10.1098/rspb.2007.1442

Cottam et al (2008) "Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007" PLoS Pathog. 2008 Apr 18;4(4):e1000050. doi: 10.1371/journal.ppat.1000050

Konig et al (2009) "Sequence data and evidence of possible airborne spread in the 2001 foot-and-mouth disease epidemic in the UK" Veterinary Record 2009;165:410-412 doi:10.1136/vr.165.14.410

Schmallenberg

Saeed et al (2001) "Phylogeny of the Simbu serogroup of the genus Bunyavirus" J Gen Virol. 2001;82:217381
PMID 11514727

Goller et al (2012) "Schmallenberg Virus as Possible Ancestor of Shamonda Virus" Emerg Infect Dis Oct 2012 18(10):16441646.
doi: 10.3201/eid1810.120835

Yanase et al (2012) "Genetic reassortment between Sathuperi and Shamonda viruses of the genus Orthobunyavirus in nature: implications for their genetic relationship to Schmallenberg virus" Arch Virol 157:8 pp 1611-1616
doi: 10.1007/s00705-012-1341-8