Fooks AR, Banyard AC, Horton DL, Johnson N, McElhinney LM, Jackson AC. Current status of rabies and prospects for elimination. Lancet. 2014;384:1389–99.
Article
PubMed
Google Scholar
Knobel DL, Cleaveland S, Coleman PG, Fèvre EM, Meltzer MI, Miranda MEG, Shaw A, Zinsstag J, Meslin F-X. Re-evaluating the burden of rabies in Africa and Asia. Bull World Health Organ. 2005;83:360–8.
PubMed
PubMed Central
Google Scholar
Tang X, Luo M, Zhang S, Fooks AR, Hu R, Tu C. Pivotal role of dogs in rabies transmission, China. Emerg Infect Dis. 2005;11:1970–2.
Article
PubMed
PubMed Central
Google Scholar
Talbi C, Lemey P, Suchard MA, Abdelatif E, Elharrak M, Jalal N, Faouzi A, Echevarría JE, Morón SV, Rambaut A. Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS Pathog. 2010;6:e1001166.
Article
PubMed
PubMed Central
Google Scholar
Bourhy H, Nakouné E, Hall M, Nouvellet P, Lepelletier A, Talbi C, Watier L, Holmes EC, Cauchemez S, Lemey P. Revealing the micro-scale signature of endemic zoonotic disease transmission in an African urban setting. PLoS Pathog. 2016;12:e1005525.
Article
PubMed
PubMed Central
Google Scholar
Pybus OG, Rambaut A. Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet. 2009;10:540–50.
Article
CAS
PubMed
Google Scholar
Meng S, Sun Y, Wu X, Tang J, Xu G, Lei Y, Wu J, Yan J, Yang X, Rupprecht CE. Evolutionary dynamics of rabies viruses highlights the importance of China rabies transmission in Asia. Virology. 2011;410:403–9.
Article
CAS
PubMed
Google Scholar
Bourhy H, Reynes J-M, Dunham EJ, Dacheux L, Larrous F, Huong VTQ, Xu G, Yan J, Miranda MEG, Holmes EC. The origin and phylogeography of dog rabies virus. J Gen Virol. 2008;89:2673–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hyun B-H, Lee K-K, Kim I-J, Lee K-W, Park H-J, Lee O-S, An S-H, Lee J-B. Molecular epidemiology of rabies virus isolates from South Korea. Virus Res. 2005;114:113–25.
Article
CAS
PubMed
Google Scholar
Nagarajan T, Mohanasubramanian B, Seshagiri E, Nagendrakumar S, Saseendranath M, Satyanarayana M, Thiagarajan D, Rangarajan P, Srinivasan V. Molecular epidemiology of rabies virus isolates in India. J Clin Microbiol. 2006;44:3218–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo Z, Tao X, Yin C, Han N, Yu J, Li H, Liu H, Fang W, Adams J, Wang J. National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries. PLoS Negl Trop Dis. 2013;7:e2039.
Article
PubMed
PubMed Central
Google Scholar
Zhang H, Zhang Y, Yang W, Tao X, Li H, Ding J, Feng Y, Yang D, Zhang J, He J. Molecular epidemiology of reemergent rabies in Yunnan Province, southwestern China. Emerg Infect Dis. 2014;20:1433.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harrison A, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Supuri M, Masta A, Teriboriki B. Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses. 2011;3:83–101.
Article
PubMed
PubMed Central
Google Scholar
Hughes GJ, Orciari LA, Rupprecht CE. Evolutionary timescale of rabies virus adaptation to North American bats inferred from the substitution rate of the nucleoprotein gene. J Gen Virol. 2005;86:1467–74.
Article
CAS
PubMed
Google Scholar
Holmes EC, Woelk CH, Kassis R, Bourhy H. Genetic constraints and the adaptive evolution of rabies virus in nature. Virology. 2002;292:247–57.
Article
CAS
PubMed
Google Scholar
Bourhy H, Dautry-Varsat A, Hotez PJ, Salomon J. Rabies, still neglected after 125 years of vaccination. PLoS Negl Trop Dis. 2010;4:e839.
Article
PubMed
PubMed Central
Google Scholar
Carlson JM, Du VY, Pfeifer N, Bansal A, Tan VY, Power K, Brumme CJ, Kreimer A, DeZiel CE, Fusi N. Impact of pre-adapted HIV transmission. Nat Med. 2016;22:606–13.
Article
PubMed
PubMed Central
Google Scholar
Nadin-Davis SA, Turner G, Paul JP, Madhusudana SN, Wandeler AI. Emergence of Arctic-like rabies lineage in India. Emerg Infect Dis. 2007;13:111–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tao X, Tang Q, Li H, Mo Z, Zhang H, Wang D, Zhang Q, Song M, Velasco-Villa A, Wu X. Molecular epidemiology of rabies in Southern People’s Republic of China. Emerg Infect Dis. 2009;15:1192–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamagata J, Ahmed K, Khawplod P, Mannen K, Xuyen DK, Loi HH, Van Dung N, Nishizono A. Molecular epidemiology of rabies in Vietnam. Microbiol Immunol. 2007;51:833–40.
Article
CAS
PubMed
Google Scholar
Smith J, McElhinney L, Parsons G, Brink N, Doherty T, Agranoff D, Miranda ME, Fooks AR. Case report: rapid ante‐mortem diagnosis of a human case of rabies imported into the UK from the Philippines. J Med Virol. 2003;69:150–5.
Article
PubMed
Google Scholar
Cuypers L, Vrancken B, Fabeni L, Marascio N, Cento V, Di Maio VC, Aragri M, Pineda-Peña AC, Schrooten Y, Van Laethem K. Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy. BMC Evol Biol. 2017;17:70.
Article
PubMed
PubMed Central
Google Scholar
Yu J, Li H, Tang Q, Rayner S, Han N, Guo Z, Liu H, Adams J, Fang W, Tao X. The spatial and temporal dynamics of rabies in China. PLoS Negl Trop Dis. 2012;6:e1640.
Article
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.
Article
PubMed
PubMed Central
Google Scholar
Martin D, Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics. 2000;16:562–3.
Article
CAS
PubMed
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme A-M, Van Laethem K, Lemey P. The genealogical population dynamics of HIV-1 in a large transmission chain: Bridging within and among host evolutionary rates. PLoS Comput Biol. 2014;10:e1003505.
Article
PubMed
PubMed Central
Google Scholar
Rambaut A, Lam TT, Carvalho LM, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2:vew007.
Article
PubMed
PubMed Central
Google Scholar
Huson DH. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 1998;14:68–73.
Article
CAS
PubMed
Google Scholar
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;7:80–9.
Article
PubMed
Google Scholar
Guindon S, Dufayard J-F, 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;59:307–21.
Article
CAS
PubMed
Google Scholar
Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27:221–4.
Article
CAS
PubMed
Google Scholar
Al-Qahtani AA, Baele G, Khalaf N, Suchard MA, Al-Anazi MR, Abdo AA, Sanai FM, Al-Ashgar HI, Khan MQ, Al-Ahdal MN. The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia. Sci Rep. 2017;7:44947.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4:e88.
Article
PubMed
PubMed Central
Google Scholar
Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol. 2013;30:713–24.
Article
CAS
PubMed
Google Scholar
Suchard MA, Kitchen CM, Sinsheimer JS, Weiss RE. Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst Biol. 2003;52:649–64.
Article
PubMed
Google Scholar
Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P. Host ecology determines the dispersal patterns of a plant virus. Virus Evol. 2015;1:vev016.
Article
PubMed
PubMed Central
Google Scholar
Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol. 2010;27:2038–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O’Connell TC, Coxon P, Monaghan N. Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol. 2011;21:1251–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shapiro B, Rambaut A, Drummond AJ. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol. 2006;23:7–9.
Article
CAS
PubMed
Google Scholar
Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P. Spread3: interactive visualization of spatiotemporal history and trait evolutionary processes. Mol Biol Evol. 2016;33:2167–9.
Article
CAS
PubMed
Google Scholar
Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol. 2008;56:391–412.
Article
PubMed
Google Scholar
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586–91.
Article
CAS
PubMed
Google Scholar
Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 2000;15:496–503.
Article
CAS
PubMed
Google Scholar
Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21:676–9.
Article
CAS
PubMed
Google Scholar
Kass RE, Raftery AE. Bayes factors. J Am Stat Assoc. 1995;90:773–95.
Article
Google Scholar