Epidemic arboviral diseases: priorities for research and public health, The Lancet Infectious Diseases, vol.17, issue.3, pp.101-107, 2017. ,
DOI : 10.1016/S1473-3099(16)30518-7
Ecological effects on arbovirus-mosquito cycles of transmission, Current Opinion in Virology, vol.21, pp.124-155, 2016. ,
DOI : 10.1016/j.coviro.2016.09.008
Dissecting vectorial capacity for mosquito-borne viruses, Current Opinion in Virology, vol.15, pp.112-120, 2015. ,
DOI : 10.1016/j.coviro.2015.10.003
URL : https://manuscript.elsevier.com/S1879625715001534/pdf/S1879625715001534.pdf
Heterogeneity, mixing, and the spatial scales of mosquito-borne pathogen transmission):e1003327. https, PLoS Comput Biol, vol.9, issue.12, 2013. ,
Differential sources of host species heterogeneity influence the transmission and control of multihost parasites, Ecology Letters, vol.94, issue.8, pp.975-84, 2013. ,
DOI : 10.1007/978-0-387-87458-6
Coupled Heterogeneities and Their Impact on Parasite Transmission and Control, Trends in Parasitology, vol.32, issue.5, pp.356-67, 2016. ,
DOI : 10.1016/j.pt.2016.01.001
URL : http://europepmc.org/articles/pmc4851872?pdf=render
Heterogeneities in the transmission of infectious agents: Implications for the design of control programs, Proceedings of the National Academy of Sciences, vol.20, issue.6306, pp.338-380, 1997. ,
DOI : 10.1097/00007435-199307000-00001
Ross, Macdonald, and a Theory for the Dynamics and Control of Mosquito-Transmitted Pathogens, PLoS Pathogens, vol.3, issue.4, 2012. ,
DOI : 10.1371/journal.ppat.1002588.s001
A systematic review of mathematical models of mosquito-borne pathogen transmission: 1970-2010, Journal of The Royal Society Interface, vol.1, issue.8, p.20120921, 2013. ,
DOI : 10.1038/ncomms1107
Impact of daily temperature fluctuations on dengue virus transmission by Aedes aegypti, Proceedings of the National Academy of Sciences, vol.273, issue.1593, pp.7460-7465, 2011. ,
DOI : 10.1098/rspb.2006.3483
URL : https://hal.archives-ouvertes.fr/pasteur-00587940
Climate Change and Aedes Vectors: 21st Century Projections for Dengue Transmission in Europe, EBioMedicine, vol.7, pp.267-77, 2016. ,
DOI : 10.1016/j.ebiom.2016.03.046
URL : https://doi.org/10.1016/j.ebiom.2016.03.046
Extrinsic Incubation Period of Dengue: Knowledge, Backlog, and Applications of Temperature Dependence, PLoS Neglected Tropical Diseases, vol.49, issue.6, 2013. ,
DOI : 10.1371/journal.pntd.0002207.s001
URL : https://doi.org/10.1371/journal.pntd.0002207
The global distribution and burden of dengue, Nature, vol.62, issue.7446, pp.504-511, 2013. ,
DOI : 10.1016/S0065-308X(05)62004-0
URL : http://www.nature.com/nature/journal/v496/n7446/pdf/nature12060.pdf
Dengue viruses cluster antigenically but not as discrete serotypes, Science, vol.346, issue.6212, pp.1338-1381, 2015. ,
DOI : 10.1126/science.1256427
URL : http://europepmc.org/articles/pmc4876809?pdf=render
Dengue?quo tu et quo vadis? Viruses, pp.1562-608, 2011. ,
DOI : 10.3390/v3091562
URL : http://www.mdpi.com/1999-4915/3/9/1562/pdf
Consequences of the expanding global distribution of Aedes albopictus for dengue virus transmission):e646. https, PLoS Negl Trop Dis, vol.4, issue.5, 2010. ,
, Evolution, vol.90, issue.11, pp.2459-69, 2016.
DOI : 10.4269/ajtmh.13-0186
Spatial and Temporal Clustering of Dengue Virus Transmission in Thai Villages, PLoS Medicine, vol.38, issue.11, p.205, 2008. ,
DOI : 10.1371/journal.pmed.0050205.sg001
Mode of transmission and the evolution of arbovirus virulence in mosquito vectors, Proceedings of the Royal Society B: Biological Sciences, vol.47, issue.5, pp.1369-78, 1660. ,
DOI : 10.4269/ajtmh.1992.47.691
Chikungunya Virus and Aedes Mosquitoes: Saliva Is Infectious as soon as Two Days after Oral Infection, PLoS ONE, vol.4, issue.6, p.5895, 2009. ,
DOI : 10.1371/journal.pone.0005895.g005
URL : https://hal.archives-ouvertes.fr/pasteur-00395262
Rapid Infection of Salivary Glands in Culiseta Melanura with Eastern Equine Encephalitis Virus: an Electron Microscopic Study *, The American Journal of Tropical Medicine and Hygiene, vol.33, issue.5, pp.961-965, 1984. ,
DOI : 10.4269/ajtmh.1984.33.961
The 5??? and 3??? Untranslated Regions of the Flaviviral Genome, Viruses, vol.71, issue.6, p.28587300 ,
DOI : 10.1016/j.virol.2010.06.014
URL : http://www.mdpi.com/1999-4915/9/6/137/pdf
Dengue virus type 2: replication and tropisms in orally infected Aedes aegypti mosquitoes, BMC Microbiol, vol.7, issue.9, 1471. ,
Flavivirus Susceptibility in Aedes aegypti, Archives of Medical Research, vol.33, issue.4, pp.379-88, 2002. ,
DOI : 10.1016/S0188-4409(02)00373-9
URL : http://eprints.uanl.mx/956/1/Flavivirus_susceptibility_in_Aedes_aegypti.pdf
Asymptomatic humans transmit dengue virus to mosquitoes, Proceedings of the National Academy of Sciences, vol.7, issue.5, pp.14688-93, 2015. ,
DOI : 10.1128/JCM.39.5.1922-1927.2001
URL : https://hal.archives-ouvertes.fr/pasteur-01239113
Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes, Proceedings of the National Academy of Sciences, vol.207, issue.9, pp.9072-9079, 2013. ,
DOI : 10.1093/infdis/jis470
Mathematical modeling of infectious disease dynamics, Virulence, vol.460, issue.4, pp.295-306, 2013. ,
DOI : 10.1016/j.amc.2011.05.067
URL : http://www.tandfonline.com/doi/pdf/10.4161/viru.24041?needAccess=true
Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses):e1003621. https, PLoS Genet, vol.9, issue.8, 2013. ,
DOI : 10.1371/journal.pgen.1003621
URL : https://doi.org/10.1371/journal.pgen.1003621
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.18, issue.15, pp.2114-2134, 2014. ,
DOI : 10.1101/gr.074492.107
URL : https://academic.oup.com/bioinformatics/article-pdf/30/15/2114/17143152/btu170.pdf
Ray Meta: scalable de novo metagenome assembly and profiling, Genome Biology, vol.13, issue.12, p.23259615, 2012. ,
DOI : 10.1093/nar/gkh021
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2012-13-12-r122?site=genomebiology.biomedcentral.com
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366, 1923. ,
DOI : 10.1093/bioinformatics/btp352
URL : http://europepmc.org/articles/pmc3322381?pdf=render
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.9, issue.11, pp.2078-2087, 2009. ,
DOI : 10.1146/annurev.genom.9.081307.164359
URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf
BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.85, issue.6, pp.841-843, 2010. ,
DOI : 10.1073/pnas.85.8.2444
URL : https://academic.oup.com/bioinformatics/article-pdf/26/6/841/16897802/btq033.pdf
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets, Nucleic Acids Research, vol.19, issue.22, pp.11189-201, 2012. ,
DOI : 10.1093/nar/gks918
URL : https://academic.oup.com/nar/article-pdf/40/22/11189/16961200/gks918.pdf
Highly divergent dengue virus type 1 genotype sets a new distance record, Scientific Reports, vol.33, issue.1, pp.22356-26924208, 2016. ,
DOI : 10.1111/j.1440-6055.1994.tb01219.x
URL : https://doi.org/10.1038/srep22356
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-80, 1994. ,
DOI : 10.1093/nar/22.22.4673
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.57, issue.9, pp.1312-1315, 2014. ,
DOI : 10.1080/10635150802429642
jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, p.772, 2012. ,
DOI : 10.1109/TAC.1974.1100705
URL : http://europepmc.org/articles/pmc4594756?pdf=render
FigTree v1.4.3, Available from http ,
package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, vol.40, issue.1, pp.28-36, 2017. ,
DOI : 10.1093/nar/gks576
phylosignal: an R package to measure, test, and explore the phylogenetic signal, Ecology and Evolution, vol.33, issue.9, pp.2774-80, 2016. ,
DOI : 10.1146/annurev.ecolsys.33.010802.150448
URL : https://hal.archives-ouvertes.fr/hal-01426773
Phylogenetic Signal, Evolutionary Process, and Rate, Systematic Biology, vol.92, issue.4, pp.591-601, 2008. ,
DOI : 10.3732/ajb.92.6.972
Carrying Capacity, Technological Forecasting and Social Change, vol.61, issue.3, pp.209-223, 1999. ,
DOI : 10.1016/S0040-1625(99)00022-0
A Primer on Logistic Growth and Substitution, Technological Forecasting and Social Change, vol.61, issue.3, pp.247-71, 1999. ,
DOI : 10.1016/S0040-1625(99)00021-9
subplex: unconstrained optimization using the subplex algorithm. R package version 3 ,
Pvclust: an R package for assessing the uncertainty in hierarchical clustering. R package version 3.4.0, 2006. ,
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.24, issue.8, pp.1647-1656, 2012. ,
DOI : 10.1093/molbev/msm092
R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing, 2014. ,
ggplot2: elegant graphics for data analysis, 2009. ,
Vertical Transmission of Dengue, Clinical Infectious Diseases, vol.25, issue.6, pp.1374-1381, 1997. ,
DOI : 10.1086/516126
Determinants of Arbovirus Vertical Transmission in Mosquitoes):e1005548. https, PLoS Pathog, vol.12, issue.5, 2016. ,
Natural History of Dengue Virus (DENV)???1 and DENV???4 Infections: Reanalysis of Classic Studies, The Journal of Infectious Diseases, vol.195, issue.7, pp.1007-1020, 2007. ,
DOI : 10.1086/511825
The Incubation Periods of Dengue Viruses, PLoS ONE, vol.9, issue.11, p.50972, 2012. ,
DOI : 10.1371/journal.pone.0050972.s003
foreach: provides foreach looping construct for R. R package 3.4.0, 2015. ,
doParallel: foreach parallel adaptor for the parallel package. R package version 3.4.0, 2014. ,
The Split-Apply-Combine Strategy for Data Analysis, Journal of Statistical Software, vol.40, issue.1, pp.1-29000289228100001, 2011. ,
DOI : 10.18637/jss.v040.i01
Reshaping data with the reshape package, J Stat Softw, vol.21, issue.12, pp.1-20000252429400001, 2007. ,
table: extension of data.frame for fast indexing, fast ordered joins, fast assignment, fast grouping and list columns ,
Caret: classification and regression training. R package version 3 ,
Integrated Development for R, 2015. ,
plotly: create interactive web graphics via Plotly's javascript graphing library. R package version 3.4.0, 2016. ,