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For: Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP. Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. PLoS Pathog 2011;7:e1002064. [PMID: 21655108 PMCID: PMC3107208 DOI: 10.1371/journal.ppat.1002064] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 03/25/2011] [Indexed: 01/19/2023]  Open
Number Cited by Other Article(s)
51
Bhoomiboonchoo P, Gibbons RV, Huang A, Yoon IK, Buddhari D, Nisalak A, Chansatiporn N, Thipayamongkolgul M, Kalanarooj S, Endy T, Rothman AL, Srikiatkhachorn A, Green S, Mammen MP, Cummings DA, Salje H. The spatial dynamics of dengue virus in Kamphaeng Phet, Thailand. PLoS Negl Trop Dis 2014;8:e3138. [PMID: 25211127 PMCID: PMC4161352 DOI: 10.1371/journal.pntd.0003138] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 07/22/2014] [Indexed: 12/16/2022]  Open
52
Le MQ, Lam HM, Cuong VD, Lam TTY, Halpin RA, Wentworth DE, Hien NT, Thanh LT, Phuong HVM, Horby P, Boni MF. Migration and persistence of human influenza A viruses, Vietnam, 2001-2008. Emerg Infect Dis 2014;19:1756-65. [PMID: 24188643 PMCID: PMC3837676 DOI: 10.3201/eid1911.130349] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
53
Nunes MRT, Palacios G, Faria NR, Sousa EC, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DBA, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PFC, Lipkin WI. Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil. PLoS Negl Trop Dis 2014;8:e2769. [PMID: 24743730 PMCID: PMC3990485 DOI: 10.1371/journal.pntd.0002769] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/18/2014] [Indexed: 01/01/2023]  Open
54
Villabona-Arenas CJ, de Oliveira JL, Capra CDS, Balarini K, Loureiro M, Fonseca CRTP, Passos SD, Zanotto PMDA. Detection of four dengue serotypes suggests rise in hyperendemicity in urban centers of Brazil. PLoS Negl Trop Dis 2014;8:e2620. [PMID: 24587454 PMCID: PMC3937275 DOI: 10.1371/journal.pntd.0002620] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
55
Messina JP, Brady OJ, Scott TW, Zou C, Pigott DM, Duda KA, Bhatt S, Katzelnick L, Howes RE, Battle KE, Simmons CP, Hay SI. Global spread of dengue virus types: mapping the 70 year history. Trends Microbiol 2014;22:138-46. [PMID: 24468533 PMCID: PMC3946041 DOI: 10.1016/j.tim.2013.12.011] [Citation(s) in RCA: 438] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 12/28/2022]
56
Guo RN, Lin JY, Li LH, Ke CW, He JF, Zhong HJ, Zhou HQ, Peng ZQ, Yang F, Liang WJ. The prevalence and endemic nature of dengue infections in Guangdong, South China: an epidemiological, serological, and etiological study from 2005-2011. PLoS One 2014;9:e85596. [PMID: 24465613 PMCID: PMC3900419 DOI: 10.1371/journal.pone.0085596] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/29/2013] [Indexed: 11/30/2022]  Open
57
Rabaa MA, Simmons CP, Fox A, Le MQ, Nguyen TTT, Le HY, Gibbons RV, Nguyen XT, Holmes EC, Aaskov JG. Dengue virus in sub-tropical northern and central Viet Nam: population immunity and climate shape patterns of viral invasion and maintenance. PLoS Negl Trop Dis 2013;7:e2581. [PMID: 24340118 PMCID: PMC3854975 DOI: 10.1371/journal.pntd.0002581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 10/29/2013] [Indexed: 11/22/2022]  Open
58
Natural, persistent oscillations in a spatial multi-strain disease system with application to dengue. PLoS Comput Biol 2013;9:e1003308. [PMID: 24204241 PMCID: PMC3812071 DOI: 10.1371/journal.pcbi.1003308] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 09/13/2013] [Indexed: 12/03/2022]  Open
59
Rasmussen DA, Boni MF, Koelle K. Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam. Mol Biol Evol 2013;31:258-71. [PMID: 24150038 PMCID: PMC3907054 DOI: 10.1093/molbev/mst203] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
60
Cuong HQ, Vu NT, Cazelles B, Boni MF, Thai KTD, Rabaa MA, Quang LC, Simmons CP, Huu TN, Anders KL. Spatiotemporal dynamics of dengue epidemics, southern Vietnam. Emerg Infect Dis 2013;19:945-53. [PMID: 23735713 PMCID: PMC3713821 DOI: 10.3201/eid1906.121323] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
61
Chu PY, Ke GM, Chen PC, Liu LT, Tsai YC, Tsai JJ. Spatiotemporal dynamics and epistatic interaction sites in dengue virus type 1: a comprehensive sequence-based analysis. PLoS One 2013;8:e74165. [PMID: 24040199 PMCID: PMC3767619 DOI: 10.1371/journal.pone.0074165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/29/2013] [Indexed: 12/26/2022]  Open
62
Camargo A, Werneck FP, Morando M, Sites JW, Avila LJ. Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling. Mol Ecol 2013;22:4038-54. [PMID: 23786355 DOI: 10.1111/mec.12369] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 12/29/2022]
63
Villabona-Arenas CJ, de Brito AF, de Andrade Zanotto PM. Genomic mosaicism in two strains of Dengue virus type 3. INFECTION GENETICS AND EVOLUTION 2013;18:202-12. [PMID: 23727343 DOI: 10.1016/j.meegid.2013.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 11/28/2022]
64
Villabona-Arenas CJ, Zanotto PMDA. Worldwide spread of Dengue virus type 1. PLoS One 2013;8:e62649. [PMID: 23675416 PMCID: PMC3652851 DOI: 10.1371/journal.pone.0062649] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/24/2013] [Indexed: 01/01/2023]  Open
65
Villabona-Arenas CJ, Mondini A, Bosch I, Schimitt D, Calzavara-Silva CE, de A Zanotto PM, Nogueira ML. Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006-2007. PLoS One 2013;8:e63496. [PMID: 23667626 PMCID: PMC3646734 DOI: 10.1371/journal.pone.0063496] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/03/2013] [Indexed: 12/26/2022]  Open
66
Stadler T, Bonhoeffer S. Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Philos Trans R Soc Lond B Biol Sci 2013;368:20120198. [PMID: 23382421 DOI: 10.1098/rstb.2012.0198] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
67
Ward MJ, Lycett SJ, Kalish ML, Rambaut A, Leigh Brown AJ. Estimating the rate of intersubtype recombination in early HIV-1 group M strains. J Virol 2013;87:1967-73. [PMID: 23236072 PMCID: PMC3571495 DOI: 10.1128/jvi.02478-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/06/2012] [Indexed: 11/20/2022]  Open
68
Rabaa MA, Klungthong C, Yoon IK, Holmes EC, Chinnawirotpisan P, Thaisomboonsuk B, Srikiatkhachorn A, Rothman AL, Tannitisupawong D, Aldstadt J, Nisalak A, Mammen MP, Gibbons RV, Endy TP, Fansiri T, Scott TW, Jarman RG. Frequent in-migration and highly focal transmission of dengue viruses among children in Kamphaeng Phet, Thailand. PLoS Negl Trop Dis 2013;7:e1990. [PMID: 23350000 PMCID: PMC3547850 DOI: 10.1371/journal.pntd.0001990] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/16/2012] [Indexed: 12/15/2022]  Open
69
Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JLN, Holmes EC, Murcia PR. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathog 2012;8:e1003081. [PMID: 23308065 PMCID: PMC3534375 DOI: 10.1371/journal.ppat.1003081] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/25/2012] [Indexed: 12/30/2022]  Open
70
Tibayrenc M, Ayala FJ. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci U S A 2012;109:E3305-13. [PMID: 22949662 PMCID: PMC3511763 DOI: 10.1073/pnas.1212452109] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
71
Lycett SJ, Baillie G, Coulter E, Bhatt S, Kellam P, McCauley JW, Wood JLN, Brown IH, Pybus OG, Leigh Brown AJ, for the Combating Swine Influenza Initiative (COSI) Consortium. Estimating reassortment rates in co-circulating Eurasian swine influenza viruses. J Gen Virol 2012;93:2326-2336. [PMID: 22971819 PMCID: PMC3542128 DOI: 10.1099/vir.0.044503-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/24/2012] [Indexed: 12/22/2022]  Open
72
Therapeutics for dengue: recommendations for design and conduct of early-phase clinical trials. PLoS Negl Trop Dis 2012;6:e1752. [PMID: 23029567 PMCID: PMC3459884 DOI: 10.1371/journal.pntd.0001752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
73
Carneiro AR, Cruz ACR, Vallinoto M, Melo DDV, Ramos RTJ, Medeiros DBA, Silva EVPD, Vasconcelos PFDC. Molecular characterisation of dengue virus type 1 reveals lineage replacement during circulation in Brazilian territory. Mem Inst Oswaldo Cruz 2012;107:805-12. [DOI: 10.1590/s0074-02762012000600016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/10/2012] [Indexed: 11/22/2022]  Open
74
Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters. INFECTION GENETICS AND EVOLUTION 2012;15:77-86. [PMID: 22677620 DOI: 10.1016/j.meegid.2012.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/13/2012] [Accepted: 05/16/2012] [Indexed: 11/23/2022]
75
Dugan VG, Saira K, Ghedin E. Large-scale sequencing and the natural history of model human RNA viruses. Future Virol 2012;7:563-573. [PMID: 23682295 DOI: 10.2217/fvl.12.45] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
76
Revealing the microscale spatial signature of dengue transmission and immunity in an urban population. Proc Natl Acad Sci U S A 2012;109:9535-8. [PMID: 22645364 DOI: 10.1073/pnas.1120621109] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
77
WHO-VMI Dengue Vaccine Modeling Group. Assessing the potential of a candidate dengue vaccine with mathematical modeling. PLoS Negl Trop Dis 2012;6:e1450. [PMID: 22479655 PMCID: PMC3313921 DOI: 10.1371/journal.pntd.0001450] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
78
Liebman KA, Stoddard ST, Morrison AC, Rocha C, Minnick S, Sihuincha M, Russell KL, Olson JG, Blair PJ, Watts DM, Kochel T, Scott TW. Spatial dimensions of dengue virus transmission across interepidemic and epidemic periods in Iquitos, Peru (1999-2003). PLoS Negl Trop Dis 2012;6:e1472. [PMID: 22363822 PMCID: PMC3283551 DOI: 10.1371/journal.pntd.0001472] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 11/29/2011] [Indexed: 11/18/2022]  Open
79
Castro-Nallar E, Pérez-Losada M, Burton GF, Crandall KA. The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol 2012;62:777-92. [PMID: 22138161 PMCID: PMC3258026 DOI: 10.1016/j.ympev.2011.11.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 12/02/2022]
80
Thai KTD, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L, de Vries PJ, Hien TT, Farrar J, van Doorn HR, de Jong MD, Birren BW, Holmes EC, Simmons CP. High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. J Virol 2012;86:835-43. [PMID: 22090119 PMCID: PMC3255838 DOI: 10.1128/jvi.05985-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 10/17/2011] [Indexed: 11/20/2022]  Open
81
Faria NR, Suchard MA, Rambaut A, Lemey P. Toward a quantitative understanding of viral phylogeography. Curr Opin Virol 2011;1:423-9. [PMID: 22440846 DOI: 10.1016/j.coviro.2011.10.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 08/22/2011] [Accepted: 10/07/2011] [Indexed: 12/11/2022]
82
Khor CC, Hibberd ML. Revealing the molecular signatures of host-pathogen interactions. Genome Biol 2011;12:229. [PMID: 22011345 PMCID: PMC3333766 DOI: 10.1186/gb-2011-12-10-229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
83
Chen R, Vasilakis N. Dengue--quo tu et quo vadis? Viruses 2011;3:1562-608. [PMID: 21994796 PMCID: PMC3187692 DOI: 10.3390/v3091562] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/12/2011] [Accepted: 08/12/2011] [Indexed: 02/08/2023]  Open
84
dos Santos FB, Nogueira FB, Castro MG, Nunes PC, de Filippis AMB, Faria NR, Simões JB, Sampaio SA, Santos CR, Nogueira RMR. First report of multiple lineages of dengue viruses type 1 in Rio de Janeiro, Brazil. Virol J 2011;8:387. [PMID: 21813012 PMCID: PMC3170301 DOI: 10.1186/1743-422x-8-387] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/03/2011] [Indexed: 01/06/2023]  Open
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