Dengue diversity across spatial and temporal scales: Local structure and the effect of host population size.
A fundamental mystery for dengue and other infectious pathogens is how observed patterns of cases relate to actual chains of individual transmission events. These pathways are intimately tied to the mechanisms by which strains interact and compete across spatial scales. Phylogeographic methods have been used to characterize pathogen dispersal at global and regional scales but have yielded few insights into the local spatiotemporal structure of endemic transmission. Using geolocated genotype (800 cases) and serotype (17,291 cases) data, we show that in Bangkok, Thailand, 60% of dengue cases living <200 meters apart come from the same transmission chain, as opposed to 3% of cases separated by 1 to 5 kilometers. At distances <200 meters from a case (encompassing an average of 1300 people in Bangkok), the effective number of chains is 1.7. This number rises by a factor of 7 for each 10-fold increase in the population of the "enclosed" region. This trend is observed regardless of whether population density or area increases, though increases in density over 7000 people per square kilometer do not lead to additional chains. Within Thailand these chains quickly mix, and by the next dengue season viral lineages are no longer highly spatially structured within the country. In contrast, viral flow to neighboring countries is limited. These findings are consistent with local, density-dependent transmission and implicate densely populated communities as key sources of viral diversity, with home location the focal point of transmission. These findings have important implications for targeted vector control and active surveillance.
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. henrik.salje@pasteur.fr justin@jhu.edu datc@ufl.edu.|Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France.|CNRS, URA3012, Paris 75015, France.|Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris 75015, France.
Henrik
0000-0003-3626-4254
H
Salje
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. henrik.salje@pasteur.fr justin@jhu.edu datc@ufl.edu.
Justin
0000-0002-9741-8109
J
Lessler
Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Irina
0000-0001-8555-5352
I
Maljkovic Berry
Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Melanie C
0000-0002-4811-4467
MC
Melendrez
Department of Medicine, Upstate Medical University of New York, Syracuse, New York, NY, 13210, USA.
Timothy
0000-0001-9152-0199
T
Endy
Queen Sirikit National Institute of Child Health, Bangkok, Thailand.
Siripen
S
Kalayanarooj
National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.
Atchareeya
0000-0003-1597-8944
A
A-Nuegoonpipat
National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.
Sumalee
0000-0002-3522-3795
S
Chanama
National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.
Somchai
S
Sangkijporn
Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
Chonticha
C
Klungthong
Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
Butsaya
B
Thaisomboonsuk
Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
Ananda
A
Nisalak
Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
Robert V
0000-0002-3368-6542
RV
Gibbons
Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand.
Sopon
0000-0002-6109-5002
S
Iamsirithaworn
Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
Louis R
LR
Macareo
Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.|International Vaccine Institute, Seoul, South Korea.
In-Kyu
0000-0001-5077-6470
IK
Yoon
National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.
Areerat
A
Sangarsang
Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
Richard G
0000-0002-5765-0173
RG
Jarman
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. henrik.salje@pasteur.fr justin@jhu.edu datc@ufl.edu.|Department of Biology, University of Florida, Gainesville, FL 32610, USA.|Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.
Derek A T
0000-0002-9437-1907
DA
Cummings
D016000:Cluster Analysis; D003715:Dengue / Q000453:epidemiology* / Q000635:transmission* / Q000821:virology; D003716:Dengue Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D062665:Epidemiological Monitoring; D006801:Humans; D000072138:Mosquito Vectors / Q000821:virology; D010802:Phylogeny; D011156:Population Density; D017423:Sequence Analysis, RNA; D062211:Spatio-Temporal Analysis; D013785:Thailand / Q000453:epidemiology