Growing airline networks in Asia.

<p>(A) Number of nodes (countries belonging to the Asian air transport network), the number of airlines, and total passenger flow in the Asian air transport network between 1982–2012. Records are not available for the period 1983–1991, so dashed lines represented imputed missing values obtained by linear interpolation. (B) Passenger flux in Asia in 1982, 2000 and 2012. The size of each node corresponds to the degree centrality of the country in the airline network. Color coded lines represent the volume of air passenger flux. Node colors correspond to the countries indicated on the right-hand side of the figure. Black points indicate countries for which no virus sequence was included in the genetic analyses. China shares one of the busiest Asian flight routes with Japan, which is indicated by an asterisk.</p

Co-circulation of dengue virus serotypes in Asia.

<p>(A). Locations of available viral sequences (within regions defined by sampling effort) and airports. Circle areas are proportional to the number of genetic sequences from a particular geographic location and for a given serotype (dark grey: DENV-1, orange: DENV-2, green: DENV-3, and yellow: DENV-4). Grey dots represent the airports for which passenger flux data was used in the analysis. Sequences obtained from patients in Japan, 2014 are indicated by asterisk. (B) The upper panel shows the proportion of sequences from each serotype per year, while the lower panel shows the number of serotypes isolated per year in Asia. Co-occurrence of multiple serotypes in a single year has become increasingly frequent.</p

Strongly supported pathways of lineage movement and histograms of the total number of location state transitions of DENV-1–3 in Asia for 1956 to 2015.

<p>(A) Strongly supported state transitions, indicating migration of DENV-1–3 lineages among discrete locations. The size of points corresponds to the number of geographic connections. The colored lines represent statistical support for a given viral movement pathway. Only those viral lineage movements supported with a BF > 6 are shown. (B) Number of expected transitions into and out of each country per serotype. Error bars represent 95% BCIs.</p

Predictors of DENV-1–3 diffusion in Asia.

<p>In the top panel bars show <i>δ</i>, an indicator variable that governs the probability of inclusion or exclusion of the predictor in the model. In the lower panel, points and error bars indicate the mean and the 95% Bayesian credible intervals, respectively, of the estimated conditional effect size of the GLM coefficients (<i>β</i>|<i>δ</i> = 1) on a log scale, for each predictor variable. <i>β</i> is the effective size of the predictor variable. GDP: Gross domestic product; LSBCI: linear shipping bilateral connectivity index; CPT: container port throughput.</p

Centrality measures of the air passenger network and number of state transitions.

<p>(A) Scatterplot of centrality measures for the air travel network based on degree and betweenness. The “degree” centrality of a given country (node) refers to the number of airlines linking it in the airline network, and the “betweenness” centrality of a given country measures the extent to which a country lies on routes between other countries in airline network (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005694#sec002" target="_blank">Methods</a>). The size of each point corresponds to the number of expected Markov jump transitions (including both importations and exportations). (B) Net Markov jump counts, summed across all 3 DENV serotypes. For each country, we summarize the average net Markov jumps (jumps to—jumps from) and their 95% credible intervals. The estimates are ordered from the lowest to highest number of net jumps.</p

Large transmission clusters over time: recent infections.

<p>As in <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001898#pmed.1001898.g002" target="_blank">Fig 2</a>, but here red dots represent patients with a documented recent infection. HT, heterosexual transmission.</p

Proportional contribution of new HIV-1 diagnoses amongst all MSM in the ATHENA cohort by decade of birth.

<p>Proportional contribution of new HIV-1 diagnoses amongst all MSM in the ATHENA cohort by decade of birth.</p

Diagnosis and growth of transmission clusters over time.

<p>Cluster types within the phylogenetic tree are defined as follows. Singletons (in blue) are clusters of size 1, or cases whose sequence solely clustered with sequences from the Los Alamos HIV Sequence Database. Small clusters (in green) comprise sequences from 2–9 ATHENA patients. Large clusters comprise sequences from ten or more patients in the ATHENA cohort. Amongst those, non-MSM-dominant clusters (in brown) contain a majority of sequences from non-MSM patients, whilst MSM-majority clusters contain a majority of sequences from MSM patients. Among large MSM-majority clusters, pre-1996 clusters (in dark orange) are defined as those in which the first diagnosed patient in the cluster was diagnosed before 1996, and post-1996 clusters are defined as those in which all patients in the cluster were diagnosed in or after 1996. Large MSM-majority post-1996 clusters are stratified as “time of MRCA pre-1996” (in light orange) when the estimated time of the MRCA is before 1996, and “time of MRCA post-1996” (in purple) when the estimated time of the MRCA is in or after 1996. (A) Number of MSM registered in the ATHENA cohort in the Netherlands with a sequence in this study by year of diagnosis and by cluster type. (B) Number of clusters of each type by year of first diagnosed case in each cluster.</p

Estimated case reproduction number over time for all MSM-majority transmission clusters of ≥10 cases.

<p>The solid lines show the mean <i>R</i>_<i>t</i> estimate for each transmission cluster. The bold black line is the mean <i>R</i>_<i>t</i> of all clusters, with the 95% confidence interval shown by the dotted lines. The shaded areas show the 95% confidence intervals for each transmission cluster: darker areas indicate overlapping intervals across different transmission clusters. Transmission clusters are shown in red if their first sequence appeared before 1991, in blue if their first sequence appeared between 1991 and 2000, and in green if their first diagnosed case appeared after 2000. The black horizontal dotted line represents the threshold value <i>R</i>_<i>t</i> = 1. (A) Main analysis. (B) Sensitivity analysis for a looser cluster definition. (C) Sensitivity analysis for a more stringent cluster definition. (D) Sensitivity analysis for the clusters defined under a single linkage branch length threshold.</p

Large transmission clusters over time: region of origin.

<p>As in <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001898#pmed.1001898.g002" target="_blank">Fig 2</a>, but here the color of each dot represents the region of origin. In large MSM-majority clusters 79% (1,673) of MSM were of Dutch origin. HT, heterosexual transmission.</p