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. 2022 Jul 26;11:e76605. doi: 10.7554/eLife.76605

Figure 3. Historical transmission dynamics analysis.

(A) Distribution of local-born cases clustered by different pairwise distance SNP thresholds. Cases are expressed as the percentage of the plotted samples. Pie charts represent the proportion of local-born (color) and foreign-born (gray) cases in each dataset. (B) Age of local transmission links over time in each setting. Circles represent median time, and lines represent 95% high probability density for each transmission link counted. Circle size represents the number of samples included in the corresponding link. Red denotes those transmission links including only samples within the same genomic transmission clusters (gClusters), green denotes links involving samples from different gClusters, blue denotes samples within gClusters and unique, and purple denotes unique cases. All links were obtained from Figure 3—figure supplements 1–6 and are summarized in Figure 3—source data 1–6.

Figure 3—source data 1. Bayesian dating results for all clusters (CL) from Oxfordshire.
Data include information of cluster date (in years AD); cluster distances (min, max, mean, and median); most recent common ancestor (MRCA) time in years (AD) with corresponding 95% highest probability density (HPD) intervals and cluster time span or duration.
Figure 3—source data 2. Number of transmission links (TLs) traced back to 150 years before 2016 for Oxfordshire dataset.
Median time of all the local TLs pointed in Figure 3—figure supplement 1 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Sampling period for Oxfordshire is 2007–2012.
Figure 3—source data 3. Bayesian dating results for all clusters (CL) from Valencia region.
Data include information of cluster date (in years AD); cluster distances (min, max, mean, and median); most recent common ancestor (MRCA) time in years (AD) with corresponding 95% highest probability density (HPD) intervals and cluster time span or duration.
Figure 3—source data 4. Number of transmission links (TLs) traced back to 150 years before 2016 for Oxfordshire dataset.
Median time of all the local TLs pointed in Figure 3—figure supplement 1 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Sampling period for Oxfordshire is 2007–2012.
Figure 3—source data 5. Number of transmission links (TLs) traced back to 150 years before 2016 for Malawi dataset.
Analysis performed for Malawi. Median time of all the TLs pointed in Figure 3—figure supplement 2 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Color code for links outside clusters (no_CL) are the same as in Figure 3—figure supplement 2. Sampling period for Malawi is 2008–2010.
Figure 3—source data 6. Number of transmission links (TLs) traced up to 150 years before 2016 for Valencia dataset.
Median time of all the TLs pointed in Figure 3—figure supplements 3–6 were classified in different time windows. The total number of links within each time window is indicated even if they were links within a genomic cluster (total_CL) or not (total_noCL). Color code for links outside clusters (no_CL) are the same as in Figure 3—figure supplements 3–6. Sampling period for Valencia is 20014–2016. The percentage of Spanish cases within each TL was evaluated in a global phylogeny as a proxi of the origin of the node.

Figure 3.

Figure 3—figure supplement 1. Bayesian time tree for Oxfordshire dataset.

Figure 3—figure supplement 1.

Sample names in bold represent local born cases. Local clusters (CLs) are highlighted in orange and mixed CLs in green (those including foreign cases). The CL numbers are crossreferenced in Figure 3—source data 1. The transmission links’ (TLs’) dates used in the analysis are indicated in bold and expressed as AD, the other TLs’ dates are indicated as years before 2016 AD. Branch colors represent Bayesian posterior values being red the highest posterior, blue median, and green the lowest values. Numbers in TLs nodes are crossreferenced in Figure 3—source data 4.
Figure 3—figure supplement 2. Bayesian time tree for Malawi dataset.

Figure 3—figure supplement 2.

Sample names in bold represent local born cases. Local clusters (CLs) are highlighted in orange and mixed CLs in green (those including foreign cases). The CL numbers are crossreferenced in Figure 3—source data 2. The transmission links’ (TLs’) dates used in the analysis are indicated in bold and expressed as AD, the other TLs’ dates are indicated as years before 2016 AD. Branch colors represent Bayesian posterior values being red the highest posterior, blue median, and green the lowest values. Numbers in TLs nodes are crossreferenced in Figure 3—source data 5.
Figure 3—figure supplement 3. Bayesian time tree for Valencia region dataset.

Figure 3—figure supplement 3.

Sample names in bold represent local born cases. Local clusters (CL) are highlighted in orange and mixed CL in green (those including foreign cases). The CL numbers are crossreferenced in Figure 3—source data 3. The transmission links’ (TLs’) dates used in the analysis are indicated in bold and expressed as AD, the other TLs’ dates are indicated as years before 2016 AD. Branch colors represent Bayesian posterior values being red the highest posterior, blue median and green the lowest values. Numbers in TLs nodes are crossreferenced in Figure 3—source data 6.
Figure 3—figure supplement 4. Bayesian time tree for Velncia Region dataset.

Figure 3—figure supplement 4.

Sample names in bold represent local born cases. Local clusters are highlighted in orange and mixed clusters in green (those including foreign cases). CL numbers are crossreferencied in Figure 3—source data 3. TLs’ dates used in the analysis are indicated in bold and expressed as AD, the other TLs’ dates are indicated as years before 2016 AD. Branch colors represent bayesian posterior values being red the highest posterior, blue median and green the lowest values. Numbers in TLs nodes are cross referencend in Figure 3—source data 6.
Figure 3—figure supplement 5. Bayesian time tree for Valencia Region dataset.

Figure 3—figure supplement 5.

Sample names in bold represent local born cases. Local clusters are highlighted in orange and mixed clusters in green (those including foreign cases). CL numbers are crossreferencied in Figure 3—source data 3. TLs’ dates used in the analysis are indicated in bold and expressed as AD, the other TLs’ dates are indicated as years before 2016 AD. Branch colors represent bayesian posterior values being red the highest posterior, blue median and green the lowest values. Numbers in TLs nodes are crossreferencend in Figure 3—source data 6.
Figure 3—figure supplement 6. Bayesian time tree for Valencia Region dataset.

Figure 3—figure supplement 6.

Sample names in bold represent local born cases. Local clusters are highlighted in orange and mixed clusters in green (those including foreign cases). CL numbers are crossreferencied in Figure 3-source data 3. TLs’ dates used in the analysis are indicated in bold and expressed as AD, the other TLs’ dates are indicated as years before 2016 AD. Branch colors represent bayesian posterior values being red the highest posterior, blue median and green the lowest values. Numbers in TLs nodes are crossreferencend in Figure 3—source data 6.