Table 1.
Dates for Rt estimation for the national and regional epidemic curves for the first 30 epidemic days.
Fig 1.
Timeline of the COVID-19 pandemic in Colombia as of October 31, 2021.
Fig 2.
Epidemic curve of the COVID-19 pandemic in Colombia as of October 31, 2021.
Table 2.
Comparison of model performance metrics by calibrating the GLM, Richards and the sub-epidemic model for 90 epidemic days (July 4, 2021 to October 1, 2021) at the national and regional level.
Higher 95% PI coverage and lower RMSE, MAE, WIS and MIS represent better performance. Best performing model is given in bold with the superscript “a”.
Table 3.
Comparison of 30-day ahead forecasting performance (October 2, 2021 to October 31, 2021) by calibrating the GLM, Richards and the sub-epidemic model for 90 epidemic days (July 4, 2021 to October 1, 2021) at the national and regional level.
Higher 95% PI coverage and lower RMSE, MAE, WIS and MIS represent better performance. Best performing model is given in bold with the superscript "a”.
Fig 3.
30-days ahead forecasts of the national and regional COVID-19 epidemic curves in Colombia by calibrating the GLM model from July 4, 2021 to October 1, 2021.
The blue circles correspond to the data points; the solid red line indicates the best model fit, and the red dashed lines represent the 95% prediction interval. The vertical black dashed line represents the time of the start of the forecast period.
Fig 4.
30-days ahead forecast of the national and regional COVID-19 epidemic curves in Colombia by calibrating the Richards model from July 4, 2021 to October 1, 2021.
The blue circles correspond to the data points; the solid red line indicates the best model fit, and the red dashed lines represent the 95% prediction interval. The vertical black dashed line represents the time of the start of the forecast period.
Fig 5.
30-days ahead forecast of the national and regional COVID-19 epidemic curves in Colombia by calibrating the sub-epidemic wave model from July 4, 2021 to October 1, 2021.
The blue circles correspond to the data points; the solid red line indicates the best model fit, and the red dashed lines represent the 95% prediction interval. The vertical black dashed line represents the time of the start of the forecast period.
Fig 6.
Upper panel: Reproduction number for Colombia with 95% CI estimated using the GGM model. The estimated reproduction number of the COVID-19 epidemic in Colombia as of March 27, 2020, is 1.30 (95% CI: 1.20, 1.50). The growth rate parameter, r, is estimated at 1.40 (95%CI: 0.91, 2.0) and the deceleration of the growth parameter, p, is estimated at 0.64 (95%CI: 0.56, 0.71) at α = 0.15. Lower panel: The lower panel shows the GGM fit to the case incidence data for the first 30 days from February 27, 2020 to March 27, 2020. The blue circles correspond to the data points; the solid red line indicates the best model fit, and the red dashed lines represent the 95% confidence interval. The cyan lines are the model fits obtained via bootstrapping.
Table 4.
Estimates of reproduction number (R), growth rate parameter (r) and deceleration of the growth parameter (p) obtained from the renewal equation method utilizing the GGM for the early ascending phase of the epidemic (30 days) at the national and regional level at α = 0.15.
Table 5.
Estimates of reproduction number (R), growth rate parameter (r) and deceleration of the growth parameter (p) obtained from the renewal equation method utilizing the GGM for the early ascending phase of the epidemic (30 days) at the national and regional level at α = 1.00.
Fig 7.
Effective (instantaneous) reproduction number with 95% CrI estimated using the Cori et al. method and the estimate of reproduction number with 95% CI utilizing the GGM for simulating the parameters employed in the renewal equation method for the COVID-19 epidemic in Colombia as of March 27, 2020 (first 30 days).
The red solid line is the mean reproduction number estimated from the renewal equation method and the red dashed lines are the 95% CI coverage around the mean reproduction number. The green solid line is the median effective reproduction number estimated from the Cori et al. method and the green dashed lines are the 95% CrI coverage around the median instantaneous reproduction.
Fig 8.
Upper panel: Effective reproduction number estimated from the Cori et al. method with 95% credible intervals for the COVID-19 pandemic in Colombia as of October 31, 2021. The red solid line represents the mean reproduction number for Colombia and the red shaded area represents the 95% credible interval around it. The blue solid line represents the mean reproduction number in the Caribbean region and the blue shaded area represents the 95% credible interval around it. The yellow solid line represents the mean reproduction number in the Pacific region and the yellow shaded area represents the 95% credible interval around it. The brown solid line represents the mean reproduction number in the Orinoquía region and the brown shaded area represents the 95% credible interval around it. The pink solid line represents the mean reproduction number in the Andean region and the pink shaded area represents the 95% credible interval around it. The green solid line represents the mean reproduction number in the Amazon and the green shaded area represents the 95% credible interval around it. Lower panel: The percentage of the COVID-19 cases in Colombia, nationally and regionally as of October 31, 2021. The red solid line represents the percentage of cases in Colombia, the blue solid line represents the percentage of cases in the Caribbean region, the yellow solid line represents the percentage of cases in the Pacific region, the brown dotted line represents the percentage of cases in the Orinoquía region, the pink dashed line represents the percentage of cases in the Andean region and the green dotted line represents the percentage of cases in the Amazon region.
Fig 9.
Global Maximum Likelihood (ML) tree for SARS-CoV-2 genomic data analyzed in the paper.
The leaves of the tree are Colombian sequences of SARS-CoV-2 sampled between February 27, 2020, and April 5, 2020 (highlighted in red) and background sequences sampled from around the globe for genomic context. Colombian sequences are distributed among different lineages, indicating multiple virus introductions. The largest estimated intra-Colombian cluster (i.e., a monophyletic clade consisting solely of Colombian sequences) was analyzed using an exponential growth coalescent model to estimate the intra-country basic reproduction number.
Fig 10.
Pre-processing COVID-19 data into incidence rate functions.
From left to right: the original lab-confirmed COVID-19 cases, curve of daily new cases, smoothed and scaled rate curves, and average of rate curves before scaling and smothing.
Fig 11.
Panel A. Clustering of states according to the shapes of their rate curves. Cluster 1 is shown in blue, cluster 2 is shown in red, the smallest cluster, cluster 3 is shown in black whereas cluster 4 is shown in green. One can see that states with similar shapes of rates curves are geographically close to each other. The panel shows the geographic distribution of the clusters created in PaintMaps.com, https://paintmaps.com/map-charts/51/Colombia-map-chart [81]. Panel B. Shows the average shape of the incidence rate curves in each cluster and the overall average. Panel C. Shows the dendrogram plot- a hierarchal clustering of states, which shows that there are four predominant clusters of states.
Fig 12.
Average shapes of the COVID-19 incidence rate curves, along with a one standard-deviation band around the average, in each of the clusters.
Fig 13.
Panel A: Apple mobility trends data showing the variation in walking and driving among the population in Colombia. Orange curve shows the driving trend, and the blue curve shows the walking trend. Panel B: Google mobility trends data showing the variation in movement of people in Colombia across the following categories: grocery and pharmacy (green solid curve), parks (pink solid curve), transit stations (purple solid curve), workplaces (red solid curve) and residential areas (golden solid curve). Panel C: The COVID-19 incidence curve in Colombia by the dates of symptoms onset as of October 31, 2021.
Fig 14.
The daily number of tweets indicating stay at home orders (blue) and the daily number of new COVID-19 cases based on the dates of symptom onset (orange) as of October 31, 2021.