An investigation of spatial-temporal patterns and predictions of the coronavirus 2019 pandemic in Colombia, 2020–2021
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 5,002,387 cases and 127,258 deaths as of October 31, 2021. The aggressive transmission dynamics of SARS-CoV-2 motivate an investigation of COVID-19 at the national and regional levels in Colombia. We utilize the case incidence and mortality data to estimate the transmission potential and generate short-term forecasts of the COVID-19 pandemic to inform the public health policies using previously validated mathematical models. The analysis is augmented by the examination of geographic heterogeneity of COVID-19 at the departmental level along with the investigation of mobility and social media trends. Overall, the national and regional reproduction numbers show sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Whereas the most recent estimates of reproduction number indicate disease containment, with R t <1.0 as of October 31, 2021. On the forecasting front, the sub-epidemic model performs best at capturing the 30-day ahead COVID-19 trajectory compared to the Richards and generalized logistic growth model. Nevertheless, the spatial variability in the incidence rate patterns across different departments can be grouped into four distinct clusters. As the case incidence surged in July 2020, an increase in mobility patterns was also observed. On the contrary, a spike in the number of tweets indicating the stay-at-home orders was observed in November 2020 when the case incidence had already plateaued, indicating the pandemic fatigue in the country.
Article activity feed
-
-
SciScore for 10.1101/2021.07.28.21261212: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources These sequences were aligned to the reference genome obtained from the literature [73] using Muscle [74] and trimmed using Mega 7 (Molecular Evolutionary Genetics Analysis version: 7) [75]. Musclesuggested: (MUSCLE, RRID:SCR_011812)Phylodynamics analysis of that cluster was carried out using BEAST version 2 (Bayesian Evolutionary Analysis by sampling trees) [76]. BEASTsuggested: (BEAST, RRID:SCR_010228)For any two rate curves, hi and hj, we compute the norm ||hi −hj||, where the double bars denote the L2 norm of the difference function, that is, To perform clustering of thirty six curves …
SciScore for 10.1101/2021.07.28.21261212: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources These sequences were aligned to the reference genome obtained from the literature [73] using Muscle [74] and trimmed using Mega 7 (Molecular Evolutionary Genetics Analysis version: 7) [75]. Musclesuggested: (MUSCLE, RRID:SCR_011812)Phylodynamics analysis of that cluster was carried out using BEAST version 2 (Bayesian Evolutionary Analysis by sampling trees) [76]. BEASTsuggested: (BEAST, RRID:SCR_010228)For any two rate curves, hi and hj, we compute the norm ||hi −hj||, where the double bars denote the L2 norm of the difference function, that is, To perform clustering of thirty six curves into smaller groups, we apply the dendrogram function in MATLAB using the “ward” linkage as explained in reference [79].
MATLABsuggested: (MATLAB, RRID:SCR_001622)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has some limitations. First, we excluded the last 30-day case counts from our study in order compare the performance of our models in the forecasting phase. Moreover, excluding the last 30 data points allows us to overcome the influence of reporting delays on our analysis. Specifically, we utilize the case counts based on the dates of onset in this study, because delays in case reporting, testing rates and factors related to the surveillance systems can influence our epidemic projections. Secondly, we relied on the daily updates of cases in the official surveillance system of Colombia, which can sometimes underreport the cases. Third, the phenomenological models applied in this study do not explicitly account for behavioral changes, and thus the results such as the predicted decline or stability in the epidemic trajectory should be interpreted with caution. Fourth, some authors [83] shifted the dates of symptom onset backwards to approximate the date of infection when applying the EpiEstim package to estimate the instantaneous reproduction number. However, in this study we stick to the date of symptoms onset for the sake of comparison across methods to estimate the reproduction number. Lastly, the unpredictable social component of the epidemic on ground was also a limiting factor for the study as we did not know the ground truth epidemic pattern when the forecasts were generated. In conclusion, the country observed a surge in case counts as the mobility increased i...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
