Modelling quarantine effects on SARS-CoV-2 epidemiological dynamics in Chilean communes and their relationship with the Social Priority Index
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Abstract
An epidemiological model (susceptible, un-quarantined infected, quarantined infected, confirmed infected (SUQC)) was previously developed and applied to incorporate quarantine measures and calculate COVID-19 contagion dynamics and pandemic control in some Chinese regions. Here, we generalized this model to incorporate the disease recovery rate and applied our model to records of the total number of confirmed cases of people infected with the SARS-CoV-2 virus in some Chilean communes.
Methods
In each commune, two consecutive stages were considered: a stage without quarantine and an immediately subsequent quarantine stage imposed by the Ministry of Health. To adjust the model, typical epidemiological parameters were determined, such as the confirmation rate and the quarantine rate. The latter allowed us to calculate the reproduction number.
Results
The mathematical model adequately reproduced the data, indicating a higher quarantine rate when quarantine was imposed by the health authority, with a corresponding decrease in the reproduction number of the virus down to values that prevent or decrease its exponential spread. In general, during this second stage, the communes with the lowest social priority indices had the highest quarantine rates, and therefore, the lowest effective viral reproduction numbers. This study provides useful evidence to address the health inequity of pandemics. The mathematical model applied here can be used in other regions or easily modified for other cases of infectious disease control by quarantine.
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SciScore for 10.1101/2022.01.21.22269658: (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 The fitting parameters β, γ, Ut=0, and Qt=0 were calculated by minimizing the error function err, which is equal to the mean squared deviation between the empirical and theoretical time series data:In fitting the parameters, to minimize err (Eq. 11), we alternatively used the MATLAB function fminsearch or fmincon [14] to optimize the fit of the model. 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: …SciScore for 10.1101/2022.01.21.22269658: (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 The fitting parameters β, γ, Ut=0, and Qt=0 were calculated by minimizing the error function err, which is equal to the mean squared deviation between the empirical and theoretical time series data:In fitting the parameters, to minimize err (Eq. 11), we alternatively used the MATLAB function fminsearch or fmincon [14] to optimize the fit of the model. 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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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