Modeling the Transmission of the SARS-CoV-2 Delta Variant in a Partially Vaccinated Population
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Abstract
In a population with ongoing vaccination, the trajectory of a pandemic is determined by how the virus spreads in unvaccinated and vaccinated individuals that exhibit distinct transmission dynamics based on different levels of natural and vaccine-induced immunity. We developed a mathematical model that considers both subpopulations and immunity parameters, including vaccination rates, vaccine effectiveness, and a gradual loss of protection. The model forecasted the spread of the SARS-CoV-2 delta variant in the US under varied transmission and vaccination rates. We further obtained the control reproduction number and conducted sensitivity analyses to determine how each parameter may affect virus transmission. Although our model has several limitations, the number of infected individuals was shown to be a magnitude greater (~10×) in the unvaccinated subpopulation compared to the vaccinated subpopulation. Our results show that a combination of strengthening vaccine-induced immunity and preventative behavioral measures like face mask-wearing and contact tracing will likely be required to deaccelerate the spread of infectious SARS-CoV-2 variants.
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SciScore for 10.1101/2021.09.23.21264032: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our model has several limitations, some of which are addressed in other mathematical models developed during this pandemic. First, our model does not consider the population heterogeneity, which has been shown to reduce the required number of vaccinated individuals to achieve herd immunity (7). Second, we do not consider seasonality (6), although the seasonal …
SciScore for 10.1101/2021.09.23.21264032: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our model has several limitations, some of which are addressed in other mathematical models developed during this pandemic. First, our model does not consider the population heterogeneity, which has been shown to reduce the required number of vaccinated individuals to achieve herd immunity (7). Second, we do not consider seasonality (6), although the seasonal trend for SARS-CoV-2 is still unclear at this point. Third, SARS-CoV-2 infections that are not reported were not included in the model and may vary based on ascertainment rates (17). Lastly, we focused the application on modeling the currently dominant delta variant in the US as of September 2021. While the analyses herein utilized the immunity parameters for the BNT162b2 vaccine and the delta variant, our model can be applied to model other vaccines and emerging virus strains in different populations. Overall, our results demonstrated that the trajectory of a pandemic is heavily influenced by natural and vaccine-induced immunity given a dominant virus strain’s level of infectiousness and response to vaccines. As variants of SARS-CoV-2 have emerged (18), VOCs capable of higher transmission rates and immune evasion may continue to arise (19-21). Tempering the spread of SARS-CoV-2 variants will require enhanced global efforts on sequencing and variant detection, establishing reproducible analysis pipelines, and rapid sharing of data across geographical boundaries (22). Given that asymptomatic but infected virus carriers ca...
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.
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