Rapid Impact Analysis of B 1.1.7 Variant on the Spread of SARS-CoV-2 in North Carolina
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Abstract
Background
Several cases of the B1.1.7 variant of the SARS-CoV-2 virus were identified in North Carolina first on January 23, 2021 in Mecklenburg County and later in Guilford County on January 28, 2021. [1,2] This variant has been associated with higher levels of transmissibility. [3–6] This study examines the potential impact of increased transmissibility as the B1.1.7 variant becomes more predominant given current vaccine distribution plans and existing non-pharmaceutical interventions (NPIs).
Method
We explored the anticipated impact on the effective reproduction number for North Carolina and Guilford County given the date of import of B1.1.7. The approximate growth rate in proportion of B1.1.7 observed in the United Kingdom was fit and used to establish the estimate share of B1.1.7 circulating in North Carolina. Using the nowcasted reproduction numbers, a stochastic discrete compartmental model was fit with the current vaccination rates and B1.1.7 transmissibility to estimate the impact on the effective reproduction number.
Results
We found that the effective reproduction number for North Carolina and Guilford County may exceed one, indicating a return to accelerating spread of infection in April as the proportion of B1.1.7 increases. The effective reproduction number will likely decrease into March, then increase as the proportion of B1.1.7 increases in circulation in the population.
Conclusions
Existing non-pharmaceutical interventions will need to remain in effect through the spring. Given the current vaccination rate and these interventions, it is likely that there will be an increase in SARS-CoV-2 infections. The impact of the variant will likely be heterogeneous across North Carolina given the reproduction number and volume of susceptible persons in each county at the time of introduction of the variant. Age-based vaccinations will likely reduce the overall impact on hospitalizations. This analysis underlines the need for population level genetic surveillance to confirm the proportion of variants circulating.
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SciScore for 10.1101/2021.02.07.21251291: (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 NHS England region was used as a group level intercept, fit using the RStanArm R package[10]. RStanArmsuggested: NoneThe models were fit using the Odin R package[11] and each simulation was run 100 times. Odinsuggested: (ODIN, RRID:SCR_001386)These scenarios included the 10%, 50%, and 90% quantile estimates for the effective reproduction number on the incubation time adjusted import date of B1.1.7 estimated using the EpiNow2 package.[ EpiNow2suggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the …SciScore for 10.1101/2021.02.07.21251291: (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 NHS England region was used as a group level intercept, fit using the RStanArm R package[10]. RStanArmsuggested: NoneThe models were fit using the Odin R package[11] and each simulation was run 100 times. Odinsuggested: (ODIN, RRID:SCR_001386)These scenarios included the 10%, 50%, and 90% quantile estimates for the effective reproduction number on the incubation time adjusted import date of B1.1.7 estimated using the EpiNow2 package.[ EpiNow2suggested: NoneResults from OddPub: Thank you for sharing your code and data.
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 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 scite Reference Check: We found no unreliable references.
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