SARS-CoV-2 Transmission in Alberta, British Columbia, and Ontario, Canada, December 25, 2019, to December 1, 2020
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Abstract
Objective:
This study aimed to investigate coronavirus disease (COVID-19) epidemiology in Alberta, British Columbia, and Ontario, Canada.
Methods:
Using data through December 1, 2020, we estimated time-varying reproduction number, R t , using EpiEstim package in R, and calculated incidence rate ratios (IRR) across the 3 provinces.
Results:
In Ontario, 76% (92 745/121 745) of cases were in Toronto, Peel, York, Ottawa, and Durham; in Alberta, 82% (49 878/61 169) in Calgary and Edmonton; in British Columbia, 90% (31 142/34 699) in Fraser and Vancouver Coastal. Across 3 provinces, R t dropped to ≤ 1 after April. In Ontario, R t would remain < 1 in April if congregate-setting-associated cases were excluded. Over summer, R t maintained < 1 in Ontario, ~1 in British Columbia, and ~1 in Alberta, except early July when R t was > 1. In all 3 provinces, R t was > 1, reflecting surges in case count from September through November. Compared with British Columbia (684.2 cases per 100 000), Alberta (IRR = 2.0; 1399.3 cases per 100 000) and Ontario (IRR = 1.2; 835.8 cases per 100 000) had a higher cumulative case count per 100 000 population.
Conclusions:
Alberta and Ontario had a higher incidence rate than British Columbia, but R t trajectories were similar across all 3 provinces.
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SciScore for 10.1101/2020.07.18.20156992: (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 Software version: Data management and analysis (except for maps) was performed using Microsoft Excel and R version 3.6.2 (R Core Team, Vienna, Austria) Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)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:44-46 Our study has several limitations. First, our Rt estimation for Alberta and British Columbia relied on data …
SciScore for 10.1101/2020.07.18.20156992: (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 Software version: Data management and analysis (except for maps) was performed using Microsoft Excel and R version 3.6.2 (R Core Team, Vienna, Austria) Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)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:44-46 Our study has several limitations. First, our Rt estimation for Alberta and British Columbia relied on data by reporting date and not date of onset, as the latter was unavailable to us. Only Ontario provided the accurate episode date. Future research can study the epidemic data by date of onset when it is available to researchers to better estimate Rt. Second, the number of reported cases per day in the Alberta and British Columbia datasets would be influenced by the testing rate, since limited testing capacity could lead to underdiagnosis. We did not attempt to do a nationwide analysis for Canada because the testing criteria has not been consistent across Canadian provinces. Third, our estimates are contingent that the testing ratio does not change significantly over the study period. However, provincial governments might have been ramping out testing capacity during the early epidemic phase in their jurisdiction. Fourth, reporting delays are known to vary over time and could influence the observed trajectory of the epidemics by date of report in Alberta and British Columbia. For Ontario, our results showed that the delay to testing has been reduced over time and Ontario achieved testing on the same or next date since symptom onset in June. It is possible that similar improvement in reduction in testing delay may have happened in Alberta and British Columbia, but we do not have such data. Fifth, improvement in testing over time could potentially reduce generation time ...
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.
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