Omicron and S‐gene target failure cases in the highest COVID‐19 case rate region in Canada—December 2021

Abstract

As the newly detected SARS-CoV-2 B.1.1.529 variant (Omicron) rapidly spreads worldwide, the Kingston, Frontenac, Lennox & Addington (KFL&A) region has had record-setting COVID-19 case numbers, with 1574 active cases as of December 21, 2021—a higher case rate than any other region in Canada (Figure 1). The Omicron variant was classified as a variant of concern by the World Health Organization on November 26, 2021.1 One of its 50+ mutations reduces PCR amplification of the S gene, allowing for S gene target failure (SGTF) to be used as an Omicron marker while awaiting sequencing.2 The rate of detection of Omicron has been faster than other strains in previous pandemic waves, suggesting Omicron may have the ability for faster growth.3 From December 3, the detection of the first case of Omicron in the KFL&A region, until December 21, 2021, there have been 1063 Omicron cases that were either confirmed or suspected.1 A total of 59% of these cases were 18–24 years old while 27% were 25–39 years old. This has corresponded with the main outbreak environments being in Postsecondary education (N = 64) and food and beverage settings (N = 106), with considerable overlap between these settings. There have only been three cases in the 70+ age group and no hospitalizations. There have been no deaths to-date in KFL&A due to Omicron. Initial modeling estimates have placed the Re for Omicron in KFL&A at 1.5 (90% credible interval: 0.78–2.34; modeling estimates conducted with R and the EpiNow2 package). In confirmed and suspect Omicron cases, 9.6% were asymptomatic. For symptomatic cases, the most common symptoms reported were nasal congestion (73%), cough (65%), headaches (54%), sore throat (48%). Of note, only 10% reported shortness of breath. Frequencies of symptom combinations between any two symptoms are displayed in Figure 2. Outside of 45 individuals not yet old enough to be double-vaccinated, 31 cases were unvaccinated, 19 cases were partially vaccinated,2 and 64 cases had unknown vaccination status. The remainder of cases were at least double-vaccinated.3 There was a median of 22 weeks between second dose and symptom onset. There were also 13 Omicron cases in individuals with a third dose: four received their booster 32–35 days before onset, two received theirs 15 days before onset, and seven cases received their booster <14 days before onset. There have been 12 confirmed reinfections with Omicron; all were symptomatic and double-vaccinated.4 These cases had a mix between suspect wild-type, alpha, and delta variants at first infection. Given the rapid propagation of the Omicron variant as well as the incidence of immune escape in double-vaccinated individuals, everyone must continue to remain cautious and vigilant in a time of rapid case surge. This includes physical distancing, limiting nonessential travel and gatherings, proper respiratory and hand hygiene, robust personal protective equipment, and adhering to testing and isolation requirements based on symptoms. Getting a booster vaccine, as able, may be an effective way to prevent breakthrough infections. Postsecondary education institutions and food and beverage settings remain high-risk transmission environments most likely due to reduced physical distancing and higher frequency of unmasking behavior. Strong collaboration and communication between public officials and citizens are needed to ensure a unified approach to mitigating community spread. All the persons and organizations affected by the COVID-19 pandemic; staff at KFL&A Public Health, including the investigators, nurses, case and contact management team, and assessment center personnel; staff at the Kingston Health Sciences Centre and the local Public Health Ontario Laboratory. This study received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors. The authors received no financial support for the research, authorship, and/or publication of this article. The authors declare there are no conflict of interests. The authors alone are responsible for the content and writing of the article. The authors confirm that the data supporting the findings of this study are available within the article. Derived data supporting the findings of this study are available from the corresponding author [THG] on request The authors confirm that the data supporting the findings of this study are available within the article. Derived data supporting the findings of this study are available from the corresponding author [THG] on request

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