The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has become widespread across the world in a flashing manner. As of December 7, 2021, a total of 758 Omicron cases were confirmed in Denmark. Using the nucleotide sequences of the Delta and Omicron variants registered from Denmark in the GISAID database, we found that the effective (instantaneous) reproduction number of Omicron is 3.19 (95% confidence interval [CI]: 2.82–3.61) times greater than that of Delta under the same epidemiological conditions. The proportion of Omicron infections among all SARS‐CoV‐2 infections in Denmark was expected to exceed 95% on December 28, 2021, with a 95% CI from December 25 to December 31, 2021. Given that the Delta variant or variants less transmissible than Delta are dominant in most countries, the rapid increase in Omicron in the virus population may be observed as soon as the Omicron is introduced. Preparing proactive control measures is vital, assuming the substantial advantage of the transmission by Omicron.

The world identified the rapidly increasing incidence of the causative variant of SARS-CoV-2 Pangolin B [...]

Using numbers of SARS-CoV-2 variants detected in Japan as at 13 June 2021, relative instantaneous reproduction numbers (RRI) of the R.1, Alpha, and Delta variants with respect to other strains circulating in Japan were estimated at 1.25, 1.44, and 1.95. Depending on the assumed serial interval distributions, RRI varies from 1.20–1.32 for R.1, 1.34–1.58 for Alpha, and 1.70–2.30 for Delta. The frequency of Delta is expected to take over Alpha in Japan before 23 July 2021.

<abstract> <p>The Omicron variant spreads fastest as ever among the severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) we had so far. The BA.1 and BA.2 sublineages of Omicron are circulating worldwide and it is urgent to evaluate the transmission advantages of these sublineages. Using a mathematical model describing trajectories of variant frequencies that assumes a constant ratio in mean generation times and a constant ratio in effective reproduction numbers among variants, trajectories of variant frequencies in Denmark from November 22, 2021 to February 26, 2022 were analyzed. We found that the mean generation time of Omicron BA.1 is 0.44–0.46 times that of Delta and the effective reproduction number of Omicron BA.1 is 1.88–2.19 times larger than Delta under the epidemiological conditions at the time. We also found that the mean generation time of Omicron BA.2 is 0.76–0.80 times that of BA.1 and the effective reproduction number of Omicron BA.2 is 1.25–1.27 times larger than Omicron BA.1. These estimates on the ratio of mean generation times and the ratio of effective reproduction numbers have epidemiologically important implications. The contact tracing for Omicron BA.2 infections must be done more quickly than that for BA.1 to stop further infections by quarantine. In the Danish population, the control measures against Omicron BA.2 need to reduce 20–21% of additional contacts compared to that against BA.1.</p> </abstract>

The B.1.1.7 strain, a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is thought to have higher transmissibility than previously circulating strains in England. The fraction of the B.1.1.7 strain among SARS-CoV-2 viruses in England have grown rapidly. In this paper, we propose a method to estimate the selective advantage of a mutant strain over previously circulating strains using the time course of the fraction of B.1.1.7 strains. Based on Wallinga-Teunis's method to estimate the instantaneous reproduction numbers, our method allows the reproduction number to change during the target period of analysis. Our approach is also based on the Maynard Smith's model of allele frequencies in adaptive evolution, which assumes that the selective advantage of a mutant strain over previously circulating strains is constant over time. Applying this method to the sequence data in England using serial intervals of COVID-19, we found that the transmissibility of the B.1.1.7 strain is 40% (with a 95% confidence interval (CI) from 40% to 41%) higher than previously circulating strains in England. The date of the emergence of B.1.1.7 strains in England was estimated to be September 20, 2020 with its 95% CI from September 11 to September 20, 2020. The result indicated that the control measure against the B.1.1.7 strain needs to be strengthened by 40% from that against previously circulating strains. To get the same control effect, contact rates between individuals need to be restricted to 0.71 of the contact rates that have been achieved form the control measure taken for previously circulating strains.