Assessing the Transmissibility of the New SARS-CoV-2 Variants: From Delta to Omicron

Abstract

Omicron, the latest SARS-CoV-2 Variant of Concern (VOC), first appeared in Africa in November 2021. At present, the question of whether a new VOC will out-compete the currently predominant variant is important for governments seeking to determine if current surveillance strategies and responses are appropriate and reasonable. Based on both virus genomes and daily-confirmed cases, we compare the additive differences in growth rates and reproductive numbers (R0) between VOCs and their predominant variants through a Bayesian framework and phylo-dynamics analysis. Faced with different variants, we evaluate the effects of current policies and vaccinations against VOCs and predominant variants. The model also predicts the date on which a VOC may become dominant based on simulation and real data in the early stage. The results suggest that the overall additive difference in growth rates of B.1.617.2 and predominant variants was 0.44 (95% confidence interval, 95% CI: -0.38, 1.25) in February 2021, and that the VOC had a relatively high R0. The additive difference in the growth rate of BA.1 in the United Kingdom was 6.82 times the difference between Delta and Alpha, and the model successfully predicted the dominating process of Alpha, Delta and Omicron. Current vaccination strategies remain similarly effective against Delta compared to the previous variants. Our model proposes a reliable Bayesian framework to predict the spread trends of VOCs based on early-stage data, and evaluates the effects of public health policies, which may help us better prepare for the upcoming Omicron variant, which is now spreading at an unprecedented speed.

Keywords: AY.4; B.1.617.2; BA.1; Delta variants; Omicron variants; nonpharmaceutical interventions; reproductive number; vaccination.

Figure 1

Number of sequences on GISAID collected from October 2020 to December 2021 globally and in each country.

Figure 2

Proportion of the main Delta variants collected from 22 February 2021 to 31 December 2021, globally and in the United Kingdom.

Figure 3

Additive difference in growth rate of B.1.617.2 compared to the predominant variants in each country: (a) Time-varying trend; and (b) Average difference in growth rate during the period. The dotted line represents the global trend for comparison. The dashed line in (b) indicates that there was no difference between the two variants.

Figure 4

Estimated values of (a) clock rate and (b) reproductive number of B.1.617.2 and its predominant variants in five countries.

Figure 5

Ratio of the reproductive numbers of B.1.617.2 and predominant variants (a) over the indicated period, and (b) time-varying trend for each country. Dotted lines represent the global level.

Figure 6

Estimated origin date (blue) and collection date (red) of the first B.1.617.2 sequence in each country on GISAID with annotated collection date.

Figure 7

Comparison between AY.4 and B.1.617.2 in the UK: (a) Ratio of the average reproductive numbers of AY.4 and B.1.617.2 over the indicated period; (b) time-varying trend of the ratio. The dashed line indicates when there was no advantage (ratio = 1).

Figure 8

Difference of weekly growth rates between VOC and its predominant variant.

Figure 9

Estimated spread trends of Alpha, Delta, and Omicron in the UK using the Bayesian model, based on GISAID data. The black dashed line suggests when each variant will become dominant (proportion > 50%). Predictions were based on data from the early stages of each VOC (proportion < 10%, below the orange dashed line). On this basis, we predicted the trends of these VOCs after they had reached 10% (after the red dot, i.e., above the orange dashed line).