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

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## Abstract

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## 1. Introduction

## 2. Materials and Methods

#### 2.1. Experimental Design

#### 2.2. Estimation of Number of Variants

#### 2.3. NPIs and Vaccination

#### 2.4. Bayesian Model and Phylo-Dynamics Analysis

## 3. Results

#### 3.1. Global Trends and Major Countries

#### 3.2. Relative Transmission Advantage of B.1.617.2 Compared to Predominant Variants

#### 3.3. Relative Transmission Advantage of AY.4 compared to B.1.617.2

#### 3.4. Differences in Growth Rates between Alpha, Delta and Omicron

#### 3.5. Effect of NPIs and Vaccination

#### 3.6. Estimating the Date on which a VOC Becomes Dominant

## 4. Conclusions

## 5. Discussion

## Supplementary Materials

## Author Contributions

## Funding

## Institutional Review Board Statement

## Informed Consent Statement

## Data Availability Statement

## Conflicts of Interest

## References

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**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 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).

n_GISAID ^{1} | n_estimated ^{2} | Name | n_GISAID ^{1} | n_estimated ^{2} | n_estimated ^{2} | Index | |
---|---|---|---|---|---|---|---|

1 Februay 2021 to 17 July 2021 | B.1.617.2 | predominant variant | all | ||||

India | $1.57\times {10}^{4}$ | $1.37\times {10}^{7}$ | B.1.617.1 | $3.89\times {10}^{3}$ | $2.56\times {10}^{7}$ | $2.01\times {10}^{7}$ | 0.0015 |

Indonesia | $9.79\times {10}^{2}$ | $5.55\times {10}^{5}$ | B.1.466.2 | $1.19\times {10}^{3}$ | $5.63\times {10}^{5}$ | $1.56\times {10}^{6}$ | 0.0021 |

Russia | $1.23\times {10}^{3}$ | $8.48\times {10}^{5}$ | B.1.1.523 | $3.69\times {10}^{2}$ | $1.93\times {10}^{5}$ | $1.75\times {10}^{6}$ | 0.0019 |

United Kingdom | $1.20\times {10}^{5}$ | $5.17\times {10}^{5}$ | B.1.1.7 | $1.42\times {10}^{5}$ | $5.77\times {10}^{5}$ | $1.29\times {10}^{6}$ | 0.2462 |

United States | $3.39\times {10}^{4}$ | $6.09\times {10}^{5}$ | B.1.1.7 | $2.04\times {10}^{5}$ | $2.82\times {10}^{6}$ | $5.95\times {10}^{6}$ | 0.0725 |

30 May 2021 to 24 July 2021 | AY.4 | predominant variant | all | ||||

India | $1.57\times {10}^{4}$ | $4.00\times {10}^{5}$ | B.1.617.2 | $3.52\times {10}^{3}$ | $2.47\times {10}^{6}$ | $3.48\times {10}^{6}$ | 0.0014 |

Indonesia | $4.56\times {10}^{2}$ | $4.12\times {10}^{5}$ | B.1.617.2 | $9.00\times {10}^{2}$ | $7.04\times {10}^{5}$ | $1.32\times {10}^{6}$ | 0.0013 |

Russia | $1.70\times {10}^{1}$ | $1.48\times {10}^{4}$ | B.1.617.2 | $8.95\times {10}^{2}$ | $5.99\times {10}^{5}$ | $8.65\times {10}^{5}$ | 0.0015 |

United Kingdom | $5.59\times {10}^{4}$ | $4.85\times {10}^{5}$ | B.1.617.2 | $1.10\times {10}^{5}$ | $7.22\times {10}^{5}$ | $1.20\times {10}^{7}$ | 0.1527 |

United States | $1.36\times {10}^{4}$ | $2.04\times {10}^{5}$ | B.1.617.2 | $3.99\times {10}^{4}$ | $5.10\times {10}^{5}$ | $1.18\times {10}^{6}$ | 0.0782 |

^{1}Number of sequences submitted to GISAID.

^{2}Estimated number of variants based on GISAID and JHU CSSE.

Intervention | Effective Size | 95% CI |
---|---|---|

Covid 19 testing policy | −0.64 | (−1.09, −0.19) |

Covid contact tracing | 0.04 | (−0.3, 0.39) |

Covid vaccination policy | 0.01 | (−0.17, 0.19) |

Debt relief | −0.07 | (−0.28, 0.14) |

Face covering policies | 0.42 | (0.05, 0.78) |

Income support | −0.09 | (−0.48, 0.29) |

International travel | −1.68 | (−2.32, −1.03) |

Public campaigns | 2.24 | (1.07, 3.4) |

Public events | 0.26 | (−0.1, 0.63) |

Public gathering rules | 0.32 | (−0.13, 0.76) |

Public transport | −0.2 | (−0.5, 0.11) |

School closures | 0.05 | (−0.25, 0.35) |

Stay at home | −0.13 | (−0.46, 0.2) |

Workplace closures | −0.32 | (−0.69, 0.05) |

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**MDPI and ACS Style**

Dong, R.; Hu, T.; Zhang, Y.; Li, Y.; Zhou, X.-H.
Assessing the Transmissibility of the New SARS-CoV-2 Variants: From Delta to Omicron. *Vaccines* **2022**, *10*, 496.
https://doi.org/10.3390/vaccines10040496

**AMA Style**

Dong R, Hu T, Zhang Y, Li Y, Zhou X-H.
Assessing the Transmissibility of the New SARS-CoV-2 Variants: From Delta to Omicron. *Vaccines*. 2022; 10(4):496.
https://doi.org/10.3390/vaccines10040496

**Chicago/Turabian Style**

Dong, Rui, Taojun Hu, Yunjun Zhang, Yang Li, and Xiao-Hua Zhou.
2022. "Assessing the Transmissibility of the New SARS-CoV-2 Variants: From Delta to Omicron" *Vaccines* 10, no. 4: 496.
https://doi.org/10.3390/vaccines10040496