# Characterisation of Omicron Variant during COVID-19 Pandemic and the Impact of Vaccination, Transmission Rate, Mortality, and Reinfection in South Africa, Germany, and Brazil

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## Abstract

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## 1. Introduction

## 2. Material and Methods

#### 2.1. Mathematical Model

#### 2.2. Numerical Simulations

#### 2.3. Data Sources

## 3. Results

#### 3.1. Brazil

#### 3.2. South Africa

#### 3.3. Germany

#### 3.4. Estimated Parameters for the Three Different Countries

## 4. Discussion

## 5. Limitations and Future Works

## 6. Conclusions

## Author Contributions

## Funding

## Data Availability Statement

## Conflicts of Interest

## References

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**Figure 1.**Weekly deaths per million people in recent since 9 October 2021 in South Africa, Germany, and Brazil. Each point represents the cumulative number of confirmed deaths over the previous week.

**Figure 2.**Choropleth map of vaccination around the globe by 15 February 2022. It presents the share of people who received all doses prescribed by the initial vaccination protocol, divided by the total population of the country.

**Figure 3.**Percentage of Omicron variant of all analysed sequences. This figure was adapted from the one generated by Our World in Data website.

**Figure 4.**Evolution of the number of active cases (

**upper left**), deaths (

**upper right**), recovered cases (

**lower left**), and confirmed cases (

**lower right**) in Brazil. All simulations with errors below $10\%$ are presented.

**Figure 5.**Evolution of the number of active cases (

**upper left**), deaths (

**upper right**), recovered cases (

**lower left**), and confirmed cases (

**lower right**) in South Africa. All simulations with errors below $10\%$ are presented.

**Figure 6.**Evolution of the number of active cases (

**upper left**), deaths (

**upper right**), recovered cases (

**lower left**), and confirmed cases (

**lower right**) in Germany. All simulations with errors below $10\%$ are presented.

**Figure 7.**Violin plots of the parameters: $b\phantom{\rule{0.166667em}{0ex}}r1$, $r2$, m, $m\phantom{\rule{0.166667em}{0ex}}{r}_{d}$, $ef{f}_{d}$, ${s}_{rate}$ for Brazil, South Africa, and Germany. (

**a**) $b\phantom{\rule{0.166667em}{0ex}}r1$. (

**b**) ${r}_{2}$. (

**c**) m. (

**d**) $m\phantom{\rule{0.166667em}{0ex}}rd$. (

**e**) $ef{f}_{d}$. (

**f**) ${s}_{rate}$.

**Table 1.**Characterisation of the COVID-19 pandemics by the best parameter values by country: b represents the basic infection rate, m, the mortality rate previous to Omicron; ${r}_{1}$, the contact reduction factor; ${t}_{{i}_{1}}$, the start time for intervention policy 1; ${\mathsf{\Delta}}_{1}$, the intervention policy duration; ${r}_{2}$, Omicron transmission rate factor; ${t}_{{i}_{2}}$, the start time for the Omicron variant; ${\mathsf{\Delta}}_{2}$, the transition to Omicron duration; ${\tau}_{1}$, the incubation period; ${\tau}_{2}$, the time from symptoms to death; ${\tau}_{3}$, the time from symptoms to recovery; $\theta $ is the notified cases; $ef{f}_{d}$ is the vaccine efficacy for prevent deaths; ${s}_{rate}$ is the potential of reinfection; $rd$ is the mortality reduction factor during Omicron.

Parameters | Brazil | South Africa | Germany |
---|---|---|---|

b | 0.049745 | 0.083456 | 0.098533 |

m | 0.002223 | 0.001614 | 0.007456 |

${r}_{1}$ | 0.999733 | 0.503252 | 0.279499 |

$t{i}_{1}$ | 37.611357 | 27.571859 | 27.361629 |

${\mathsf{\Delta}}_{1}$ | 43.476986 | 7.465598 | 25.647412 |

${r}_{2}$ | 5.422328 | 7.993557 | 4.961679 |

$t{i}_{2}$ | 139.978414 | 86.668599 | 65.600770 |

${\mathsf{\Delta}}_{2}$ | 21.272066 | 34.562475 | 17.164128 |

${\tau}_{1}$ | 6.305544 | 4.653837 | 11.486396 |

${\tau}_{2}$ | 18.950821 | 33.184733 | 27.741349 |

${\tau}_{3}$ | 11.803360 | 9.761925 | 10.689566 |

$\theta $ | 0.052279 | 0.019445 | 0.241283 |

$ef{f}_{d}$ | 0.702603 | 0.753452 | 0.761646 |

${s}_{rate}$ | 0.133930 | 0.419652 | 0.211434 |

$rd$ | 0.410348 | 0.283680 | 0.278265 |

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**MDPI and ACS Style**

Ribeiro Xavier, C.; Sachetto Oliveira, R.; da Fonseca Vieira, V.; Lobosco, M.; Weber dos Santos, R.
Characterisation of Omicron Variant during COVID-19 Pandemic and the Impact of Vaccination, Transmission Rate, Mortality, and Reinfection in South Africa, Germany, and Brazil. *BioTech* **2022**, *11*, 12.
https://doi.org/10.3390/biotech11020012

**AMA Style**

Ribeiro Xavier C, Sachetto Oliveira R, da Fonseca Vieira V, Lobosco M, Weber dos Santos R.
Characterisation of Omicron Variant during COVID-19 Pandemic and the Impact of Vaccination, Transmission Rate, Mortality, and Reinfection in South Africa, Germany, and Brazil. *BioTech*. 2022; 11(2):12.
https://doi.org/10.3390/biotech11020012

**Chicago/Turabian Style**

Ribeiro Xavier, Carolina, Rafael Sachetto Oliveira, Vinícius da Fonseca Vieira, Marcelo Lobosco, and Rodrigo Weber dos Santos.
2022. "Characterisation of Omicron Variant during COVID-19 Pandemic and the Impact of Vaccination, Transmission Rate, Mortality, and Reinfection in South Africa, Germany, and Brazil" *BioTech* 11, no. 2: 12.
https://doi.org/10.3390/biotech11020012