Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany
Abstract
:1. Introduction
2. Materials and Methods
2.1. Definitions—Outbreaks, Cases, Clusters, and Hotspots
2.2. Sample Selection and RNA Extraction
2.3. IAV-End-RT-PCR
2.4. Next-Generation Sequencing and Consensus Generation
2.5. Phylogenetic and Phylogeographic Analysis
3. Results
3.1. Background Information
3.2. Direct Wild Bird Introductions and Spread—H5N8 Ger-11-16 and Ger-12-16.1
3.2.1. H5N8 Ger-11-16
Epidemiological Data
Phylogenetic Analysis of Ger-11-16
Wild Bird-Mediated Transmissions of Ger-11-16
Farm-to-Farm Transmissions within Ger-11-16
Circulation Period of Ger-11-16
3.2.2. H5N8 Ger-12-16.1
Epidemiological Data, Genetic Distinction, and Phylogenetic Analysis
3.3. Cluster I and II: Cluster Development and Modification by Genetic Drift—H5N8 Ger-10-16.2
3.3.1. Cluster I—“Brandenburg (BB)”
3.3.2. Cluster II—“Cloppenburg/Oldenburg (CLOL)”
3.4. Cluster III: Genetic Modification by Reassortment in Poultry Holdings—H5N5 Ger-12-16-N5.1 and Ger-12-16-N5.2
3.4.1. Epidemiological Data
3.4.2. Genetic Modification by Reassortment
3.5. Cluster IV, V, and VI: Cluster Development and Distant Spread—H5N8 Ger-10-20-N8
Epidemiological Data and Time-Scaled Phylogeny Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Reassortant | Subtype | First Date | Last Date | Total | Poultry | Wild |
---|---|---|---|---|---|---|
Ger-11-16-N8 | H5N8 | 7 November 2016 | 22 August 2017 | 34 | 25 | 9 |
Ger-12-16-N8.1 | H5N8 | 1 January 2017 | 24 February 2017 | 8 | 2 | 6 |
Ger-12-16-N8.2 | H5N8 | 13 December 2016 | 9 May 2017 | 71 | 61 | 10 |
Ger-12-16-N5.1 | H5N5 | 13 December 2016 | 23 January 2017 | 7 | 2 | 5 |
Ger-12-16-N5.2 | H5N5 | 22 January 2017 | 9 March 2017 | 22 | 15 | 7 |
Ger-10-20-N8 | H5N8 | 26 October 2020 | 20 July 2021 | 161 | 122 | 39 |
Ger-02-21-N8 | H5N8 | 26 February 2021 | 10 March 2021 | 3 | 3 | 0 |
Ger-03-21-N8 | H5N8 | 2 March 2021 | 2 March 2021 | 1 | 1 | 0 |
Ger-10-20-N5 | H5N5 | 26 October 2020 | 9 November 2020 | 2 | 1 | 1 |
Ger-12-20-N3 | H5N3 | 14 December 2020 | 26 January 2021 | 5 | 0 | 5 |
Ger-02-21-N4 | H5N4 | 17 February 2021 | 17 February 2021 | 2 | 0 | 2 |
Ger-02-21-N1 | H5N1 | 17 February 2021 | 17 July 2021 | 9 | 4 | 5 |
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King, J.; Staubach, C.; Lüder, C.; Koethe, S.; Günther, A.; Stacker, L.; Rubbenstroth, D.; Dietze, K.; Grund, C.; Conraths, F.J.; et al. Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany. Viruses 2022, 14, 1849. https://doi.org/10.3390/v14091849
King J, Staubach C, Lüder C, Koethe S, Günther A, Stacker L, Rubbenstroth D, Dietze K, Grund C, Conraths FJ, et al. Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany. Viruses. 2022; 14(9):1849. https://doi.org/10.3390/v14091849
Chicago/Turabian StyleKing, Jacqueline, Christoph Staubach, Christiane Lüder, Susanne Koethe, Anne Günther, Lina Stacker, Dennis Rubbenstroth, Klaas Dietze, Christian Grund, Franz J. Conraths, and et al. 2022. "Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany" Viruses 14, no. 9: 1849. https://doi.org/10.3390/v14091849