Table 1 List of analysed samples from domestic pig outbreaks and genetically related wild Boar cases. Sequencing strategies are specified in the corresponding materials and methods section.
ASFV domestic pig outbreaks in Germany | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Outbreak farm | Location | Animal sample | Lib-no. | Sample matrix | Sequencing strategy | Mean coverage [reads/site]* | Reads ASFV* | Genome length [bp] | Comments | Accession |
1, 2 | Brandenburg | 2021ASP03384 | lib05117 | EDTA blood | Illumina | 202 | 260.256 | 190.517 | Complete genome published in previous study20 | OX376265 |
3 | Brandenburg | 2021ASP03286 | lib05058 + lib05059 | Blood swap | Enrichment + Illumina / Amplicon Sanger sequencing | - | 524 (Illumina) 3 (Sanger) | n.d. | Only partial sequences available (Sanger) | |
4 | Mecklenburg-Western Pomerania | 2021ASP05548 | lib05327 | Organ pool | Enrichment + Illumina | 222 | 282.069 | 190.591 | Low coverage of EP402R gene | OZ335133 |
5 | Baden-Wuerttemberg | 2022ASP01802 | lib05910 | EDTA blood | Illumina | 213 | 280.531 | 190.598 | No German genetic markers identified | OZ335129 |
6 | Lower Saxony | 2022ASP01931 | lib05777 | EDTA blood | Illumina | 244 | 313.365 | 190.609 | OZ335128 | |
7 | Brandenburg | 2022ASP01938 | lib05778 | Lung tissue | Illumina | 53 | 68.560 | 190.602 | OZ335136 | |
8 | Brandenburg | 2023ASP00680 2023ASP00683 | lib06111-12 + lib06119-22 | Lung + spleen tissue | Enrichment + Illumina | 28 | 36.451 | 190.571 | OZ335137 | |
9 | Mecklenburg-Western Pomerania | 2024ASP01428 | lib06609 (Nanopore) lib06605 (Illumina) | Spleen tissue | Nanopore + Illumina | 9 (Nanopore) 423 (Illumina) | 2.239 (Nanopore) 541.829 (Illumina) | 190.621 | OZ335132 | |
ASFV wild boar cases genetically related to outbreaks in domestic pigs | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Related outbreak farms | Location | Animal sample | Lib-No. | Sample matrix | Sequencing strategy | Mean coverage [reads/site]* | Reads ASFV* | Genome length [bp] | Loci of shared characteristic mutations | |
6, 7, 9 | Brandenburg | 2022ASP01516 | lib05907 | EDTA blood | Illumina | 20 | 25.402 | 190.591 | MGF 505-6R | OZ335138 |
8 | Brandenburg | 2022ASP03250 | lib05995 | EDTA blood | Illumina | 48 | 63.186 | 190.597 | MGF 505-2R, EP424R, M448R, I267L | OZ335135 |
8 | Brandenburg | 2022ASP03254 | lib05996 | EDTA blood | Illumina | 18 | 22.824 | 190.569 | MGF 505-2R, EP424R, M448R, I267L | OZ335134 |
8 | Brandenburg | 2022ASP03260 | Lib05997 | EDTA blood | Illumina | 160 | 211.707 | 190.593 | MGF 505-2R, EP424R, M448R, I267L, MGF 360-21R | OZ335130 |
6, 7, 9 | Brandenburg | 2024ASP06001 | lib06964 (Nanopore) lib07083 (Illumina) | Tonsil | Nanopore + Illumina | 4 (Nanopore) 75 (Illumina) | 1.202 (Nanopore) 96.119 (Illumina) | 190.574 | MGF 505-6R | OZ335131 |
