Genome Sequences and Sequence Data of African Swine Fever virus from the Dominican Republic 2021

Diagnostic samples from swine were provided to the USDA Foreign Animal Disease Diagnostic Laboratory (FADDL) for testing originating from the Dominican Republic. Initial tests indicated the presence of African Swine Fever virus, which was subsequently submitted for whole genome sequencing for confirmation and characterization. Samples were provided as blood and tissue obtained from affected swine in May through early August 2021. Samples were sequenced on the Oxford Nanopore PromethION and the Illumina MiSeq platforms. The best reference from the NCBI RefSeq database was determined by aligning reads against all references and selecting the reference genome with the closest identity and breadth of coverage. The closest reference genome by identity was Georgia 2007/1 (NC_044959.2). Reference-guided alignment was performed using BWA-MEM (0.7.17-r1188) for Illumina data and Minimap2 (version 2.21-r1071) for Oxford Nanopore data. Variant calling against the Georgia 2007/1 reference was performed using Freebayes (version 1.3.4) against the population of samples. Variants were filtered based on quality score, depth, and log-odds ratio to remove low-confidence variants. This produced a sample set with 21 total variant sites, all of which were single nucleotide polymorphisms. These variants were applied to the Georgia 2007/1 genome to produce the final consensuses. Annotations were transferred from the Georgia 2007/1 genome, and changes in gene coding sequences were modified accordingly. The BioSamples in this BioProject include raw data files and genome consensus sequences against Georgia 2007/1 based on reference-guided assembly. These genomes have not been finished and may contain additional structural variations that were not detected by the sequencing performed here.

自多米尼加共和国提供的猪只诊断样本被提交至美国农业部外国动物疾病诊断实验室（FADDL）进行检测。初步检测结果显示非洲猪瘟病毒的存在，随后进行了全基因组测序以确认和鉴定。样本包括2021年5月至8月初从受影响的猪只中采集的血液和组织。样本在牛津纳米孔PromethION和Illumina MiSeq平台上进行测序。通过将测序读段与所有参考基因组进行比对，并选取与参考基因组同源性最高且覆盖范围最广的基因组作为最佳参考，从而确定了NCBI RefSeq数据库中的最佳参考。通过同源性比对，最接近的参考基因组为Georgia 2007/1（NC_044959.2）。针对Illumina数据，使用BWA-MEM（版本0.7.17-r1188）和针对牛津纳米孔数据使用Minimap2（版本2.21-r1071）进行了参考指导的比对。利用Freebayes（版本1.3.4）针对样本群体进行了基于Georgia 2007/1参考基因组的变异检测。根据质量分数、深度和对数优势比对变异进行了过滤，以去除低置信度的变异。这产生了包含21个总变异位点的样本集，所有这些位点均为单核苷酸多态性。这些变异被应用于Georgia 2007/1基因组，以生成最终的共识序列。基因编码序列的变化根据Georgia 2007/1基因组的注释进行了相应的调整。该BioProject中的BioSamples包括原始数据文件和基于参考指导组装的针对Georgia 2007/1基因组的基因组共识序列。这些基因组尚未完成组装，可能包含未被此处测序检测到的额外结构变异。