Salman Muhammad, Venkateswaran Dhithya, Prakash Anwesha, Nguyen Quynh Anh, Suntisukwattana Roypim, Atthaapa Waranya, Tantituvanont Angkana, Songkasupa Tapanut, Deemagarn Taweewat, Bhakha Kultyarat, Pengpetch Nuttun, Saenboonrueng Janya, Thaweerattanasinp Theeradej, Jongkaewwattana Anan, Nilubol Dachrit
Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand.
Department of Pharmaceutic and Industrial Pharmacies, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
Animals (Basel). 2024 Sep 6;14(17):2602. doi: 10.3390/ani14172602.
African swine fever virus (ASFV) has been responsible for the globally devastating epidemics in wild and domesticated pigs. Of the 24 identified ASFV genotypes, genotype II is the primary cause for the pandemic occurring in Europe and Asia since its emergence in Georgia in 2007. The current study aimed to characterize the full-length genomic pattern of the ASFV strain from Thailand, TH1_22/CR (Accession No. PP915735), which was then compared with genomic diversity across other Asian isolates using Georgia 2007/1 (Accession No. FR682468) as the reference. Viral DNA was isolated from the pig spleen sample following library preparation and paired-end sequencing using the MiSeq Illumina platform. The sequenced TH1_22/CR isolate spanned 189,395 nucleotides encoding 193 open reading frames (ORFs), exhibiting maximum nucleotide similarity (99.99%) with Georgian (Georgia 2007/1) and Chinese (Wuhan 2019-1 and China HLJ) isolates. Based on phylogenetic analysis, the TH1_22/CR isolate (Accession No. PP915735) was characterized as genotype II, serogroup 8, and IGR-II due to the presence of three tandem repeat sequences (TRSs). Genetic variations including SNPs and single and polynucleotide indels were identified in TH1_22/CR in agreement with other Asian isolates. For comprehensive analysis, the genome was divided into four regions (I-IV) based on gene location. Overall, the TH1_22/CR isolate demonstrated eight SNPs and indels in its genome. Two unique SNPs were reported in the coding regions of the TH1_22/CR isolate, out of which, a C-591-T substitution was seen in MGF 360-4L and a C-297-T was found in A238L, and four unique SNPs were reported in non-coding regions (NCRs). Furthermore, a 29 bp deletion was observed in the IGR between MGF 110-13La and MGF 110-13Lb, as well as 52 bp deletion in the ASFV G ACD 00350 gene. This comparative analysis establishes the foundational information for future studies on the diversity and phylogeography of this regionally significant genetic sub-group of ASFV.
非洲猪瘟病毒（ASFV）已导致全球范围内野猪和家猪的毁灭性疫情。在已确定的24种ASFV基因型中，II型基因型是自2007年在格鲁吉亚出现以来在欧洲和亚洲发生大流行的主要原因。本研究旨在对来自泰国的ASFV毒株TH1_22/CR（登录号PP915735）的全长基因组模式进行表征，然后以格鲁吉亚2007/1（登录号FR682468）为参考，与其他亚洲分离株的基因组多样性进行比较。使用Illumina MiSeq平台进行文库制备和双端测序后，从猪脾脏样本中分离出病毒DNA。测序的TH1_22/CR分离株跨度为189,395个核苷酸，编码193个开放阅读框（ORF），与格鲁吉亚（格鲁吉亚2007/1）和中国（武汉2019 - 1和中国HLJ）分离株表现出最大核苷酸相似性（99.99%）。基于系统发育分析，由于存在三个串联重复序列（TRS），TH1_22/CR分离株（登录号PP915735）被鉴定为II型基因型、血清群8和IGR - II。在TH1_22/CR中鉴定出包括单核苷酸多态性（SNP）以及单核苷酸和多核苷酸插入缺失在内的遗传变异，这与其他亚洲分离株一致。为了进行全面分析，根据基因位置将基因组分为四个区域（I - IV）。总体而言，TH1_22/CR分离株在其基因组中显示出8个SNP和插入缺失。在TH1_22/CR分离株的编码区报告了两个独特的SNP，其中在MGF 360 - 4L中观察到C - 591 - T替换，在A238L中发现C - 297 - T，在非编码区（NCR）报告了4个独特的SNP。此外，在MGF 110 - 13La和MGF 110 - 13Lb之间的间隔区（IGR）观察到29 bp的缺失，以及在ASFV G ACD 00350基因中观察到52 bp的缺失。这种比较分析为该地区重要的ASFV遗传亚群的多样性和系统地理学的未来研究奠定了基础信息。
