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The Comparative Full-Length Genome Characterization of African Swine Fever Virus Detected in Thailand
by
, , , , and
Muhammad Salman
1,
Dhithya Venkateswaran
1,
Anwesha Prakash
1,
Quynh Anh Nguyen
1,
Roypim Suntisukwattana
1,
Waranya Atthaapa
1,
Angkana Tantituvanont
2,
Tapanut Songkasupa
3,
Taweewat Deemagarn
3,
Kultyarat Bhakha
3,
Nuttun Pengpetch
3,
Janya Saenboonrueng
4,
Theeradej Thaweerattanasinp
4,
Anan Jongkaewwattana
4 and
Dachrit Nilubol
1,* 1
Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
2
Department of Pharmaceutic and Industrial Pharmacies, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
3
Department of Livestock Development, National Institute of Animal Health, 50/2 Kasetklang, Phahonyothin 45-15, Chatuchak, Bangkok 10900, Thailand
4
National Center for Genetic Engineering and Biotechnology, Pathum Thani 12120, Thailand
*
Author to whom correspondence should be addressed.
Animals 2024, 14(17), 2602; https://doi.org/10.3390/ani14172602
Submission received: 30 July 2024
/
Revised: 2 September 2024
/
Accepted: 3 September 2024
/
Published: 6 September 2024
(This article belongs to the Topic Animal Diseases in Agricultural Production Systems, 2nd Edition)
Simple Summary
African swine fever is a deadly disease affecting pigs worldwide, causing major economic losses. The virus strain causing the current outbreak in Europe and Asia, known as genotype II, was first identified in Georgia in 2007. This study aimed to analyze the genetic makeup of a strain found in Thailand to better understand its characteristics and how it compares to other strains in Asia. The viral DNA from an infected pig was analyzed and was found to be almost identical to strains from Georgia and China. The Thai strain had eight unique genetic changes, including small mutations in specific genes and deletions in others. This detailed genetic analysis helps track the spread and evolution of the virus, providing important information for developing strategies to control future outbreaks. By understanding these genetic differences, improved measures to protect pig populations can be implemented, thereby reducing the economic impact on the agricultural industry.
Abstract
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.
