Analysis of codon usage bias of lumpy skin disease virus causing livestock infection

Siddiq Ur Rahman; Hassan Ur Rehman; Inayat Ur Rahman; Abdur Rauf; Abdulrahman Alshammari; Metab Alharbi; Noor Ul Haq; Hafiz Ansar Rasul Suleria; Sayed Haidar Abbas Raza

doi:10.3389/fvets.2022.1071097

Analysis of codon usage bias of lumpy skin disease virus causing livestock infection

Front Vet Sci. 2022 Dec 5:9:1071097. doi: 10.3389/fvets.2022.1071097. eCollection 2022.

Authors

Siddiq Ur Rahman¹, Hassan Ur Rehman¹, Inayat Ur Rahman², Abdur Rauf³, Abdulrahman Alshammari⁴, Metab Alharbi⁴, Noor Ul Haq¹, Hafiz Ansar Rasul Suleria⁵, Sayed Haidar Abbas Raza^{6

7}

Affiliations

¹ Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan.
² Department of Botany, Khushal Khan Khattak University, Karak, Pakistan.
³ Department of Chemistry, University of Swabi, Swabi, Pakistan.
⁴ Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.
⁵ Faculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia.
⁶ College of Animal Science and Technology, Northwest A&F University, Xianyang, China.
⁷ Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, China.

Abstract

Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them.

Keywords: codon usage bias (CUB); effective number of codons (ENC); lumpy skin disease virus; mutation pressure; natural selection.