Abstract
The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV.
Highlights
The torque teno virus (TTV) was first identified in Homo sapiens and in numerous host species and, was considered to have a broad host range [1,2]
The TTSuV1a and TTSuV1b species belong to the Iotatorquevirus genera, while TTSuVk2a and TTSuVk2b belong to the Kappatorquevirus genera, based on nucleotide divergence [5]
Evolutionary analysis on DNA viruses has been revealed that the high nucleotide substitution rate of torque teno sus virus (TTSuV) is consistent with the porcine circovirus type 3 (PCV3) [10], as well as other ssDNA and RNA viruses suspected to be driven by natural selection and drift [8,11], and higher than the pseudorabies virus (PRV) [12]
Summary
The torque teno virus (TTV) was first identified in Homo sapiens and in numerous host species and, was considered to have a broad host range [1,2]. Evolutionary analysis on DNA viruses has been revealed that the high nucleotide substitution rate of TTSuV is consistent with the porcine circovirus type 3 (PCV3) [10], as well as other ssDNA and RNA viruses suspected to be driven by natural selection and drift [8,11], and higher than the pseudorabies virus (PRV) [12]. A direct way to display the evolutionary changes of viruses is the analysis of the codon usage pattern [13]. TTSuV, as any other virus, depends on the host for survival and transmission; the TTSuV codon usage pattern could influence virus infection, adaptation, and escape from host immune responses. We performed a comprehensive codon usage analysis that could aid the understanding of virus-host inter-adaption and inform surveillance and prevention strategies
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