Abstract
Sabia and Chapare viruses in the Arenavirus family cause viral hemorrhagic fever among humans with a fatality rate of 30% with no treatment models. Therefore, it is of interest to document the codon usage, amino acid patterns and associated factors influencing the observed variations in Sabia and Chapare viruses for host adaptation. Multivariate statistical analysis revealed compositional constraint and host selection pressure influencing the viral codon usage patterns. These data suggests the codon usage signatures in Sabia and Chapare viruses for host adaptation in the human host implying its role in the rapid progression of the infection. Dinucleotides UpG and CpA were noted to be over-represented among the Sabia, Chapare viruses and human genomes. Strong restraint from the usage of CpG dinucleotides among viruses is linked with the molecular mimicry of the human immune system. Thus, the data reported from this study help in understanding the mechanism of viral adaptation inside the host genome for further consideration in drug discovery.
Highlights
Study of viruses to eradicate them globally is of great concern considering their highly detrimental association with all type of life forms including bacteria, archaea, and eukaryotes [1]
It is of interest to document the codon usage, amino acid patterns and associated factors influencing the observed variations in Sabia and Chapare viruses for host adaptation
Assessment of parameters pertaining to Nucleotide composition and codon usage analysis: Nucleotide composition properties like %A (Adenine),%G (Guanine), %C(Cytosine) and %T(Thymine); occurrence of GC (Guanine + Cytosine) at all the three positions of synonymous codons (GC1, GC2 and GC3); overall occurrence of AT and GC in Effective number of codons: Effective number of codons (ENc) computed from CodonW [21] can have values from 20 to 61.Value equal to or close to 20 depicts that each amino acid has been encoded by one single codon only and there is no biasness whereas, value equal to or close to 61 shows that a particular amino acid can be encoded by more than one codon which is the case with no codon biasness
Summary
Study of viruses to eradicate them globally is of great concern considering their highly detrimental association with all type of life forms including bacteria, archaea, and eukaryotes (human and agricultural sector, zoonotic threats) [1]. Include total 10 strains causing diseases among humans and are examined as polyphyletic [6, 7].Further New World Arenaviruse have been sub grouped into clades: A, B, C and D. Five viruses of clade B of NW Arenaviruse; known to be pathogenic among humans are Junin, Machupo, Guanarito, Sabia and Chapare [8]. Deciphering the variations and factors regulating the complicated patterns of codons and amino acids of viral genome may stimulate information regarding the regulation of host by viruses which may be utilized to design therapeutics and vaccines against virus with high accuracy [17]. It is of interest to document the codon usage, amino acid patterns and associated factors influencing the observed variations in Sabia and Chapare viruses for host adaptation
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