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A detailed analysis of synonymous codon usage in human bocavirus

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Abstract

Human bocavirus (HBoV) is a recently discovered parvovirus associated with respiratory and gastroenteric infections in children. To date, four distinct subtypes have been identified worldwide. HBoV1 is the most frequently detected bocavirus in clinical samples derived from the respiratory tract. HBoV has a single-stranded DNA genome, which encodes two nonstructural proteins, NS1 and NP1, and two structural proteins, VP1 and VP2. Despite a large number of available HBoV sequences, the molecular evolution of this virus remains enigmatic. Here, we applied bioinformatic methods to measure the codon usage bias in 156 HBoV genomes and analyzed the factors responsible for preferential use of various synonymous codons. The effective number of codons (ENC) indicates a highly conserved, gene-specific codon usage bias in the HBoV genome. The structural genes exhibit a higher degree of codon usage bias than the non-structural genes. Natural selection emerged as dominant factor influencing the codon usage bias in the HBoV genome. Other factors that influence the codon usage include mutational pressure, gene length, protein properties, and the relative abundance of dinucleotides. The results presented in this study provide important insight into the molecular evolution of HBoV and may serve as a primer for HBoV gene expression studies and development of safe and effective vaccines to prevent infection.

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Acknowledgements

We thank the College of Clinical Pharmacy for providing necessary support to conduct this research. This research was supported by the Deanship of Scientific Research, King Faisal University, grant #160009.

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  1. Department of Biomedical Science, College of Clinical Pharmacy, King Faisal University, P.O Box 400, Al-Ahsa, 31982, Kingdom of Saudi Arabia

    Snawar Hussain, Sahibzada Tasleem Rasool & Afzal Haq Asif

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  1. Snawar Hussain
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  3. Afzal Haq Asif
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SH, STR and AHA identified the research topic and designed the study. SH collected the data and conducted the analysis. SH, STR and AHA prepared the manuscript.

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Correspondence to Snawar Hussain.

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Handling Editor: Sheela Ramamoorthy.

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Hussain, S., Rasool, S.T. & Asif, A.H. A detailed analysis of synonymous codon usage in human bocavirus. Arch Virol 164, 335–347 (2019). https://doi.org/10.1007/s00705-018-4063-8

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