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Archives of Virology

, Volume 164, Issue 10, pp 2479–2491 | Cite as

The relationship of codon usage to the replication strategy of parvoviruses

  • Thanyaporn Sirihongthong
  • Kunlakanya Jitobaom
  • Supinya Phakaratsakul
  • Chompunuch Boonarkart
  • Ornpreya Suptawiwat
  • Prasert AuewarakulEmail author
Original Article

Abstract

Codon usage is biased in most species, and the pattern of codon usage bias is specific to each species or group of closely related species. Although viruses use the host translational machinery for synthesis of their proteins, their codon usage patterns do not match those of their host. Viral codon usage is determined by a complex interplay of mutational bias, genome composition constraints, translational adaptation to the host, and host cellular innate defense. The codon usage of parvoviruses was previously shown not to be strongly biased and selective pressure was found to be a dominating factor driving codon usage. The family Parvoviridae includes the genus Dependoparvovirus, some of the members of which require a helper virus to complete their replication cycle, whereas the rest of the family can replicate without the need for helper viruses. Here, we show that difference in the replication strategy of these viruses may be an important factor determining viral codon usage. Hierarchical clustering and principal component analysis revealed that the codon usage pattern of adeno-associated viruses (AAVs) of the genus Dependoparvovirus is distinct from that of members of the other genera of vertebrate parvoviruses, and even from that of independent viruses of the genus Dependoparvovirus. Furthermore, the codon usage of human AAVs was found to be similar to that of some human adenoviruses in hierarchical clustering and principal component analysis. This suggests that the codon usage of AAVs is different from that of other parvoviruses because of their distinctive replication strategy and that their codon usage is probably driven by forces similar to those that shaped the codon usage pattern of their helper viruses.

Notes

Acknowledgements

This work was supported financially by Siriraj Graduate Scholarship and the Thailand Research Fund (Grant No. IRN60W0002).

Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest.

Research involving human participants and/or animals

No part of this study was performed with human participants or animals.

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Microbiology, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
  2. 2.Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical ScienceChulabhorn Royal AcademyBangkokThailand

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