Genetic variation in the 3′ non-coding region of dengue viruses

Amy C. Shurtleff, David Beasley, Jenny J Y Chen, Haolin Ni, Miguel T. Suderman, Heiman Wang, Renling Xu, Eryu Wang, Scott Weaver, Douglas M. Watts, Kevin L. Russell, Alan Barrett

Research output: Contribution to journalArticle

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Abstract

The 3′ non-coding region (3′NCR) of strains of dengue 1 (DEN 1), DEN 2, DEN 3, and DEN 4 viruses, isolated in different geographical regions, was sequenced and compared to published sequences of the four dengue viruses. A total of 50 DEN 2 strains was compared: 7 West African strains, 3 Indonesian mosquito strains, 1 Indonesian macaque isolate, and 39 human isolates from Southeast Asia, the South Pacific, and the Caribbean and Americas. Nucleotide sequence alignment revealed few deletions and no repeat sequences in the 3′ NCR of DEN 2 viruses and showed that much of the 3′ NCR was well conserved. The strains could be divided into two groups, sylvatic and human/mosquito/macaque, based on nucleotide sequence homology. A hypervariable region was identified immediately following the NS5 stop codon, which involved a 2-10 nucleotide deletion in human, mosquito, and macaque isolates compared with the sylvatic strains. The DEN 2 3′NCR was also compared with 3′NCR sequences from strains of DEN 1, DEN 3, and DEN 4 viruses. DEN 1 was found to have four copies of an eight nucleotide imperfect repeat following the NS5 stop codon, while DEN 4 virus had a deletion of 75 nucleotides in the 3′NCR. We propose that the variation in nucleotide sequence in the 3′NCR may have evolved as a function of DEN virus transmission and replication in different mosquito and non-human primate/human host cycles. The results from this study are consistent with the hypothesis that DEN viruses arose from sylvatic progenitors and evolved into human epidemic strains. However, the data do not support the hypothesis that variation in the 3′NCR correlates with DEN virus pathogenesis.

Original languageEnglish (US)
Pages (from-to)75-87
Number of pages13
JournalVirology
Volume281
Issue number1
DOIs
StatePublished - Mar 1 2001

Fingerprint

Dengue Virus
Viruses
Culicidae
Dengue
Macaca
Nucleotides
Terminator Codon
Southeastern Asia
Sequence Alignment
Virus Replication
Sequence Homology
Primates

Keywords

  • 3′ non-coding region
  • Dengue virus
  • Flaviviruses
  • Reverse transcription-polymerase chain reaction

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

Shurtleff, A. C., Beasley, D., Chen, J. J. Y., Ni, H., Suderman, M. T., Wang, H., ... Barrett, A. (2001). Genetic variation in the 3′ non-coding region of dengue viruses. Virology, 281(1), 75-87. https://doi.org/10.1006/viro.2000.0748

Genetic variation in the 3′ non-coding region of dengue viruses. / Shurtleff, Amy C.; Beasley, David; Chen, Jenny J Y; Ni, Haolin; Suderman, Miguel T.; Wang, Heiman; Xu, Renling; Wang, Eryu; Weaver, Scott; Watts, Douglas M.; Russell, Kevin L.; Barrett, Alan.

In: Virology, Vol. 281, No. 1, 01.03.2001, p. 75-87.

Research output: Contribution to journalArticle

Shurtleff, AC, Beasley, D, Chen, JJY, Ni, H, Suderman, MT, Wang, H, Xu, R, Wang, E, Weaver, S, Watts, DM, Russell, KL & Barrett, A 2001, 'Genetic variation in the 3′ non-coding region of dengue viruses', Virology, vol. 281, no. 1, pp. 75-87. https://doi.org/10.1006/viro.2000.0748
Shurtleff AC, Beasley D, Chen JJY, Ni H, Suderman MT, Wang H et al. Genetic variation in the 3′ non-coding region of dengue viruses. Virology. 2001 Mar 1;281(1):75-87. https://doi.org/10.1006/viro.2000.0748
Shurtleff, Amy C. ; Beasley, David ; Chen, Jenny J Y ; Ni, Haolin ; Suderman, Miguel T. ; Wang, Heiman ; Xu, Renling ; Wang, Eryu ; Weaver, Scott ; Watts, Douglas M. ; Russell, Kevin L. ; Barrett, Alan. / Genetic variation in the 3′ non-coding region of dengue viruses. In: Virology. 2001 ; Vol. 281, No. 1. pp. 75-87.
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