Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum [version 2; referees: 2 approved]

Mary Dias, Chitra Pattabiraman, Shilpa Siddappa, Malali Gowda, Anita Shet, Derek Smith, Barbara Muehlemann, Krishnapriya Tamma, Tom Solomon, Terry Jones, Sudhir Krishna

Research output: Contribution to journalArticle

Abstract

Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.

Original languageEnglish (US)
Article number44
JournalWellcome Open Research
Volume3
DOIs
StatePublished - Jan 1 2019

Fingerprint

Metagenomics
Dengue Virus
Japanese Encephalitis Virus
Dengue
Viruses
Severe Dengue
Fever
Genes
Genotype
Genome
Dengue Vaccines
Serum
RNA Sequence Analysis
Flavivirus
Tropics
Amino Acid Substitution
Culicidae
Tertiary Care Centers
India
Substitution reactions

Keywords

  • DENV3
  • Febrile illness
  • Metagnomics

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum [version 2; referees : 2 approved]. / Dias, Mary; Pattabiraman, Chitra; Siddappa, Shilpa; Gowda, Malali; Shet, Anita; Smith, Derek; Muehlemann, Barbara; Tamma, Krishnapriya; Solomon, Tom; Jones, Terry; Krishna, Sudhir.

In: Wellcome Open Research, Vol. 3, 44, 01.01.2019.

Research output: Contribution to journalArticle

Dias, Mary ; Pattabiraman, Chitra ; Siddappa, Shilpa ; Gowda, Malali ; Shet, Anita ; Smith, Derek ; Muehlemann, Barbara ; Tamma, Krishnapriya ; Solomon, Tom ; Jones, Terry ; Krishna, Sudhir. / Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum [version 2; referees : 2 approved]. In: Wellcome Open Research. 2019 ; Vol. 3.
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