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Wellcome Open Res. 2018 Apr 23;3:44. doi: 10.12688/wellcomeopenres.14438.1. eCollection 2018.

Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.

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St. John's Medical College and Hospital, Bangalore, 560034, India.
National Institute of Mental Health and Neurosciences, India, Bangalore, 560029, India.
Centre for Cellular and Molecular Platforms, Bangalore, 560065, India.
Trans-Disciplinary University, Foundation for Revitalization of Local Health Traditions, Bangalore, 560064, India.
Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA.
Center for Pathogen Evolution, Department of 
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
World Health Organization 
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK.
Indian Institute of Science, Bangalore, 560012, India.
Institute of Infection and Global Health, and National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK.
National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India.
Contributed equally


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.


DENV3; febrile illness; metagnomics

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