TY - JOUR
T1 - Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum [version 2; referees
T2 - 2 approved]
AU - Dias, Mary
AU - Pattabiraman, Chitra
AU - Siddappa, Shilpa
AU - Gowda, Malali
AU - Shet, Anita
AU - Smith, Derek
AU - Muehlemann, Barbara
AU - Tamma, Krishnapriya
AU - Solomon, Tom
AU - Jones, Terry
AU - Krishna, Sudhir
N1 - Publisher Copyright:
© 2019 Dias M et al.
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
KW - DENV3
KW - Febrile illness
KW - Metagnomics
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U2 - 10.12688/wellcomeopenres.14438.2
DO - 10.12688/wellcomeopenres.14438.2
M3 - Article
C2 - 30167467
AN - SCOPUS:85060101058
SN - 2398-502X
VL - 3
JO - Wellcome Open Research
JF - Wellcome Open Research
M1 - 44
ER -