Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.
Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.
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DOI：
10.12688/wellcomeopenres.14438.2
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发表时间：
2018
影响因子：
--
通讯作者：
Krishna S
中科院分区：
文献类型：
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作者：
Dias M;Pattabiraman C;Siddappa S;Gowda M;Shet A;Smith D;Muehlemann B;Tamma K;Solomon T;Jones T;Krishna S
背景：蚊媒黄病毒，例如登革热和日本脑炎病毒（JEV），会引起危及生命的疾病，特别是在热带地区。 方法：我们对 2014 年四名患者的血清和一名患者的血浆中提取的 RNA 进行了无偏倚的宏基因组测序，这些患者均因严重或长期发热性疾病而住院于印度南部的三级护理中心，并与一名健康对照者的血清一起进行。结果：我们从一例严重登革热病例中鉴定并组装了完整的登革热病毒 3 型序列。我们还在两名患有发热性疾病的成年人（其中一名患有严重登革热）的血清中发现了少量 JEV 序列。系统发育分析显示登革热序列属于基因型III。它与最相关的印度菌株的估计分化时间为 13.86 年。与用于开发第一个商业登革热疫苗的亲本菌株相比，预计该菌株的抗原包膜蛋白中总共有 11 个氨基酸取代。 结论：我们证明，通过对临床材料进行公正的测序，基因组组装和少量病毒序列的检测都是可能的。这些方法可能有助于确定不明原因发热性疾病的病因。
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.