ISSN 1003-8280 CN 10-1522/R 中国疾病预防控制中心 主办
Chinese Journal of Vector Biology and Control >
Screening for Japanese encephalitis virus in mosquitoes by high-throughput sequencing of viral RNA
Received date: 2015-06-24
Online published: 2015-10-20
Supported by
Supported by the National Natural Science Foundation of China (No. 81290343)
Objective To use RNA-seq library construction and high-throughput sequencing approach to identify and characterize Japanese encephalitis virus (JEV) within mosquito samples. Methods Thirty-two mosquito pools (around 480 females in total) were collected in Wuhan, Hubei, China. Total RNA was extracted using TRIzol LS reagent and E.Z.N.A. Total RNA Kit and these extractions were further merged into 1 pool for RNA-seq library construction and sequencing. To obtain the full-length genome and reconstruct the phylogenetic tree, we used software including Trinity, Blast, SeqMan, MAFFT_7, MegAlign and PhyML. Results Within the sequencing results, we were able to identify a JEV which we named as WH-JEV strain. The genome of WH-JEV strain was 10 947 nucleotides long, which covers the complete open reading frame from 81 to 10 376 nt of the genome and encodes for a 3432 amino acid polyprotein. The virus has a low abundance (with a coverage of 40X and a TPM of 4.19) comparing to other viruses with the same mosquito RNA library. Subsequent genome analyses suggests that the WH strain belongs to genotypeⅠ, and has 99.5% nucleotide identity and 100% amino acid identity with the strain LN0716. Conclusion High-throughput technology could be used to rapidly detect and characterize JEV within mosquitoes.
LI Ci-xiu, SHI Mang, TIAN Jun-hua, LI Ming-hui, QIN Xin-cheng . Screening for Japanese encephalitis virus in mosquitoes by high-throughput sequencing of viral RNA[J]. Chinese Journal of Vector Biology and Control, 2015 , 26(5) : 439 -442 . DOI: 10.11853/j.issn.1003.4692.2015.05.002
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