Intra-host dynamics of Ebola virus during 2014



Nature Microbiology


Intra-host dynamics of Ebola virus during 2014


Ming Ni, Chen Chen, Jun Qian, Hai-Xia Xiao, Wei-Feng Shi, Yang Luo, Hai-Yin Wang, Zhen Li, Jun Wu, Pei-Song Xu, Su-Hong Chen, Gary Wong, Yuhai Bi, Zhi-Ping Xia, Wei Li, Hui-jun Lu, Juncai Ma, Yi-Gang Tong, Hui Zeng, Sheng-Qi Wang, George F. Gao, Xiao-Chen Bo & Di Liu


Since 2013, West Africa has encountered the largest Ebola virus (EBOV) disease outbreak on record, and Sierra Leone is the worst-affected country, with nearly half of the infections. By means of next-generation sequencing and phylogeographic analysis, the epidemiology and transmission of EBOV have been well elucidated. However, the intra-host dynamics that mainly reflect viral–host interactions still need to be studied. Here, we show a total of 710 intra-host single nucleotide variations (iSNVs) from deep-sequenced samples from EBOV-infected patients, through a well-tailored bioinformatics pipeline. We present a comprehensive distribution of iSNVs during this outbreak and along the EBOV genome. Analyses of iSNV and its allele frequency reveal that VP40 is the most conserved gene during this outbreak, and thus it would be an ideal therapeutic target. In the co-occurring iSNV network, varied iSNV sites present different selection features. Intriguingly, the T-to-C substitutions at the 3′-UTR of the nucleoprotein (NP; positions 3008 and 3011), observed in many patients, result in the upregulation of the transcription of NP through an Ebola mini-genome reporting system. Additionally, no iSNV enrichment within B-cell epitopes of GP has been observed.




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