High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics.
Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from metatranscriptomics data is key to the development of new control strategies for these diseases. Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5'-UTR and 3'-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification.
['I Sardi|Silvia|S|', 'H Carvalho|Rejane|R|0000-0002-2178-8226', 'C Pacheco|Luis G|LG|', 'P D Almeida|João P|JP|0000-0001-7532-8420', 'M D A Belitardo|Emilia M|EM|0000-0003-0818-1582', 'S Pinheiro|Carina|C|', 'S Campos|Gúbio|G|', 'R G R Aguiar|Eric|E|0000-0002-8143-5756']
D001103:Arboviruses D004196:Disease Outbreaks D020869:Gene Expression Profiling D016679:Genome, Viral D059014:High-Throughput Nucleotide Sequencing D006801:Humans D000072138:Mosquito Vectors D028381:Nidovirales D010802:Phylogeny D016133:Polymerase Chain Reaction D000071244:Zika Virus D000071243:Zika Virus Infection
Zika virus metatranscriptomics Ion Torrent RNA deep sequencing virus identification