Abstract
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.
Highlights
Arthropode-borne viral infections, transmitted to mammals by hematophagous arthropod vectors, have recently emerged as one of the most important threats to human health.Due to their worldwide occurrence and fast adaptation to environmental changes, mosquitoes from the Aedes genus play an important role in the transmission of viral etiological agents of emerging human infections, including Dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHYKV) and Viruses 2020, 12, 782; doi:10.3390/v12070782 www.mdpi.com/journal/virusesYellow fever virus (YFV) [1,2]
The cells were inoculated with a Zika virus strain derived from a serum sample collected from a patient in the Brazilian outbreak of 2015 with MOI 1, and after observation of the cytophatic effect (4 days), the supernatant of the infected cells was centrifugated
We first tried to use SPAdes with the default parameters referred here as ‘regular.’ we identified many contigs derived from the Zika virus, we were not able to reconstitute the viral genome as a single segment
Summary
Arthropode-borne viral infections (arboviroses), transmitted to mammals by hematophagous arthropod vectors, have recently emerged as one of the most important threats to human health.Due to their worldwide occurrence and fast adaptation to environmental changes, mosquitoes from the Aedes genus play an important role in the transmission of viral etiological agents of emerging human infections, including Dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHYKV) and Viruses 2020, 12, 782; doi:10.3390/v12070782 www.mdpi.com/journal/virusesYellow fever virus (YFV) [1,2]. Arthropode-borne viral infections (arboviroses), transmitted to mammals by hematophagous arthropod vectors, have recently emerged as one of the most important threats to human health Due to their worldwide occurrence and fast adaptation to environmental changes, mosquitoes from the Aedes genus play an important role in the transmission of viral etiological agents of emerging human infections, including Dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHYKV) and Viruses 2020, 12, 782; doi:10.3390/v12070782 www.mdpi.com/journal/viruses. Different from African lineage, the Asian lineage of Zika virus, supposedly the origin of the strains circulating in Brazil, exhibits a different profile with lower pathogenicity and prolonged infections [4]. These differences have been attributed to mutations in the viral genome, mainly in untranslated regions [5,6]. The long-term infection, which could facilitate mosquito transmission, associated with the high susceptibility of the population likely explains the rapid spread of the virus that reached almost all Brazilian states in only a few months, different, for example, to the Dengue virus whose spread took decades [7]
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