Metagenomic approaches for arbovirus surveillance in Brazil
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Emerging and re-emerging viruses transmitted by arthropods (arboviruses) are a global concern to human health especially in tropical and subtropical regions.
Recently, Brazil has been affected by a wave of severe overlapping arbovirus epidemics including the viruses Zika (ZIKV), Chikungunya (CHIKV), Dengue (DENV) and Yellow Fever (YFV). However, epidemiological surveillance is limited due to the difficulty of making definitive clinical diagnoses, coupled with limited availability of molecular diagnostic capacity in Brazil. We have previously employed specific pathogen-targeted sequencing approaches coupled with mobile diagnostic surveillance to help collect important epidemiological information. However, such approaches are only suitable for detecting already known viral outbreaks.
Recently, improvements in yield of nanopore sequencing has meant that untargeted metagenomic sequencing of clinical samples is now viable, potentially meaning that new viruses and lineages can be detected with a single, universal test. We describe here a full-length, low-input, long-read approach we term “SMART-metagenomics” to sequence RNA arboviruses directly from clinical samples by MinION nanopore sequencing.