Assessment of Metagenomic MinION and Illumina sequencing as an approach for the recovery of whole genome sequences of chikungunya and dengue viruses directly from clinical samples.

The recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. We performed metagenomicsequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinIONto study the feasibility of whole genome sequencingfrom clinical samples containing chikungunyaor dengue virus, two of the most important arboviruses. Direct metagenomicsequencing of nucleic acid extracts from serum and plasma without viral enrichment allowed for virus and coinfectionidentification, subtype determination and in the majority of cases elucidated complete or near-complete genomes adequate for phylogenetic analysis. This work demonstrates that metagenomic whole genome sequencingis feasible for over 90% and 80% of chikungunyaand dengue virusPCR-positive patient samples respectively. It confirms the feasibility of field metagenomicsequencing for these and likely other RNA viruses, highlighting the applicability of this approach to front-linepublic health.