Figure 2. Challenges to in-field clinical metagenomics for rapid diagnosis and outbreak response.
A mobile medical unit deploying a portable clinical metagenomics platform has been established at the epicentre of an infectious disease outbreak, but the team faces challenges throughout the diagnostic process and epidemiological response. For example, in the case of Zika virus, samples, such as blood, with low viral titres, a small genome of <11 kb and transient viraemia120 combine to complicate detection of viral nucleic acid by use of a strictly metagenomic approach. Furthermore, obtaining a sufficient amount of viral nucleic acids for genome sequencing beyond simple diagnostics requires a tiling PCR and amplicon sequencing approach14. Other challenges include, for example, access to a reliable Internet connection, the ability to collect sample metadata and translating genomic findings into real-time, actionable recommendations.