Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains

Multiplex PCR assays for respiratory viruses are widely used in routine diagnostics, as they are highly sensitive, rapid, and cost effective. However, depending on the assay system, cross-reactivity between viruses that share a high sequence homology as well as detection of rare virus isolates with sequence variations can be problematic. Virus sequence-independent metagenomic high-throughput sequencing allows for accurate detection of all virus species in a given sample, as we demonstrate here for human Enterovirus and Rhinovirus in a lung transplant patient. While early in infection a commercial PCR assay recorded Rhinovirus, high-throughput sequencing correctly identified human Enterovirus C104 as the source of infection, highlighting the potential of the technology and the benefit of applying open assay formats in complex diagnostic situations.
Highlights • Commercial test produced ambivalent results regarding Enterovirus/Rhinovirus infection. • To resolve etiology of infection, we performed unbiased metagenomic sequencing. • We detected HEV-C104 and other coinfecting viruses. • We identified sequence variations in HEV-C104 responsible for low sensitivity. • Metagenomics can complement specific routine diagnostics in complex cases.