Virome capture sequencing for enhanced detection of respiratory and other viruses in PCR-negative influenza-like illness cases : a cross-sectional study

Conventional multiplex PCR diagnostics for influenza-like illness (ILI) frequently yield negative results, leaving the etiology of respiratory infections undetermined. Virome Capture Sequencing for Vertebrate Viruses (VCS) offers a comprehensive agnostic approach for detecting known and unexpected vertebrate viruses in clinical samples. We retrospectively analyzed 440 nasal swab samples from adults enrolled in the ILI002 cohort in Mexico (2010–2014) who tested negative for respiratory pathogens by Respifinder multiplex PCR. Total nucleic acids (DNA and RNA) were extracted and sequenced using VCS. Bioinformatic analysis was conducted using the Rapid Identification of Microbes (RIM) pipeline. Detected viruses were classified by pathogenicity and disease association. Of 440 samples, 208 (48%) yielded viral hits, identifying 314 viruses. A respiratory virus consistent with clinical symptoms was identified in 17% of samples. Rhinoviruses were the most frequent respiratory viruses identified. Influenza C virus (ICV) was detected in five cases, revealing previously unrecognized circulation. Additionally, there was observed a high frequency of non-respiratory viruses, particularly Epstein-Barr virus (EBV) and papillomaviruses. Phylogenetic analyses of rhinoviruses showed high diversity, and genotyping of ICV strains confirmed lineage conservation. VCS is able to detect common respiratory pathogens missed by conventional diagnostic methods and also identify unusual viruses of epidemiological relevance, such as ICV, underscoring its potential value for pandemic preparedness. This technique represents a promising approach to broaden our understanding of the full spectrum of viruses present in the human respiratory tract and to advance insights into host-pathogen/microbiota interactions. NCT01418287