Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples

• Published in: Cell reports methods Vol. 1; no. 6; p. 100091
• Main Authors: Rajagopala, Seesandra V., Bakhoum, Nicole G., Pakala, Suman B., Shilts, Meghan H., Rosas-Salazar, Christian, Mai, Annie, Boone, Helen H., McHenry, Rendie, Yooseph, Shibu, Halasa, Natasha, Das, Suman R.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 25.10.2021; Elsevier
• Subjects: acute respiratory infection; ARI; Child; coronavirus; Humans; metatranscriptomics; microbiome; Microbiota - genetics; next-generation sequencing; respiratory syncytial virus; Respiratory Syncytial Virus Infections - genetics; Respiratory Syncytial Virus, Human - genetics; RNA-seq; RSV; Transcriptome - genetics; virome; Virome - genetics; virome; RNA-seq; RSV; metatranscriptomics; next-generation sequencing; ARI; coronavirus; acute respiratory infection; microbiome; respiratory syncytial virus
• ISSN: 2667-2375; 2667-2375
• DOI: 10.1016/j.crmeth.2021.100091

We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that H. influenzae was highly active in symptomatic RSV subjects. The host nasal transcriptome reveled upregulation of the innate immune system, anti-viral response and inflammasome pathway, and downregulation of fatty acid pathways in children with symptomatic RSV. Overall, we demonstrate that our method is broadly applicable to infer the transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples. [Display omitted] •Develop metatranscriptomics to characterize virome, microbiome, and host response•High prevalence of RSV and coronavirus is observed in healthy children•RSV-A and RSV-B are co-detected in 56% of children with symptomatic RSV•H. influenzae is highly active in children with symptomatic RSV Metatranscriptomics is a powerful method to study the entire transcriptome landscape; however, the feasibility of using this approach to describe the entire respiratory RNA virome, microbiome, and host response from low biomass clinical samples remains elusive. Here, we present an optimized metatranscriptomics method and an accompanying computational workflow to simultaneously characterize the respiratory virome, microbiome, and host response directly from nasal samples. Although this method is optimized for nasal swab samples, further optimization of sample preservation and RNA extraction might be needed to obtain high-quality RNA for other clinical samples. Rajagopala et al. develop a metatranscriptomic approach for simultaneously and directly characterizing the respiratory virome, microbiome, and host response from low biomass clinical samples such as nasal swabs.