Single-cell RNA-seq methods to interrogate virus-host interactions

Abstract

The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.

Keywords: Antiviral immunity; Single-cell RNA sequencing; Transcriptomics; Virus.

Fig. 1

Transcriptomic approaches to profile antiviral immunity

Fig. 2

Table summarizing the advantages and disadvantages of different scRNA-seq methods in viral immunology research

Fig. 3

Schematic demonstrating key differences between host and viral RNA that can require alternative approaches for sequencing virus transcripts

Fig. 4

Overview of ways in which scRNA-seq can enable a deeper understanding of cellular antiviral responses and viral dynamics

Fig. 5

Overview of scRNA-seq analytic approaches to understanding intracellular and multicellular signaling

Fig. 6

Venn diagram demonstrating the information that can be derived from epigenetic, transcriptomic, and proteomic measurements. Overlapping regions contain unique information that can be derived from integrative analyses of multiple omics in the same cell. CITE-seq, cellular indexing of transcriptomes and epitopes by sequencing; trx, transcription; scATAC-seq, single-cell resolution in assay for transposase-accessible chromatin using sequencing; SNP, single nucleotide polymorphism

Fig. 7

Virus-related scRNA-seq publications from 2013 to October 2022. SCOPUS database search for publications associated with “scRNA-seq” and “viruses,” with publications relating to HIV, influenza, and SARS-CoV-2 highlighted within the identified total