A review of virus host factor discovery using CRISPR screening

Abstract

The emergence of genome-scale forward genetic screening techniques, such as Haploid Genetic screen and clustered regularly interspaced short palindromic repeats (CRISPR) knockout screen has opened new horizons in our understanding of virus infection biology. CRISPR screening has become a popular tool for the discovery of novel host factors for several viruses due to its specificity and efficiency in genome editing. Here, we review how CRISPR screening has revolutionized our understanding of virus-host interactions from scientific and technological viewpoints. A summary of the published screens conducted thus far to uncover virus host factors is presented, highlighting their experimental design and significant findings. We will outline relevant methods for customizing the CRISPR screening process to answer more specific hypotheses and compile a glossary of conducted CRISPR screens to show their design aspects. Furthermore, using flaviviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as examples, we hope to offer a broad-based perspective on the capabilities of CRISPR screening to serve as a reference point to guide future unbiased discovery of virus host factors.

Keywords: CRISPR screening; SARS-CoV-2; flavivirus; functional genomics; host factors; virus-host interactions.

Fig 1

Illustration of the CRISPR screening workflow. Key steps of a CRISPR screening workflow, from selection of suitable cells, the delivery of a pooled sgRNA library, selection of infected cells, to the hit validation after NGS and bioinformatics data analysis.