CRISPR-based screening of host factors in veterinary viral infections: from target discovery to host-directed antiviral strategies

Abstract

Viral infectious diseases in livestock and poultry cause substantial economic losses worldwide and pose persistent zoonotic threats to public health. Elucidating virus-host interactions is essential for understanding viral pathogenesis and developing effective control strategies. In recent years, genome-wide CRISPR/Cas9 functional screening has emerged as a powerful and unbiased high-throughput approach for identifying host dependency and restriction factors. Enabled by the development of species-specific sgRNA libraries, this technology has significantly advanced research in veterinary virology. In this review, we systematically summarize recent progress in CRISPR/Cas9-based screening studies of major livestock and poultry viruses, including foot-and-mouth disease virus (FMDV), swine enteric coronaviruses, African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), avian leukosis virus (ALV), and other zoonotic pathogens. We highlight key host factors involved in viral entry, replication, and egress, and integrate these findings to delineate conserved cross-viral dependency networks, such as sialic acid biosynthesis, endosomal–lysosomal trafficking, double-membrane vesicle (DMV) formation, and interferon signaling pathways. Furthermore, we discuss the translational potential of these genomic discoveries for practical agricultural applications, particularly in the development of host-targeted broad-spectrum antivirals and the generation of disease-resistant livestock (e.g., receptor-edited pigs and chickens) through precise genome editing. Finally, we outline future perspectives, including the integration of single-cell transcriptomics and in vivo validation, thereby providing a comprehensive framework for advancing disease control and sustainable breeding in animal agriculture.