Diversity and Complexity of Internally Deleted Viral Genomes in Influenza A Virus Subpopulations with Enhanced Interferon-Inducing Phenotypes

Abstract

Influenza A virus (IAV) populations harbor large subpopulations of defective-interfering particles characterized by internally deleted viral genomes. These internally deleted genomes have demonstrated the ability to suppress infectivity and boost innate immunity, rendering them promising for therapeutic and immunogenic applications. In this study, we aimed to investigate the diversity and complexity of the internally deleted IAV genomes within a panel of plaque-purified avian influenza viruses selected for their enhanced interferon-inducing phenotypes. Our findings unveiled that the abundance and diversity of internally deleted viral genomes were contingent upon the viral subculture and plaque purification processes. We observed a heightened occurrence of internally deleted genomes with distinct junctions in viral clones exhibiting enhanced interferon-inducing phenotypes, accompanied by additional truncation in the nonstructural 1 protein linker region (NS1Δ76-86). Computational analyses suggest the internally deleted IAV genomes can encode a broad range of carboxy-terminally truncated and intrinsically disordered proteins with variable lengths and amino acid composition. Further research is imperative to unravel the underlying mechanisms driving the increased diversity of internal deletions within the genomes of viral clones exhibiting enhanced interferon-inducing capacities and to explore their potential for modulating cellular processes and immunity.

INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance

“…These exercises in a real context not only provided a good complement to the multiple tests performed during the TELEVIR pipeline development, benchmarking, and final refinement, but also introduced it as a bioinformatics resource of reference among several Public Health and Veterinary institutes across Europe. The achieved INSaFLU-TELEVIR versatility and functionality has also captured the attention of the international scientific community and key stakeholders in the field of public and animal health, leading to a considerable increase in the number of accounts created and published applications (e.g., [ 89 – 97 ]). This is well reflected by the multiple national and international activities that were conducted (or are being planned) to support the capacity building of several countries/laboratories in viral metagenomic detection and genomic surveillance through specific training in INSaFLU-TELEVIR.…”

Defective viral genomes: advances in understanding their generation, function, and impact on infection outcomes

“…Given the inherent error-prone nature of viral RNA-dependent RNA polymerases (RdRps), it was historically accepted that DVG generation is a random process. However, the dissociation (break point) and re-initiation (rejoin point) positions of both deletion and cbDVGs are consistently observed to cluster in certain genomic regions across different virus families ( 8 , 20 – 26 ), strongly arguing against the completely random generation theory. Additionally, microhomologies and specific nucleotide compositions have been observed to flank DVG break and rejoin points ( 3 , 6 , 27 ), further suggesting a sequence dependency for DVG generation ( Fig.…”