Insect cypoviruses: advances in structural characterization, evolutionary genomics, and host interaction dynamics

Cypoviruses are insect-specific, double-stranded RNA viruses belonging to the genus Cypovirus within the family Spinareoviridae. Cypoviruses primarily infect insects of the orders Lepidoptera, Diptera, and Hymenoptera. These viruses replicate in midgut epithelial cells, forming polyhedrin-based occlusion bodies. Cypovirus genomes typically consist of 10-16 linear double-stranded RNA (dsRNA) segments that encodes distinct viral proteins; however, the number of genomic segments may vary among species. Each genomic segment encodes a functionally specialized distinct viral protein, with high intra-species conservation but notable divergence between species, reflecting genomic plasticity and evolutionary divergence. This review presents a comprehensive comparative genomic analysis of representative Cypovirus species, focusing on segment-wise assignments. Segment 1 universally encodes the major capsid protein, while segment 2 encodes the RNA-dependent RNA polymerase (RdRP) and segment 3 encodes the minor capsid protein. Segments 4 and 5 typically encode enzymes with methyltransferase and guanylyl transferase, which are essential for RNA capping. Segments 6 to 8 encodes for other structural or accessory proteins. Segment 9 frequently encodes a non-structural protein and segment 10 consistently encodes structural polyhedrin protein. Conserved protein domains and sequence motifs are identified across cypovirus genomic segments. Analysis of nonsynonymous to synonymous substitutions (Ka/Ks ratios) reveals evidence of both purifying and positive selection in viral genomic segments. Phylogenetic analysis demonstrates lineage diversification and species-specific clustering. Genotypic and phenotypic variability among viral strains correlates with host insect species, co-infection and geographic isolation, whereas functional convergence in protein roles is observed across species. This study consolidates electrophoretic migration patterns and genomic demarcation criteria for Cypovirus species into a practical reference framework that enables rapid species identification without the need for complete genome sequencing. The current review provides structural, genomic, and evolutionary insights that collectively advance the current understanding of cypovirus biology and diversity.