Extended Data Fig. 5: Newly characterized delta virus and delta-virus-like genomes.

Structure and organization of selected examples from the 14 delta virus-, 39 epsilon virus- and 311 zeta virus-like genomes identified in our study. a Similar to human delta virus (HDV), delta virus-like genomes from vertebrates (PmacDV SRR7910143; MmonDV SRR2136906; TgutDV SRR5001850; IchiDV SRR8954566 and BglaDV SRR8242383) and environmental datasets (SRR7286070 and SRR6943136) share similar predicted stable rod-like folding, a predicted ORF coding for the delta antigen (δAg) and a delta ribozyme (dvrbz) on each polarity. Folding of the circular DNA virus Porcine Circovirus 2 (PCV2) and a shuffled MmonDV sequence are shown as negative controls. b Epsilon virus-like genomes detected in invertebrates (SulaEV SRR8739608; GsulEV SRR7170939 and BaerEV SRR12300397) and environmental datasets (SRR8840728 and SRR6943136) show similar structure and organization to delta viruses, with one or two predicted ORFs (epsilon antigen or Ag) and two hammerhead ribozymes (hhrbz) in equivalent genomic regions. c Zeta virus-like genomes detected in invertebrate (Ocassitermes sp. ZVs SRR8924823) and environmental datasets (SRR7286070, SRR6943136, SRR8840728, SRR6201737, SRR5864109 and SRR12063536) are smaller than delta and epsilon agents. Up to 90% of the zeta genomes have sizes multiple of 3 and predicted ORFs without stop codons, capable to encode endless tandem-repeated zeta antigens in both polarities (ζAg+ and ζAg– shown as yellow and red arrows, respectively). Both genomic zeta polarities keep hhrbzs (shown as arrows overlapping the ORFs) similar to the epsilon ribozymes (Extended Fig 6). Larger zeta virus-like genomes (>651 nt) were less abundant (7% of all zeta genomes) and frequently show stop codons, or their sizes are not multiple of 3.