Expanding the size limit of RNA viruses: Evidence of a novel divergent nidovirus in California sea hare, with a ~35.9 kb virus genome

Humberto J Debat

The RdRP-ZBD-HEL predicted region of the ORF1ab protein appears to be the more similar to reported nidoviruses (Fig 1.D) . Lastly, a divergent methyltransferasa region, similar to that of nsp14 or nsp10, exoribonuclease and transferase (MT; PDB structure: 5C8T_B of Human SARS coronavirus guanine-N7 methyltransferase; Probability: 90.11; E-value = 0.12) was found at the 7,642-7,937 aa coordinates. In sum, the predicted ORF1ab protein presents an array of characteristic domains in an architecture typically associated to nidoviruses (NH2-PL-TM1-TM2-3CLpro-TM3-RdRP-ZBD-HEL-MT-COOH) this specific domain order is essential for diverse aspects of the replicative cycle of nidoviruses (Gorbalenya, 2001) . Further characterization of ORF2 encoded protein (PP2) suggests a clear divergence between this polyprotein and ordinary nidoviruses. Nevertheless, divergent but consistent signatures were identified which supports its affinity with BNLV-1. ORF2 encodes a 3,224 polyprotein with an N-terminal signal peptide with a predicted cleavage site between residues Ala 21 and Gly 22 ( Fig.1. A.i-ii). HHPred searches identified at 276-471 aa coordinates of PP2 a Trypsin (TryP; E.C.3.4.21.4) serine protease domain (PDB structure: 5KWM_A; Probability: 98.88; E-value = 4.3e-12). At an equilocal position (128-308 aa coordinates), the ORF2 product of BNLV-1 presents a related domain (Trypsin-like serine protease; Superfamily = SSF50494; E-value = 5.9e-07). While proteases involved in post-translational processing of PP1ab are a hallmark of nidoviruses, evolutionary insights of the detected domain suggest that this peptidase is significantly related to the ones found in the digestive system of many vertebrates, where they hydrolyzes diverse proteins. Future studies should explore the potential source of the detected TryP domain, which might be associated to horizontal transmission from an eventual host. In addition, the C-region of ORF2 of BNLV-1 presents an alphavirus glycoprotein like domain (Superfamily = SSF56983; 1,335-1,546 aa). The A. californica ORF2 product presents an analogous, but highly divergent region with similarity with Torovirinae spike glycoprotein (Sgp; 2,185-3,092 aa; FFAS03 = PF17072.3; 17 % id) at the C-region of the predicted PP2, which could be associated with structural functions.