Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle-shaped viruses that putatively infect mesophilic ammonia-oxidizing archaea

The genome of a putative Nitrosopumilaceae virus with a hypothetical spindle-shaped particle morphology was identified in the Yangshan Harbour metavirome from the East China Sea through protein similarity comparison and structure analysis. This discovery was accompanied by a set of 10 geographically dispersed close relatives found in the environmental virus datasets from typical locations of ammonia-oxidizing archaeon distribution. Its host prediction was supported by iPHoP prediction and protein sequence similarity. The structure of the predicted major capsid protein, together with the overall N-glycosylation site, the transmembrane helices prediction, the hydrophilicity profile, and the docking simulation of the major capsid proteins, indicate that these viruses resemble spindle-shaped viruses. It suggests a similarly assembled structure and, consequently, a possibly spindle-shaped morphology of these newly discovered archaeal viruses. A putative Nitrosopumilaceae virus with a spindle-shaped morphology was identified in the Yangshan Harbour metavirome. Its potential major capsid protein was annotated manually through structural comparison, N-glycosylation site recognition, hydrophilicity prediction, transmembrane helices prediction, and docking simulation. Its host prediction was supported by iPHoP prediction and protein sequence similarity. Its 10 close relatives were found in geographically diverse locations of typical ammonia-oxidizing archaea distribution, representing a new branch of archaeal viruses of putatively spindle-shaped morphology and global distribution.image