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

Given the considerable number of viral reads, a tentative assessment of AcNV variability was generated. Polymorphic sites were defined with a conservative estimated frequency of at least ≥ 0.05 and a Phred score of 20 or higher to filter raw reads. Considering that sequencing errors of the diverse platforms reach at most ~1 % (Ion Torrent data), thus a 5% frequency threshold enables the detection of probable true variants in the virus RNA genome with high confidence. Cotten et al (2013) , with a similar strategy, explored virus variants of human betacoronavirus using as threshold 1 %. A 5% frequency threshold was used by Van den Hoecke et al (2015) to assess the variation landscape of Influenza virus A. The detected variability among bioprojects appears to be non-significant or within the levels of intra-host variability. While dispersed in time, most NGS libraries were generated from lab reared animals from the same provider. Thus it is tempting to suggest (this is pure speculation) that the low intrinsic variability observed could be linked with a single virus lineage maintained inadvertently through the years at the breeder facilities.