Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

Abstract

The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55–58% sequence diversity threshold range for genera and at the 23–36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses

“…We suggest the species be named Bombali ebolavirus to reflect the location of first detection, as is consistent with the naming of other ebolavirus species. Assessment using NCBI’s PASC tool supported this new species assignment and it meets all criteria for a novel virus species suggested by Bao et al 10 (Supplemental Figure 3). Overall, the virus showed 55–59% nucleotide identity (64–72% amino acid) to other ebolaviruses, though areas of high sequence conservation and high variability were identified throughout the genome (Supplemental Figure 4).…”

“…Alignments and trees were created separately for each gene and a concatenation was used for the complete genome. Sequences were also analyzed using the PASC tool (NCBI) to classify sequences taxonomically 10 . The nucleotide alignment of the ebolavirus genomes was screened for recombination using the seven algorithms in the Recombination Detection Program (RDP version 4.87).…”

Minimum Information about an Uncultivated Virus Genome (MIUViG)

“…5). In addition, vOTU reports should include the clustering method and cutoff, the reference database used (if any), and the genome alignment approach because small differences have been observed between different methods 61 (Supplementary Table 1).…”

First Evidence of Antibodies Against Lloviu Virus in Schreiber’s Bent-Winged Insectivorous Bats Demonstrate a Wide Circulation of the Virus in Spain

“…This family is composed of five genera, Ebolavirus , Marburgvirus , Cuevavirus, Striavirus and Thamnovirus . The only member of the Cuevavirus genus discovered to date, Lloviu virus (LLOV), was described in 2011 [1,2,3]. LLOV is believed to be the first filovirus detected in Europe that was not imported from an endemic area in Africa or Asia.…”