Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis

Abstract

During the last decade, genome sequence-based classification of viruses has become increasingly prominent. Viruses can be even classified based on coding-complete genome sequence data alone. Nevertheless, classification remains arduous as experts are required to establish phylogenetic trees to depict the evolutionary relationships of such sequences for preliminary taxonomic placement. Pairwise sequence comparison (PASC) of genomes is one of several novel methods for establishing relationships among viruses. This method, provided by the US National Center for Biotechnology Information as an open-access tool, circumvents phylogenetics, and yet PASC results are often in agreement with those of phylogenetic analyses. Computationally inexpensive, PASC can be easily performed by non-taxonomists. Here we describe how to use the PASC tool for the preliminary classification of novel viral hemorrhagic fever-causing viruses.

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

“…Redundant filovirus genome sequences (here defined as sequences with PASC identities >99.5%) were removed, leaving 112 filovirus genome sequences for further analysis [ 20 ]. PASC analysis was performed with those 112 genome sequences as previously described [ 18 ] using the open-access PASC tool (NCBI). The new taxon demarcation algorithm/flowchart was developed based on the previously developed chart presented in [ 10 ] using type filoviruses [ 4 ] and type filovirus genome sequences (RefSeq, NCBI) [ 10 ].…”

“…The number of GenBank-deposited near-complete, coding-complete, and complete filovirus genome sequences has increased substantially in recent years (from the ≈50 in 2012 to ≈1400 at the time of writing in 2017). We analyzed these sequences using PASC, a method that can be easily used by any scientist using an open-access software platform [ 16 , 17 , 18 ]. We created inferred objective filovirus taxon demarcation criteria and updated the algorithm/flowchart for filovirus taxon assignment using the recently decided type filovirus sequences (NCBI RefSeq database sequences) [ 10 ] as starting points.…”