Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names

Abstract

Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information's (NCBI's) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [<virus name> (<strain>)/<isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.

Figure 1

Genome-based classification of novel filoviruses or filovirus genomic sequences. Viruses are classified in the family Filoviridae (order Mononegavirales) based on a list of biophysical criteria, genomic organization, the type of disease the viruses cause in primates, geographic distribution, and morphology of their virions (outlined in [11,12]). Once a novel virus isolate clearly belongs to this family, genomic sequence comparison can help classification into lower taxa. Novel isolates are classified by comparing the genomic sequence of the new isolate first to the genomic sequences to the type viruses of the ICTV-accepted genera, and then to viruses of the ICTV-accepted species. Using taxon-specific genomic sequence divergence cut-offs, the novel isolate can then be automatically classified into existing taxa, unless they require the establishment of novel taxa through existing ICTV mechanisms.