Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names.

Kuhn JH1, Andersen KG2, Bào Y3, Bavari S4, Becker S5, Bennett RS6, Bergman NH7, Blinkova O8, Bradfute S9, Brister JR10, Bukreyev A11, Chandran K12,Chepurnov AA13, Davey RA14, Dietzgen RG15, Doggett NA16, Dolnik O17, Dye JM18, Enterlein S19, Fenimore PW20, Formenty P21, Freiberg AN22, Garry RF23,Garza NL24, Gire SK25, Gonzalez JP26, Griffiths A27, Happi CT28, Hensley LE29, Herbert AS30, Hevey MC31, Hoenen T32, Honko AN33, Ignatyev GM34, Jahrling PB35, Johnson JC36, Johnson KM37, Kindrachuk J38, Klenk HD39, Kobinger G40, Kochel TJ41, Lackemeyer MG42, Leroy EM43, Lever MS44, Mühlberger E45,Netesov SV46, Olinger GG47, Omilabu SA48, Palacios G49, Panchal RG50, Park DJ51, Patterson JL52, Paweska JT53, Peters CJ54, Pettitt J55, Pitt L56,Radoshitzky SR57, Ryabchikova EI58, Saphire EO59, Sabeti PC60, Sealfon R61, Smither SJ62, Sullivan NJ63, Swanepoel R64, Takada A65, Towner JS66, van der Groen G67, Volchkov VE68, Volchkova VA69, Wahl-Jensen V70, Warren TK71, Warfield KL72, Weidmann M73, Nichol ST74, Fackner DF75, Shestopalov AM76.

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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.