Taxonomy of prokaryotic viruses update from the I

Authors: Mart Krupovic Bas E Dutilh Evelien M Adriaenssens Johannes Wittmann Finn K Vogensen Mathew B Sullivan Janis Rumnieks David Prangishvili Rob Lavigne Andrew M Kropinski Jochen Klumpp Annika Gillis Francois Enault Rob A Edwards Siobain Duffy Martha R C Clokie Jakub Barylski HansWolfgang Ackermann Jens H Kuhn

Publish Date: 2016/01/05

Volume: 161, Issue: 4, Pages: 1095-1099

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Abstract

The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or the institutions and companies affiliated with the authors The taxonomic changes summarized here have been submitted as official taxonomic proposals to the International Committee on Taxonomy of Viruses ICTV wwwictvonlineorg and are by now accepted but not yet ratified These changes therefore may differ from any new taxonomy that is ultimately approved by the ICTVreplacement of “ phage ” with “ virus ” in prokaryotic virus taxon names In recognition of the fact that phages are first and foremost genuine viruses and to adhere to ICTV’s International Code of Virus Classification and Nomenclature ICVCN the word “phage” will disappear from taxon names but not from phage names For instance the current taxon Escherichia phage T4 will be renamed Escherichia virus T4 while the name of this taxon’s member will remain unchanged Escherichia phage T4 It is important that the community remembers the ICVCN distinction between viral taxa such as species genera families or orders and their members the actual viruses/phages “viruses are real physical entities produced by biological evolution and genetics whereas virus species and higher taxa are abstract concepts produced by rational thought and logic”elimination of the infix “ like ” from prokaryotic virus genus names The naming of phage taxa has been an evolving process with genus names in the form “P22like virus” which was always considered to be a stopgap measure being replaced by P22likevirus However the latter convention is also problematic since it was only applied to genera included in the order Caudovirales and the infix “like” was unnecessary since the grouping of viruses in genera implies per se that their constituent members are alike Consequently the infix “like” will be removed from the names of phage genera and genus names such as Lambdalikevirus and T4likevirus will become Lambdavirus and T4virus respectively It will of course remain correct to refer to “lambdalike viruses” and “T4like phages” during discussions regarding specific groups of phages classified in these taxa There have also been discussions in the Subcommittee whether all prokaryotic virus genera should adopt the system used for some archaeal and eukaryotic viruses in which names of genera are created from the root of the corresponding family name with sequentially appended transliterated Greek letters eg Alphabaculovirus Betabaculovirus etc However it was decided that recognition of new genus names is of paramount importance and that further drastic changes in one setting might overly confuse the community Thus in most cases the infix “like” was merely removed and the name of the founding member of the genus was retained as a root of the taxon namediscontinuation of the use of “ Phi ” and other transliterated Greek letters in the naming of new prokaryotic virus genera Since some scientists are under the impression that “Phi” in its various forms phi φ Φ indicates a phage over the years many phages were given names containing the prefix “Phi” However the prefix “Phi” adds no informational value when naming phage genera Consequently the Subcommittee decided that unless there was sufficient historical precedent eg Φ29 or ΦX174 Phi would no longer be added to genus names In addition Greek letters can create problems in electronic databases as exemplified by a PubMed search for references on Bacillus phage Φ29 1 which retrieved articles on phi 29 phi29 Phi 29 Phi29 29 phi phi29 φ29 and φ29 phages Therefore the Subcommittee strongly discourages phage scientists from using Phi or any other Greek letter in virus and virus taxon names in the futureelimination of hyphens from taxon names The ICVCN discourages hyphens in virus taxon names Accordingly taxon names such as Yersinia phage L413C have been renamed in this instance to Yersinia virus L413C However hyphens are retained when appearing in a number string Thermus phage P2345 becomes Thermus virus P2345 its correct name 2inclusion of the isolation host name in the taxon name On several occasions terms such as “Enterobacteria” or “Pseudomonad” have been used in phage taxon names However such terms do not refer to a specific bacterial host nor do they indicate whether the phage in question was tested upon a variety of members of the particular host group To improve the situation terms such as “Enterobacteria” or “Pseudomonad” in taxon names will be replaced with the isolation host genus name for instance Enterobacteria phage T7 will become Escherichia virus T7 In addition host species names will be eliminated from taxon names For example Thermus thermophilus phage IN93 will become Thermus virus IN93DNADNA relatedness is the gold standard in the classification of all prokaryotes 3 4 5 6 7 and efforts are underway to move towards a completely genomic taxonomy in that field 8 The Bacterial and Archaeal Viruses Subcommittee has previously used overall proteome similarity to define genera and subfamilies with 40  homologous proteins indicating membership in the same genus 9 10 11 This has resulted in spurious taxonomic lumping 12 13 14 Furthermore EMBOSS Stretcher 15 16 which has been used for calculating nucleotide similarities between related phages eg 17 suffers from certain limitations in particular the requirement for the genomes to be collinear Problems with EMBOSS Stretcher are highlighted when an alignment of the phage T7 genome with a randomly shuffled T7 DNA sequence http//wwwbioinformaticsorg/sms2/shuffle dnahtml is attempted The resulting value 476  identity demonstrates that EMBOSS Stretcher values below a certain threshold are meaningless Accordingly more recent phage classification efforts have explored alternative approaches Specifically BLASTN 19 was found to be superior to EMBOSS Stretcher for identification and quantitative comparison of closely related phages 16 Indeed a BLASTN search seeded with the shuffled sequence of phage T7 specifically against “Enterobacteria phage T7” results in no detectable similarity as expected from a randomized sequence with 484  GC content Moreover BLASTN has also been used to determine relationships between phages at larger phylogenetic distances 17 18 although the meaning of a similarity search hit in the absence of a trueshared ancestry remains unclear Most of the newer programs that calculate phylogenetic relationships between genome sequences including CLANS 20 GEGENEES 21 and mVISTA 22 are based upon sequence similarity analyses such as provided by BLASTN 19 Complete and nearcomplete viral genome and protein homologies will be the focus of the Bacterial and Archaeal Viruses Subcommittee’s attention in 2016 to develop clearer parameters for the molecular definition of genera subfamilies and families

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