The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [8], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.

  1. 1.

    New appointments. The committee has been enlarged through the additions of Drs. J. Rodney Brister (Chair—Molecular Typing), Ho Bin Jang (Member), Petar Knezevic (Chair—ICTV Inoviridae Study Group), Hanna M. Oksanen (Chair—ICTV Corticoviridae Study Group), and Minna M. Poranen (Chair—ICTV Cystoviridae Study Group). In addition, Dr. Mart Krupovic has taken over the Chairmanship of the ICTV Plasmaviridae Study Group.

  2. 2.

    Future of the order Caudovirales. With the dramatic increase in the number of characterized tailed bacterial and archaeal viruses, it is becoming increasingly clear that the order Caudovirales (and the three included families Myoviridae, Siphoviridae and Podoviridae) can no longer sustain the huge genetic diversity within this virus group [5] and has to be adequately reorganized. Indeed, taxonomic hurdles with this and some other expansive groups of viruses, prompted ICTV to explore the possibility of introducing additional taxonomic levels. Initial ideas and plans were presented to the microbial viruses community at the 2016 EMBO conference “Viruses of Microbes IV” (Liverpool, UK). Currently, the Bacterial and Archaeal Viruses Subcommittee is examining the consistency of the order Caudovirales on the example of a diverse group of phages currently classified in the subfamily Spounavirinae [2, 6, 7, 9, 12]. We applied a range of complementary DNA and protein sequence analysis tools as well as phylogenetic methods to the analysis of 93 Bacillus, Enterococcus, Listeria, and Staphylococcus phages with large genomes (≈110–160 kb). A manuscript describing our findings is in preparation, and the appropriate TaxoProps will be submitted.

  3. 3.

    Taxonomy of prokaryotic viruses found in GenBank. Genome sequences of prokaryotic viruses are accumulating in public sequence databases, such as GenBank, at an increasing rate. Oftentimes, these sequences are being deposited without or with only minimal taxonomy descriptions. To appropriately classify these viruses, the Subcommittee adopted a holistic approach with the first-line discriminator being DNA sequence identity (calculated using NCBI BLASTN [3, 10] or Gegenees BLASTN [1]) of the genome in question to those of previously classified viruses. Next, overall protein identity was calculated using Gegenees TBLASTX for large datasets and CoreGenes 3.5 [11] for smaller sets. Lastly, phylogenetic analyses of one to three conserved phage proteins, often including the large subunit of the terminase and major capsid proteins or DNA-replication-associated proteins, were carried out using maximum-likelihood method as implemented at Phylogeny.fr [4]. The changes described here were formalized and submitted in more than 80 ICTV TaxoProps for consideration by the ICTV EC (http://www.ictvonline.org). One new archaeal virus family (Tristromaviridae), six new bacteriophage subfamilies (Ounavirinae [Salmonella phage FelixO1], Sepvirinae [Escherichia phage 933 W], Arquatrovirinae [Streptomyces phage R4], Bclasvirinae [Mycobacterium phage Acadian], Mclasvirinae [Mycobacterium phage Pipefish] and Pclasvirinae [Mycobacterium phage Fishburne]), and 88 new genera including 249 species are covered in these proposals (Table 1). These proposals were submitted to the ICTV EC in 2016 for approval. In addition, another 70 phages and one archaeal virus belonging to existing genera were classified. Of particular note is a fundamental reorganization of the family Inoviridae by Petar Knezevic, Chair of the Inoviridae Study Group, who has rearranged the two existing genera (Inovirus and Plectovirus), created five new genera and 17 new species, reassigned 12 previously approved species, and deleted 29 species.

    Table 1 Taxonomy proposals (TaxoProps) describing new taxa (families, subfamilies, genera) submitted to the ICTV Executive Committee in 2016