Virus genome assemblies from GenBank and RefSeq are downloaded from NCBI (Kitts et al., 2016) using genome_updater v. 0.5.1 software¹. The information on the assembly level of each genome (Complete Genome/Chromosome, Scaffold, Contig) is extracted from assembly report files. Nucleotide sequences of viruses present in GenBank or RefSeq but not in the Assembly database are retrieved in FASTA and flat-file formats from NCBI Virus (Hatcher et al., 2017) and the RefSeq FTP server. The obtained sequences are assigned as a “Complete Genome” if they were included in the monthly-update of complete phage genomes in INPHARED (Cook et al., 2021).

National Center for Biotechnology Information (NCBI) taxonomy tables are downloaded from the NCBI FTP server. The ICTV taxonomy of viruses is retrieved from the Virus Metadata Resource at the ICTV website, and species are mapped to the corresponding NCBI taxonomy identifiers based on the RefSeq/GenBank genome accessions provided by ICTV. The GTDB taxonomy of Bacteria and Archaea is obtained from metadata files provided in the latest GTDB release. The bacterial and archaeal lineages are mapped between NCBI and GTDB taxonomies based on the NCBI taxonomy identifiers provided in the GTDB archaeal and bacterial metadata files.

Virus-host assignments are retrieved from: (i) the NCBI Virus website, (ii) the TSV file provided by VirusHost DB, (iii) the text files from MVP, (iv) the GenBank flat files (in the “/isolated_host = “ or “/host = “ qualifiers), (v) the protein-protein interactions from the IntAct FTP server, and (vi) the protein sequence entries in UniProt-SwissProt (“OH” line in UniProt entry). The extracted names and taxonomy identifiers of hosts are queried against NCBI Taxonomy using TaxonKit v. 0.10.1 (Shen and Ren, 2021) to retrieve complete host lineages. Only bacterial and archaeal hosts specified at the species level are included.

For a prokaryotic virus infecting only one host species, the host range is set to this species. For a virus infecting multiple host species, we defined the host range as the taxonomic rank of the last common ancestor of all its hosts in the NCBI taxonomic database.

The PHD web interface was developed in React.js (v. 17.0.2), Next.js (v. 11.1.3) and Highcharts.js (v. 10.0.0). The database querying system was developed in Django (v. 4.0.0), Django REST framework (v. 3.13.1), and Python (v. 3.9.5) using SQLite database as a management system.

As of May 1, 2022, 12,123 virus species have prokaryotic hosts reported at the species level. Only one-quarter of these viruses (24%) have been classified by ICTV, indicating a significant delay between NCBI submissions and classification by the committee. However, the number of taxa at higher ranks, from genus to phylum, is similar between NCBI and ICTV taxonomies (Figure 1A). Both systems classify prokaryotic viruses into 47 families. More than three-quarters of virus species remain in the morphotype-based Siphoviridae, Myoviridae, and Podoviridae families (Figure 1B). These umbrella groups of historical importance gather phages that are without properly resolved phylogenetic taxonomy and are scheduled for dissolution (Adriaenssens, 2021; Turner et al., 2021). Aside from these, the largest family is Autographiviridae, which represents 6% of the total viral species.

Consequently, most sequences in the database come from double-stranded DNA (dsDNA) viruses (Figure 1C). Single-stranded DNA (ssDNA) accounts for only 1% of viral genomes and belong to three orders: Tubulavirales (n = 71), Petitvirales (n = 67), and Haloruvirales (n = 8; two betapleolipovirus species in Haloruvirales have circular dsDNA genomes containing single-stranded discontinuities), and lower taxonomic units not classified at the order level (n = 3). RNA viruses correspond to fewer than one percent of virus species (n = 27) and belong to five families: Cystoviridae (n = 16), Leviviridae (n = 5), Fiersviridae (n = 4), Steitzviridae (n = 1), and Duinviridae (n = 1).

Most virus species (92%) are represented by single genome assembly. The remaining species mainly have two (4%) or three (1%) genomes assigned. The highest number of genomes have been reported for two closely related species, Escherichia virus G4/Gequatrovirus G4 (n = 343) and Escherichia virus phiX174/Sinsheimervirus phiX174 (n = 105). In both cases, the majority of retrieved sequences represents strains obtained during in vitro evolution experiments (Cuevas et al., 2009; Domingo-Calap et al., 2009). Over 92% of virus species (n = 11,195) have complete genomes, and the remaining viruses are represented by genomic fragments (7%; n = 884) or partial genomes at the contig and scaffold levels (1%; n = 44) (Figure 1D). Most virus species are represented only by assemblies from GenBank, but 34% are also covered by the RefSeq database.

The size of complete genomes varies between 1.4 and 551.6 kb, with no homogenous distribution (Figure 1E), which may be due to a bias linked to isolation techniques, sparse sampling of different virus taxa, or natural constraints on the size of viral genomes. Although Campylobacter phage C10 is the shortest phage genome sequence (1,417 bp) submitted to NCBI, the record itself (accession: MG065651) is flagged by the GenBank staff as “unverified”. The second smallest phage genome (2,435 bp) belongs to Leuconostoc phage L5, which is often cited as the phage with the smallest known genome (Dion et al., 2020). At the other end of the distribution (Figure 1E), there are 267 phage species (2%) with genomes of more than 200 kb, often referred to as “jumbo” or “giant” phages (Yuan and Gao, 2017; Al-Shayeb et al., 2020). Such phages have been isolated only for 73 bacterial species from 38 genera, mostly from Erwinia, Vibrio, Aeoromans, Pseudomonas, and Klebsiella. Phages with genomes > 500 kb (Devoto et al., 2019), n = 12) have been isolated from Prevotella species (e.g., Prevotella phage Lak-B8 has the largest genome of 551,627 bp).

Sequenced viruses appear to represent only a small fraction of the actual phage diversity as half of the virus species infect only eight host genera (Mycolicibacterium, Escherichia, Streptococcus, Vibrio, Pseudomonas, Salmonella, Klebsiella, and Staphylococcus) (Figure 1F). One of the reasons for such a disproportion may be biased toward culturable host taxa in isolation efforts, e.g., the SEA-PHAGES program (Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science) that focuses mainly on phages infecting Mycolicibacterium smegmatis (Jordan et al., 2014). In total, the viruses were isolated on 944 prokaryotic species including 875 bacteria and 69 archaea, accounting for 1.5% of all bacterial species (n = 60,136) and 2.7% archaeal species (n = 2,597) reported in NCBI Assembly (Figure 1G). Compared to NCBI Taxonomy, the fraction of bacterial and archaeal species with known viruses is even smaller and corresponds to only 0.2% of bacterial (n = 471,815) and 0.5% of archaeal species (n = 12,718), respectively. Although collectively, host species represent 34 classes, three-quarters of the host species fall into five classes (Gammaproteobacteria, Bacilli, Alphaproteobacteria, Actinomycetia, and Betaproteobacteria) (Figure 1H). Given that all cellular organisms are most likely prey to viral attack (Fuhrman, 1999), these gaps in host diversity indicate that phage genomic diversity and the scope of virus-host interactions remain widely uncharacterized.

To date, there are 12,725 pairwise linkages between 12,123 viral and 944 prokaryotic species. Most viruses (96.1%; n = 11,640) were isolated from single hosts, followed by viruses infecting two host species (3.4%; n = 419) (Figure 1I) mostly from the same genus or family, and sporadically with a broader host range (Pseudomonas virus PB1 reported in two species from different phyla, Pseudomonas and Chryseobacterium). The remaining virus species (0.5%; n = 64) were reported to infect more than two host species (Figure 1I). The record-holder is the Pseudomonas virus PRD1, known to infect nine bacteria species from the Proteobacteria phylum carrying the IncN plasmid.

Most assignments between viral and host species were retrieved from NCBI Virus (93%) and GenBank (87%), followed by Virus-Host DB (35%) and RefSeq (31%) (Figure 1J), indicating that Refseq lags behind the submission of new virus genomes (because sequence records in RefSeq additionally undergo NCBI curation). Over a quarter (29%) of the assignments were covered by all source databases (Figure 1I). Despite this overlap, these databases differ in the content of virus-host assignments. NCBI Virus provides 1,069 virus-host assignments (8%) that were not present in the other source databases. Similarly, GenBank and Virus-Host DB also have specific assignments that correspond to 3 and 2% of all interactions, respectively. The remaining source databases – RefSeq, MVP, UniProt, and IntAct – do not contain unique virus-host assignments, but provide support for 33% of the existing interactions.

Phage & Host Daily (PHD) offers two ways to access information on interactions between virus and host species: by searching for a particular virus/host taxon and browsing taxonomic trees.

The Search view allows users to look for viruses targeting bacterial or archaeal taxa of interest or prokaryotic taxa that are infected by phages from a given viral taxon. The view allows for searches corresponding to the names and identifiers used in NCBI, GTDB, and ICTV taxonomies. For convenience, the search box features an autocomplete functionality that suggests terms matching the user query. The Browse view provides a hierarchical exploration of virus-host interactions through virus or host taxonomies based on NCBI or GTDB Taxonomy. The interactive interface allows users to expand branches of virus or host trees and view the number of virus-host interactions associated with each node.

Once the query taxon is selected from either the Search or Browse view, PHD presents a table of pairwise interactions between viral and host species belonging to the query viral/host. For each virus-host interaction, PHD lists the source database(s), taxonomic affiliations for both viruses and hosts, as well as information on the virus’ genome composition and assembly completeness of the representative virus genome. This is a central component of PHD that can be filtered using multiple combinations of parameters (e.g., all virus-host interactions within Enterobacterales that are supported by RefSeq and Virus-Host DB and contain viruses with complete genomes).

Each virus species has an associated web page indicating host range, genomic sequences, taxonomy, and nomenclature. The available sequence data for a given virus species are organized into genome assemblies with information on assembly level, sequence length, and an indication of a representative genome, and links to NCBI Assembly and NCBI Nucleotide resources.

All virus-host interaction data and viral sequences available through the web interface can be downloaded as JSON, GenBank, and FASTA files.