Volvereviria

Volvereviria is a realm of bacterial viruses (bacteriophages) that have single-stranded DNA (ssDNA) genomes and a hallmark single jelly roll fold (SJR) major capsid protein (MCP). Viruses in the realm are commonly called microviruses. They are known for their small, circular ssDNA genomes and small physical size of 25–30 nanometers in diameter, which is why they are called microviruses. The MCP is the primary component of the capsid, a protein shell that surrounds the genome. In addition to the MCP, microviruses encode an endonuclease that is involved in rolling circle replication (RCR) of the genome. Most microviruses also encode a DNA pilot protein that transports the genome into cells. Microvirus extracellular particles (virions) consist of the genome encased in an icosahedral capsid. Virions also contain numerous copies of the DNA pilot protein as well as protrusions, such as spikes, on the surface of the capsid. Microvirus virions do not have a viral envelope. They infect cells by binding to receptors on the cell surface, after which pilot proteins guide the genome into the cell. The genome is converted to a double-stranded DNA form and replicated through RCR. Progeny genomes are packaged into newly constructed capsids, which leave the bacterium through the rupturing of the cell membrane (lysis). Compared to double-stranded DNA viruses and other DNA bacteriophages, microviruses have a high mutation rate, albeit lower than that of RNA viruses. Microviruses are widespread in bacteria, but individual microviruses tend to have narrow host ranges, infecting only a few species or strains of a species. They are the most abundant ssDNA viruses in the world and have been found in nearly every environment analyzed. Microviruses are believed to originate from a RCR plasmid that recombined with an RNA virus or host DNA to obtain the SJR MCP. The first to be discovered was phiX174, in the 1930s. Microviruses were first grouped together in the family Microviridae, which became official in 1978. In 2020, they were assigned to the kingdom Sangervirae in the realm Monodnaviria. In 2026, Monodnaviria was split into four realms corresponding to its four kingdoms after evidence showed the kingdoms had different evolutionary origins. This gave microviruses their own realm, Volvereviria.

Classification Volvereviria is monotypic down to the rank of its sole class, Microviricetes, which has seven orders. This is shown hereafter:

Realm: Volvereviria Kingdom: Sangervirae Phylum: Phixviricota Class: Microviricetes Order: Alpavirales Order: Amoyvirales Order: Bullavirales, which contains phiX174 Order: Gokushovirales Order: Reekeekeevirales Order: Roodoodoovirales Order: Secretvirales

Characteristics

Genome

Volverevirians, i.e. microviruses, have circular, positive-sense, single-stranded DNA genomes. Isolated microvirus genomes range from about 4,200 to 6,100 nucleotides in length, whereas genomes derived from metagenomics expand the range to 3,000 to 8,900 nucleotides in length. Most of the genome is made of three core genes that encode a major capsid protein (MCP), an endonuclease, and a DNA pilot protein. Varying numbers of smaller genes that encode other proteins are also present. Genomes have many overlapping reading frames.

Proteins

Major capsid protein Microviruses encode a major capisd protein, called F or VP1 (viral protein 1) for certain phages, numerous copies of which form the capsid. The MCP has a single jelly roll (SJR) motif that consists of eight antiparallel beta-barrel strands connected by loops. The eight beta strands are organized into two beta sheets named βBIDG and βCHEF. The two sheets are arranged in such a manner that the βBIDG sheet forms the interior surface of the capsid, while the βCHEF sheet is mostly buried within the walls of the capsid. The loops of the MCP contribute to the features of the capsid's exterior surface and mediate interactions with specific cellular receptors.

Replication-initiator protein Microviruses encode a replication-initiator protein that contains a HUH superfamily endonuclease domain. Endonucleases are enzymes that can cleave phosphodiester bonds within a polynucleotide chain. HUH endonucleases contain three conserved motifs: a UUTU motif, which is believed to be involved in recognizing replication origins; the HUH motif, made of two histidine (H) residues separated by a hydrophobic residue (U), which is involved with coordinating Mg2+ or Mn2+ ions, which are necessary for endonuclease activity; and the YxxK/YxxKY motif, which is involved in dsDNA cleavage and covalent attachment of Rep to DNA through its tyrosine (Y) residue. The HUH endonuclease of ssDNA viruses is often called the replication-initiator protein, or Rep, because of its role in commencing replication. Other names of the microvirus Rep protein include A and VP4.

Other proteins Most microviruses also encode a multifunctional alpha-helical DNA pilot protein (F or VP2). The pilot protein guides genomic ssDNA from the capsid into the host by organizing into multimers that form an extendable tunnel through which ssDNA passes. Although the pilot protein is a hallmark trait of microviruses, its gene's sequence diversity means it can't be used to identify viruses belonging to the realm. Other common proteins encoded by microviruses include scaffold folding and DNA-binding and packaging proteins, used for assembling virions, as well as spike proteins. There are also predicted, nonessential coding sequences related to host cell lysis, anti-immune system proteins, and secretion signals. The vast majority of these minor proteins, however, do not have known functions. Unlike other DNA phages, microviruses do not have genes that encode supplementary metabolic proteins.

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