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Viruses are small compared to the wavelength of visible light; indeed, while the largest virus can be discerned in a good light microscope, the vast majority of viruses can only be visualized in detail using an electron microscope. A size scale with some important landmarks is shown in Figure 5.1.

Virus particles are composed of a nucleic acid genome or core, which is the genetic material of the virus, surrounded by a capsid made up of virus‐encoded proteins. Viral genetic material encodes the structural proteins of the capsid and other viral proteins essential for other functions in initiating virus replication. The entire structure of the virus (the genome, the capsid, and – where present – the envelope) makes up the virion or virus particle. The exterior of this virion contains proteins that interact with specific proteins on the surface of the cell in which the virus replicates. The schematic structures of some well‐characterized viruses are shown in Figure 5.2.

To date, more than 5000 different genotypes of viruses have been identified, and it is estimated that there may be as many as 10⁶ in a kilogram of marine sediment. The National Center for Biological Information (NCBI) database contains more than 8000 complete viral genomes as February 2019. Although perhaps not as overwhelming, the number of different types of viruses associated with terrestrial plants and animals is very high, and, of course, bacteria and protists all have their own populations of associated viruses. Further, there are a very large number of subviral entities, which depend on viruses themselves for replication – these are subviral infectious agents and plant satellite nucleic acid elements that share at least some features of their replication strategies with viruses. And, finally, as we have noted briefly in Part I, there are infectious proteins (prions), which also can be studied using the techniques of virology.

Figure 5.1 A scale of dimensions for biologists. The wavelength of a photon or other subatomic particle is a measure of its energy and its resolving power. An object with dimensions smaller than the wavelength of a photon cannot interact with it, and thus is invisible to it. The dimensions of some important biological features of the natural world are shown. Note that the wavelength of ultraviolet (UV) light is between 400 and 280 nm; objects smaller than that, such as viruses and macromolecules, cannot be seen in visible or UV light. The electron microscope can accelerate electrons to high energies; the resulting short wavelengths can resolve viruses and biological molecules. Note that the length of DNA is a measure of its information content, but since DNA is essentially “one‐dimensional,” it cannot be resolved by light.

The development of self‐consistent classification schemes for this plethora of entities is a major challenge for virologists. Good classification schemes have a major role in helping organize the growing flood of detailed genetic and molecular information concerning viruses and their genes. Further, a valid classification scheme provides an important framework for understanding the different ways that viruses can utilize cellular and their own genes in maintaining themselves within the biosphere. Finally, valid classifications provide useful guides to our understanding of the origins of various virus groups, and the relationships between viruses in the same group and divergent groups.

Figure 5.2 The structure and relative sizes of a number of (a) DNA and (b) RNA viruses. The largest viruses shown have dimensions approaching 300–400 nm and can be just resolved as refractile points in a high‐quality ultraviolet‐light microscope. The smallest dimensions of viruses shown here are on the order of 25 nm. Classifications of viruses based on the type of nucleic acid serving as the genome and the shape of the capsid are described in the text. ss: Single stranded; ds: double stranded.

The International Committee on Taxonomy of Viruses (ICTV) was created at an international conference on microbiology in Moscow in 1966 in order to develop a single, universal taxonomic scheme for all the viruses infecting animals (vertebrates, invertebrates, and protozoa), plants (higher plants and algae), fungi, bacteria, and archaea. Its membership is made up of distinguished virologists throughout the world, and it has issued periodic reports describing its progress, and its problems, as well as databases containing the properties of viruses and appropriate computer‐based tools for utilizing such databases. One of the notable achievements of this group and the community of virologists that it represents is the recognition of a limited number of viral features that can be used for classification; these include the nature of the viral genome, the presence of an envelope, and the morphology of the virus particle. The classification scheme uses the designation of “family,” even though these phylogenetic terms do not strictly apply in the case of viruses. Table 5.1 lists the families of this scheme, in alphabetical order, as of their 2018 report.

Table 5.1 Classification of viruses according to the ICTV.

Family	Nature of the genome	Presence of an envelope	Morphology	Genome configuration	Genome size (kbp or kb)	Host
Abyssoviridae	ssRNA			+
Ackermannviridae	dsDNA	−	Icosahedral tailed	1 linear	155	Bacteria
Adenoviridae	dsDNA	−	Isometric	1 linear	28–45	Vertebrates
Alloherpesviridae	dsDNA	+	Isometric	1 linear	134–248	Vertebrates
Alphaflexiviridae	ssRNA	−	Filamentous	1 + segment	7–9	Plants
Alphasatellitidae	ssDNA	−	N/A	1 linear	1.3–1.4	Plants
Alphatetraviridae	ssRNA	−	Isometric	1 linear	6.5	Invertebrates
Alvernaviridae	ssRNA	−	Isometric	1 linear	4.4	Dinoflagellates
Amalgaviridae	dsRNA	−	Isometric	1 linear	3.5	Plants
Ampullaviridae	dsDNA	+	Bottle‐shaped	1 linear	23.8	Archaea
Anelloviridae	ssDNA	−	Isometric	1 linear	3–4	Vertebrates
Arenaviridae	NssRNA	+	Spherical	2 ± segments	11	Vertebrates
Arteriviridae	ssRNA	+	Isometric	1 + segment	13–16	Vertebrates
Artoviridae	ssRNA	+	Spherical	1 − linear	12.3	Invertebrates and vertebrates
Ascoviridae	dsDNA	+	Reniform	1 linear	100–180	Invertebrates
Asfarviridae	dsDNA	+	Spherical	1 circular	170–190	Vertebrates
Aspiviridae	ssRNA	−	Filamentous	3–4 – linear	11.3–12.5	Plants
Astroviridae	ssRNA	−	Isometric	1 + segment	7–8	Vertebrates
Avsunviroidae	ssRNA	N/A	N/A	1 + circular	0.25	Plant viroids
Bacilladnaviridae	ssDNA	−	Isometric	1 circular	5–6	Diatoms
Baculoviridae	dsDNA	+	Bacilliform	1 circular supercoiled	80–180	Invertebrates
Barnaviridae	ssRNA	−	Bacilliform	1 + segment	4	Fungi
Belpaoviridae	ssRNA (RT)	N/A	N/A	1 linear	?	Invertebrates
Benyviridae	ssRNA	−	Rod‐shaped	4/5 + segments	14–16	Plants
Betaflexiviridae	ssRNA	−	Filamentous	1 linear	6.5–9	Plants, fungi
Bicaudaviridae	dsDNA	+	Lemon‐shaped	1 circular	62	Archaea
Bidnaviridae	ssDNA	−	Isometric	2 linear	6 and 6.5	Invertebrates
Birnaviridae	dsRNA	−	Isometric	2 segments	6	Vertebrates and invertebrates
Bornaviridae	NssRNA	+	Spherical	1 − segment	6	Vertebrates
Bromoviridae	ssRNA	−	Isometric	3 + segments	8–9	Plants
Caliciviridae	ssRNA	−	Isometric	1 + segment	7–8	Vertebrates
Carmotetraviridae	ssRNA	−	Isometric	1 linear	6.1	Invertebrates
Caulimoviridae	dsDNA‐RT	−	Isometric, bacilliform	1 circular	8	Plants
Chrysoviridae	dsRNA	−	Isometric	4 linear	2.9–3.6	Fungi
Chuviridae	ssRNA	?	?	? (negative sense)	?	Invertebrates
Circoviridae	ssDNA	−	Isometric	1 circular	2	Vertebrates
Clavaviridae	dsDNA		Bacilliform	1 circular	5.3	Archaea
Closteroviridae	ssRNA	−	Filamentous	1/2 + segments	15–19	Plants
Coronaviridae	ssRNA	+	Isometric	1 + segment	27–31	Vertebrates
Corticoviridae	dsDNA	−	Isometric	1 circular supercoiled	9	Bacteria
Cruliviridae	ssRNA	?	?	? (negative sense)	?	Invertebrates
Cystoviridae	dsRNA	+	Spherical	3 segments	13	Bacteria
Deltaflexiviridae	ssRNA	?	?	1 + sense	6–8	Fungi, plants
Dicistroviridase	ssRNA	−	Isometric	1 linear	8.5–10.2	Invertebrates
Endornaviridae	dsRNA	N/A	No true capsid	1 linear	14	Plants
Euroniviridae	ssRNA	?	?	?	?	?
Filoviridae	NssRNA	+	Bacilliform	1 − segment	19	Vertebrates
Fimoviridae	ssRNA	+	Spherical	4 − sense segments	12	Plants
Flaviviridae	ssRNA	+	Isometric	1 + segment	10–12	Vertebrates
Fuselloviridae	dsDNA	+	Lemon‐shaped	1 circular supercoiled	15	Archaea
Gammaflexiviridae	ssRNA	−	Filamentous	1 linear	6.8	Plants
Geminiviridae	ssDNA	−	Isometric	1 or 2 circular	3–6	Plants
Genomoviridae	ssDNA	−	Isometric	1 circular +/−	2.17	Mammals, birds, fungi
Globuloviridae	dsDNA	+	Spherical	1 circular	20–30	Archaea
Guttaviridae	dsDNA	+	Ovoid	1 circular	20	Archaea
Hantaviridae	ssRNA	+	Spherical	3 linear negative sense	11–20	Humans, rodents
Hepadnaviridae	dsDNA‐RT	+	Spherical	1 circular	3	Vertebrates
Hepeviridae	ssRNA	−	Isometric	1 linear	7.2	Vertebrates
Herpesviridae	dsDNA	+	Isometric	1 linear	125–240	Vertebrates
Hypoviridae	dsRNA	−	Pleomorphic	1 segment	12	Fungi
Hytrosaviridae	dsDNA	+	Filamentous	1 circular	120–190	Insects
Iflaviridae	ssRNA	−	Isometric	1 linear	8.8–9.7	Invertebrates
Inoviridae	ssDNA	−	Filamentous	1 + circular	7–9	Bacteria, mycoplasmas
Iridoviridae	dsDNA	−	Isometric	1 linear	140–383	Vertebrates and invertebrates
Lavidaviridae	dsDNA	−	Isometric	1 circular	17–30	Protists
Leviviridae	ssRNA	−	Isometric	1 + segment	3–4	Bacteria
Lipothrixviridae	dsDNA	+	Rod‐shaped	1 linear	16	Archaea
Lispiviridae	ssRNA	+ (?)	Spherical (?)	1, linear	12	Arachnids
Luteoviridae	ssRNA	−	Isometric	1 + segment	6	Plants
Malacoherpesviridae	dsDNA	+	Spherical	1 linear	150	Mollusks
Marnaviridae	ssRNA	−	Isometric	1 linear	8.6	Seaweed
Marseilleviridae	dsDNA	−	Isometric	1 circular	368	Amoeba
Medioniviridae	ssRNA	?	?	?	?	Tunicates
Megabirnaviridae	dsRNA	−	Isometric	Linear, segmented	7	Fungi
Mesoniviridae	ssRNA	+	Spherical	1 linear	20	Vertebrates
Metaviridae	ssRNA	−	RT‐spherical	1 + segment	4–10	Fungi, plants, invertebrates
Microviridae	ssDNA	−	Isometric	1 + circular	4–6	Bacteria, spiroplasmas
Mimiviridae	dsDNA	−	Isometric	1 linear	1200	Amoeba
Mymonaviridae	ssRNA	+	Filamentous	1 linear	10	Fungi
Myoviridae	dsDNA	−	Tailed phage	1 linear	39–169	Bacteria, archaea
Nairoviridae	ssRNA	+	Spherical	3 linear negative sense	11–20	Vertebrates, arthropods
Nanoviridae	ssDNA	−	Isometric	6–9 circular	6–9	Plants
Narnaviridae	ssRNA	−	RNP complex	1 + segment	2–3	Fungi
Nimaviridae	dsDNA	+	Ovoid	1 circular	293	Crustaceans
Nodaviridae	ssRNA	−	Isometric	2 + segments	4–5	Vertebrates and invertebrates
Nudiviridae	dsDNA	+	Rod‐shaped	1 circular	96–231	Invertebrates
Nyamiviridae	ssRNA	+	Spherical	1 linear	11.6	Birds, invertebrates
Orthomyxoviridae	NssRNA	+	Pleomorphic	6–8 − segments	10–15	Vertebrates
Papillomaviridae	dsDNA	−	Isometric	1 circular	7–8	Vertebrates
Paramyxoviridae	NssRNA	+	Pleomorphic	1 − segment	15	Vertebrates
Partitiviridae	dsRNA	−	Isometric	2 segments	4–6	Plants, fungi
Parvoviridae	ssDNA	−	Isometric	1 +/− circular	4–6	Vertebrates and invertebrates
Peribunyaviridae	ssRNA	+	Spherical	3, linear, negative sense	11–20	Humans, rodents, arthropods
Permutotetraviridae	ssRNA	−	Isometric	1 linear	5.6	Invertebrates
Phasmaviridae	ssRNA	+	Spherical	3, linear, negative sense	10.3	Insects
Phenuiviridae	ssRNA	+	Spherical	3, linear, negative sense	11–20	Ruminants, camels, humans, mosquitos
Phycodnaviridae	dsDNA	−	Isometric	1 linear	160–380	Algae
Picobirnaviridae	dsRNA	−	Isometric	2 linear segments	2.5 + 1.7	Mammals
Picornaviridae	ssRNA	−	Isometric	1 + segment	7–8	Vertebrates
Plasmaviridae	dsDNA	+	Pleomorphic	1 circular	12	Mycoplasmas
Pleolipoviridae	ssDNA or dsDNA	+	Pleomorphic	1 circular or linear	7–16	Archaea
Pneumoviridae	ssRNA	+	Spherical	1 linear	15	Vertebrates
Podoviridae	dsDNA	−	Tailed phage	1 linear	19–44	Bacteria
Polycipiviridae	ssRNA	−	Isometric	1 linear + sense	11	Insects
Polydnaviridae	dsDNA	+	Rod, fusiform	Multiple supercoiled	150–250	Invertebrates
Polyomaviridae	dsDNA	−	Isometric	1 circular	5	Vertebrates
Portogloboviridae	dsDNA	−	Isometric	1 circular	20	Sulfolobus S38A archaea
Pospiviroidae	ssRNA	N/A	N/A	1 circular	0.24–0.4	Plants
Potyviridae	ssRNA	−	Filamentous	1/2 + segments	8–12	Plants
Poxviridae	dsDNA	+	Pleomorphic	1 linear	130–375	Vertebrates and invertebrates
Pseudoviridae	ssRNA	−	RT‐spherical	1 + segment	5–8	Fungi, plants, invertebrates
Qinviridae	ssRNA	?	?	?	?	?
Quadriviridae	dsRNA	+	Spherical	Linear, 4 segments	16.8	Fungi
Reoviridae	dsRNA	−	Isometric	10–12 segments	19–32	Vertebrates and invertebrates, plants
Retroviridae	ssRNA	−	RT + spherical	1 dimer + segment	7–12	Vertebrates
Rhabdoviridae	NssRNA	+	Bullet‐shaped	1 − segment	11–15	Vertebrates, plants
Roniviridae	ssRNA	+	Bacilliform	1 linear	26	Crustaceans
Rudiviridae	dsDNA	+	Rod‐shaped	1 linear	33–36	Archaea
Sarthroviridae	ssRNA	−	Isometric	1 linear	0.9	Crustaceans
Secoviridae	ssRNA	−	Isometric	Linear/segmented	24	Plants
Siphoviridae	dsDNA	−	Tailed phage	1 linear	22–121	Bacteria, archaea
Smacoviridae	ssDNA	−	Isometric	1 circular	2.3–2.8	Vertebrates (?)
Sphaerolipoviridae	dsDNA	−	Isometric	1 circular	16–19	Bacteria, archaea
Spiraviridae	ssDNA	−	Cylindrical	1 circular	25	Archaea
Sunviridae	ssRNA	?	?	?	17	Vertebrates
Tectiviridae	dsDNA	−	Isometric	1 linear	15	Bacteria
Tobaniviridae	ssRNA	+	Spherical	1 + segment	28	Vertebrates
Togaviridae	ssRNA	+	Isometric	1 + segment	10–12	Vertebrates
Tolecusatellitidae	ssDNA	N/A	N/A	1	0.7–1.35	Plants
Tombusviridae	ssRNA	−	Isometric	1/2 + segments	4–5	Plants
Totiviridae	dsRNA	−	Isometric	1 segment	5–7	Fungi, protozoa
Tristromaviridae	dsDNA	+	Rod‐shaped	1 linear	15.9	Archaea
Turriviridae	dsDNA	−	Isometric	1 circular	17.6	Archaea
Tymoviridae	ssRNA	−	Isometric	1 linear	6.5–7	Plants
Virgaviridae	ssRNA	−	Rod‐shaped	Linear, segmented, or nonsegmented	3.3–6.5	Plants
Wupedeviridae	ssRNA	?	?	?	?	Insects
Xinmoviridae	ssRNA	?	?	1 linear, − sense	12	Mosquitoes
Yueviridae	ssRNA	?	?	− sense	?	?

+ sense: Positive‐sense; − sense: negative‐sense; dsRNA: double‐stranded RNA; N/A: not applicable; NssRNA: negative‐sense single‐stranded RNA; RNP: ribonucleoprotein; RT: reverse transcriptase; ssRNA: single‐stranded RNA.