Orthomyxoviridae

The family Orthomyxoviridae (Greek μύξα myxa, German 'slime') comprises enveloped viruses with single-stranded RNA with negative polarity as genome. Their RNA genome is distributed over several segments, which is why they are not classified in the order Mononegavirales, unlike the Paramyxoviridae. The segmentation of their genome allows the Orthomyxoviridae a high genetic flexibility and adaptability to new host species due to the intermixing of the different segments of different subtypes and mutants by the so-called reassortment.

The Orthomyxoviridae include virus genera that infect and replicate in the respiratory system of a host mainly via droplet infection. This is particularly true for the genera of influenza viruses, which can cause asymptomatic infections or severe disease in mammals and birds. Only the species of the genus Thogotovirus do not cause respiratory infections and are transmitted to vertebrates by ticks. Some aquatic hosts of the genera Influenza virus A (baleen whales) and Isavirus (salmon) are infected by contaminated water, direct contact, or (in the case of infectious salmon anemia virus) by fish lice. Tilapia pond virus has also been scientifically described as "orthomyxovirus-like" and placed by the ICTV in a new sister family Amnoonviridae, genus Tilapinevirus.

Morphology

The virus particles (virions) of the Orthomyxoviridae are spherical to irregular and 80-120 nm in diameter. Filamentous forms with lengths of up to a few µm are also observed. The lipid-containing viral envelope contains 1-3 glycoproteins and 1-2 non-glycosylated proteins. These form visible "spikes" 10-14 nm long and 4-6 nm in diameter on the surface. Anchored in the envelope, but with the larger part pointing inwards, are so-called matrix proteins, which line the space between the envelope and the capsids (matrix space).
Depending on the segmentation of the genome, virions also contain several helical capsids, at one end of
 which several subunits of the viral polymerase proteins (PA, PB1 and PB2) are associated. These viral enzymes show different activities depending on the viral genus, e.g. PB1 is an endonuclease in influenza viruses and additionally an RNA polymerase (transcriptase) in these and the genus Thogotovirus. After release in the cytoplasm, the capsids are transported into the cell nucleus by specific nuclear transport ("nuclear import").

The (-)ssRNA genome is linear and segmented; the number of segments varies between genera. For example, the species of the genera Influenzavirus A, Influenzavirus B and Isavirus each have 8 segments, Influenzavirus C and from the genus Thogotovirus the species Dhori virus has 7, the species Thogoto virus has 6 segments. The size of the segments ranges from 874 to 2396 nt, the total genome size from 10.0 to 14.6 kb. Due to distribution and synthesis errors during virus replication, many virions have shorter, defective RNA pieces or do not have a complete set of segments. This is particularly observed in mutations of the polymerase subunit PA, which appears to play a crucial role in the correct packaging and distribution of genome segments.

Systematics

As of March 2019, the systematics of Orthomyxoviridae according to the International Committee on Taxonomy of Viruses (ICTV) is as follows:

·         Family Orthomyxoviridae

·         Genus Alphainfluenza virus

·         Species Influenza virus A

·         Genus Betaine fluenza virus

·         Species Influenza virus B

·         Genus Gammainfluenza virus

·         Species Influenza virus C

·         Genus Deltainfluenzavirus

·         Species Influenza virus D

·         genus Isavirus

·         Species Infectious salmon anaemia virus (officially Salmon isavirus)

·         Genus Quaranjavirus

·         Species Quaranfil quaranjavirus (Quaranfil virus, QRFV, type species)

·         Species Johnston Atoll quaranjavirus (Johnston Atoll virus, JAV)

·         Genus Thogotovirus

·         Species Dhori virus

·         Species Thogoto virus (officially Thogoto thogotovirus, type species including the as yet unclassified 'Bourbon virus')

The individual virus lineages and other unclassified candidates can be found at NCBI.

Phylogenetic tree of Orthomyxoviridae with confirmed and proposed representatives (black and red, respectively).