Nyamiviridae


Nyamiviridae

Ralf G. Dietzgen​, Dàohóng Jiāng, Hideki Kondo, Jens H. Kuhn​ and Nikos Vasilakis

Chapter contents

Posted December 2017, revised June 2019

Nyamiviridae: The family

Member taxa

Supporting information

  • Authors - corresponding author: Ralf G. Dietzgen (r.dietzgen@uq.edu.au)
  • Resources - sequence alignments and tree files
  • References

Citation

A summary of this ICTV Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows:

Dietzgen, R.G., Ghedin, E., Jiāng, D., Kuhn, J.H., Song, T., Vasilakis, N., Wang, D., and ICTV Report Consortium. 2017, ICTV Virus Taxonomy Profile: NyamiviridaeJournal of General Virology, 98, 29142915.

Summary

The Nyamiviridae is a family of viruses in the order Mononegavirales with non-segmented or segmented, negative-sense RNA genomes of approximately 10–12 kb. The Nyamiviridae was recently expanded by the inclusion of viruses identified by next generation sequencing (Shi et al., 2016) and now includes the genera Berhavirus, Crustavirus, Nyavirus, Orinovirus, Socyvirus, and Tapwovirus that form monophyletic clades on phylogenetic analysis of the RNA polymerase. Nyamiviruses have a similar genome organization, including the number and locations of genes identified by homology with those of other mononegaviruses. Only viruses of the genus Tapwovirus have segmented genomes. Viruses of the genus Nyavirus are tick-borne and some of them also infect birds (Takahashi et al., 1982). Members of the Socyvirus genus infect plant parasitic nematodes (Bekal et al., 2011). Other nyamiviruses were identified in marine animals, and have been classified in the genus Berhavirus (echinoderms and sipunculids) and Crustavirus (crustaceans). Nyamiviruses found in moths are members of the genus Orinovirus, and those associated with tapeworms belong to the genus Tapwovirus. Members of the genera Nyavirus and Socyvirus produce enveloped, spherical virions (Kuhn et al., 2013). For the other nyamiviruses, no virion information is available.

Table 1.Nyamiviridae. Characteristics of members of the family Nyamiviridae.

Characteristic

Description

Typical member

Nyamanini virus (FJ554526), species Nyamanini nyavirus, genus Nyavirus

Virion

Enveloped, spherical particles, approximately 100–130 nm in diameter

Genome

Negative-sense, non-segmented or bi-segmented RNA of up to 12.2 kb

Replication

Nuclear: the RNA-directed RNA polymerase engages with ribonucleoprotein at the genome 3′-end

Translation

Individual putatively polyadenylated mRNAs are translated in the cytoplasm

Host Range

Invertebrates: ticks, insects, echinonoderms, sipunculids, crustaceans, nematodes, tapeworms; vertebrates: land- and seabirds

Taxonomy

Realm Riboviria, phylum Negarnaviricota, subphylum Haploviricotina, class Monjiviricetesorder Mononegavirales. The genera Berhavirus, Crustavirus, and Nyavirus include 3 species each, whereas the genera Orinovirus, Socyvirus and Tapwovirus include 1 species each

Virion

Morphology

Virions are enveloped and spherical with a diameter of 100–130 nm (Figure 1.Nyamiviridae).

Figure 1.Nyamiviridae. Transmission electron micrograph of Vero E6 cells infected with Sierra Nevada virus. High magnification of virions (V) budding from the cell surface. M indicates mitochondria. Bar = 1 μm. Contributed by Dr Vsevolod Popov, Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.

Physicochemical and physical properties

None reported.

Nucleic acid

Non-segmented, negative-sense RNA of 10–12 kb.

Proteins

Nyamiviruses encode 5 or 6 structural proteins. Among them are the nucleocapsid protein (N), glycoprotein (G) and RNA-directed RNA polymerase (L) that are identified based on sequence similarity and structural properties shared with mononegavirus homologues. Functions of the other encoded proteins are largely unknown, but may be those of matrix and polymerase cofactor proteins. 

Lipids

None reported.

Carbohydrates

None reported. 

Genome organization and replication

Nyamivirus negative-sense RNA genomes range from 10–12 kb (Figure 2.Nyamiviridae). All nyamiviruses in the genera Nyavirus and Socyvirus have non-segmented genomes with 5 or 6 open reading frames (ORFs) that encode structural proteins. Nyamiviruses in the genera Berhavirus, Crustavirus, and Orinovirus also have non-segmented genomes with up to 5 ORFs. The only known member of Tapwovirus has a bisegmented genome with RNA 1 encoding the large protein (L) and the other ORFs located on RNA 2. Knowledge about nyamivirus replication is limited. Nyamanini virus (genus Nyavirus) replicates in the nucleus of infected cells.

Figure 2.Nyamiviridae. Genome organization of viruses in the family Nyamiviridae, genera Berhavirus, Crustavirus, Nyavirus, Orinovirus, Socyvirus and Tapwovirus. Box arrows indicate the position and length of each ORF. Putative nucleocapsid protein (N), phosphoprotein (P), glycoprotein (G) and RNA-directed RNA polymerase (L) ORFs are indicated; ORFs encoding hypothetical proteins with unknown function are numbered U1, U2; int - internal ORF, X - ORF with unknown function.

Antigenicity

An antigenic relationship between Nyamanini virus and Midway virus (genus Nyavirus) was demonstrated by complement fixation tests.

Biology

Viruses of the genus Nyavirus are tick-borne and some of them also infect birds, whereas members of the Socyvirus genus infect plant parasitic nematodes. Viruses of the genus Berhavirus are associated with marine echinoderms and sipunculids, viruses of the genus Crustavirus are associated with crustaceans, viruses of the genus Orinovirus with moths, and viruses of the genus Tapwovirus with tapeworms.

Genus demarcation criteria

Due to the small number of genus members, no firm genus demarcation criteria have been established beyond phylogeny and the hosts the viruses infect.

Derivation of names

Nyamiviridae: from Nyamanini Pan (place of isolation of Nyamanini virus in South Africa) and Midway Atoll (place of isolation of Midway virus in the USA), and the suffix -viridae (ending denoting a virus family) → Neo-Lat. n. fem. pl. Nyamiviridae – the family of nyamiviruses. 

Phylogenetic relationships

Viruses assigned to each genus appear to form monophyletic clades but bootstrap support in the phylogenetic analyses of L polymerase amino acid sequences is weak (Figure 3.Nyamiviridae). Nyamiviruses have a similar genome organization, including the number and locations of genes identified by homology with those of other mononegaviruses (Figure 2.Nyamiviridae).

Figure 3.Nyamiviridae. Phylogenetic maximum likelihood tree of mononegavirus L polymerase protein sequences highlighting Nyamiviridae and its genera. Amino acid sequences were aligned using MAFFT version 7 (Katoh et al., 2017) and then the alignment was filtered using Gblocks 0.91b (Talavera and Castresana 2007). The resulting alignment was used to generate a phylogenetic tree using PhyML 3.0 (Guindon et al., 2010) with the best-fit model LG + G + I +F. The colors indicate the different mononegavirus families and nyamivirus genera. The currently unassigned putative nyamiviruses San Jacinto virus, Formica fusca virus 1 and Formica exsecta virus 4 have been included in addition to the currently recognized nyamiviruses. Numbers at the nodes indicate bootstrap support over 50% (100 replicates).

Similarity with other taxa

Some biological properties of nyamiviruses appear to be similar to those of filoviruses (mononegavirus family Filoviridae) and bornaviruses (mononegavirus family Bornaviridae).