Family: Nyamiviridae

 

Ralf G. Dietzgen, Andrew E. Firth, Dàohóng Jiāng, Sandra Junglen, Hideki Kondo, Jens H. Kuhn, Sofia Paraskevopoulou and Nikos Vasilakis

The citation for this ICTV Report chapter is the summary published as Dietzgen et al., (2021):
ICTV Virus Taxonomy Profile: Nyamiviridae 2021Journal of General Virology, 2021 102(11) 001681

Corresponding author: Ralf G. Dietzgen (r.dietzgen@uq.edu.au)
Edited by: Stuart G. Siddell and Peter Simmonds
Posted: December 2017, updated June 2019, August 2021, June 2022
PDF: ICTV_Nyamiviridae.pdf (2019 version)

Summary

Nyamiviridae is a family of viruses in the order Mononegavirales with non-segmented or segmented, negative-sense RNA genomes of approximately 10–13 kb (Table 1.Nyamiviridae). Several viruses in the family Nyamiviridae have been identified by next generation sequencing (Shi et al., 2016) and the family was recently expanded to include the genus Formivirus. Nyamiviridae now includes the additional genera Berhavirus, Crustavirus, Formivirus, NyavirusOrinovirus, Socyvirus, and Tapwovirus that form monophyletic clades on phylogenetic analysis of the RNA-directed RNA polymerase. Nyamivirids have a similar genome organization, including the number and locations of genes identified by homology with those of other mononegavirals. 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 nyamivirids were identified in marine animals and have been classified in the genus Berhavirus (echinoderms and sipunculids) and Crustavirus (crustaceans). Nyamivirids found in moths are members of the genus Orinovirus, and those associated with tapeworms belong to the genus Tapwovirus. Members of the genus Formivirus are associated with ants and wasps. Members of the genera Nyavirus and Socyvirus produce enveloped, spherical virions (Kuhn et al., 2013). For the other nyamivirids, no virion information is available.

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

Characteristic

Description

Example

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

Virion

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

Genome

Negative-sense, non-segmented or bi-segmented RNA of up to 13.3 kb

Replication

Nuclear: the large protein, which contains an RNA-directed RNA polymerase domain, 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 Monjiviricetes, order Mononegavirales. The genera Berhavirus and Crustavirus include 3 species each, the genus Nyavirus includes 6 species, and the genus Formivirus include 5 species, whereas the genera OrinovirusSocyvirus, and Tapwovirus include 1 species each

Virion

Morphology

Virions of Nyamanini virus are enveloped and spherical with a diameter of 100–130 nm; virions of Sierra Nevada virus are of similar appearance (Figure 1.Nyamiviridae). San Jacinto virus-infected Vero E6 cells release large spherical (320–800 nm) or pleomorphic and elongated particles (350 × 540 nm to 280 × 1120 nm and 3280 × 1275 nm).

Figure 1. NyamiviridaeTransmission 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 10–13 kb.

Proteins

Nyamivirids encode 4 to 8 structural proteins. Among them are the nucleocapsid protein (N), glycoprotein (G) and large protein (L), which contains an RNA-directed RNA polymerase (RdRP) domain, 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

Nyamivirid negative-sense RNA genomes range from 10–13 kb (Figure 2.Nyamiviridae). All nyamivirids in the genera Nyavirus and Socyvirus have non-segmented genomes with 4 to 8 open reading frames (ORFs) that encode mostly structural proteins. Nyamivirids in the genera BerhavirusCrustavirus, and Orinovirus also have non-segmented genomes with up to 5 ORFs. The only known member of Tapwovirus has a bi-segmented genome with RNA 1 encoding the large protein (L) and the other ORFs located on RNA 2. Knowledge about nyamivirid replication is limited. Nyamanini virus (genus Nyavirus) replicates in the nucleus of infected cells.

Genome diagram Nyamiviridae

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

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, viruses of the genus Formivirus are associated with ants and wasps, and viruses of the genus Tapwovirus with tapeworms.

Antigenicity

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

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

Berhavirus: from Běihǎi rhabdo-like virus 3.

Crustavirus: from Crustacea.

Formivirus: from Formica, the ant genus name associated with the ant hosts in which Formica fusca virus 1 and Formica exsecta virus 4 were discovered.

Orinovirus: from Orinoco virus.

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). 

Nyavirus: from Nyamanini Pan (place of isolation of Nyamanini virus in South Africa. Species in the genus are named after the location where species members were first identified.

Socyvirus: from soybean cyst nematode virus. Species in the genus are named after the host.

Tapwovirus: from Wēnzhōu tapeworm virus 1.

Relationships within the family

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). Nyamivirids have a similar genome organization, including the number and locations of genes identified by homology with those of other mononegaviruses (Figure 2.Nyamiviridae).

Phylogenetic tree 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  MUSCLE (Edgar 2004). The resulting alignment was used to generate a phylogenetic tree using MEGA7 (Kumar et al., 2016)  with the best-fit model JTT + G + I +F. The colors indicate the different mononegavirus families and nyamivirid genera. Numbers at the nodes indicate bootstrap support over 70% (100 replicates).

Relationships with other taxa

Some biological properties of nyamivirids appear to be similar to those of filovirids (mononegaviral family Filoviridae) and bornavirids (mononegaviral family Bornaviridae).