Arenaviridae


Arenaviridae

Chapter contents

Posted May 2019

Arenaviridae: The family

Member taxa

Supporting information

  • Authors - corresponding author: Juan Carlos de la Torre (juanct@scripps.edu)
  • 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:

Sheli R. Radoshitzky, Michael J. Buchmeier, Rémi N. Charrel, J. Christopher S. Clegg, Jean-Paul J. Gonzalez, Stephan Günther, Jussi Hepojoki, Jens H. Kuhn, Igor S. Lukashevich, Víctor Romanowski, Maria S. Salvato, Manuela Sironi, Mark D. Stenglein, Juan Carlos de la Torre, and the ICTV Report Consortium, 2019, ICTV Virus Taxonomy Profile: ArenaviridaeJournal of General Virology, 100, 12001201.

Summary

Members of the family Arenaviridae produce enveloped virions containing genomes consisting of at least 2 single-stranded RNA segments totaling about 10.5 kb. Arenaviruses are currently classified into four genera (Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus). These viruses infect mainly fish (antennaviruses), snakes (hartmaniviruses and reptarenaviruses) and rodents (mammarenaviruses). Some reptarenaviruses cause boid inclusion body disease in captive snakes, whereas some mammarenaviruses can infect humans and other primates, causing severe and sometimes fatal diseases.

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

Characteristic

Description

Typical member

lymphocytic choriomeningitis virus Armstrong 53b [S segment: AY847350; L segment: AY847351], species Lymphocytic choriomeningitis mammarenavirus, genus Mammarenavirus.

Virion

Enveloped, pleomorphic virions 40–200 nm in diameter with trimeric surface spikes

Genome

Two or three single-stranded, usually ambisense, RNA molecules called small (S), (M [medium]), and large (L)

Replication

Ribonucleoprotein (RNP) complexes are generated that contain anti-genomic RNA serving as templates for synthesis of genomic RNA

Translation

Proteins produced from capped and not-polyadenylated mRNAs. The 5′-cap structure is derived by polymerase slippage or cap-snatching from cellular mRNAs

Host range

Predominantly fish (antennaviruses), mammals (mammarenaviruses) and reptiles (hartmaniviruses and reptarenaviruses), but possibly also bats and ticks

Taxonomy

Realm Riboviria, phylum Negarnaviricota, subphylum Polyploviricotina, class Ellioviricetes, order Bunyavirales. The family includes several genera and > 40 species

Viruses assigned to each of the 4 genera form a monophyletic clade based on phylogenetic analysis of RNA-dependent RNA polymerase (L) and nucleoprotein (NP) sequences. Viruses from all four genera share one or more of the following characteristics: (i) enveloped spherical or pleomorphic virions; (ii) segmented single-stranded, ambisense RNA genome without polyadenylated tracts at the 3′-termini; (iii) genomic 5′- and 3′-end sequence complementarity; (iv) nucleotide sequences that could form one or more hairpin configurations within non-coding intergenic regions (IGRs) of genomic segments; (v) capped but not polyadenylated virus mRNAs; and (vi) induction of a persistent and frequently asymptomatic infection in reservoir hosts, in which chronic viremia and/or viruria occur (Radoshitzky et al., 2015).

Piscine host

Genus Antennavirus. This recently established genus currently includes 2 species for 2 viruses discovered in actinopterygian fish. Antennaviruses are notable for having genomes consisting of 3, rather than 2, genomic segments and likely not encoding the zinc finger matrix (Z) protein, which is encoded by mammarenaviruses and reptarenaviruses.

Reptilian host

Genus Hartmanivirus. This recently established genus currently includes 1 species for Hartmaan Institute snake virus 1 (HISV-1) discovered in captive snakes with boid inclusion body disease (BIBD). Hartmaniviruses are notable for genomes lacking a gene encoding the Z protein, which is encoded by mammarenaviruses and reptarenaviruses.

Genus Reptarenavirus. This genus currently includes 5 species for 8 viruses discovered in captive snakes, some of which were suffering from BIBD. Reptarenaviruses are notable for their surface glycoproteins (GPs), which are more closely related to that of Ebola virus (order Mononegavirales, family Filoviridae) than to those of antennaviruses, hartmaniviruses, mammarenaviruses or other bunyaviruses. 

Mammalian host

Genus Mammarenavirus. The genus currently includes 35 species for 42 viruses. These viruses have been detected in rodent hosts, apart from Tacaribe virus (TCRV) which has been found in phyllostomid bats and ixodid lone star ticks. Mammarenavirus infections of their natural rodent hosts are generally asymptomatic. However, some mammarenaviruses, such as Western African Lassa virus (LASV) and several viruses of South American origin, can also infect humans and cause severe and often fatal disease. Lymphocytic choriomeningitis virus (LCMV) can also cause disease in humans and poses a serious threat to immunocompromised individuals, including transplant recipients

Virion

Morphology

Virions are spherical or pleomorphic in shape, 40–200 nm in diameter, with dense lipid envelopes (Table 1.Arenaviridae., Figure 1.Arenaviridae.). The virion surface layer is covered with club-shaped projections with distinctive stalk and head regions. These projections are made of trimeric spike structures of two virus-encoded membrane glycoprotein (GP) subunits (GP1 and GP2) and in case of some arenaviruses, a third component (stable signal peptide [SSP]). Isolated RNP complexes are organized into “beads-on-a-string”-like structures (Hetzel et al., 2013, Li et al., 2016, Neuman et al., 2005, Buchmeier 2002, Charrel and de Lamballerie 2003, Jay et al., 2005, Meyer et al., 2002, Hepojoki et al., 2018).

Figure 1.Arenaviridae. A) Electron micrograph of (mammalian) arenavirus particles, showing dark internal inclusion bodies, budding from an infected cell. B) Schematic illustration of an arenavirus particle. Shown is the spherical and enveloped (grey) particle that is spiked with glycoproteins (GP, gold) around a layer of zinc finger matrix proteins (Z, brown; missing in hartmaniviruses). The small (S) and large (L) ribonucleoprotein (RNP) complexes inside the particle consist of nucleoprotein (NP, blue) and RNA-dependent RNA polymerase (L, green).

Physicochemical and physical properties

Only known for members of the genus Mammarenavirus (see section on genus page).

Nucleic acid

Arenavirions typically contain 2 or 3 linear, ambisense or negative-sense single-stranded RNA segments that are encapsidated independently. These RNAs are uncapped (Leung et al., 1977) and contain a single non-templated G at each of the 5′-ends (Garcin and Kolakofsky 1990, Raju et al., 1990, Shi et al., 2018). No poly(A) tracts are present at the 3′-termini. The termini of the RNAs ends have inverted complementary sequences encoding transcription and replication initiation signals  (Hepojoki et al., 2018, Salvato et al., 1989, Harnish et al., 1993, Young and Howard 1983).

Proteins

Arenaviruses express 3 (hartmaniviruses) or 4 (antennaviruses, mammarenaviruses, reptarenaviruses) structural proteins. The most abundant structural protein in virions is the nucleoprotein (NP), which encapsidates the virus genomic segments. The least abundant protein is the RNA-dependent RNA polymerase (L), which mediates virus genome replication and transcription. The zinc finger matrix protein Z, which is absent in antennaviruses and hartmaniviruses, is a matrix protein. Glycoproteins (GP1 or G1, GP2 or G2) are derived by post-translational cleavage of an intracellular GP precursor (GPC) by the cellular S1P/SKI protease. A third GPC product, the signal peptide, stays attached to the GP complex in hartmaniviruses and mammarenaviruses (stable signal peptide [SSP]), but not in reptarenaviruses (signal peptide [SP]). The GPC structure of antennaviruses is unknown (Hepojoki et al., 2018, Shi et al., 2018, Buchmeier et al., 1987, Kunz et al., 2003, Lenz et al., 2001, Koellhoffer et al., 2014, Bederka et al., 2014, Eichler et al., 2003, York et al., 2004).

Lipids

Only known for members of the genus Mammarenavirus (see section on genus page). 

Carbohydrates

Only known for members of the genus Mammarenavirus (see section on genus page).

Genome organization and replication 

The arenavirus genome typically consists of two or three single-stranded, typically ambisense RNA molecules, termed S, (M), and L. Some of these RNAs encode two proteins in non-overlapping open reading frames (ORF) of opposite polarities (ambisense coding arrangement) that are separated by non-coding intergenic regions (IGRs) (Figure 2.Arenaviridae.). The S RNA encodes NP in the virus genome-complementary sequence, and, in many cases, the virus glycoprotein precursor (GPC) in the virus genome-sense sequence. The L RNA encodes L in the virus genome-complementary sequence, and, in some case, Z in the virus genome-sense sequence. Antennaviruses and hartmaniviruses lack the Z ORF, and antennaviruses encode at least one protein of unknown function. The IGRs form one or more energetically stable stem-loop (hairpin) structures and function in structure-dependent transcription termination and in virion assembly and budding.

Figure 2.Arenaviridae. Schematic representation of the bi- or tri-segmented arenavirus genome organization. The 5′- and 3′-ends of all segments (S, [M], and L) are complementary at their termini, likely promoting the formation of circular ribonucleoprotein complexes within the virion. GPC, glycoprotein precursor; L, RNA-dependent RNA polymerase; NP, nucleoprotein; Z, zinc finger matrix protein. Open reading frames are separated by non-coding intergenic regions (IGRs), with predicted hairpin structures (not shown).

Arenavirus infection starts with attachment to cell-surface receptors and entry via the endosomal route (Martinez et al., 2007, Vela et al., 2007, Borrow and Oldstone 1994, Radoshitzky et al., 2007, Cao et al., 1998, Raaben et al., 2017) (Figure 3.Arenaviridae). pH-dependent fusion with late endosomes releases the virion RNP complex into the cytoplasm. In the case of some arenaviruses, this pH-dependent fusion event requires the previous participation of an intracellular receptor (Jae et al., 2014). The virus RNP directs both RNA genome replication and gene transcription (Meyer et al., 2002). During replication, L reads through the IGR transcription-termination signal and generates uncapped antigenomic and genomic RNAs (Leung et al., 1977). Because these RNAs contain a single non-templated G at the 5′-ends  (Garcin and Kolakofsky 1990, Raju et al., 1990), replication initiation might involve a slippage mechanism of L on the nascent RNA (Garcin and Kolakofsky 1992). In case of ambisense coding arrangements, only mRNAs encoding NP or L can be synthesized from genomic RNAs. Transcription of mRNAs encoding GPC or Z occurs only after the first round of virus replication, during which S and L antigenomes are produced.

Virus proteins are synthesized from subgenomic capped mRNAs that lack terminal poly(A) (Meyer and Southern 1993, Singh et al., 1987, Southern et al., 1987). The 5′-ends  of virus mRNAs contain several non-templated bases, suggesting that arenaviruses use either polymerase slippage or a cap-snatching mechanism similar to that used by other members of the subphylum Polyploviricotina (Garcin and Kolakofsky 1990, Raju et al., 1990, Meyer and Southern 1993). Cap-snatching would require an endonuclease presumed to be present in the N-terminal part of L, which cleaves cellular mRNAs to generate a cap leader that is subsequently used to prime arenavirus transcription. The 3′-termini of the mRNAs have been mapped to locations in the IGRs.

Virion budding occurs from the cellular plasma membrane, thereby providing the virion envelope (Dalton et al., 1968, Eichler et al., 2004, Perez et al., 2003, Strecker et al., 2003).

Figure 3.Arenaviridae. Lifecycle of arenaviruses. (1) Virion uptake; (2) virus-cell membrane fusion; (3) uncoating; (4) transcription, translation, and replication; (5) virion assembly; and (6) virion budding. GP, glycoprotein; IGR, intergenic region; L, RNA-dependent RNA polymerase; NP, nucleoprotein; RNP, ribonucleoprotein; Z, zinc finger matrix protein. Note that antennaviruses and hartmaniviruses do not encode Z.

Antigenicity

Systematic antigenicity studies have only been reported for mammarenavirions (see section on genus page).

Biology

Arenaviruses are ecologically diverse: they have been isolated from fish (antennaviruses) (Shi et al., 2018), rodents, bats, and ticks (mammarenaviruses) (Downs et al., 1963, Sayler et al., 2014), and snakes (reptarenaviruses, hartmaniviruses) (Hetzel et al., 2013, Hepojoki et al., 2018, Hepojoki et al., 2015, Stenglein et al., 2012). The geographic distribution of arenaviruses correlates with the distribution of their hosts. Most mammalian arenaviruses infect rodents of only one or a few species and are, therefore, geographically constrained, but LCMV, which infects the ubiquitous house mouse (Mus musculus Linnaeus, 1758) is distributed globally (Childs 1993). The natural distribution of reptilian arenaviruses is unknown as they have only been detected in captive snakes thus far (Hetzel et al., 2013, Hepojoki et al., 2018, Hepojoki et al., 2015, Stenglein et al., 2012). A diverse range of vertebrate cell lines are permissive to mammalian arenavirus infection in vitro; certain reptilian cell lines support replication of reptilian arenaviruses (Hepojoki et al., 2018, Stenglein et al., 2012, Lukashevich et al., 1983).

Genus demarcation criteria 

Classification of arenaviruses is currently based on pairwise sequence comparisons (PASC) of coding-complete genomes. Based on the most current sequence dataset, S segment and L segment nucleotide sequence identities for viruses within the same genus need to be higher than 40% and 35%, respectively (Radoshitzky et al., 2015). Four genera have been established to date. Viruses assigned to a genus form a monophyletic clade in well-supported maximum likelihood trees using complete L and NP nucleotide sequences and/or core L palm domain sequences. Use of L and NP for taxonomic purposes is justified by the presence of broadly conserved domains and the rarity of reassortment between genetic segments, at least in mammarenaviruses. Hence, the availability of at least coding-complete sequences of all genome segments may be sufficient for arenavirus classification in the absence of a cultured isolate. Classification is also possible when a coding-complete genomic S segment sequence is available together with a cultured isolate (Radoshitzky et al., 2015). However, at the present time, classification also includes the consideration of phenotypic characters such as significant differences in member virus genome architecture, virion antigenicity, and virus ecology (e.g., host range, pathobiology, and transmission patterns).

Derivation of names

Arenaviridae: from the Latin arenosus meaning “sandy” and arena meaning “sand,” in recognition of the “sandy” appearance of mammarenavirus particles observed in electron-microscopic thin sections (Rowe et al., 1970a).

Phylogenetic relationships

Phylogenetic relationships across the family have been established from maximum likelihood trees generated using complete L amino acid sequences (Figure 4.Arenaviridae). Phylogenetic relationships between viruses assigned to more closely related genera and within genera can also be established using other structural protein genes, notably NP.

Figure 4.Arenaviridae. Maximum likelihood phylogenetic tree inferred from PRANK alignment (Löytynoja and Goldman 2008) of the complete L amino acid sequences of 43 arenaviruses (red dots) assigned to 4 genera. Representative viruses of other bunyavirus families are also included (dots in colors other than red). The best-fit model of protein evolution (LG+G) was selected using ProtTest 3 (v. 3.4.2) (Darriba et al., 2011). The maximum likelihood tree with 1,000 bootstrap replicates was produced using RAxML (v. 8) (Stamatakis 2014). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap is shown next to branch nodes (when ≥ 70%). The tree was visualized using FigTree (http://tree.bio.ed.ac.uk) and is mid-point rooted. This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page.

Similarity with other taxa

Arenaviruses are closely related to Húběi myriapoda virus 5 (Bunyavirales: Mypoviridae) (Shi et al., 2016).

Related, unclassified viruses

Table 2.Arenaviridae. Unclassified arenaviruses (additional unclassified arenaviruses that are probable members of existing genera are listed under individual genus descriptions).

Virus name

Accession number

Virus abbreviation

DF 20/00 virus (Granzow et al., 2014)

Not available

-

DF 26/02 virus (Granzow et al., 2014)

Not available

-

Virus names and virus abbreviations are not official ICTV designations.