Arenaviridae

Arenaviridae

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 and Juan Carlos de la Torre

The citation for this ICTV Report chapter is the summary published as Radoshitzky et al., (2019):
ICTV Virus Taxonomy Profile: Arenaviridae, Journal of General Virology, 100, 12001201.

Corresponding author: Juan Carlos de la Torre (juanct@scripps.edu)
Edited by: Jens H. Kuhn, Stuart G. Siddell and Peter J. Walker
Posted: May 2019, updated September 2020

Summary

Members of the family Arenaviridae produce enveloped virions containing genomes consisting of 2 to 3 single-stranded RNA segments totaling about 10.5 kb (Table 1.Arenaviridae). Arenaviruses are currently classified into four genera (Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus). These viruses infect fish (antennaviruses), snakes (hartmaniviruses and reptarenaviruses) and mammals (mammarenaviruses). Some reptarenaviruses cause boid inclusion body disease in captive snakes, whereas some mammarenaviruses can infect humans and other primates, causing mild, 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 coding arrangement, RNA molecules called small (S), medium (M), and large (L)

Replication

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

Translation

Proteins are produced from capped and non-polyadenylated mRNAs. The 5′-cap structure is derived by polymerase slippage or cap-snatching from cellular mRNAs

Host range

Fish (antennaviruses), predominantly small mammals (mammarenaviruses), and reptiles (hartmaniviruses and reptarenaviruses), but potentially also bats and ticks

Taxonomy

Realm Riboviria, phylum Negarnaviricota, subphylum Polyploviricotina, class Ellioviricetes, order Bunyavirales. The family includes 4 genera and 50 species

* mostly based on experiments with mammalian arenaviruses

Viruses assigned to each of the 4 genera form a monophyletic clade based on phylogenetic analysis of large protein/RNA-directed RNA polymerase (L/RdRP) 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 -binding matrix (Z) protein, which is encoded by mammarenaviruses and reptarenaviruses.

Reptilian host

Genus Hartmanivirus. This recently established genus currently includes 4 species for 6 viruses 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 transmembrane surface GP2 glycoproteins, which are more closely related to those of ebolaviruses (order Mononegavirales, family Filoviridae) than to those of antennaviruses, hartmaniviruses, mammarenaviruses or other bunyaviruses. Reptarenaviruses are also unusual in that they are prone to cause co-infections, with multiple distinct S and L segments, not necessarily in a 1:1 ratio, being detectable in snakes.

Mammalian host

Genus Mammarenavirus. The genus currently includes 39 species for 46 viruses. These viruses have been detected in rodent hosts, apart from Tacaribe virus (TCRV) which has been found only in phyllostomid bats and ixodid lone star ticks. Mammarenavirus infections of their natural rodent hosts are generally asymptomatic. In humans, some mammarenaviruses, such as Western African Lassa virus (LASV) or several viruses of South American origin, can cause severe and often fatal diseases with hemorrhagic manifestations. Lymphocytic choriomeningitis virus (LCMV), the typical mammalian arenavirus, can also cause disease in humans and poses a serious threat to immunocompromised individuals.

Virion

Morphology

Virions are spherical or pleomorphic in shape, 40–200 nm in diameter, with dense lipid envelopes (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 (Latin: arena, sand), 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-binding 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-directed RNA polymerase (L, green).

Physicochemical and physical properties

Mainly 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-directed RNA polymerase (L), which mediates virus genome replication and transcription. The zinc-binding matrix (Z) protein, 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, the “glycoprotein-cell-associated” preprotein (GPC) by the cellular S1P/SKI protease. A third GPC cleavage 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 GP 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 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 which 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-directed RNA polymerase; NP, nucleoprotein; Z, zinc-binding 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, Glushakova and Lukashevich 1989) (Figure 3.Arenaviridae). pH-dependent fusion with late endosomes releases the virion RNP complex into the cytoplasm. In the case of some mammalian arenaviruses (LASV), this fusion event involves a pH-dependent switch to an intracellular receptor, lysosomal associated membrane protein 1 (LAMP1) (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-directed RNA polymerase; NP, nucleoprotein; RNP, ribonucleoprotein; Z, zinc-binding matrix protein. Note that antennaviruses and hartmaniviruses do not encode Z.

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 overlaps with the distribution of their hosts. Most mammalian arenaviruses infect rodents of preferentially one or a few species and are, therefore, geographically constrained to their hosts, but LCMV, which infects the ubiquitous house mouse (Mus musculus Linnaeus, 1758) appears 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).

Antigenicity

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

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 at least 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).

Relationships within the family

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 50 arenaviruses assigned to the genera Antennavirus (blue dots, blue rings for unclassified viruses the genus), Hartmanivirus (green dots), Mammarenavirus (red dots) and Reptarenavirus (yellow dots), along with representative viruses of other bunyavirus families (other colors of dots). 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.

Relationships with other taxa 

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

Related, unclassified viruses 

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

-

Hyriopsis cumingii Lea plague virus (Carella et al., 2016, Zhong et al., 2011)

Not available

HcPV

Virus names and abbreviations are not official ICTV designations.

Member taxa