Marnaviridae

Marnaviridae

Andrew S. Lang, Marli Vlok, Alexander I. Culley, Curtis A. Suttle, Yoshitake Takao and Yuji Tomaru

The citation for this ICTV Report chapter is the summary published as Lang et al., (2021):
ICTV Virus Taxonomy Profile: Marnaviridae, Journal of General Virology, (In Press)

Corresponding author: Andrew S. Lang (aslang@mun.ca)
Edited by: Sead Sabanadovic and Stuart G. Siddell
Posted: June 2021
PDF: TBA

Summary

Marnaviridae is a family of small non-enveloped viruses with positive-sense RNA genomes of 8.6–9.6 kb (Table 1.Marnaviridae). Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Also, some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets from marine and freshwater environments.

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

Characteristic

Description

Example

Heterosigma akashiwo RNA virus (AY337486), species Heterosigma akashiwo RNA virus, genus Marnavirus

Virion

Non-enveloped, 22–35 nm virions with four structural proteins

Genome

8.6–9.6 kb of positive-sense, non-segmented RNA

Replication

Cytoplasmic, involving RNA-directed RNA polymerase and helicase; cytolytic

Translation

Directly from genomic RNA containing one or more internal ribosomal entry sites (IRES)

Host range

Single-celled eukaryotes (protists) from marine environments

Taxonomy

Realm Riboviria, kingdom Orthornavirae, phylum Pisuviricota, class Pisoniviricetes, order Picornavirales; 7 genera and 20 species

Virion

Morphology

Those members of the family Marnaviridae that have been isolated and structurally characterized have polyhedral virions that range from 22 to 35 nm in diameter, do not appear to have an envelope, and have no discernible projections (Figure 1.Marnaviridae; Table 2.Marnaviridae). 

Figure 1.Marnaviridae. virion structures. A. Negatively-stained transmission electron micrograph of Heterosigma akashiwo RNA virus (species Heterosigma akashiwo RNA virus) particles (scale bar = 50 nm). B. Cryo-electron microscopy reconstructed capsid structure at 3.1 Å resolution of Chaetoceros tenuissimus RNA virus type II (species Chaetenuissarnavirus II) (PDB structure 6SHL viewed in NGL-WebGL). The three major capsid proteins are represented in dark blue (VP1), light blue (VP2) and yellow (VP3). C. Ribbon depiction of the protein subunits from the reconstruction in B, including the minor capsid protein VP4 (red). 

Physicochemical and physical properties

Virions are not sensitive to chloroform.

Nucleic acid

Members of the family Marnaviridae possess monopartite, positive-sense RNA genomes containing either one or two open reading frames (ORFs) (Figure 2.Marnaviridae). One exception is Aurantiochytrium single-stranded RNA virus 01 (AuRNAV01, species Aurantiochytrium single-stranded RNA virus 01, genus Labyrnavirus), which has an additional ORF at the 3′-end of the genome. Among the isolated viruses the genome lengths range from 8.6 to 9.6 kb including a 3′-poly(A) tail (Table 2.Marnaviridae). Genome lengths for viruses known only from metagenomic sequencing data fall within this range, although some of these genome sequences are not complete (Table 3.Marnaviridae). Predicted secondary structures within the 5′-non-coding regions (NCRs) and intergenic regions (IGRs) suggest the presence of internal ribosome entry sites (IRES) (Figure 2.Marnaviridae), a feature observed in other members of other families in the order Picornavirales

Figure 2.Marnaviridae. Genome architecture of members of the family Marnaviridae. All genomes are organized with the non-structural proteins, including RNA helicase, 3C protease and RNA-directed RNA polymerase domains, at the 5′-ends. The structural proteins (VP2, VP4, VP3 and VP1) are encoded at the 3′-ends of the genomes, downstream of a putative internal ribosome entry site in the intergenic region in the di-cistronic genomes.

Proteins

Members of the family Marnaviridae encode four conserved proteins, VP1–4, with recognizable similarities to the structural proteins of other members of the order Picornavirales. The three largest of these (VP1–3) have been visualized by SDS-PAGE for some isolates (Tai et al., 2003, Shirai et al., 2008, Nagasaki et al., 2004). The structure of all four capsid proteins as well as the virion structure have been resolved by cryo-electron microscopy for Chaetoceros tenuissimus RNA virus type II (species Chaetenuissarnavirus II, genus Sogarnavirus) (Munke et al., 2020) (Figure 1.Marnaviridae).

Table 2.Marnaviridae. Properties of Marnaviridae isolates

Genus
Species
Virus name (abbreviation)
Host species (type)a
Virion diameter (nm)
Genome length (kb)
Latent period (hours)
Burst size
References
Marnavirus
Heterosigma akashiwo RNA virus
Heterosigma akashiwo RNA virus (HaRNAV)
Heterosigma akashiwo (R)
25
8.6
48
460–520
(Tai et al., 2003, Lang et al., 2004)
Bacillarnavirus
Rhizosolenia setigera RNA virus 01
Rhizosolenia setigera RNA virus 01 (RsRNAV01)
Rhizosolenia setigera (D)
32
8.9
48
1.0–3.1×103
(Nagasaki et al., 2004, Shirai et al., 2006)
Bacillarnavirus
Chaetoceros tenuissimus RNA virus 01
Chaetoceros tenuissimus RNA virus 01  (CtenRNAV01)
Chaetoceros tenuissimus (D)
31
9.4
<24
1.0×105
(Shirai et al., 2008)
Bacillarnavirus
Chaetoceros socialis forma radians RNA virus 1
Chaetoceros socialis f. radians RNA virus 01  (CsfrRNAV01)
Chaetoceros socialis f. radians (D)
22
9.5
<48
66
(Tomaru et al., 2009)
Sogarnavirus
Chaetenuissarnavirus II
Chaetoceros tenuissimus RNA virus type II  (CtenRNAVII)
Chaetoceros tenuissimus (D)
35
9.6
24–48
287
(Kimura and Tomaru 2015)
Sogarnavirus
Chaetarnavirus 2
Chaetoceros species RNA virus 02 (CspRNAV02)
Chaetoceros sp. (D)
32
9.4
<48
NDb
(Tomaru et al., 2013)
Labyrnavirus
Aurantiochytrium single-stranded RNA virus 01
Aurantiochytrium single-stranded RNA virus 01 (AuRNAV01)
Aurantiochytrium (T)
25
9.0
8
0.58–6.4×104
(Takao et al., 2006, Takao et al., 2005)
Kusarnavirus
Astarnavirus
Asterionellopsis glacialis RNA virus (AglaRNAV)
Asterionellopsis glacialis (D)
31
8.8
48
ND
(Tomaru et al., 2012)
a R, raphidophyte; D, diatom; T, thraustochytrid
b ND, not determined

Table 3.Marnaviridae. Marnaviridae members discovered by metagenomics.

Genus
Species
Virus name (abbreviation)
Genome length (nt)a
Genome completenessb
Source
References
Locarnavirus
Jericarnavirus B
marine RNA virus JP-B (JP-B)
8926
CG
Coastal marine
(Culley et al., 2007)
Sanfarnavirus 2
marine RNA virus SF-2 (SF-2)
[9321]
CCG
Coastal wastewater
(Greninger and DeRisi 2015)
Sanfarnavirus 1
marine RNA virus SF-1 (SF-1)
[8970]
CCG
Coastal wastewater
(Greninger and DeRisi 2015)
Sanfarnavirus 3
marine RNA virus SF-3 (SF-3)
[8648]
CCG
Coastal wastewater
(Greninger and DeRisi 2015)
Salisharnavirus
Britarnavirus 4
marine RNA virus BC-4 (BC-4)
[8593]
CCG
Coastal/oceanic marine
(Vlok et al., 2019)
Palmarnavirus 473
marine RNA virus PAL473 (PAL473)
[6360]
CCG
Coastal marine
(Miranda et al., 2016)
Britarnavirus 1
marine RNA virus BC-1 (BC-1)
[8638]
PG
Coastal marine
(Vlok et al., 2019)
Palmarnavirus 128
marine RNA virus PAL128 (PAL128)
[8660]
CCG
Coastal marine
(Miranda et al., 2016)
Sogarnavirus
Britarnavirus 2
marine RNA virus BC-2 (BC-2)
[8843]
CCG
Coastal marine
(Vlok et al., 2019)
Palmarnavirus 156
marine RNA virus PAL156 (PAL156)
[7897]
CCG
Coastal marine
(Miranda et al., 2016)
Britarnavirus 3
marine RNA virus BC-3 (BC-3)
[8496]
PG
Coastal marine
(Vlok et al., 2019)
Jericarnavirus A
marine RNA virus JP-A (JP-A)
9236
CG
Coastal marine
(Culley et al., 2007)
a Brackets indicate the genome sequence is not complete
b CG, complete genome; CCG, complete coding genome, protein-coding region(s) complete; PG, partial genome, protein-coding region(s) not complete

Genome organization and replication

Among the members of the 20 species and 7 genera in the family, there is a mixture of mono- and di-cistronic genome organizations (Figure 2.Marnaviridae). The majority of viruses have a di-cistronic genome organization, whereas Heterosigma akashiwo RNA virus (HaRNAV, genus Marnavirus) and marine RNA virus SF-3 (SF-3, genus Locarnavirus) have a single predicted polyprotein encoded in their genomes. Aurantiochytrium single-stranded RNA virus 01 (AuRNAV01, genus Labyrnavirus) contains an additional ORF at the 3′-end of the genome, which is transcribed as a sub-genomic mRNA during infection (Takao et al., 2006). Maps of protein domain organization within the polyprotein sequences are shown in Figure 2.Marnaviridae. Domains were identified using profile hidden Markov models (HMMs) based on similarities with conserved domains from other members of the order Picornavirales, including helicase, RNA-directed RNA polymerase (RdRP), and structural (VP) domains. Some genomes of viruses in the family also contain regions that resemble the 3C cysteine proteinases of members of the family Picornaviridae. Regardless of whether the genomes are mono- or di-cistronic, the non-structural proteins are encoded in the 5′-region and the structural proteins are encoded in the 3′region. Members of family Marniviridae do not appear to encode virus protein genome-linked (VPg)-like proteins, characteristic of some members of the order Picornavirales.

Biology

Where known, virus hosts are marine, single-celled, eukaryotic microbes (protists) (Table 2.Marnaviridae). Replication is cytolytic, with latent periods ranging from 8 to 48 hours. Cytopathic effects have been observed, with ultrastructural changes including swelling of the endoplasmic reticulum, the formation of crystalline arrays in the cytoplasm, vacuolation and disintegration of the cytoplasm, and the appearance of fibrous material in vacuolated areas (Tai et al., 2003, Nagasaki et al., 2004, Tomaru et al., 2009, Takao et al., 2005, Tomaru et al., 2012, Tomaru et al., 2004) . Large numbers of viral particles have been observed in the cytoplasm of infected cells (Shirai et al., 2008, Nagasaki et al., 2004, Takao et al., 2005). Burst sizes of these viruses vary from 66 to 105 particles per cell (Table 2.Marnaviridae). 

Derivation of names

Bacillarnavirus: from Bacillariophyceae, the class of diatoms that are hosts of these RNA viruses

Kusarnavirus: from the Afrikaans word kus meaning coastal and RNA virus

Labyrnavirus: from Labyrinthulid, the host name and RNA virus

Locarnavirus: from Locarno Beach where samples for the first marine RNA virus metagenomes in this genus were collected

Marnaviridae, Marnavirus: from Latin mare, meaning “sea”, and RNA virus

Salisharnavirus: from Salish Sea, the water mass around coastal southern British Columbia, Canada, from which the first marine RNA virus sequences in this genus were amplified

Sogarnavirus: from the Strait of Georgia, a major water body of the Salish Sea, the water mass around coastal southern British Columbia, Canada, from which the first marine RNA virus sequences in this genus were amplified

Genus demarcation criteria

Genera are defined based on phylogenetic relationships between virus amino acid sequences. Phylogenetic analysis of RdRP domain sequences place the viruses in seven clades that correspond to genera (Figure 3.Marnaviridae).

Figure 3.Marnaviridae. Maximum likelihood phylogeny of RdRP amino acid sequences of members of the family Marniviridae. Branches containing sequences from viruses in other families in the order Picornavirales and the Potyviridae (outgroup) are collapsed. SH-like branch support values are indicated at the nodes when >0.70. The scale bar indicates average residue substitution per site. Modified from (Vlok et al., 2019).

Species demarcation criteria

In genera with more than one species, species demarcation cut-offs are based on pairwise comparisons of the RdRP and capsid amino acid sequences. The cut-offs are 90% identity for the RdRP and 75% identity for the capsid.

Relationships within the family

Phylogenetic analysis of RdRP domain sequences place the 20 classified viruses in seven clades that correspond to genera (Figure 4.Marnaviridae, Figure 5.Marnaviridae).

Figure 4.Marnaviridae. RdRP phylogeny of viruses in the family Marnaviridae. Sequences outside of the clades of established genera are not highlighted in colour. Triangles indicate viruses classified into species. The RdRP conserved domains (Koonin and Dolja 1993) were aligned using MUSCLE v3.8.425 with default parameters (Edgar 2004) and manually curated with Aliview version 1.17.1 (Larsson 2014). The maximum-likelihood tree was constructed with PhyML 3.0 (Guindon et al., 2010) and the LG+I+G+F amino acid model (selected with Smart Model Selection (Lefort et al., 2017). Branch support was evaluated with the Shimodaira-Hasegawa approximate-likelihood ratio test and values are indicated at the nodes when >0.70. The maximum-likelihood scale bar indicates average residue substitution per site. The tree was edited in iTOL v3 (Letunic and Bork 2016). Accession numbers of individual viruses are given in the trees in the genera sections and in Figure 5.Marnaviridae. Modified from (Vlok et al., 2019). This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page.

Figure 5.Marnaviridae. Collapsed version of Figure 4.Marnaviridae. Collapsed genus clades include viruses classified into species in a genus and unclassified viruses also likely belonging to that genus. This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page.

Relationships with other taxa

Members of the family Marnaviridae share many properties with other viruses in the order Picornavirales. For example, their genomes are composed of one molecule of positive-sense RNA, have a 2C-3Cpro-3Dpol non-structural gene organization (Figure 2.Marnaviridae), and the virions of isolated representatives are icosahedral with a diameter of 22–35 nm (Figure 1.Marnaviridae; Table 2.Marnaviridae). However, phylogenetic analysis of RdRP amino acid sequences shows that members of the family Marnaviridae form a monophyletic group relative to viruses from other families within the Picornavirales (Figure 3.Marnaviridae). 

Related, unclassified viruses 

Virus name

Accession number

Beihai paphia shell virus 1 strain BHZY60696

KX884512

Beihai paphia shell virus 1 strain BWBFG40339

KX884527

Beihai paphia shell virus 2 strain YYSZX17625

KX884389

Beihai paphia shell virus 2 strain BWBFG38484

KX884525

Beihai picorna-like virus 20

KX883365

Beihai picorna-like virus 30

KX883402

Beihai picorna-like virus 36

KX883373

Beihai picorna-like virus 37

KX883426

Beihai picorna-like virus 38

KX884495

Beihai picorna-like virus 39

KX883410

Hubei picorna-like virus 6

KX884262

N OV 001

KY130492

N OV 013

KY130495

N OV 064

KY130497

Sanxia picorna-like virus 6

KX883713

Sanxia picorna-like virus 7

KX883716

Shahe picorna-like virus 3

KX883667

Shahe picorna-like virus 14 strain SHWC0209c12767

KX883647

Shahe picorna-like virus 14 strain SHWC13617

KX883664

Wenling picorna-like virus 1

KX884311

Wenzhou gastropodes virus 1

KX884372

Wenzhou picorna-like virus 5 strain WZSLuoI84329

KX884369

Wenzhou picorna-like virus 5 strain BHZC35527

KX884476

Wenzhou picorna-like virus 11

KX884333

Wenzhou picorna-like virus 17

KX884358

Wenzhou picorna-like virus 20

KX884356

Wenzhou picorna-like virus 21

KX884351

Wenzhou picorna-like virus 53

KX884373

Virus names and virus abbreviations are not official ICTV designations.

Metagenomic approaches targeting marine RNA viruses (Lachnit et al., 2015, López-Bueno et al., 2015, Moniruzzaman et al., 2017, Shi et al., 2016) have uncovered a diverse collection of viruses that are closely related to members of various families in the Picornavirales, including some that form a well-supported clade with members of the family Marnaviridae (Vlok et al., 2019). These are likely to represent additional members of the established genera as well as possible new genera (Figure 4.Marnaviridae, Figure 5.Marnaviridae).

Member taxa