Nimaviridae


Nimaviridae

Chapter contents

Posted February 2019

Nimaviridae: The family

Member taxa

Supporting information

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:

Wang, H.C., Hirono, I., Maningas, M.B.B., Somboonwiwat, K., Stentiford, G., and ICTV Report Consortium. 2019, ICTV Virus Taxonomy Profile: NimaviridaeJournal of General Virology, 100: 10531054.

Summary

The family Nimaviridae includes the single genus Whispovirus and the single species, White spot syndrome virus isolates of which infect a wide range of aquatic crustaceans and cause substantial economic losses. Virions are ellipsoid to bacilliform with a terminal extension, and contain more than 40 structural proteins ranging in mass from 11 to 664 kDa. These assemble into three structural layers (an outer envelope, a tegument and a nucleocapsid) that surround the core genomic DNA. The circular dsDNA genome is 280–307 kbp and contains several homologous repeat regions. Despite some genotypic variability, all isolates are classified within the same species.

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

Characteristic

Description

Typical member

white spot syndrome virus-CN (AF332093), species White spot syndrome virus, genus Whispovirus

Virion

Ellipsoid-to-bacilliform virion consisting of envelope, tegument, rod-shaped nucleocapsid and, sometimes, a thread-like terminal extension, 70–170 nm × 210–420 nm, containing >40 structural proteins

Genome

A single circular dsDNA of 280–307 kbp with 9 internal homologous repeat regions

Replication

Formation of the nucleocapsid and assembly of the intact virion occur in the nucleus; only virus protein translation occurs in the cytoplasm

Translation

Most virus mRNAs are capped, polyadenylated and translated via the canonical cap-dependent pathway; some genes, including structural genes, are expressed via mRNAs translated by the canonical cap-independent pathway using internal ribosome entry site elements

Host range

Wide range of crustaceans (order Decapoda) from marine, brackish or freshwater sources

Taxonomy

Single genus and species

Virion

Morphology

Virions of white spot syndrome virus (WSSV) are enveloped, ellipsoid-to-bacilliform particles of 70–170 nm in width and 210–420 nm in length (Table 1.Nimaviridae  and Figure 1.Nimaviridae). A thread or flagellum-like projection (or extension) is present at one end of most virions (Chou et al., 1995, Durand et al., 1997, Lu et al., 1997). The virion consists of an inner, rod-shaped nucleocapsid with a tight-fitting capsid layer, an intermediate tegument layer and an outer lipid-containing trilaminar envelope (Tsai et al., 2006). In virions purified from the crayfish Procambarus clarkii, the virion lipids are apparently derived from host cell nuclei (Zhou et al., 2008). There is currently no evidence to suggest that the lipid components of virions are derived from the host cell membrane. The purified nucleocapsid is 50–80 nm in width and 300–420 nm in length.

Figure 1.Nimaviridae. (Top) Morphology of virions of white spot syndrome virus (WSSV). (Left) Schematic illustration of the structure of a typical whispovirus virion using a cutaway section to show the locations of major virion proteins. (Top center and right) Negative-contrast electron micrographs of WSSV virions (center, courtesy of Marielle van Hulten) and nucleocapsids (right, courtesy of Don Lightner) from hemolymph of infected Penaeus monodon. The bars represent 100 nm. (Bottom left) Thin section of WSSV-infected stomach epithelium showing the parallel arrangement of virions in the nucleoplasm (the bar represents 1 µm) and (bottom right) a cross-section of virions (the bar represents 100 nm) (courtesy of Don Lightner).

Physicochemical and physical properties

WSSV virions have a buoyant density of 1.22 g cm−3 in CsCl, whereas nucleocapsids have a buoyant density of 1.31 g cm−3. Virions are viable for at least 1 month at 30°C in seawater under laboratory conditions and in ponds for at least 3–4 days. They are inactivated by pH <3.0 for 1 h and pH 12 for 10 min, exposure to UV irradiation at 9.3 x 105 µW s/cm2 for 1 h, and by incubation for <1 min at 60°C. Virions are also sensitive to sodium hypochlorite, benzalkonium chloride, iodophore and ozone (Chang et al., 1998, Nakano et al., 1998, Balasubramanian et al., 2006).

Nucleic acid

The nucleocapsid contains a single molecule of circular dsDNA of 280–307 kbp. The G+C content of WSSV genome DNA is about 41% (van Hulten et al., 2001, Yang et al., 2001).

Proteins

High-throughput proteomic analysis indicates that WSSV virions contain more than 40 structural proteins ranging in mass from 11 to 664 kDa and arranged in three structural layers that surround the core genomic DNA: an outer envelope, a tegument and a nucleocapsid (Table 2.Nimaviridae) (Tsai et al., 2006, Tsai et al., 2004, Xie et al., 2006). There are six major structural proteins: VP28 and VP19 in the envelope; VP26 and VP24 in the tegument; and VP664 and VP15 in the nucleocapsid. The three major proteins, VP28, VP26 and VP24, are phylogenetically related. VP664, which has a theoretical mass of 664 kDa, is the largest viral structural protein known. It forms unique stacked rings in the nucleocapsid (Leu et al., 2005). VP15 is a very basic, histone-like DNA-binding nucleoprotein (Witteveldt et al., 2005). Two structural proteins, VP38B and VP36A, also block shrimp caspase-induced apoptosis (Leu et al., 2010, Bowornsakulwong et al., 2017). One envelope protein, VP22, shows relatively high similarity to TATA-box binding protein. WSSV458 is a tegument protein that can bind to the shrimp protein PmVRP15 to facilitate viral trafficking and assembly (Jaree et al., 2016). Other WSSV structural proteins, including three envelope proteins (WSSV189, VP39 and WSSV471), a nucleocapsid protein (WSSV186) and a tegument protein (WSSV458), are targeted by the shrimp antimicrobial peptide, ALFPm3 (Suraprasit et al., 2014, Methatham et al., 2017). Curiously, silencing of the genes encoding VP28, VP26, VP19 and VP15 by RNA interference also leads to a reduction in WSSV replication (Escobedo-Bonilla 2011).

Table 2.Nimaviridae. WSSV-encoded structural proteins.

No.

Sub-category

Protein namea

WSSV ORF

WSSV-CN

(AF332093)

WSSV-TW

(AF440570)

1

Envelope proteinsb

 

VP187

wsv209

wssv264

2

VP180

wsv001

wssv052

3

VP150

wsv011

wssv067

4

VP136B

wvs465

wssv524

5

VP124

wsv216

wssv271

6

VP110

wsv035

wssv092

7

VP90

wsv327

wssv383

8

VP75

wsv332

wssv388

9

VP56 (VP60A)

wsv325

wssv381

10

VP55

wsv526

wssv051

11

VP53A

wsv011

wssv067

12

VP53B

wsv115

wssv171

13

VP53C

wsv269

wssv324

14

VP52A (VP51A)

wsv238

wssv294

15

VP52B (VP51B)

wsv256

wssv311

16

VP41A

wsv237

wssv293

17

VP41B

wsv242

wssv298

18

VP39 (VP39B)

wsv339

wssv395

19

VP38 (VP38A)

wsv259

wssv314

20

VP38B

wsv390

wssv449

21

VP33 (VP36B)

wsv254

wssv309

22

VP32

wsv198

wssv253

23

VP31

wsv340

wssv396

24

VP28

wsv421

wssv480

25

VP22

wsv303

wssv359

26

VP19

wsv414

wssv473

27

VP16 (VP13B)

wsv321

wssv377

28

VP14

wsv293a

wssv349

29

VP13A

wsv284

wssv339

30

VP12 (VP12A)

wsv009

wssv065

31

VP12B

wsv386

wssv445

32

VP11

wsv338

wssv394

33

 

WSSV189

wsv134

wssv189

33

 

WSSV471

wsv412

wssv471

34

Tegument proteins

VP95

wsv442

wssv502

35

VP39A

wsv306

wssv362

36

VP36A

wsv077

wssv134

37

VP26

wsv311

wssv367

38

VP24

wsv002

wssv058

39

 

WSSV458

wsv399

wssv458

40

Nucleocapsid proteins

VP664

wsv360

wssv419

41

VP190 (VP160A)

wsv289

wssv344

42

VP160B

wsv037

wssv094

43

VP136 (VP136A)

wsv271

wssv326

44

VP76 (VP73)

wsv220

wssv275

45

VP60 (VP60B)

wsv415

wssv474

46

VP51 (VP51C)

wsv308

wssv364

47

VP15

wsv214

wssv269

48

 

WSSV186

wsv131

wssv186

a: Structural protein names are from (Tsai et al., 2004, Tsai et al., 2006, Xie et al., 2006). Some structural proteins have alternative names; these aliases are shown in parentheses (Tsai et al., 2004, Tsai et al., 2006).
b: Some proteins listed as envelope proteins may in fact turn out to be tegument proteins.

Lipids

Virion lipid components include neutral lipids and the phospoholipids phosphatidylcholine and phosphatidylethanolamine (Zhou et al., 2008). A GC/MS analysis of the fatty acids in crayfish stomach and WSSV virions suggested that, although the respective compositions of their long chain fatty acids are broadly similar, WSSV virions contain more saturated C18:0 (stearic acid) and less C20:5n-3 (eicosapentaenoic acid) and C22:6n-3 (docosahexaenoic acid) fatty acids (Hsieh et al., 2015).

Carbohydrates

None of the major virion proteins is glycosylated.

Genome organization and replication

Genotypic variants exist that can be distinguished by restriction length polymorphism and genomic sequence data. Several WSSV isolates have been sequenced, and their genomes are variously 280,591 bp (WSSV-IN_AP4RU; MG702567), 297,967 bp (WSSV-TH; AF369029), 305,119 bp (WSSV-CN; AF332093) and 307,287 bp (WSSV-TW; AF440570). In the case of WSSV-TH, major differences can be attributed to deletions between positions 275,238 and 287,285, and between 267,203 and 268,046, and also to insertion of a 1.3 kb transposase sequence in the WSSV-TW genome at positions 204,978–204,979. The WSSV genome is further characterized by the presence of nine homologous repeat (Hr) regions (Hr1-9; Figure 2.Nimaviridae). The number of imperfect palindromic repeats (each of 250 bp) within an Hr varies among isolates (Marks et al., 2004).

Figure 2.Nimaviridae. Schematic map of the circular dsDNA genome of white spot syndrome virus type strain CN. Solid arrows indicate the positions and direction of transcription of ORFs.

WSSV enters host cells via caveola- or clathrin-mediated endocytosis (Huang et al., 2013, Huang et al., 2015). After entering, WSSV triggers host metabolic changes in order to complete its replication, affecting aerobic glycolysis, glutaminolysis and lipid metabolism (Hsieh et al., 2015, Su et al., 2014, Li et al., 2016, Chen et al., 2016, Fan et al., 2016). Transcription of virus mRNA, replication of virus DNA, formation of nucleocapsids and assembly of virions take place in the nucleus; virus proteins are translated in the cytoplasm (Leu et al., 2009). Transcription of WSSV genes is temporally regulated, and four main gene classes are assigned according to the time of mRNA expression: immediate early (IE), early, late and very late genes. Most virus mRNA is 5′-capped and 3′-polyadenylated. There is no evidence for RNA splicing. The virion protein genes are dispersed on both strands of the genome, and some, such as vp31/vp39b/vp11, are arranged in clusters with non-structural genes. These produce polycistronic mRNAs and use an IRES (internal ribosome entry site element) mechanism to regulate translation. Several IRES elements have been identified in the WSSV genome: upstream from vp28, upstream from wsv493 (icp35) and an extension across the coding regions of vp31 and vp39b (Han and Zhang 2006, Kang et al., 2009, Kang et al., 2013). 

WSSV ie1 has a promoter motif ([A/C][A/C]TCANT) that matches the RNA polII core promoter in arthropods. The WSSV late gene consensus promoter (A[A/T][A/T/G]AC) is usually situated less than 100 bp upstream from the transcriptional start site. Consensus TATA box sequences have been found about 25 bp upstream from early gene transcription initiation sites. Late transcripts seem to start 25 bp downstream from an A- or T-rich region (Marks et al., 2006).

Genomic analysis reveals that, of the 531 ORFs of 60 codons or more in the WSSV genome, only 181 seem likely to encode functional proteins (WSSV-CN; Figure 2.Nimaviridae). Only a few functional genes have been identified: these encode virion proteins, proteins involved in initiating virus replication (IE proteins), proteins involved in virus DNA replication (DNA polymerase, ribonucleotide reductase subunits [RR1 and RR2], dUTPase, thymidylate synthase [TS], thymidine kinase-thymidylate kinase [TK-TMK]), protein-modifying proteins (protein kinase), anti-apoptotic proteins and a histone-binding DNA mimic, ICP11 (Tables 2.Nimaviridae and 3.Nimaviridae). A total of 18 IE genes have been proposed. IE1 has a transactivation activity and interacts with shrimp TATA box-binding protein, STAT and Yin Yang 1 protein (Liu et al., 2011, Yao et al., 2016, Huang et al., 2017b). WSSV164 and WSSV453 are anti-melanization proteins that interact with proteins involved in the proPO system (Sutthangkul et al., 2017, Sangsuriya et al., 2018). Four genes, AAP1–AAP4, show anti-apoptotic activity (Leu et al., 2010, Bowornsakulwong et al., 2017, He et al., 2009, Lertwimol et al., 2014). WSV152 is a mitochondrion-targeting protein that localizes specifically on the outer mitochondrial membrane (Yan et al., 2016). The most highly expressed WSSV nonstructural protein is ICP11 (Wang et al., 2008).

Table 3.Nimaviridae. WSSV-encoded non-structural proteins

No.

Sub-category

WSSV ORF

Protein name

WSSV-CN

(AF332093)

WSSV-TW

(AF440570)

1

IE proteins

IE1

wsv069

wssv126

2

IE2

wsv187.

wssv242

3

IE3

wsv359

wssv418

4

Ubiquitin E3 ligase

wsv249

wssv304

5

IE candidate

wsv051

wssv108

6

IE candidate

wsv078

wssv135

7

IE candidate

wsv079

wssv136

8

IE candidate

wsv080

wssv137

9

IE candidate

wsv083

wssv140

10

IE candidate

wsv091

wssv148/149.

11

IE candidate

wsv094

wssv150

12

IE candidate

wsv098

wssv154

13

IE candidate

wsv099

wssv155

14

IE candidate

wsv100

wssv156

15

IE candidate

wsv101

wssv157

16

IE candidate

wsv103

wssv159

17

IE candidate

wsv108

wssv164

18

IE candidate

wsv178

wssv234

19

Anti-apoptotic proteins (AAP)

AAP1

wsv390

wssv449

20

AAP2

wsv077

wssv134

21

AAP3

wsv166

wssv222

22

AAP4

wsv267

wssv322

23

Anti-melanization proteins

WSSV164

wsv108

wssv164

24

WSSV453

wsv394

wssv453

25

Latency-related genes

ORF89

wsv151

wssv207

26

ORF427

wsv427

wssv486

27

Enzymes

 

Thymidylate synthase (TS)

wsv067

wssv124

28

Protein kinase 2 (PK2)

wsv083

wssv140

29

dUTPase

wsv112

wssv168

30

Ribonucleotide reductase 1 (RR1)

wsv172

wssv228

31

Ribonucleotide reductase 2 (RR2)

wsv188

wssv243

32

Nuclease

wsv191

wssv246

33

Thymidine kinase thymidylate kinase (TK-TMK)

wsv395

wssv454

34

Protein kinase 1 (PK1)

wsv423

wssv482

35

DNA polymerase

wsv514

wssv037

36

Others

RING-H2 protein

wsv194.

wssv249

37

Collagen-like protein

wsv001

wssv052

38

Histone-binding DNA mimic (ICP11)

wsv230

wssv285

39

Mitochondria targeting protein (MTP)

wsv152

wssv208

40

TATA-box binding protein (TBP)

wsv303

wssv359

41

ICP35

wsv493

wssv019

To regulate its replication, WSSV expresses several virus microRNAs that target either its own genes or those of the host. WSSV-miR-N32 targets wsv459 and wsv322 to suppress virus replication, possibly as a strategy to avoid stimulating host innate immunity (He et al., 2017). Conversely, WSSV-miR-66 and WSSV-miR-68 promote virus replication by targeting wsv094 and wsv 177, and wsv248 and wsv309, respectively (He et al., 2014). WSSV-miR-N13 and WSSV-miR-N23 target Dorsal, the key gene of the Toll pathway, and this results in suppression of Toll-mediated shrimp immunity (Ren et al., 2017), while WSSV-miR-22 targets the shrimp STAT gene to promote WSSV replication (Ren et al., 2015). Shrimp microRNAs also regulate WSSV replication by targeting WSSV genes. The expression of shrimp miR-965 decreases WSSV copy number and WSSV-induced mortality by targeting the wsv240 gene (Shu et al., 2016). Shrimp miR-10A enhances the translation of at least three WSSV genes (vp26, vp28 and wssv102) by targeting the 5-UTRs of these genes (Huang et al., 2017a).

WSSV has also been shown to contain genes homologous to those of its hosts Marsupenaeus japonicus (Dang et al., 2010) and Penaeus monodon. These may be instances of mimicry of the structure and function of host genes, e.g. to avoid detection and destruction by the host immune system, a stratagem used by other dsDNA viruses. Alternatively, the host genes may be degenerate proviral remnants.

Antigenicity 

Polyclonal and monoclonal antibodies have been raised against WSSV virions, and these can be used as diagnostic tools. Viruses can be neutralized with antisera against the WSSV structural proteins VP12B, VP19, VP28, VP31, VP36A, VP33 (VP36B) and VP51 (Wu et al., 2005, Li et al., 2006, Patil et al., 2011). Recombinant proteins have been widely used as vaccines against WSSV infection. In shrimps, vaccines containing recombinant WSSV structural proteins VP19, VP26, VP28 and VP41A have been shown to improve survival after WSSV infection (Chang et al., 2018). It can be inferred from this that these proteins are involved in WSSV infection. 

Biology

Host range

WSSV can infect a wide range of aquatic crustaceans, including salt, brackish and fresh water penaeids, crabs, crayfish and hermit crabs (Lo et al., 1996, Flegel 2006, Sánchez-Paz 2010).

Transmission

The virus is transmitted by cannibalism of diseased individuals or via water passing through the gills. The virus can also be transmitted vertically from adults to offspring by being released from non-viable WSSV-infected eggs or from supporting cells in ovarian tissue (Lo et al., 1997).

Geographical distribution

WSSV has been identified from crustaceans in China, Japan, Korea, Southeast Asia, South Asia, the Middle East and the Americas. An unusual property of the virus is the extremely wide host range despite a very low level of genetic polymorphism. The latter suggests that white spot disease (WSD) is a relatively recent epizootic (Nadala and Loh 1998, Pradeep et al., 2012).

Cytopathic effects

The major targets of WSSV infection are tissues of ectodermal and mesodermal embryonic origin, such as subcuticular epithelial cells (including those of the shrimp stomach), gills, lymphoid organ and connective tissue. Although WSSV infects the underlying connective tissue in the shrimp hepatopancreas and midgut, the columnar epithelial cells of these two organs are of endodermal origin and do not become infected. WSSV can be propagated in primary cultures of lymphoid organ and ovary. Whether or not infection causes disease depends upon factors that are poorly understood but related to species tolerance and environmental triggers. Shrimp and other crustaceans susceptible to disease from this virus show gross signs of lethargy, such as lack of appetite, slow movement and often a reddish coloration of the whole body together with “white spots” embedded within the exoskeleton. These spots are the result of calcified deposits that range in diameter from 0.5 to 3.0 mm. However, in some cases, such as acute experimental infections resulting from injected virus preparations, there may be no gross signs of infection other than lethargy and lack of appetite. Most affected animals die 3–10 days after infection. With a lower infection dose to allow sufficient time before mortality, animals susceptible to disease have large numbers of virions circulating in the hemolymph, but this may also occur for tolerant species showing no mortality. Thus, high virus loads per se do not cause disease or mortality in all susceptible species (Durand et al., 1997, Leu et al., 2009, Lo et al., 1996, Sánchez-Paz 2010, Lo et al., 1997).

Derivation of names

Nima: Greek for “thread”; referring to the thread- or tail-like polar extension (appendage) on some virus particles.

The name white spot syndrome virus has been arrived at after the use of various earlier names, such as Chinese baculo-like virus, hypodermic and hematopoietic necrosis baculovirus, Penaeus monodon non-occluded baculovirus II, Penaeus monodon non-occluded baculovirus III, Penaeus monodon rod-shaped nuclear virus, systemic ectodermal and mesodermal baculovirus, white spot bacilliform virus and white spot baculovirus.

Phylogenetic relationships

Despite some genotypic variability, the amino acid sequences of DNA polymerase from geographically distinct WSSV isolates are approximately 99% identical, and all isolates are classified in the same species. Various isolates with small genetic polymorphisms have been identified (variants). Because of the high level of similarity among variants, their evolutionary histories have not yet been clearly established.

Similarity with other taxa

Morphologically, virions and rod-shaped nucleocapsids resemble the budded virus particles of baculoviruses, polydnaviruses and the alphanudivirus Oryctes rhinoceros nudivirus. The presence of Hrs dispersed throughout the genome is a property shared with members of the families Baculoviridae, Ascoviridae, Hytrosaviridae and Nudiviridae. Phylogenetic analysis based on the DNA polymerase from WSSV and a number of other dsDNA viruses shows that WSSV is phylogenetically highly distinct.


Genus: Whispovirus


Since only one genus (Whispovirus) is currently recognized in the family Nimaviridae, the family description above corresponds to the genus description. For clarity, the additional information that can be found on the genus page is also presented below.

Species demarcation criteria 

There is a single species in the genus.

Member species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
White spot syndrome viruswhite spot syndrome virusCNAF332093Complete genomeWSSV-CN
White spot syndrome viruswhite spot syndrome virusTaiwanAF440570WSSV-TW
White spot syndrome viruswhite spot syndrome virusTHAF369029WSSV-TH
White spot syndrome viruswhite spot syndrome virusK-LV1JX515788WSSV-K-LV1
White spot syndrome viruswhite spot syndrome virusCN01KT995472WSSV-CN01
White spot syndrome viruswhite spot syndrome virusCN02KT995470WSSV-CN02
White spot syndrome viruswhite spot syndrome virusCN03KT995471WSSV-CN03
White spot syndrome viruswhite spot syndrome virusCN04KY827813WSSV-CN04
White spot syndrome viruswhite spot syndrome virusMEX2008KU216744WSSV-MEX2008
White spot syndrome viruswhite spot syndrome virusEG3KR083866WSSV-EG3
White spot syndrome viruswhite spot syndrome virusCN-PcKX686117WSSV-CN-Pc
White spot syndrome viruswhite spot syndrome virusAUMF768985WSSV-AU
White spot syndrome viruswhite spot syndrome virusIN_AP4RUMG702567WSSV-IN_AP4RU
White spot syndrome viruswhite spot syndrome virusEC-15098MH090824WSSV-EC-15098

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Derivation of names 

Whispo: derived from white spot syndrome virus