Nudiviridae


Nudiviridae

Robert L. Harrison, Elisabeth A. Herniou, Annie Bézier, Johannes A. Jehle, John P. Burand, David A. Theilmann, Peter J. Krell, Monique M. van Oers and Madoka Nakai

Chapter contents

Posted December 2019

Nudiviridae: The family

Member taxa

Supporting information

  • Authors - corresponding author: Robert L. Harrison (Robert.L.Harrison@ars.usda.gov)
  • Resources - study group wiki, sequence alignments and tree files
  • Further reading - reviews and additional information
  • 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:

Robert L. Harrison, Elisabeth A. Herniou, Annie Bézier, Johannes A. Jehle, John P. Burand, David A. Theilmann, Peter J. Krell, Monique M. van Oers, Madoka Nakai, and ICTV Report Consortium. 2020, ICTV Virus Taxonomy Profile: NudiviridaeJournal of General Virology, 101, 3–4.

Summary

Members of the family Nudiviridae are large dsDNA viruses with distinctive rod-shaped nucleocapsids and circular genomes of 96 to 232 kbp.  Nudiviruses have been identified from a diverse range of insects and crustaceans.  Although nudiviruses resemble baculoviruses and share some core genes, they are part of a separate, distinct lineage.

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

Characteristic

Description

Typical member

Oryctes rhinoceros nudivirus Ma07 (EU747721), species Oryctes rhinoceros nudivirus, genus Alphanudivirus

Virion

Enveloped, rod-shaped or ellipsoidal, compact (approximately 100 nm × 200 nm) or elongated (approximately 81 nm × 415 nm)

Genome

A single covalently-closed circular dsDNA molecule of 96–232 kbp encoding 89–155 proteins

Replication

Nuclear, with nucleocapsids assembled and enveloped within the nucleus

Translation

From mRNAs transcribed from viral DNA

Host range

Immature and adult stages of insects and crustaceans

Taxonomy

Two genera with three species

Virion

Morphology

Virions consist of bacilliform nucleocapsids surrounded by an envelope.  The virions can be relatively compact (100 nm × 200 nm; (Payne et al., 1977)) or elongated (81 × 415 nm) (Hamm et al., 1996).  Tail-like appendages extending from the nucleocapsid are sometimes observed (Payne et al., 1977, Hamm et al., 1996).  Virions assembled into occlusion bodies have been noted in nudivirus-infected hosts in some instances (Smith 1956, Lightner and Redman 1981, Huger 1991, Raina et al., 2000, Bézier et al., 2015). 

Physicochemical and physical properties

Virions have a buoyant density of 1.18–1.23 g/mL in sucrose gradients (Payne 1974, Huger 1985) and 1.28 g/mL in CsCl gradients (Payne et al., 1977).  The envelope surrounding the virion is removed upon treatment with the detergent NP-40, and the remaining nucleocapsids possess a density of 1.47 g/mL in CsCl gradients (Payne et al., 1977).

Nucleic acid

Nudivirus DNA consists of a supercoiled, circular double-stranded molecule (Huang et al., 1982), of 96 to 232 kbp.

Proteins

Annotations of nudivirus genomes indicate that nudiviruses encode approximately 89 to 155 proteins.  Protein gels of purified virions have distinguished 26–28 structural proteins (Burand et al., 1983, Crawford and Sheehan 1985), and proteomic analysis determined that the occlusion bodies of an unclassified nudivirus from a crane fly, Tipula oleracea, consist of at least 48 proteins (Bézier et al., 2017).  Genes encoding homologs of the lepidopteran and hymenopteran baculovirus polyhedrin matrix protein have been identified in nudivirus genomes (Bézier et al., 2015, Wang et al., 2011).  However, the nudivirus occlusion body matrix in some cases may consist of a protein unrelated to baculovirus polyhedrin (Chaivisuthangkura et al., 2008).  Nudivirus genes also encode several homologs of proteins demonstrated to be structural components of baculovirus virions, such as the major capsid protein VP39 and the envelope protein P74, or to have roles in viral replication, such as DNA polymerase and RNA polymerase components LEF-8, LEF-9, and P47.

Lipids

Lipids are likely present in the envelope, but have not been characterized.

Carbohydrates

Carbohydrates are present in nudiviral glycoproteins (Burand et al., 1983).

Genome organization and replication

ORFs are distributed throughout the genome, with approximately equal numbers of the ORFs occurring in either orientation (Figure 1.Nudiviridae) (Bézier et al., 2015, Wang et al., 2011, Cheng et al., 2002, Wang et al., 2007, Burand et al., 2012, Yang et al., 2014, Hill and Unckless 2018, Holt et al., 2019).  The order of homologs shared among nudivirus genomes is poorly conserved.  Thirty-two core genes have been identified as being present in all nudivirus genomes, including 21 homologs of baculovirus core genes (Table 2.Nudiviridae) (Bézier et al., 2015).  In addition, intergenic regions of direct or tandem repeated sequences are present. TATA box and Initiator promoter motifs are located upstream of some of the ORFs, as well as the baculovirus late promoter motif TAAG (Bézier et al., 2015, Cheng et al., 2002, Wang et al., 2007).  

Figure 1.Nudiviridae. Genome map of Oryctes rhinoceros nudivirus isolate Ma07, the exemplar isolate of the species Oryctes rhinoceros nudivirus (genus Alphanudivirus), and typical member of the family Nudiviridae.  The map is illustrated with locations and orientations of annotated ORFs (arrows). ORFs corresponding to the core genes of members of the family Nudiviridae, and ORFs conserved among subsets of nudiviruses are indicated.  Locations of direct (dr) and tandem (tr) repeat sequence regions are also shown.

Nudivirus infection of cells is characterized by cytopathology consisting of cellular rounding and nuclear hypertrophy (Crawford and Sheehan 1985, Huger 1966, Burand and Lu 1997, Rallis and Burand 2002).  Virus-specific transcripts and infected cell-specific proteins appear at different times during infection (Burand et al., 1983, Crawford and Sheehan 1985, Chao et al., 1992), suggesting that there is temporal regulation of viral gene expression.  Envelopment of nucleocapsids takes place in the nucleus (Crawford and Sheehan 1985, Kelly et al., 1981), and the resulting progeny virions accumulate, often in paracrystalline arrays, within the nucleus or within vesicles (Hamm et al., 1996, Huger 1966, Burand and Lu 1997, Rallis and Burand 2002).  This is followed by cell lysis (Burand et al., 1983, McIntosh et al., 2007).  Virions bud from infected cells (Crawford and Sheehan 1985) or are released upon cell lysis (Burand and Lu 1997).

Table 2.Nudiviridae. Core genes of members of the family Nudiviridae

Oryctes rhinoceros nudivirus (OrNV) ORF

Gene name

Inferred activity or function of encoded protein

ORF1a

dnapol

DNA polymerase

ORF4a

ac81

Nucleocapsid envelopment

ORF15a

vp39

Major capsid protein

ORF16

fen-1

FEN-1/FLAP endonuclease

ORF17a

pif-2

Per os infectivity factor

ORF18

GbNV_gp67-like

Unknown

ORF20a

p47

RNA polymerase subunit

ORF22a, b

p6.9

Nucleocapsid packaging/assembly

ORF30a

vlf-1

Very late gene expression factor

ORF33a

pif-4

Per os infectivity factor

ORF34a

helicase

DNA helicase

ORF41

11K-like

Occlusion body component

ORF42a

lef-4

RNA polymerase subunit

ORF47

GbNV_gp19-like

Unknown

ORF52a

lef-5

Transcription initiation factor

ORF60a

pif-1

Per os infectivity factor

ORF61

GbNV_gp51-like

Unknown

ORF64a

lef-8

RNA polymerase subunit

ORF72a

pif-6

Per os infectivity factor

ORF75

integrase

DNA processing

ORF76

GbNV_gp58-like

Unknown

ORF87a

38k

Nucleocapsid protein

ORF96a

lef-9

RNA polymerase subunit

ORF106a

vp91/p95

Nucleocapsid protein

ORF107a

pif-3

Per os infectivity factor

ORF108

helicase-2

DNA helicase

ORF113a

p33

Sulfhydryl oxidase

ORF115a

odv-e56/pif-5

Per os infectivity factor

ORF117

tk2

Thymidine kinase

ORF125

tk3

Thymidine kinase

ORF126a

p74/pif-0

Per os infectivity factor

ORF137

tk1

Thymidine kinase

aAlso conserved among members of family Baculoviridae
bThe p6.9 homolog of OrNV and related alphanudiviruses from drosophilid hosts is a fusion of the homologs of Gryllus bimaculatus nudivirus (GbNV) p6.9 (ORF73) and the upstream GbNV ORF72.  In other nudiviruses, it exists as an independent ORF. 

Antigenicity 

Antigenic similarities have been detected between virions of Oryctes rhinoceros nudivirus and baculoviruses (Payne et al., 1977). 

Biology 

Nudiviruses have been isolated from insects of the orders Coleoptera, Diptera, Lepidoptera, and Orthoptera, and from crustaceans of the order Decapoda.  Infections of both adult and immature stages of the host can occur.  Transmission occurs horizontally and is initiated by oral ingestion of virions and infection of the midgut (Hamm et al., 1996, Bézier et al., 2015, Huger 1985, Zelazny 1976, Raina and Lupiani 2006).  Also, horizontal transmission occurring via sexual contact between adults has been documented, as has vertical transmission from infected adults to progeny (Hamm et al., 1996, Burand et al., 2004).  Viral DNA by itself can initiate an infection when transfected into cells in culture (McIntosh et al., 2007). The outcome of infection ranges from cell lysis and mortality of the infected host to establishment of a persistent, asymptomatic infection.

Genus demarcation criteria

Because relatively low numbers of nudiviruses have been identified and studied, criteria for the demarcation of nudivirus genera are not well-defined.  Currently, nudivirus genera can be broadly distinguished by molecular phylogeny and differences in genome characteristics (size and gene content), hosts of origin, and virion width and length.  Analysis that includes sequences of additional unclassified nudiviruses suggests the possibility that pairwise amino acid distances of selected core genes and the presence or absence of core gene synteny may be used to develop demarcation criteria for nudivirus genera with more precision.

Derivation of names

Alpha, Beta: Greek letters α and β, the first two letters of the Greek alphabet.

Nudi-: From the Latin “nudus”, meaning “naked”, referring to virions that are not occluded in a baculovirus-like occlusion protein matrix.  This prefix is taken from “Nudibaculovirinae”, the name of the former subfamily of Baculoviridae into which nudiviruses had been previously classified in the 5th Report of the ICTV.  At that time, it was not known that some nudiviruses form occlusion bodies.

Phylogenetic relationships

Phylogenetic analysis based on core genes shared with baculoviruses shows that members of the family Nudiviridae comprise a monophyletic group distinguishable from baculoviruses (Wang et al., 2007). Figure 2.Nudiviridae illustrates the relationships of nudiviruses to each other, including exemplar nudiviruses of species classified into the genera Alphanudivirus and Betanudivirus.

Figure 2.Nudiviridae. Phylogeny of family Nudiviridae. Amino acid sequences of all nudivirus core genes except p6.9 were aligned individually by MUSCLE and concatenated, and phylogeny was inferred from the concatenated alignments by maximum likelihood using MEGA X with the Le_Gascuel_2008 (LG) substitution model and a discrete Gamma distribution to account for evolutionary rate differences among sites.  The percentage of 500 bootstrap replications in which the associated taxa clustered together is shown next to the branches. Filled circles indicate viruses that are classified into species in the genus Alphanudivirus (blue) or Betanudivirus (orange); unclassified viruses are indicated by open circles. This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page.

Similarity with other taxa

Nudiviruses were classified within the family Baculoviridae as “non-occluded baculoviruses” until the 5th Report of the ICTV, but were removed from Baculoviridae upon the publication of the 6th Report in 1995 due to differences in virion morphology and the lack of an occlusion body.  After being “unassigned viruses” for 18 years, members of the family Nudiviridae were grouped together in two genera in 2013. Nevertheless, nudiviruses share structural, genetic and biological characters with viruses of family Baculoviridae.  Nudivirus genomes possess homologs of at least 21 baculovirus core genes (Wang et al., 2011).  In addition, viruses of the genus Bracovirus in the family Polydnaviridae appear to be derived from an ancestral nudivirus that was integrated into the genome of a parasitoid wasp (Herniou et al., 2013).   

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

Homarus gammarus nudivirus

MK439999

HgNV

Penaeus monodon nudivirus

KJ184318

PmNV

Tipula oleracea nudivirus

KM610234

ToNV

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