Genus: Protoparvovirus


Genus: Protoparvovirus

Distinguishing features 

Members of genus Protoparvovirus are monophyletic and share standard NS1 sequence identity criteria. The genus is split into two branches (Figure 6B.Parvoviridae), one occupied by founder members of the family that have been studied in great detail, whereas the second branch is occupied exclusively by predicted viruses whose coding sequences were identified recently in the wild using virus discovery approaches, but whose biology remains minimally explored. Genomes of the founder protoparvoviruses are distinctive because they contain many reiterations of the tetranucleotide sequence 5′-TGGT-3′ (or its complement 5′-ACCA-3′), which is the modular binding motif of the NS1 duplex DNA recognition site, generally depicted as (TGGT)2-3 (Cotmore et al., 1995). Minute virus of mice (MVM) NS1 recognizes variably spaced, tandem and inverted, clusters of the TGGT motif, allowing it to bind to a wide variety of sequences distributed throughout replicative-form viral DNA. TGGT/ACCA tetranucleotide clusters are also dispersed throughout the genomes of the new viruses, suggesting significant biological similarities with founder members. For example, in the 4822 nt sequence of bufavirus 1a (human) (JX027296) there are 95 copies of ACCA or TGGT, while in the 4452 nt sequence of a melanoma-associated human cutavirus (KX685945) there are 105 separate copies.

Protoparvoviruses exhibit a wide range of pathologies; some founder viruses, such as canine, feline and porcine parvovirus can be significantly pathogenic and are of major veterinary or agricultural significance, but many other infections can be asymptomatic. 

Virion

See discussion under family description and Figures 1.Parvoviridae and 2.Parvoviridae therein. X-ray reconstructions indicate that the first ordered VP residues in protoparvovirus capsids are located inside the particle at the base of the 5-fold pore, leaving unresolved VP1 and VP2 N-termini of ~180 and 37 residues, respectively (Halder et al., 2013, Agbandje-McKenna et al., 1998, Xie and Chapman 1996). The C-terminal region of this unresolved sequence forms a slender glycine-rich chain, present in both VP1 and VP2, which in minute virus of mice (MVM) variant VLPs can be modeled into claw-like densities positioned inside the capsid below the 5-fold channels in some cryoEM reconstructions (Subramanian et al., 2017). However, in X-ray structures of MVM virions, but not empty particles, the first 10 amino acids from a single copy of this sequence (VP2 G37–G28) can be modeled into submolar density that occupies the central pore of most 5-fold cylinders. Although all VP1 and VP2 N-terminal peptides are sequestered in empty particles, a subset of MVM VP2 N-termini become exposed at the virion surface early during genome encapsidation (Cotmore and Tattersall 2005a),  presumably via a poorly understood conformational shift that involves expansion of the 5-fold cylinders. These externalized VP2 N-termini contain a nuclear export signal (Maroto et al., 2004) that in some cells effectively converts the trafficking-neutral capsid into a nuclear export-competent particle. Virions are released from infected cells in this form (Cotmore and Tattersall 2005a), but both in the extracellular environment and during cell entry, exposed N-termini undergo proteolytic cleavage, which removes ~25 amino acids and converts VP2 to a form called VP3. Because X-ray structures show slightly less than one polyglycine tract threaded through each cylinder, it is significant that ~90% of the ~50 MVM VP2 termini eventually become surface exposed and cleaved. X-ray structures of cleaved, predominantly VP3, virions indicate that this proteolysis allows the polyglycine tract of cleaved proteins to be retracted into the capsid interior, where it folds back and assumes additional icosahedral ordering extending to residue G30, while being replaced in the cylinders by a new cluster of VP2 N-termini (Govindasamy L, Gurda BL, Halder S, Van Vliet K, McKenna R, Cotmore SF, Tattersall P, Agbandje-McKenna M. 2010, unpublished observations). Externalized VP2 N-termini also serve an important structural role, stabilizing the cylinders prior to cell entry and preventing premature exposure of VP1 N-termini and ultimately the genome (Cotmore and Tattersall 2012). Thus, in members of the genus Protoparvovirus, the 5-fold cylinders serve as portals for three different forms of cargo, mediating 1) genome translocation into and out of the intact particle, 2) VP1SR extrusion prior to bilayer transit, and 3) early externalization of some VP2 N-termini concomitant with genome encapsidation. This is in sharp contrast to viruses in many other parvovirus genera, which rely on just one or two of these portal functions. 

A second distinctive feature of protoparvovirus virions is that in X-ray structures not only is the capsid icosahedrally ordered, but so is ~11–34% of the single-stranded DNA genome, forming patches in each asymmetric unit that are positioned below a cavity on the interior capsid surface. This ordered DNA comprises 2–3 short (8–11 nt) single-strands, which adopt an inverted-loop configuration with phosphates chelated in the interior by two Mg++ ions while the bases point outwards towards the capsid shell where they establish non-covalent interactions with specific amino acid side chains (Halder et al., 2013, Agbandje-McKenna et al., 1998, Chapman and Rossmann 1995). Atomic force microscopy has been used to probe the rigidity of individual MVM particles along their 5-fold, 3-fold and 2-fold symmetry axes, which showed that in empty particles, but not in DNA-containing virions, the two-fold axes can be easily distorted by nanoindentation, suggesting that the genome has a major influence on capsid rigidity of this region (Carrasco et al., 2006). Single alanine mutations that did not compromise intracapsid interactions but did disrupt major interactions between the capsid and bound DNA patches, had no effect on empty particles but abrogated the genome-enhanced 2-fold rigidity seen in full particles, indicating that it derives predominantly from these ordered DNA:capsid interactions (Carrasco et al., 2008). This perhaps indicates the importance of a full-length, 5kb genome in establishing wild-type capsid dynamics, as also suggested by in vitro uncoating studies (Cotmore et al., 2010).

Genome organization and replication 

Protoparvoviruses have heterotelomeric genomes of around 5 kb (Figure 3A.Parvoviridae), flanked by hairpin telomeres of ~120 nt at their left-end, generally in a single sequence orientation, while the right-end hairpin is ~250 nt and can be present as either of two inverted-complementary sequences dubbed “flip” and “flop”. The right-end of protoparvovirus genomes can be excised from replication intermediates in the hairpin configuration by hairpin transfer, which in MVM involves the binding of NS1 complexes to two separate clusters of (TGGT)2-3 binding sites, one that positions NS1 over the cleavage site (5′-CTATCA-3′) and a second that is ~120 bp away, at the hairpin axis. For cleavage to occur, NS1 complexes at these two sites must be co-ordinated, and the origin refolded, by recruiting DNA bending proteins from the host HMGB family, which bind to NS1 and create an essential ~30 bp double-helical loop in the intervening G-rich origin DNA (Cotmore et al., 2000). In contrast, origin sequences generated from the left end of this virus are not cleaved in the hairpin configuration because there is a critical TC/GAA mismatch in the hairpin stem. To create an active origin, the left hairpin must be unfolded and copied to form a base-paired junction region that spans adjacent genomes in dimer RF, in which the two arms of the hairpin are effectively segregated on either side of the symmetry axis. However, only the TC arm gives rise to an active origin because the dinucleotide serves as a spacer element that is positioned between the NS1 binding site and the binding site for an essential co-factor, called parvovirus initiation factor (PIF, also known as glucocorticoid modulatory element binding protein GMEB). PIF is a heterodimeric host complex that binds to two spaced 5′-ACGT-3′ half sites positioned near the axis of the DNA palindrome. In the active origin, PIF is able to interact with NS1 across the TC dinucleotide, stabilizing its binding to the relatively weak NS1 binding site, but it cannot stabilize NS1 binding to an identical binding site across the GAA trinucleotide in the inactive (GAA) arm (Christensen et al., 2001). In consequence, sequences in the hairpin configuration or perfectly-duplex hairpin arms carrying the GAA sequence are not cleaved, making them potentially available for alternative roles such as driving transcription from the adjacent P4 promoter (Gu et al., 1995). Due to major disparities in cleavage efficiency between the left- and right-end origins, progeny negative-sense single-strands are preferentially displaced from the right end of the genome, with the result that protoparvoviruses typically displace and package predominantly (~99%) negative-sense progeny ssDNA.  

Viruses in this genus use two transcriptional promoters at map units (mu) 4 and 38, and a single polyadenylation site corresponding to mu 95 (see Figure 3A.Parvoviridae), to create 3 major size classes of mRNAs, all of which have a short intron sequence between 46–48 mu removed (Pintel et al., 1983). In MVM this splice has alternative donors (D1 and D2) and acceptors (A1 and A2) of different strengths, which are positioned within a region of 120 nt so that a potential D2:A1 splice is eliminated by minimal intron size constraints. Splicing therefore creates 3 forms of each mRNA size class that are expressed with different stoichiometry (Haut and Pintel 1999). Transcripts arising from P4 that have just this central intron removed encode a single form of NS1, translation of which terminates upstream of D1. In some P4 transcripts however, a second, long intron between 10–40 mu is also excised, creating mRNAs that encode NS2 proteins of ~25 kDa. These share 85 amino acids of N-terminal sequence with NS1, but are then spliced into a different reading frame and finally reach the short central intron where 2 disparate C-terminal hexapeptides can be added. This generates variants called NS2P and NS2Y that are expressed in a ~5:1 ratio. P38 transcription is strongly transactivated by the C-terminal domain of NS1, mediated by NS1 binding to upstream 5′-TGGT-3′ repeat sequences (Christensen et al., 1995, Lorson et al., 1996). Alternative splicing at the short intron also causes two size variants of the capsid protein to be expressed with ~1:5 stoichiometry, with VP1 (~83 kDa) initiating at an ATG codon positioned between the two acceptor sites while VP2 (~64 kDa) initiates downstream of the splice.  

During infection, newly synthesized capsid proteins assemble as two types of trimers (VP2-only and 1xVP1+2xVP2) in the cytoplasm, and are transported into the nucleus for capsid-assembly using a non-conventional, structure-dependent trafficking motif (Lombardo et al., 2000). However, this translocation is restricted to S-phase (Gil-Ranedo et al., 2015), and is dependent upon trimer phosphorylation by the cellular Raf-1 kinase (Riolobos et al., 2010).  

Ancillary proteins encoded by protoparvoviruses include the NS2 variants, which appear to have multiple functions that are mostly mediated by interactions with host proteins, and a small alternatively translated (SAT) protein (Zádori et al., 2005). MVM NS2 is not essential in transformed human cell lines, but its absence in murine cells leads to rapid cessation of duplex DNA amplification early in the infectious cycle by an unknown mechanism (Naeger et al., 1990, Ruiz et al., 2006). This early defect can be abrogated by relatively low levels of NS2 expression, but much higher levels of NS2 are required later in the cycle to enable efficient capsid assembly (Cotmore et al., 1997), which is a pre-requisite for the subsequent accumulation of progeny DNA single-strands, and for virion release. In the late capsid defect, VP proteins are expressed, but most fail to assemble into capsids and are rapidly degraded, perhaps reflecting inadequacies in the nuclear translocation of precursor subunits linked to a severe dislocation in normal nuclear/cytoplasmic protein trafficking, as discussed below. During MVM infection NS2 associates with proteins from the cellular 14-3-3 family (Brockhaus et al., 1996) and with the nuclear export factor CRM1 (Bodendorf et al., 1999). Significantly, the NS2 nuclear export signal (NES) engages CRM1 with "supraphysiological" affinity, which is independent of the presence of RanGTP and thus can potentially resist cytoplasmic release (Engelsma et al., 2008). During wildtype MVM infection CRM1 can be detected in the perinuclear cytoplasm, but this redistribution is exacerbated in infections with mutant viruses that carry point mutations close to the NS2 NES that cause CRM1 to bind at even higher affinity (López-Bueno et al., 2004). These mutations also accelerate the onset of a late step in infection, which is characterized by the cytoplasmic accumulation of large, typically nuclear structures including NS1 and empty capsids, again suggesting major disruptions in normal nuclear/cytoplasmic trafficking pathways. Following transfection into A9 fibroblasts, wildtype MVMi genomes express low levels of NS2, but when these genomes were engineered to express one of the NS2-NES mutations, the resulting low levels of mutant NS2 were able to drive wildtype levels of virus progeny accumulation, confirming that the cumulative late infection blocks seen in cells expressing insufficient NS2 result from the stoichiometric limitation of NS2:CRM1 interactions (Choi et al., 2005). Studies with mutant viruses in which NS2:CRM1 binding was impaired, rather than enhanced, similarly indicate that during infection this interaction is required for the efficient release of virions (Eichwald et al., 2002, Miller and Pintel 2002).

The second protoparvovirus ancillary protein, SAT, is encoded within the capsid gene and is expressed late, from the same mRNA as VP2. SAT accumulates in the endoplasmic reticulum (ER) of the infected cell (Zádori et al., 2005). Like NS2, it enhances the rate at which virus spreads through cultures but it acts via a different mechanism that involves induction of irreversible ER-stress and is linked to enhanced cell necrosis (Mészáros et al., 2017b). Although both SAT and the dependoparvovirus ancillary protein, AAP, occupy similar positions in the capsid gene and contain essential N-terminal hydrophobic domains, these proteins are not known to exhibit functional homology. Thus, in protoparvoviruses early virion export is a distinctive feature that can be driven by multiple mechanisms, either occurring prior to cell lysis and mediated by VP2 signals or Crm1 interactions that vary with cell type, or linked to enhanced cell necrosis and driven by SAT. During export, some virions are known to be internalized in COPII vesicles in the endoplasmic reticulum and undergo gelsolin-dependent trafficking to the Golgi, where they undergo tyrosine phosphorylation, and perhaps by other modifications that enhance their subsequent particle-to-infectivity ratios (Bär et al., 2008, Bär et al., 2013). Release at early times in the cycle allows infection to spread rapidly, potentially enhancing overall progeny production from infected tissues and prior to the accumulation of neutralizing antibodies.

Antigenicity

See discussion under family description.  

Biology 

See discussion under family description. Kilham rat virus (KRV), one of the original viruses used to establish family Parvoviridae, was isolated in 1959 from lysates of an experimental rat tumor (Kilham and Olivier 1959). Over the next decade, a succession of similar single-stranded DNA viruses were discovered in transplantable tumors, tissue culture cell lines, or laboratory stocks of other viruses. Some of these, such as MVM, closely resemble viruses now known to infect wild rodents, while other members of the same species (Rodent protoparvovirus 1), such as LuIII (M81888), appear to be distant recombinants of viruses found in nature. Studied extensively in the intervening years, these viruses have served as important model systems for defining the basic characteristics and underlying biology of the family. In rodents, viruses from species Rodent protoparvovirus 1 exhibit a range of pathologies, from asymptomatic viremia to teratogenesis and fetal or neonatal cell death. While these viruses fail to infect normal human cells, host restrictions are often relaxed when human cells undergo oncogenic transformation, allowing the viruses to become preferentially oncolytic, and suggesting their potential for use in clinical cancer virotherapy. To this end, Phase I/IIa clinical trials were recently completed using virus H-1 (X01457) to target advanced glioblastoma, which provided evidence that the virus was well tolerated and could partially disrupt the local immune suppression commonly associated with this cancer (Geletneky et al., 2017, Angelova et al., 2017). 

In some cells parvovirus infection results in delayed but significant type 1 IFN release, whereas pretreatment with exogenous IFN-beta strongly inhibits the viral life cycle (Grekova et al., 2010, Mattei et al., 2013). During MVMp infection of mouse embryonic fibroblasts (MEFs) the IFN response did not involve mitochondrial antiviral signaling protein (MAVS) and RIG-I sensing and did not conspicuously inhibit viral DNA replication (Mattei et al., 2013), although pretreatment of cells with IFN-beta-neutralizing antibody did enhance infection in another study (Grekova et al., 2010). However, infected MEFs become unresponsive to Poly (I:C) stimulation, suggesting that the virus is able to inactivate antiviral immune mechanisms elicited by type I IFNs.

Important pathogens in this genus include feline parvovirus (FPV), also known as feline panleukopenia virus, and closely related mink and raccoon parvoviruses, which have existed for over 100 years, and canine parvovirus (CPV), which arose as a variant in the mid 1970s and in 1978 spread worldwide, causing a disease pandemic among dogs, wolves and coyotes. These variants all belong to a single species, Carnivore protoparvovirus 1. CPV achieved its canine host range by acquiring a small number of capsid surface mutations (Chang et al., 1992) that allow it to bind the canine form of its host cell receptor, transferrin receptor type 1, which largely determines the precise carnivore host range of these variants (Parker et al., 2001). In adult animals, viruses in this species predominantly infect lymphoid tissues, leading to leukopenia or lymphopenia, and intestinal epithelia, resulting in severe diarrhea, dehydration and fever. In contrast, infection of neonates is characterized by cerebellar lesions in kittens or ferrets, potentially leading to ataxia, or by myocarditis in puppies. Disease is well controlled by vaccination, but mortality in affected litters varies between 20 and 100 percent (reviewed in (Kailasan et al., 2015a)). 

Porcine parvovirus (PPV), a member of the species Ungulate protoparvovirus 1, is a major cause of fetal death and infertility in pigs worldwide, although PPV infection alone rarely causes disease in non-pregnant pigs or piglets. However, when seronegative pregnant sows are exposed to a virulent PPV strain during the first 70 days of gestation, transplacental infection can lead to a syndrome called SMEDI (stillbirths, mummification, embryonic death, and infertility) (Mészáros et al., 2017a). Weakly pathogenic and vaccine strains of PPV exist (e.g., NADL-2), which are lethal if injected into the amniotic fluid but they do not cross the placental barrier as efficiently as pathogenic strains (e.g., Kresse), so disease is rare. Widespread vaccination programs are in place to prevent SMEDI, but some newly emerging virulent PPV variants cannot be neutralized by antibodies raised by exposure to current vaccine strains (Mészáros et al., 2017a).  Co-infection with PPV can also potentiate the effect of porcine circovirus type 2 (PCV-2, Porcine circovirus 2, family Circoviridae) in the development of post-weaning multisystemic wasting syndrome (PMWS).

Most of the newly discovered viruses segregate to species in a new branch of the Protoparvovirus tree, established for bufavirus 1a (human) (BuV1a, see tree in Figure 6B.Parvoviridae). Two genotypes of this virus, BuV1 and BuV2, were identified in 2012 in viral metagenomic analysis of fecal samples from diarrheic children in Burkina Faso and Tunisia (hence the name “bufavirus”) (Phan et al., 2012), while a third genotype, BuV3, was later discovered in the diarrheal feces of Bhutanese children (Yahiro et al., 2014). To date, BuV DNA has been detected in the diarrhea of children from Burkina Faso, Tunisia, Bhutan, Thailand, Turkey, China, and Finland, and of adults from Finland, the Netherlands, Thailand, and China, but has not been found in non-diarrheal feces, suggesting a causal relationship (Väisänen et al., 2017). When analyzed for the presence of anti-BuV1 capsid IgG, the seroprevalences of adults from Finland and the USA were low (~2–4%), but much higher rates were found for adults in Iraq (~85%), Iran (~56%) and Kenya (~72%) (Väisänen et al., 2018).  

A second human protoparvovirus in the bufavirus branch, called cutavirus (CuV), was detected in a small number of diarrheal samples from Brazilian and Botswanan children, and in four French skin biopsies of cutaneous T-cell lymphomas, from which the virus derives its name (Phan et al., 2016), and in malignant skin lesions from a Danish melanoma patient (Mollerup et al., 2017). The etiological significance of CuV in human disease has yet to be determined.  

Prevalence rates for IgG against CuV were evenly low (0–~6%) in the same sample series mentioned above for bufavirus, confirming that CuV is widely distributed through human populations (Väisänen et al., 2018). In contrast, IgG directed against a third new, as yet unclassified protoparvovirus that was detected in a Tunisian human fecal sample (hence tusavirus, TuV) (Phan et al., 2014) was not present in the same panels of sera, and its DNA has yet to be detected in other fecal samples (Väisänen et al., 2017, Väisänen et al., 2018), so evidence for TuV being a human virus is thus, so far, insufficient. It segregates phylogenetically with viruses occupying the original branch of the protoparvovirus phylogenetic tree, discussed previously.

Species demarcation criteria

Viruses within a species are monophyletic and encode replication initiator proteins (called NS1 or Rep1, 68, or 78) that show >85% amino acid sequence identity.

Member species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
Carnivore protoparvovirus 1canine parvovirusNM19296NC_001539Complete genomeCPV
Chiropteran protoparvovirus 1megabat bufavirus 1MAG12-57LC085675NC_029797Complete coding genomeBtBuV1
Eulipotyphla protoparvovirus 1Mpulungu (shrew) bufavirusshrew ZM38AB937988NC_026815Complete coding genomeMpBuV
Primate protoparvovirus 1bufavirus 1a (human)human BF86JX027296NC_038544Complete coding genomeBuV1a
Primate protoparvovirus 2Wuharv (rhesus) parvovirus 1rhesusJX627576NC_039049Complete coding genomeWuBuV1
Primate protoparvovirus 3cutavirus (human)human BR-337KT868811NC_039050Complete coding genomeCutaV
Rodent protoparvovirus 1minute virus of miceprototype; pJ02275NC_001510Complete genomeMVM
Rodent protoparvovirus 2rat parvovirus 1AF036710NC_038545Complete genomeRPV1
Rodent protoparvovirus 3rat bufavirus SY-20157911002KT716186NC_028650Complete coding genomeRatBuV
Ungulate protoparvovirus 1porcine parvovirusNADL2L23427NC_001718Complete genomePPV
Ungulate protoparvovirus 2porcine bufavirus; protoparvovirus (porcine)Zsana/2013/HUNKT965075Complete coding genomePBuV

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

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

sea otter parvovirus 1

KU561552

SOP1

canine bufavirus

MF198244

CBuV

Virus names and virus abbreviations are not official ICTV designations.