Parvovirus Diversity and DNA Damage Responses

Parvoviruses have a linear single-stranded DNA genome, around 5 kb in length, with short imperfect terminal palindromes that fold back on themselves to form duplex hairpin telomeres. These contain most of the cis-acting information required for viral “rolling hairpin” DNA replication, an evolutionary adaptation of rolling-circle synthesis in which the hairpins create duplex replication origins, prime complementary strand synthesis, and act as hinges to reverse the direction of the unidirectional cellular fork. Genomes are packaged vectorially into small, rugged protein capsids ∼260 Å in diameter, which mediate their delivery directly into the cell nucleus, where they await their host cell’s entry into S phase under its own cell cycle control. Here we focus on genus-specific variations in genome structure and replication, and review host cell responses that modulate the nuclear environment.Viruses from the family Parvoviridae are unique in having a linear single-stranded DNA genome, ∼5 kb in length, which terminates in short (120–420 base) imperfect palindromes that fold into self-priming hairpin telomeres. These viruses replicate via a “rolling hairpin” mechanism, with strong evolutionary and mechanistic links to “rolling-circle” replication, as reviewed in detail in previous editions of this work (Cotmore and Tattersall 1996, 2006). Rolling hairpin synthesis relies on the ability of each hairpin to give rise to a duplex origin sequence, which can be nicked by a viral initiator nuclease to create a base-paired DNA primer, and to function as a hinge, allowing quasi-circular synthesis by alternately folding and unfolding to shuttle a continuous unidirectional replication fork back and forth along linear DNA. Together with a few adjacent nucleotides, these palindromes provide all of the cis-acting information required for viral DNA replication and packaging. However, the size, sequence, and predicted structures of the hairpins can vary substantially between genera, or even between the two ends of a single genome, and they appear to have adapted to fulfill multiple additional roles in the life cycle of specific viruses. Parvoviral DNA amplification proceeds via a unidirectional single-strand displacement mechanism through a series of monomeric and concatemeric duplex replicative-form (RF) intermediates, and while the viral initiator protein, variously called NS1 or Rep, serves both as a site- and strand-specific nickase and as a 3′-to-5′ helicase, all other replicative functions are co-opted from the host cell. This mechanism benefits from suppression of host DNA synthesis, and generates long stretches of single-stranded DNA with alien terminal structures that invoke host damage responses, which impact both positively and negatively on viral replication. Although details of the mechanisms that mediate parvoviral replication have received relatively little attention since our previous review (Cotmore and Tattersall 2006), recognition that infection is invariably associated with host DNA damage responses (DDRs), some of which are specifically required for efficient viral DNA amplification, has led to significant reappraisal of the nuclear environment and replicative machinery available to these viruses. In parallel, major advances have occurred in our knowledge of genome diversity and cell specificity in this ever-expanding family, which provide novel insight into mechanisms of replication control.The International Committee on Taxonomy of Viruses (ICTV, Tijssen et al. 2011), classifies viruses in the family Parvoviridae that infect vertebrates as the subfamily Parvovirinae, which currently contains just five genera: the Parvoviruses, Dependoviruses, Amdoviruses, Erythroviruses, and Bocaviruses, although there are at least two additional genera, tentatively called Partetraviruses and Avetalviruses, that await ICTV recognition. This reflects a major jump in known virus diversity, with many new species and genera first identified in clinical or veterinary samples using PCR-based virus discovery methods (Allander et al. 2005; Jones et al. 2005; Day and Zsak 2010). Potential human pathogens that are still pending recognition include genetic variants of Human Bocavirus (HBoV 1–4), which are particularly common in the respiratory and gastrointestinal tracts of children (Kapoor et al. 2010; Kantola et al. 2011), and two broadly distributed genotypes of a “PARV4”-based genus (the aforementioned Partetraviruses), parenterally transmitted among injecting drug users, hemophiliacs, and polytransfused individuals (Sharp et al. 2009; Lahtinen et al. 2011). Most recently, viruses from another potential genus, with sequences resembling both Parvoviruses and Amdoviruses, were detected in fecal samples from children in Burkina Faso, and tentatively named Bufaviruses (Phan et al. 2012). In vitro culture systems or high titer clinical samples are often not available for new members, which can thus only be studied by PCR amplification from patient tissue.Although the vast majority of parvoviruses replicate without the aid of a helper virus, the adeno-associated viruses (AAVs) from the genus Dependovirus establish latent infections that only become productive when cells are coinfected with a more complex virus, typically an adeno- or herpesvirus. To date the replication mechanisms of adeno-associated virus 2 (AAV2) and minute virus of mice (MVM), from the genus Parvovirus, have been studied in detail, as documented in previous editions of this work. Here we adopt a broader perspective, discussing inter-genera variations that shed light on replication control, and reviewing host cell responses to viral infection that modulate the nuclear environment.