A novel flavivirus in the soybean cyst nematode

Bekal, Sadia; Domier, Leslie L.; Gonfa, Biruk; McCoppin, Nancy K.; Lambert, Kris N.; Bhalerao, Kaustubh

doi:10.1099/vir.0.060889-0

Cited by 49 publications

(43 citation statements)

References 48 publications

(62 reference statements)

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“…2C). BLAST searches indicated that AFV has 20% amino acid identity to gentian Kobu-sho-associated virus (GKaV), a recently identified flavi-like virus originally thought to be a dsRNA virus (Table 2) (35, 57, 58). Similarly to GKaV and other newly identified flaviviruses, the 20.4-kb AFV-1 genome is longer than the typical length of previously characterized members of the Flaviviridae (35).…”

Section: Resultsmentioning

confidence: 99%

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

Remnant

Shī

Buchmann

et al. 2017

J Virol

138

135

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Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa. This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales. Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.

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Section: Resultsmentioning

confidence: 99%

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

Remnant

Shī

Buchmann

et al. 2017

J Virol

138

135

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“…Moreover, virome analysis of bats has provided indications for novel pestiviruses in these mammals , but the significance of these findings still has to be supported by further analyses. A recent publication reports on a novel flavivirus with homology to pestiviruses in a soybean cyst nematode (Bekal et al, 2014).…”

Section: General Properties Hosts and Transmissionmentioning

confidence: 99%

The Molecular Biology of Pestiviruses

Tautz

Tews

Meyers

2015

Advances in Virus Research

200

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“…Despite possessing exceptionally long genomes (23 and 19 kb, respectively), these two viruses have the basic flavi-like genome/proteome structure, as well as sequence homology in the serine protease, helicase, and RNAdependent RNA polymerase (RdRp) domains of the polyprotein. Although GKaV was reported to be a double-stranded RNA (dsRNA) virus (14), the RNA digestion experiment was performed on crude plant extracts where the dsRNA is more likely to be the replication complex rather than the genome itself (15). More remarkable was the recent demonstration that Jingmen tick virus (JMTV) and Toxocara canis larva agent (TCLA) are clearly related to flaviviruses but possess a very different genomic plan comprising four distinct segments (11), in turn raising questions about the evolutionary link between segmented and unsegmented genomes.…”

mentioning

confidence: 99%

Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses

Shī

Lin²,

Vasilakis

et al. 2016

J Virol

259

308

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Viruses of the family Flaviviridae are important pathogens of humans and other animals and are currently classified into four genera. To better understand their diversity, evolutionary history, and genomic flexibility, we used transcriptome sequencing (RNA-seq) to search for the viruses related to the Flaviviridae in a range of potential invertebrate and vertebrate hosts. Accordingly, we recovered the full genomes of five segmented jingmenviruses and 12 distant relatives of the known Flaviviridae ("flavilike" viruses) from a range of arthropod species. Although these viruses are highly divergent, they share a similar genomic plan and common ancestry with the Flaviviridae in the NS3 and NS5 regions. Remarkably, although these viruses fill in major gaps in the phylogenetic diversity of the Flaviviridae, genomic comparisons reveal important changes in genome structure, genome size, and replication/gene regulation strategy during evolutionary history. In addition, the wide diversity of flavi-like viruses found in invertebrates, as well as their deep phylogenetic positions, suggests that they may represent the ancestral forms from which the vertebrate-infecting viruses evolved. For the vertebrate viruses, we expanded the previously mammal-only pegivirus-hepacivirus group to include a virus from the graceful catshark (Proscyllium habereri), which in turn implies that these viruses possess a larger host range than is currently known. In sum, our data show that the Flaviviridae infect a far wider range of hosts and exhibit greater diversity in genome structure than previously anticipated. IMPORTANCEThe family Flaviviridae of RNA viruses contains several notorious human pathogens, including dengue virus, West Nile virus, and hepatitis C virus. To date, however, our understanding of the biodiversity and evolution of the Flaviviridae has largely been directed toward vertebrate hosts and their blood-feeding arthropod vectors. Therefore, we investigated an expanded group of potential arthropod and vertebrate host species that have generally been ignored by surveillance programs. Remarkably, these species contained diverse flaviviruses and related viruses that are characterized by major changes in genome size and genome structure, such that these traits are more flexible than previously thought. More generally, these data suggest that arthropods may be the ultimate reservoir of the Flaviviridae and related viruses, harboring considerable genetic and phenotypic diversity. In sum, this study revises the traditional view on the evolutionary history, host range, and genomic structures of a major group of RNA viruses. Since the discovery of the virological cause of yellow fever in the 1920s, viruses of the family Flaviviridae have been well documented as the cause of major vector-borne and hepatic diseases in humans (1). The family as currently classified comprises four genera: Flavivirus, Hepacivirus, Pestivirus, and the newly proposed genus Pegivirus (2). Despite the extensive divergence between these viruses, they share...

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A novel flavivirus in the soybean cyst nematode

Cited by 49 publications

References 48 publications

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

The Molecular Biology of Pestiviruses

Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses

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