Double-stranded ribonucleic acid from rice dwarf virus

Diaphorina citri reovirus is most closely related to fijiviruses

The Asian citrus psyllid, Diaphorina citri Kuwayama, is an important insect vector of Candidatus Liberibacter asiaticus, the causal agent of Huanglongbing, which is the most destructive disease of citrus worldwide. Sequences for putative Diaphorina citri reovirus (DcRV) were identified from some worldwide populations of D. citri. Here, field surveys indicated that the virus was common in D. citri populations from Hawaii and Fuzhou of PR China. Electron microscopy showed that DcRV virions possessed a typical reovirus-like morphology. The U. S. and Chinese DcRV isolates both showed 10 segments of double-stranded RNA sharing >96% nucleotide sequence identity, and encoding 11 deduced proteins. All genome segments contained conserved 5' and 3' terminal nucleotide sequences and inverted repeats that are hallmarks of reovirus sequence. Phylogenetic analysis showed that DcRV may be considered a new species of the genus Fijivirus sharing a most recent common ancestor with the insect-specific fijivirus Nilaparvata lugens reovirus.

Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

The Asian citrus psyllid, Diaphorina citri, is the natural vector of the causal agent of Huanglongbing (HLB), or citrus greening disease. Together; HLB and D. citri represent a major threat to world citrus production. As there is no cure for HLB, insect vector management is considered one strategy to help control the disease, and D. citri viruses might be useful. In this study, we used a metagenomic approach to analyze viral sequences associated with the global population of D. citri. By sequencing small RNAs and the transcriptome coupled with bioinformatics analysis, we showed that the virus-like sequences of D. citri are diverse. We identified novel viral sequences belonging to the picornavirus superfamily, the Reoviridae, Parvoviridae, and Bunyaviridae families, and an unclassified positive-sense single-stranded RNA virus. Moreover, a Wolbachia prophage-related sequence was identified. This is the first comprehensive survey to assess the viral community from worldwide populations of an agricultural insect pest. Our results provide valuable information on new putative viruses, some of which may have the potential to be used as biocontrol agents.

IMPORTANCE

Insects have the most species of all animals, and are hosts to, and vectors of, a great variety of known and unknown viruses. Some of these most likely have the potential to be important fundamental and/or practical resources. In this study, we used high-throughput next-generation sequencing (NGS) technology and bioinformatics analysis to identify putative viruses associated with Diaphorina citri, the Asian citrus psyllid. D. citri is the vector of the bacterium causing Huanglongbing (HLB), currently the most serious threat to citrus worldwide. Here, we report several novel viral sequences associated with D. citri.

Reovirus genomes from plant-feeding insects represent a newly discovered lineage within the family Reoviridae

A complex set of double-stranded RNAs (dsRNAs) was isolated from threecornered alfalfa hopper (Spissistilus festinus), a plant-feeding hemipteran pest. A subset of these dsRNAs constitute the genome of a new reovirus, provisionally designated Spissistilus festinus reovirus (SpFRV). SpFRV was present in threecornered alfalfa hopper populations in the San Joaquin Valley of California, with incidence ranging from 10% to 60% in 24 of 25 sample sets analyzed. The 10 dsRNA segments of SpFRV were completely sequenced and shown to share conserved terminal sequences (5'-AGAGA and CGAUGUUGU-3') of the positive-sense strand that are distinct from known species of the family Reoviridae. Comparisons of the RNA directed RNA polymerase (RdRp) indicated SpFRV is most closely related (39.1% amino acid identity) to another new reovirus infecting the angulate leafhopper (Acinopterus angulatus) and provisionally designated Acinopterus angulatus reovirus (AcARV). The RdRp of both viruses was distantly related to Raspberry latent virus RdRp at 27.0% (SpFRV) and 30.0% (AcARV) or Rice ragged stunt virus RdRp at 26.2% (SpFRV) and 29.0% (AcARV) amino acid identity. RdRp phylogeny confirmed that SpFRV and AcARV are sister taxa sharing a most recent common ancestor. SpFRV segment 6 encodes a protein containing two NTP binding motifs that are conserved in homologs of reoviruses in the subfamily Spinareovirinae. The protein encoded by SpFRV segment 4 was identified as a guanylyltransferase homolog. SpFRV segments 1, 3, and 10 encode homologs of reovirus structural proteins. No homologs were identified for proteins encoded by SpFRV segments 5, 7, 8, and 9. Collectively, the low level of sequence identity with other reoviruses, similar segment terminal sequences, RdRp phylogeny, and host taxa indicate that SpFRV and AcARV may be considered members of a proposed new genus of the family Reoviridae (subfamily Spinareovirinae), with SpFRV assigned as the type species.

The stability of satellite viral RNAs in vivo and in vitro

Like the satellite RNA (Sat-RNA) of cucumber mosaic virus (CMV), the RNA of satellite tobacco necrosis virus (STNV-RNA) was shown to be capable of surviving in vivo without replication for at least 10 days in the absence of its helper tobacco necrosis virus (TNV). However, under similar conditions, the genomic RNA 3 of CMV failed to survive for 48 hr. It has been demonstrated that both STNV-RNA and Sat-RNA are significantly more resistant to inactivation in vitro than the RNAs of their helper viruses. The thermal denaturation kinetics of STNV-RNA and Sat-RNA, unlike those of TNV-RNA and CMV-RNA, are more like those of transfer RNA (tRNA) indicating that a high proportion of their nucleotides are involved in base pairing. STNV-RNA, Sat-RNA, and tRNA also show similar degrees of resistance to degradation by the single strand-specific S(1) nuclease. It is suggested that both STNV-RNA and Sat-RNA may owe their in vitro stability to features of their molecular structure which may also account for their ability to survive in vivo for prolonged periods without replication. Similarities and differences between satellites and viroids are discussed and it is concluded that these two classes of RNAs are unlikely to be related. The possible evolutionary origins of the satellites are also considered.

Antiviral effects of double-stranded RNA from rice dwarf virus on infection of mice with western equine encephalitis virus

A single administration (1 to 10 mg/kg) of rice dwarf virus RNA (RDV-RNA) prior to virus challenge reduced the mortality of mice infected with western equine encephalitis (WEE) virus. The protective effect of RDV-RNA was significantly higher than that of polyinosinic-polycytidylic acid. However, when these RNAs were given after virus infection, the protective effect was negligible. The titer of circulating interferon in mice reached a peak about 5 hr after injection of these RNAs and remained at this level for about 24 hr. Viremia in mice infected with a lethal dose of WEE virus was markedly suppressed by the treatment of mice with these RNAs. A pathological examination of mice treated with a lethal dose of RDV-RNA revealed marked changes including degeneration and karyorrhexis in the lymphoid tissues of the spleen.

Transcription of double-stranded RNA by Escherichia coli DNA-dependent RNA polymerase

Double-stranded RNA of some virus genomes can be used as template for the DNA-dependent RNA polymerase purified from Escherichia coli. The RNA synthesis requires all four nucleoside triphosphates and manganese ions and is dependent on the presence of sigma subunit. The reaction is inhibited by rifampicin, streptolydigin and ethidium bromide, but not by DNase and actinomycin D which does not bind to double-stranded RNA. The template activity of double-stranded RNA from various viruses is different in each case. The order of template efficiency is Penicillum chrysogenum virus greater than cytoplasmic polyhedrosis virus greater than rice dwarf virus greater than reovirus. The product obtained using cytoplasmic polyhedrosis virus double-stranded RNA as template is single-stranded and hybridizes specifically to the denatured template RNA. One of the major 5'-starting nucleotide sequences of the product RNA is pppA-A-Y--. These results indicate that transcription in vitro of double-stranded RNA by E. Coli RNA polymerase is initiated at specific sites on the template.

Ultrastructural characterization of genome of epizootic hemorrhagic disease virus

Purified epizootic hemorrhagic disease (EHD) virus preparations were treated with urea and sodium perchlorate. The viral ribonucleic acid (RNA) released when spread on protein monolayers according to the Kleinschmidt technique was examined by rotary shadow-casting electron microscopy. The viral RNA released by urea treatment had filaments which frequently formed three to five loop-shaped figures of varied length. In 80% of the virus particles the lengths of the viral RNA released were 2.5 to 4.5 mum. The sodium perchlorate-released viral nucleic acid also appeared linear, and about 70% had lengths of 0.1 to 2.0 mum, the longest filament measuring 5.8 mum. Evidence was obtained that EHD virus contains double-stranded RNA as its genetic material and the molecular weight of the EHD viral RNA was calculated to be 12.2 x to 10(6) to 15.1 x 10(6) daltons.

Double-stranded Ribonucleic Acid from Cytoplasmic Polyhedrosis Virus of the Silkworm

Ribonucleic acid (RNA) was extracted by phenol treatment from cytoplasmic polyhedrosis virus isolated from the midgut of infected silkworms. This RNA appears as threads when precipitated in alcohol. Two components having different sedimentation constants were observed. The molecular weight of the RNA preparation obtained by sedimentation coefficient (weight-averaged) and intrinsic viscosity was about 2 × 10 6 to 3 × 10 6 . It was one-half to one-third the size of the calculated molecular weight for an entire RNA molecule in a virion. Electron micrographs of this RNA preparation showed two peaks in the distribution of contour length, at 0.4 and 1.3 μm, which would correspond to molecular weights of 10 6 and 3 × 10 6 , respectively. The extracted RNA seemed to split into segments at a preferential breaking point. This RNA was soluble in concentrated salt solution, differing from single stranded high-molecular-weight RNA. The base composition of this RNA was complementary in the ratios of adenosine to uridine and guanosine to cytosine. It contained 43% guanosine plus cytosine. Based on its filamentous appearance by electron microscopy, typical pattern of optical rotatory dispersion and circular dichroism, sharp transition of the optical properties on heating, great hyperchromicity on degradation, nonreactivity with formaldehyde, and resistance to ribonucleases, it is concluded that this RNA is double-stranded and has regular base pairings of guanosine-cytosine and adenosine-uridine.

Potato spindle tuber virus: a plant virus with properties of a free nucleic acid

Infectious entities, extractable, with phosphate buffer, from tissue infected with potato spindle tuber virus and inciting symptoms on tomato that are typical of this virus, have properties incompatible with those of conventional virus particles. The infectious particles sediment in sucrose density gradients at approximately the same rate as particles with a sedimentation coefficient of 10S, are insensitive to treatment with organic solvents, and can be concentrated by ethanol precipitation. Treatment with phenol changes neither their infectivity nor their sedimentation properties. Infectivity is insensitive to deoxyribonuclease, but at low ionic strength it is sensitive to ribonuclease. At high ionic strength, infectivity partially survives incubation with ribonuclease. These properties, as well as elution patterns from columns of methylated serum albumin, suggest that the extractable infectious agent may be a double-stranded RNA.

Reovirus-directed ribonucleic acid synthesis in infected L cells

Reovirus replication in L-929 mouse fibroblasts was unaffected by 0.5 mug of actinomycin per ml, a concentration which inhibited cell ribonucleic acid (RNA) synthesis by more than 90%. Under these conditions of selective inhibition, the formation of both single-stranded and double-stranded virus-specific RNA was detected beginning at 6 hr after infection. The purified double-stranded RNA was similar in size and base composition to virus RNA and presumably was incorporated into mature virus. The single-stranded RNA formed ribonuclease-resistant duplexes when annealed with denatured virus RNA but did not self-anneal, thus indicating that it includes copies of only one strand of the duplex. The single-stranded RNA was polyribosome-associated and may function as the virus messenger RNA. Production of both types of virus-induced RNA required protein synthesis 6 to 9 hr after infection. At later times in the infectious cycle, only double-stranded RNA synthesis was dependent on continued protein formation.