Aphis glycines virus 1, a new bicistronic virus with two functional internal ribosome entry sites, is related to a group of unclassified viruses in the Picornavirales

Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites

Viral internal ribosomal entry sites (IRESs) form several classes that use distinct mechanisms to mediate end-independent initiation of translation. The origin of viral IRESs is a longstanding question. The simplest IRESs comprise tandem pseudoknots and occur in the intergenic region (IGR) of Dicistroviridae genomes (order Picornavirales ). Larger IGR IRESs contain additional elements that determine specific properties such as binding to the head of the ribosoma l 40S subunit. Metagenomic analyses reported here identified novel groups of structurally distinct IGR-like IRESs. The smallest of these (∼120nt long) comprise three pseudoknots and bind directly to the ribosomal P site. Others are up to 260nt long: insertions occurred at specific loci, possibly reflecting non-templated nucleotide insertion during replication. Various groups can be arranged in order, differing by the cumulative addition of single structural elements, suggesting an accretion mechanism for the structural elaboration of IRESs. Identification of chimeric IRESs implicates recombinational exchange of domains as a second mechanism for the diversification of IRES structure. Recombination likely also accounts for the presence of IGR-like IRESs at the 5'-end of some dicistrovirus-like genomes (e.g. Hangzhou dicistrovirus 3) and in the RNA genomes of Tombusviridae (order Tolivirales ), Marnaviridae (order Picornavirale s), and the 'Ripiresk' picorna-like clade (order Picornavirale s).

RNA Viruses Are Prevalent and Active Tenants of the Predatory Mite Phytoseiulus persimilis (Acari: Phytoseiidae)

Many arthropod species harbor a diverse range of viruses. While much is known about pathogenic viruses of some economically important insects and arthropods involved in disease transmission, viruses associated with mites have rarely been studied. The main objective of this study was to characterize the virome of Phytoseiulus persimilis (Phytoseiidae), a predatory mite commercially used worldwide for the biological control of the key pest Tetranychus urticae (Tetranichidae). A combination of de novo transcriptome assembly and virion sequencing, revealed that RNA viruses are highly prevalent and active tenants of commercial populations of P. persimilis, comprising on average 9% of the mite's total mRNA. Seventeen RNA viruses dominated the mite's virome (i.e., were highly transcribed) with over half (n = 10) belonging to the order Picornavirales, + ssRNA viruses that infect a large range of hosts, including arthropods. Screening of the 17 dominant virus sequences in P. persimilis and T. urticae revealed that three viruses (two Picornavirales of the families Iflaviridae and Dicistroviridae, and one unclassified Riboviria) are unique to P. persimilis and three others (two unclassified Picornavirales and one unclassified Riboviria) are present in both mite species. Most of the sequences were related to viruses previously documented in economically important arthropods, while others have rarely been documented before in arthropods. These findings demonstrate that P. persimilis, like many other arthropods, harbors a diverse RNA virome, which might affect the mite's physiology and consequently its efficiency as a biological control agent.

Discovery of a widespread presence bunyavirus that may have symbiont-like relationships with different species of aphids

Aphids are important agricultural pests, vectors of many plant viruses and have sophisticated relationships with symbiotic microorganisms. Abundant asymptomatic RNA viruses have been reported in aphids due to the application of RNA-seq, but aphid-virus interactions remain unclear. Bunyavirales is the most abundant RNA virus order, which can infect mammals, arthropods, and plants. However, many bunyaviruses have specific hosts, such as insects. Here, we discovered 18 viruses from 10 aphid species by RNA-seq. Importantly, a widespread presence bunyavirus, Aphid bunyavirus 1 (ABV-1), was determined to have a wide host range, infecting and replicating in all 10 tested aphid species. ABV-1 may be transmitted horizontally during feeding on plant leaves and vertically through reproduction. In a comparison of the physiological parameters of ABV-1^high and ABV-1^low strains of pea aphid, higher ABV-1 titers reduced the total nymphal duration and induced the reproduction. Moreover, viral titer significantly affected the lipid and protein contents in pea aphids. In summary, we proposed that ABV-1 may have stable symbiont-like relationships with aphids, and these observations may provide a new direction for studying bunyaviruses in aphids and establishing a model for virus-aphid interactions.

Novel viral RNA genomes of the vine mealybug Planococcus ficus

The vine mealybug, Planococcus ficus (Signoret, 1875), is the most important insect pest in growing areas of the grapevine Vitis vinifera L. in several countries, including Mexico. In Mexico, Baja California (B.C.) is the region with the highest production of V. vinifera L. grapes for industrial purposes. Recently, the diversity of viruses infecting insects only (insect-specific viruses) has been broadly explored to elucidate further ecological viral-host interactions in many insect species, which in some cases has resulted in the application of virus-based biological control agents for insect pests. However, a survey of the Pl. ficus virome has not been done yet. In the present study, we pooled Pl. ficus individuals collected through different vineyards of Ensenada, B.C., Mexico and analysed them by meta-transcriptomics. Novel nearly complete genomes of five RNA viruses were retrieved. These viruses were related to the Iflaviridae and Reoviridae families, and to the Picornavirales and Tolivirales orders. A new isolate belonging to the Dicistroviridae family was also found. Phylogenetic analyses showed that these putative viral genomes group with viruses having hemipteran (including a mealybug species) or other insect hosts, or with viruses associated with insects. Our results suggest that the identified novel RNA viruses could be insect-specific viruses of Pl. ficus. This work is the first insight into the Pl. ficus virome; it guarantees further studies aimed to characterize those viruses with potential for application in biological control of this economically important insect.

Aphid Viruses: A Brief View of a Long History

Aphids are common agricultural pests with a wide range of hosts from agriculture to forestry plants. As known, aphids also serve as the major vectors to transmit plant viruses. Although numerous studies have focused on interactions between aphids and plant viruses, little is known about the aphid viruses, i.e., the insect viruses that are infectious to aphids. In the past four decades, several aphid viruses have been identified in diverse aphid species. In this review, we present a brief view of the aphid pathogenic viruses from several aspects, including classification of aphid viruses and characters of the viral genome, integration of viral sequences in host genomes, infection symptoms and influence on aphids, as well as host range and transmission modes. Taken together, these studies have increased our understanding of the rarely known aphid viruses, and will potentially contribute to the development of new strategies for controlling aphid populations.

A Novel Rice Curl Dwarf-Associated Picornavirus Encodes a 3C Serine Protease Recognizing Uncommon EPT/S Cleavage Sites

Picornaviruses cause diseases in a wide range of vertebrates, invertebrates and plants. Here, a novel picornavirus was identified by RNA-seq technology from rice plants showing dwarfing and curling symptoms, and the name rice curl dwarf-associated virus (RCDaV) is tentatively proposed. The RCDaV genome consists of an 8,987 nt positive-stranded RNA molecule, excluding a poly(A) tail, that encodes two large polyproteins. Using in vitro cleavage assays, we have identified that the RCDaV 3C protease (3Cpro) as a serine protease recognizes the conserved EPT/S cleavage site which differs from the classic Q(E)/G(S) sites cleaved by most picornaviral 3C chymotrypsin-like cysteine proteases. Therefore, we comprehensively deciphered the RCDaV genome organization and showed that the two polyproteins of RCDaV can be cleaved into 12 mature proteins. We found that seven unclassified picornaviruses also encode a 3Cpro similar to RCDaV, and use the highly conserved EPT/S as the cleavage site. The precise genome organizations of these viruses were illustrated. Moreover, RCDaV and the seven unclassified picornaviruses share high sequence identities and similar genome organizations, and cluster into a distinct clade in the order Picornavirales. Our study provides valuable information for the understanding of picornaviral 3Cpros, deciphers the genome organization of a few relatively obscure picornaviruses, and lays the foundation for further pathogenesis research on these viruses.

Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses

Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. The novel viruses were predicted to have positive-sense RNA, negative-stranded RNA, double-stranded RNA, and single-stranded DNA genomes. The assembled sequences included 100 contigs that represented at least 95% coverage of a virus genome or genome segment. Sequences represented 12 previously described arthropod viruses including eight viruses reported from Hubei Province in China, and 12 plant virus sequences of which six have been previously described. The presence of diverse populations of plant viruses within soybean thrips suggests they feed on and acquire viruses from multiple host plant species that could be transmitted to soybean. Assessment of the virome of soybean thrips provides, for the first time, information on the diversity of viruses present in thrips.

First Report of a Mesonivirus and Its Derived Small RNAs in an Aphid Species Aphis citricidus (Hemiptera: Aphididae), Implying Viral Infection Activity

We report a new positive-sense single-stranded RNA (ss RNA+) virus from the brown citrus aphid Aphis citricidus. The 20,300 nucleotide (nt)-long viral genome contains five open-reading frames and encodes six conserved domains (TM2, 3CLpro, TM3, RdRp, Zm, and HEL1). Phylogenetic analysis and amino acid sequence analysis revealed this virus might belong to an unassigned genus in the family Mesoniviridae. The presence of the virus was also confirmed in the field population. Importantly, analysis of the virus-derived small RNAs showed a 22-nt peak, implying that viral infection triggers the small interfering RNA pathway as antiviral immunity in aphids. This is the first report of a mesonivirus in invertebrates other than mosquitoes.