Discovery of Known and Novel Viral Genomes in Soybean Aphid by Deep Sequencing

Abstract

The phytobiome includes not just cellular microorganisms, but also all viruses associated with plants: the virome. Plants and aphids exchange viruses regularly and efficiently; thus, the plant virome is tightly linked with the aphid virome. Yet, little is known about aphid viromes, particularly that of the soybean aphid (Aphis glycines), one of the most economically important pest insects of soybean. To sample the soybean aphid virome, and to seek new viruses as potential biological control agents, we employed next-generation sequencing. Genomes isolated from viruses in soybean aphids collected at four sites revealed many viruses, and six complete or nearly complete genomes were assembled. Most abundant were the picornavirus-like dicistroviruses Aphid lethal paralysis virus and Rhopalosiphum padi virus. We also sequenced the genome of a new dicistrovirus, Big Sioux River virus, fragments of which had been found previously in honey bee. Genome sequences that represent two entirely new virus families were obtained. These include an abundant tetravirus-like virus and a virus distantly related to cileviruses of plants and negeviruses of insects. Surprisingly, Cotton leafroll dwarf virus, a member of the genus Polerovirus, was found in soybean aphids from China, suggesting that the soybean aphid may be a vector of this virus. This virus had not been reported previously in China or in soybean. This study provides a peek into the rapidly expanding, largely unexplored world of insect viromes that will provide valuable knowledge for future understanding of plant−virus−vector interactions. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

“…The BSRV-like sequences from Kenya cluster phylogenetically with viruses of the genus Cripavirus . From previous reports, BSRV appears to be a multi-host pathogen; having been previously detected in honeybees, mosquitoes and soybean aphids [ 16 – 18 ]. All discoveries of BSRV have been through metagenomic studies and hence BSRV is yet to be formally classified by the International Committee on Taxonomy of Viruses (ICTV), which until recently has required evidence of biological properties such as pathogenicity, host range and epidemiology.…”

“…Big Sioux River virus (BSRV) was first isolated from honeybees ( Apis mellifera ) following a study of the bee microbiome to identify potential causes of bee colony collapse disorder in the United States [ 16 ]. BSRV has also been isolated from mosquitoes ( Culex tritaeniorhynchus ) and in the soybean aphid ( Aphis glycines ) in China [ 17 , 18 ]. Neither the diversity of aphids nor the range of viruses infecting them has been examined in East Africa.…”

Next-Generation Sequencing on Insectivorous Bat Guano: An Accurate Tool to Identify Arthropod Viruses of Potential Agricultural Concern

“…ABPV CR-026 presented 83% of nucleotide identity and 91 to 93% of amino acid identities with these viruses ( Figure 2B), which together shared 94 to 97% of nucleotide identities. BSRV-Like CR-026 clustered with the previously described BSRV [12], as well as with the Wuhan insect virus (WIV) [22] and Aphis glycines virus (AGLV) [18] characterized in China and Aphid gossypii virus (AGV) isolated in Israel (Figure 1). Sequences of AGLV were available in the GenBank but with no publication associated.…”

“…BSRVs have been described in diverse arthropod hosts worldwide [12,18,21,22]. Nonetheless, their pathogenicity in hosts is yet to be clarified.…”

“…Beyond the classified Dicistrovirus species, numerous dicistroviruses which are yet to be classified have been characterized in the last two decades mainly owing to the advent of high-throughput sequencing technologies (HTS). Although numbers of them were identified in insects [12,[17][18][19][20][21][22], some were found in mammalian stools, including human beings. However, the presence of such viruses in mammalian faeces were likely linked to their dietary habits [23][24][25][26][27][28].…”