Characterization of a Virus from Pigeonpea with Affinities to Species in the Genus Aureusvirus, Family Tombusviridae

Updates on cowpea viruses in Southwest Nigeria: distribution, prevalence and coinfection

Cowpea is an important source of dietary proteins in the semi-arid regions of sub-Saharan Africa. Its productivity is constrained by several viral diseases and there are limited updates on the incidence and distribution of these diseases in Nigeria. This study assessed the distribution and prevalence of cowpea viruses in Southwest Nigeria. Field surveys were conducted in 2017 and 2018, in which a total of 600 leaf samples were randomly collected from 60 cowpea fields in four (Oyo, Ogun, Ondo and Osun) states at 15 fields per state and 10 samples per field. Disease incidence and severity were recorded while virus infections were confirmed by enzyme-linked immunosorbent assay or reverse transcription polymerase chain reaction. Viral disease symptoms of systemic mosaic, mottling, puckering, vein-banding, leaf deformation and stunted growth were observed. Highest virus incidence and severity (100% and 4.8 ± 0.4) were observed at Adeosun Avenue, Ondo state, whereas Boredun, Osun state had the least (80% and 3.8 ± 0.7), with some symptomless fields found among the states. Seven viruses, viz.: cowpea aphid-borne mosaic virus (CABMV), cowpea mild mottle virus (CPMMV), bean common mosaic virus-blackeye cowpea mosaic strain (BCMV-BlCM), cucumber mosaic virus (CMV), southern bean mosaic virus (SBMV), cowpea mottle virus (CMoV) and cowpea yellow mosaic virus (CYMV) were detected from 173 (28.8%) samples collected from 32 (53.3%) fields across the states. CPMMV was prevalent, detected from 30.0% of surveyed fields, whereas CYMV was the least prevalent (3.3%). Multiple infections of two to four viruses were observed among 12.5% of samples from 51.7% of fields. Highest incidence of single and multiple virus infections were observed in Ondo state. This updates on virus distributions in Southwest Nigeria will be useful for multiple virus resistance-breeding programs and other viral disease management strategies for improved cowpea productivity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42360-022-00576-8.

First report of pothos latent virus infecting upland cotton (Gossypium hirsutum) in the United States

Pothos latent virus (PoLV) is a virus with isometric virions and a positive-sense RNA genome, approximately 4.4 kb in size, currently classified in the genus Aureusvirus, family Tombusviridae (Martelli et al. 1998; Rubino et al. 1995). After its original discovery from hydroponic-grown pothos plants (Scindapsus aureus) in Italy (Sabanadzovic et al. 1995), additional PoLV isolates were reported from pigeonpea (Cajanus cajan) and lisianthus (Eustoma grandiflorum) in India and Taiwan, respectively (Chen et al. 2016; Kumar et al. 2001). PoLV has not been previously reported on the American continent. During 2019, we carried out a state-wide, RT-PCR-based survey for cotton leafroll dwarf virus (CLRDV), as previously described (Aboughanem-Sabanadzovic et al. 2019). Plants exhibiting symptoms reported associated with CLRDV (Avelar et al. 2019) were collected from cotton fields throughout Mississippi. Samples consisted of individually bagged, six inch-long, apical portions collected from five to twelve cotton plants per field. At the end of the season, the total RNAs extracted from a subset of CLRDV-infected samples using a Spectrum RNA extraction kit (Sigma, St Louis, MO), were randomly selected for additional characterization by Illumina 150 nt paired-end high-throughput sequencing at the UIUC Core Sequencing Facility (University of Illinois, Urbana, IL). De novo assembly of 46 to 60 million raw reads/sample was performed by metaSPAdes (Nurk et al. 2017). In addition to several CLRDV-specific contigs, analyses of 184,173 contigs assembled from a sample collected in Clay County (lab code CL-112) revealed a large contig # 63556 of 4298 nt in size with identities ranging from 90.5% to 94.3% with three PoLV genome sequences available in GenBank, suggesting that an isolate of this virus (PoLV-cot; GenBank OP584699) was coinfecting the sample along with CLRDV. Sequence analyses showed that contig #63556 represents approx. 97-98% of the entire PoLV-cot genome. To verify HTS data, specific primers (PoLV-F 5'ACATATATCAGAGAGAGCTCAGGTC3' and PoLV-R 5'GCTCCCATGACAGACCTCACT3') were designed on conserved sequences of all four PoLV genomes and used in a single-tube RT-PCR. The initial tests on RNAs from CL-112 and six other samples from the same field confirmed PoLV-cot infections in the original and an additional cotton plant. Sanger sequencing of the two 294 bp-long RT-PCR products revealed >99% nt mutual identity and 97.5-99% with PoLV isolates. However, none of the additional 226 cotton samples collected in 2019 across the state of Mississippi and 12 samples collected in the same field in 2020 tested positive for PoLV-cot. At this moment, it is not clear whether the PoLV infections originated from infected seeds or, more likely, from soil-borne inoculum. Indeed, several aureusviruses are known to be transmitted by soil either involving vectors belonging to the fungal genera Olpidium and/or Polymyxa (i.e., cucumber leaf spot virus, maize white line mosaic virus), or in a vectorless manner (Rochon et al. 2012). Previous studies on this virus demonstrated low-rate experimental transmission through the soil with no apparent involvement of specific vectors (Chen et al. 2016; Kumar et al. 2001; Sabanadzovic et al. 1995). In summary, results of our study indicate an original report of PoLV on the North American continent, along with description of a new host. Possible impact of PoLV-cot on the cotton industry, or any other susceptible crop in the US, is yet to be understood. Funding: This work has been partially supported by financial support from Cotton Inc, Cotton Foundation, USDA-ARS 58-6066-9-033 and 2020 MAFES-SRI grants. NAS and SS acknowledge partial support from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Projects Numbers 7001412 and1021494, respectively. The author(s) declare no conflict of interest. 1. Aboughanem-Sabanadzovic, N., et al. 2019. Plant Dis 103: 1798. 2. Avelar, S., et al. 2019. Plant Dis 103: 592. 3. Chen, Y-K., et al. 2016. J Phytopath 164: 650. 4. Kumar, P.L., et al. 2001. Plant Dis 85: 208. 5. Martelli, G.P., et al. 1998. Arch Virol 143: 1847. 6. Nurk, S., et al. 2017. Genome Res 27: 824. 7. Rochon, D., et al. 2012. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Amsterdam, NL, Elsevier Academic Press, pp 1111-1138. 8. Rubino, L., et al. 1995. J Gen Virol 76: 2835. 9. Sabanadzovic, S., et al.1995. Eur J Plant Pathol 101:171.

Salient Findings on Host Range, Resistance Screening, and Molecular Studies on Sterility Mosaic Disease of Pigeonpea Induced by Pigeonpea sterility mosaic viruses (PPSMV-I and PPSMV-II)

Two distinct emaraviruses, Pigeonpea sterility mosaic virus-I (PPSMV-I) and Pigeonpea sterility mosaic virus-II (PPSMV-II) were found to be associated with sterility mosaic disease (SMD) of pigeonpea [Cajanus cajan (L.) Millsp.]. The host range of both these viruses and their vector are narrow, confined to Nicotiana benthamiana identified through mechanical transmission, and to Phaseolus vulgaris cvs. Top Crop, Kintoki, and Bountiful (F: Fabaceae) through mite transmission. A weed host Chrozophora rottleri (F: Euphorbiaceae) was also infected and tested positive for both the viruses in RT-PCR. Among the wild Cajanus species tested, Cajanus platycarpus accessions 15661, 15668, and 15671, and Cajanus scarabaeoides accessions 15683, 15686, and 15922 were infected by both the viruses and mite vector suggesting possible sources of SMD inoculum. Though accession 15666 of C. platycarpus, 15696 of C. scarabaeoides, and 15639 of Cajanus lanceolatus were infected by both the viruses, no mite infestation was observed on them. Phylogenetic analysis of nucleotide sequences of RNA-1 and RNA-2 of PPSMV-I and PPSMV-II isolates in southern India revealed significant divergence especially PPSMV-II, which is closely related to the Fig mosaic virus (FMV) than PPSMV-I. In multilocation testing of pigeonpea genotypes for their broad-based resistance to SMD for two consecutive years, genotypes ICPL-16086 and ICPL-16087 showed resistance reaction (<10% incidence) in all three locations studied. Overall, the present study gives a clear idea about the host range of PPSMV-I and PPSMV-II, their molecular relationship, and sources of resistance. This information is critical for the development of reliable diagnostic tools and improved disease management strategies.

Molecular characterization of a novel Aureusvirus infecting elderberry (Sambucus nigra L.)

A novel virus infecting elderberry was identified by high-throughput Illumina sequencing of double strand RNAs isolated form elderberry leaves. The complete genome sequence obtained (4512 nucleotides in length) shows an organization typical for aureusviruses, with five open reading frames (ORFs) and the typical ORF1-RT expression by the readthrough of an amber stop codon. The analysis of the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) sequences showed the highest identity (respectively 75.7% and 55%) with the corresponding amino acid sequences of Pothos latent virus. These two values, below the species demarcation criteria for the genus, indicate that the detected virus is a new member of genus Aureusvirus, family Tombusviridae, with the proposed name Elderberry aureusvirus 1 (ElAV1). A survey confirmed the wide distribution of ElAV1 in elderberry in the Czech Republic. Phylogenetic analyses of RdRp and CP sequences showed distinct microevolution of geographically separated isolates, with a tendency for isolates coming from close localities or from the same region to cluster together but heterogeneity of viral populations down to a local scale was also observed. The symptomatology of the new virus is not fully clear, but many infected trees were either asymptomatic or showed mild chlorotic mosaics. More severe symptoms, potentially impacting yields of flowers or berries, were observed in plants with mixed infections of ElAV1 and other elderberry viruses. Further efforts are now needed to determine ElAV1 prevalence outside the Czech Republic and to unravel its epidemiology.

Molecular characterization of emaraviruses associated with Pigeonpea sterility mosaic disease

Sterility Mosaic Disease (SMD) of pigeonpea (Cajanus cajan (L.) Millspaugh) is a complex disease due to various factors including the presence of a mixed infection. Comparison of dsRNA profile and small RNA (sRNA) deep sequencing analysis of samples from three locations revealed the presence of Pigeonpea sterility mosaic virus-I and II (PPSMV-I and II) from Chevella and only PPSMV-II from Bengaluru and Coimbatore. PPSMV-I genome consisted of four while PPSMV-II encompassed six RNAs. The two viruses have modest sequence homology between their corresponding RNA 1-4 encoding RdRp, glycoprotein precursor, nucleocapsid and movement proteins and the corresponding orthologs of other emaraviruses. However, PPSMV-II is more related to Fig mosaic virus (FMV) than to PPSMV-I. ELISA based detection methodology was standardized to identify these two viruses, uniquely. Mite inoculation of sub-isolate Chevella sometimes resulted in few- to- many pigeonpea plants containing PPSMV-I alone. The study shows that (i) the N-terminal region of RdRp (SRD-1) of both the viruses contain "cap-snatching" endonuclease domain and a 13 AA cap binding site at the C-terminal, essential for viral cap-dependent transcription similar to the members of Bunyaviridae family and (ii) P4 is the movement protein and may belong to '30 K superfamily' of MPs.

Sterility Mosaic Disease-the "Green Plague" of Pigeonpea: Advances in Understanding the Etiology, Transmission and Control of a Major Virus Disease

Pigeonpea (Cajanus cajan), is a grain legume that is a very important subsistence crop in marginal farming systems adopted by millions of smallholder farmers in the Indian subcontinent. It is grown for its seed for human consumption and for income generation by trading surpluses in local and commercial markets, but is widely used for diverse purposes, including as animal fodder and for soil conservation. Sterility mosaic (SMD) is the most damaging disease of pigeonpea endemic in the Indian subcontinent. It causes yield losses of >US$300 million per annum in India and Nepal alone. SMD-affected plants show severe stunting and mosaic symptoms on leaves, with complete or partial cessation of flowering. The SMD causal agent is spread by the arthropod mite vector Aceria cajani (Acari: Eriophyidae). Cultivating SMD-resistant genotypes is the most viable way to manage this serious disease of pigeonpea. Progress in developing broad-based SMD resistant material has been hindered by the lack of knowledge of the causal agent, the absence of diagnostic tools, and factors influencing host-plant resistance. After seven decades of research, vital breakthroughs made on the identification, detection, transmission, and epidemiology of the SMD causal agent, Pigeonpea sterility mosaic virus (PPSMV), are enabling the development of broad-based durable resistant pigeonpea cultivars. These breakthroughs will contribute greatly to sustainable pigeonpea production and enhance the income and livelihood of poor farmers in the semi-arid tropics of the Indian subcontinent.

A novel mite-transmitted virus with a divided RNA genome closely associated with pigeonpea sterility mosaic disease

ABSTRACT The agent of sterility mosaic, a disease that is a major constraint on pigeonpea (Cajanus cajan) production in the Indian subcontinent, is transmitted by the eriophyid mite, Aceria cajani. This agent has remained elusive for decades despite intensive efforts but we report the isolation of highly flexuous filamentous virus-like particles (VLPs) of 3 to 10 nm in width and of undefined lengths from sterility mosaic disease (SMD)-affected pigeonpea plants. Purified VLP preparations from virus-infected pigeonpea and Nicotiana benthamiana had a buoyant density in cesium chloride of 1.22 to 1.23 g cm(-3) and contained a major virus-specific protein species of approximately 32 kDa and 5 to 7 RNA species of approximately 6.8 to 1.1 kb. The sequence of some complementary DNA clones to RNA from purified VLP preparations had no significant matches in database searches. Two oligonucleotide primers derived from one such sequence, when used in reverse transcriptase-polymerase chain reaction assays, amplified a product of 321 bp specifically from SMD-affected pigeonpea plants. Purified VLP preparations were used to produce polyclonal antibodies that, in infected plants, detected the virus using enzyme-linked immuno-sorbent assay (ELISA) and the virus-specific 32-kDa protein in western immunoblotting (WIB). In such assays, the virus was detected consistently in all SMD-affected pigeonpea plant samples from several different locations in India, but not in samples from symptom-free pigeonpea plants from the same locations. In experimental studies, all pigeonpea plants inoculated with viruliferous A. cajani and those plants graft-inoculated with SMD-affected tissue were infected with the virus as assessed by ELISA and WIB, but not any uninfected pigeonpea plants. This virus, tentatively named Pigeonpea sterility mosaic virus (PPSMV), has some properties similar to virus species in the genera Tospovirus and Tenuivirus and with the eriophyid mite-transmitted High plains virus (HPV) but is distinct from these and from all other characterized viruses. The combination of novel properties shown by PPSMV and HPV suggest that they may constitute species in a new genus of plant viruses.