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Cotton leafroll dwarf virus (CLRDV) was first reported in the United States (US) in 2017 from cotton plants in Alabama (AL) and has become widespread in cotton-growing states of the southern US. To investigate the genomic variability among CLRDV isolates in the US, complete genomes of the virus were obtained from infected cotton plants displaying m...
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... predict possible recombination among CLRDV isolates, and identify the respective breakpoints and parents, all available CLRDV complete genomes were aligned and analyzed using the RDP software package. At least 11 independent recombination events Viruses 2021Viruses , 13, 2230 were predicted among the CLRDV isolates, with most recombination breakpoints having occurred in the second half of ORF2 and ORF5, and in the first half of ORF3 (events 1-9 and 11) (Figure 2b; Table S3). The CLRDV-GA isolates (subclade 3-US) were identified as putative recombinants in three events (1, 4, and 9) and as possible parental sequences in eight recombination events (1-4, 6, 8, 9, and 11). ...Context 2
... CLRDV isolates in subclade 1-US were identified as recombinants, with sequences of isolates from TX (subclade 2-US) or GA (subclade 3-US) implicated as possible minor and major parents (events 2, 3, 6, 8, and 11). The CLRDV-typical isolates from Brazil (BR) and Argentina (AR) were also identified as putative recombinants, with CLRDV-atypical (BR) as the predicted minor parent, but the major parent was unidentified (Figure 2b; Table S3). ...Context 3
... on Fst and Nst values, extensive population structure was evident between most of the subpopulations, indicative of genetic divergence. In contrast, relatively low Fst and Nst indices were obtained when subclades 1-US and 3-US were compared with the entire US subpopulation, at 0.07 and 0.06, respectively (Table 3). Finally, a comparison of atypical-SA with SA subpopulations revealed negative Fst and Nst values of − 0.07 (Table 3). ...Context 4
... contrast, relatively low Fst and Nst indices were obtained when subclades 1-US and 3-US were compared with the entire US subpopulation, at 0.07 and 0.06, respectively (Table 3). Finally, a comparison of atypical-SA with SA subpopulations revealed negative Fst and Nst values of − 0.07 (Table 3). Statistically significant differences for pairwise comparisons of π values calculated from full-length genomes of CLRDV subpopulations of different sample sizes were analyzed with a 95% bootstrap confidence interval (CIs) using the approach described by [73], where no statistically significant differences were observed for CI values including zero (grey line) (Figure 3). ...Context 5
... Materials: The following are available online at https://www.mdpi.com/article/ 10.3390/v13112230/s1, Table S1: Primers used for the genome amplification of complete cotton leafroll dwarf virus (CLRDV) and its 5 /3 untranslated regions (UTRs) by random amplification of cDNA ends; Table S2: Cotton leafroll dwarf virus (CLRDV) genome sequences retrieved from NCBI-GenBank; Table S3: Predicted recombination events detected for cotton leafroll dwarf virus (CLRDV) isolates. ...Similar publications
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... In 2017, CLRDV was confirmed in Alabama (Avelar et al. 2019) followed by Georgia and Mississippi (Aboughanem-Sabanadzovic et al. 2019;Tabassum et al. 2019). Molecular analysis following that initial detection determined that the strains of the virus in the United States were genetically different from strains reported in South America (Ali and Mokhtari 2020b; Avelar et al. 2020;Ramos-Sobrinho et al. 2021;Sedhain et al. 2021;Tabassum et al. 2020). Despite finding CLRDV in the United States, it did not appear to result in symptoms of cotton blue disease like those observed in South America. ...
Cotton leafroll dwarf virus (CLRDV), transmitted by the cotton aphid (Aphis gossypii Glover), was first confirmed in upland cotton (Gossypium hirsutum L.) in Alabama, United States, in 2017. Subsequent observations of symptomatic plants followed by confirmation via reverse transcriptase PCR (RT-PCR) were made in neighboring states in 2018. To assess the distribution and incidence of CLRDV, and incidence of presumed symptoms across the southern cotton belt, a multidisciplinary team established sentinel plot survey sites at 16 experiment stations in 11 states stretching from Texas to Virginia and Tennessee to Florida beginning in 2019. Field trials were conducted over a three-year period using multiple cotton cultivars that were adjusted annually. Cotton plots were evaluated at each location by a single evaluator to attempt to correlate symptom severity across the cotton growing region with virus incidence in cotton plant tissues using RTPCR. Symptom incidence, based on visual estimation of plants in each plot with presumed symptoms, differed across the region and ranged from 0% to 75% with a low average from all locations of 11.4% in 2021 to an average high of 28.0% in 2020. Though symptom severity suggested the presence of CLRDV, there were instances where symptoms were observed but virus presence was not confirmed by PCR. CLRDV has since been confirmed from all locations, which suggests that it has become endemic in cotton production areas throughout the eastern range of the United States.
... Remarkably, P0 V72I demonstrated a robust silencing suppression potency similar to that of P0 ty . This suggests that a naturally occurring mutation at this residue during viral replication in the field could give rise to a variant with increased VSR potency, potentially causing more severe disease [57,58]. It is noteworthy, and also concerning, that a variant carrying such substitution at this residue has recently been isolated in Texas, resulting in severe symptoms in the host [58]. ...
The P0 proteins encoded by Cotton leafroll dwarf virus (CLRDV) serve as viral suppressors of RNA silencing (VSR). CLRDV P0 proteins share a VSR-associated F-box-like motif. This study investigated the role of specific amino acid (aa) residues within the F-box-like motif, elucidating their implications for VSR potency, pathogenicity, and intracellular localization. Analysis of various single aa substitution mutants within the F-box-like motif to understand their effect on P0 proteins’ VSR potency revealed that specific mutations significantly affect P0’s ability to suppress RNA silencing, emphasizing the crucial role of the F-box-like motif. Subcellular localization examinations indicated that the P0 proteins associate with the nucleus and endoplasmic reticulum, which may be linked to their VSR function. Also, the induction of hypersensitive response (HR)-like symptoms and the accumulation of reactive oxygen species by P0 proteins was observed, suggesting their role as pathogenicity factors. These results indicated that specific mutations significantly affect the functions of multifaceted P0 proteins, highlighting the F-box-like motif’s crucial role. Our study highlights the importance of further molecular investigations to elucidate how different CLRDV strains manifest various disease symptoms and severity. This is crucial considering the global economic importance of cotton and the potential emergence of more threatening CLRDV isolates.
... In 2017, CLRDV was reported first time in the United States in Alabama, and the genome sequence analysis identified it as a new strain (CLRDV-AL) (Avelar et al., 2019). Since the first incidence, CLRDV has been reported in many other cotton-growing states (Aboughanem-Sabanadzovic et al., 2019;Alabi et al., 2020;Faske et al., 2020;Iriarte et al., 2020;Price et al., 2020;Tabassum et al., 2020;Thiessen et al., 2020;Wang et al., 2020;Ramos-Sobrinho et al., 2021;Ferguson and Ali, 2022). All cotton varieties grown in the United States are susceptible to this virus (Edula et al., 2023), and the presence of this pathogen poses a considerable threat. ...
Cotton is a multipurpose crop grown globally, including the United States. Cotton leafroll dwarf virus (CLRDV), a phloem-limited virus (Solemoviridae) transmitted by aphids, causes significant economic losses to cotton cultivation. CLRDV strains (CLRDV-typical and atypical) that were previously prevalent in other countries cause severe symptoms leading to high yield loss. Recently, a new isolate of CLRDV (CLRDV-AL) has been characterized from infected cotton plants in Alabama that are often asymptomatic and difficult to detect, implying a low titer and pathogenicity within the host. Different pathogenicity among certain strains within the same species often correlates with both environmental and molecular factors. Thus, better management and control of the vector-borne disease can be achieved by elucidating host-pathogen interaction, such as host immune response and pathogen counter-response. In this study, we demonstrate the ability of CLRDV-AL to suppress a major host defense response known as RNA silencing and compare the potency of silencing suppression to other strains of the same virus. Also, we discuss the difference in pathogenicity among them by evaluating the observations based on the amino acid variation within the functional domain. Our study provides and suggests a future direction for specifying the strategy to mitigate potential cotton disease severity.
... Analysis of genetic variation across the viral population can provide insight to better understand its epidemiology, evolution and host adaptation. Previously the genomic variability of a single nucleotide among cotton leafroll dwarf virus (CLRDV) isolates, that belong to the genus Polerovirus, was estimated to be π = 0.02831, from analysis of 17 fulllength genomic sequences (n = 17) [32]. Our findings estimated the genomic variability for CVEV populations to be π = 0.01981 (n = 23), suggesting that the CVEV population is less variable than the CLRDV. ...
... For instance, the coding region of ORF4 of maize yellow mosaic virus (MaYMV) was under positive selection pressure, while the rest of the genes were under negative selection pressure [26]. For poleroviruses, similar report revealed that negative selection was the dominant selective force driving genomic variation in the viral coding regions of CLRDV [32]. However, analysis of the mean dn/ds ratios revealed that all coding regions of CVEV were under negative selection pressure. ...
In this study, we identified a new citrus vein enation virus (CVEV) isolate (named CVEV-DT1) through sRNA high-throughput sequencing and traditional sequencing. Phylogenetic analysis based on whole genome sequences of all known CVEV isolates revealed that CVEV-DT1 was in an evolutionary branch with other isolates from China. Molecular variation analysis showed that the single nucleotide variability along CVEV full-length sequences was less than 8%, with more transitions (60.55%) than transversions (39.43%), indicating a genetically homogeneous CVEV population. In addition, non-synonymous nucleotide mutations mainly occurred in ORF1 and ORF2. Based on disorder analysis of all encoded ORF by CVEV-DT1, we identified that the CVEV-DT1 coat protein (CP) formed spherical granules, mainly in the cell nucleus and partly throughout the cytoplasm, with liquid properties through subcellular localization and photobleaching assay. Furthermore, we also confirmed that the CVEV P0 protein has weak post-transcriptional RNA-silencing suppressor activity and could elicit a strong hypersensitive response (HR) in tobacco plants. Collectively, to the best of our knowledge, our study was the first to profile the genomic variation in all the reported CVEV isolates and reveal the functions of CVEV-DT1-encoded proteins.
... The cotton leaf roll dwarf virus (CLRDV, Genus: Polerovirus; Family: Solemoviridae), a positive sense (+) ssRNA virus, causes the Cotton Blue Disease (CBD) that affects cotton crops in South America and Africa (Distéfano et al., 2010;Parkash et al., 2021). Aphis gossypii (Glover; Hemiptera: Aphididae), one of the most polyphagous aphid species and worldwide-distributed, hosts over 40 viruses (Quan et al., 2019) and is the exclusive vector of CLRDV (Michelotto and Busoli, 2007;Ramos-sobrinho et al., 2021). ...
... Since 2017, CBD has spread in important cotton grower states in the United States (Avelar et al., 2019;Parkash et al., 2021;Ramos-sobrinho et al., 2021). Curiously, due to very rigorous winters, A. gossypii does not impose high pressure in the United States cotton fields (Carletto et al., 2009), suggesting two hypotheses: first, CLRDV may have adapted to a new viral vector and second, even in low aphid pressure, the insects can perpetuate disease spread and maintenance. ...
Cotton (Gossypium spp. L., Malvaceae) is the world’s largest source of natural fibers. Virus outbreaks are fast and economically devasting regarding cotton. Identifying new viruses is challenging as virus symptoms usually mimic nutrient deficiency, insect damage, and auxin herbicide injury. Traditional viral identification methods are costly and time-consuming. Developing new resistant cotton lines to face viral threats has been slow until the recent use of molecular virology, genomics, new breeding techniques (NBT), remote sensing, and artificial intelligence (AI). This perspective article demonstrates rapid, sensitive, and cheap technologies to identify viral diseases and propose their use for virus resistance breeding.
Cotton leafroll dwarf virus (CLRDV), a threat to the cotton industry, was first reported in the United States (US) as an emergent pathogen in 2017. Phylogenetic analysis supports the hypothesis that US CLRDV strains are genetically distinct from strains in South America and elsewhere, which is not consistent with the hypothesis that the virus is newly introduced into the country. Therefore, using database mining, we evaluated the timeline and geographic distribution of CLRDV in the country. We uncovered evidence that shows that CLRDV had been in the US for over a decade before its official first report. CLRDV sequences were detected in datasets derived from Mississippi in 2006, Louisiana in 2015, and California in 2018. Additionally, through field surveys of upland cotton in 2023, we confirmed that CLRDV is present in California, which had no prior reports of the virus. Viral sequences from these old and new datasets exhibited high nucleotide identities (>98%) with recently characterized US isolates, and phylogenetic analyses with their homologs placed these sequences within a US-specific clade, further supporting the earlier presence of CLRDV in the country. Moreover, potential new hosts, including another fiber crop, flax, were determined through data mining. Retrospective analysis suggests CLRDV presence in the US since at least 2006 (Mississippi). These findings necessitate a reevaluation of spread patterns, inoculum sources, symptomology variations, and control strategies. Our findings challenge the current understanding of the arrival and spread of CLRDV in the US, highlight the power of data mining for virus discovery, and underscore the need for further investigation into CLRDV’s impact on US cotton.
The aphid-transmitted polerovirus, cotton leafroll dwarf virus (CLRDV), first characterized from symptomatic cotton plants in South America (S.A.), has recently been identified in commercial cotton plantings in the United States (U.S.). Here, the CLRDV intra-specific diversity was investigated by comparative sequence analysis of the most divergent CLRDV coding region, ORF0/P0. Bayesian analysis of ORF0 sequences for U.S. and reference populations resolved three well-supported sister clades comprising one U.S. and two South America lineages. Principal component analysis (PCA) identified seven statistically-supported intra-specific populations. The Bayesian phylogeny- and principal component analysis (PCA) dendrogram-inferred relationships were congruent. Population analysis of ORF0 sequences indicated most lineages have evolved under negative selection, albeit certain sites/isolates evolved under positive selection. Both U.S. and South American isolates exhibited extensive ORF0 diversity. At least two U.S. invasion foci were associated with their founder populations in Alabama-Georgia (AL-GA) and eastern Texas (TX). The AL-GA founder is implicated as the source of recent widespread expansion and establishment of secondary disease foci throughout the southeastern-central U.S. Based on the geographically-restricted distribution, spread of another extant TX population appeared impeded by a population bottleneck. Extant CLRDV isolates represent several putative introductions potentially associated with catastrophic weather events dispersing viruliferous cotton aphids of unknown origin(s).
Cotton is a leading agricultural crop, grown in about 2.5% of the world’s arable land. Leaf curl disease caused by whitefly Bemisia tabaci transmitted monopartite and bipartite begomoviruses (BBV) has emerged as a serious constraint in cotton production in parts of Africa and the Indian subcontinent, assisted by the inadvertent introduction of susceptible genotypes in the cotton cropping system. A similar leaf crumple disease caused by the New World BBV is a disease of concern in North America. The cotton leaf-roll dwarf disease caused by a Polerovirus transmitted by aphids in a persistent manner, is the fastest spreading cotton virus, affecting cotton production in Argentina, Brazil, India, Thailand, Timor-Leste, and the USA. This chapter gives a brief status of the characteristics of the viral diseases threatening cotton production and their management.
Cotton leafroll dwarf virus (CLRDV) is a yield-limiting, aphid-transmitted virus that was identified in cotton, Gossypium hirsutum L., in the United States of America in 2017. CLRDV is currently classified in the genus Polerovirus, family Solemoviridae. Although 8 species of aphids (Hemiptera: Aphididae) are reported to infest cotton, Aphis gossypii Glover is the only known vector of CLRDV to this crop. Aphis gossypii transmits CLRDV in a persistent and nonpropagative manner, but acquisition and retention times have only been partially characterized in Brazil. The main objectives of this study were to characterize the acquisition access period, the inoculation access period, and retention times for a U.S. strain of CLRDV and A. gossypii population. A sub-objective was to test the vector competence of Myzus persicae Sulzer and Aphis craccivora Koch. In our study, A. gossypii apterous and alate morphs were able to acquire CLRDV in 30 min and 24 h, inoculate CLRDV in 45 and 15 min, and retain CLRDV for 15 and 23 days, respectively. Neither M. persicae nor A. craccivora acquired or transmitted CLRDV to cotton.
Taxonomy:
Cotton leafroll dwarf virus (CLRDV) is a member of the genus Polerovirus, family Solemoviridae. Geographical Distribution: CLRDV is present in most cotton-producing regions worldwide, prominently in North and South America.
Physical properties:
The virion is a nonenveloped icosahedron with T = 3 icosahedral lattice symmetry that has a diameter of 26-34 nm and comprises 180 molecules of the capsid protein. The CsCl buoyant density of the virion is 1.39-1.42 g/cm3 and S20w is 115-127S. Genome: CLRDV shares genomic features with other poleroviruses; its genome consists of monopartite, single-stranded, positive-sense RNA, is approximately 5.7-5.8 kb in length, and is composed of seven open reading frames (ORFs) with an intergenic region between ORF2 and ORF3a.
Transmission:
CLRDV is transmitted efficiently by the cotton aphid (Aphis gossypii Glover) in a circulative and nonpropagative manner. Host: CLRDV has a limited host range. Cotton is the primary host, and it has also been detected in different weeds in and around commercial cotton fields in Georgia, USA.
Symptoms:
Cotton plants infected early in the growth stage exhibit reddening or bronzing of foliage, maroon stems and petioles, and drooping. Plants infected in later growth stages exhibit intense green foliage with leaf rugosity, moderate to severe stunting, shortened internodes, and increased boll shedding/abortion, resulting in poor boll retention. These symptoms are variable and are probably influenced by the time of infection, plant growth stage, varieties, soil health, and geographical location. CLRDV is also often detected in symptomless plants.
Control:
Vector management with the application of chemical insecticides is ineffective. Some host plant varieties grown in South America are resistant, but all varieties grown in the United States are susceptible. Integrated disease management strategies, including weed management and removal of volunteer stalks, could reduce the abundance of virus inoculum in the field.
