scholarly journals Fitness Declines in Tobacco Etch Virus upon Serial Bottleneck Transfers

2007 ◽  
Vol 81 (10) ◽  
pp. 4941-4947 ◽  
Author(s):  
Francisca de la Iglesia ◽  
Santiago F. Elena
Keyword(s):  
Rna Viruses ◽  
Average Rate ◽  
Random Noise ◽  
Chenopodium Quinoa ◽  
Tobacco Etch Virus ◽  
Deleterious Mutations ◽  
Local Lesions ◽  
Underlying Processes ◽  
Infectious Cycle ◽  
Independent Mutation

ABSTRACT It has been well established that populations of RNA viruses transmitted throughout serial bottlenecks suffer from significant fitness declines as a consequence of the accumulation of deleterious mutations by the onset of Muller's ratchet. Bottlenecks are unavoidably linked to different steps of the infectious cycle of most plant RNA viruses, such as vector-mediated transmissions and systemic colonization of new leaves. Here we report evidence for fitness declines by the accumulation of deleterious mutations in the potyvirus Tobacco etch virus (TEV). TEV was inoculated into the nonsystemic host Chenopodium quinoa, and local lesions were isolated and used to initiate 20 independent mutation accumulation lineages. Weekly, a random lesion from each lineage was isolated and used to inoculate the next set of plants. At each transfer, the Malthusian growth rate was estimated. After 11 consecutive transfers, all lineages suffered significant fitness losses, and one even became extinct. The average rate of fitness decline was 5% per day. The average pattern of fitness decline was consistent with antagonistic epistasis between deleterious mutations, as postulated for antiredundant genomes. Temporal fitness fluctuations were not explained by random noise but reflected more complex underlying processes related to emergence and self-organization phenomena.

scholarly journals On the Rate and Linearity of Viability Declines in Drosophila Mutation-Accumulation Experiments: Genomic Mutation Rates and Synergistic Epistasis Revisited

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 797-806 ◽  
Author(s):  
James D Fry
Keyword(s):  
Mutation Rate ◽  
Average Rate ◽  
Natural Populations ◽  
Mutation Accumulation ◽  
High Rate ◽  
Deleterious Mutations ◽  
Order Of Magnitude ◽  
Contamination Event ◽  
Genomic Mutation ◽  
The 1960S

Abstract High rates of deleterious mutations could severely reduce the fitness of populations, even endangering their persistence; these effects would be mitigated if mutations synergize each others’ effects. An experiment by Mukai in the 1960s gave evidence that in Drosophila melanogaster, viability-depressing mutations occur at the surprisingly high rate of around one per zygote and that the mutations interact synergistically. A later experiment by Ohnishi seemed to support the high mutation rate, but gave no evidence for synergistic epistasis. Both of these studies, however, were flawed by the lack of suitable controls for assessing viability declines of the mutation-accumulation (MA) lines. By comparing homozygous viability of the MA lines to simultaneously estimated heterozygous viability and using estimates of the dominance of mutations in the experiments, I estimate the viability declines relative to an appropriate control. This approach yields two unexpected conclusions. First, in Ohnishi’s experiment as well as in Mukai’s, MA lines showed faster-than-linear declines in viability, indicative of synergistic epistasis. Second, while Mukai’s estimate of the genomic mutation rate is supported, that from Ohnishi’s experiment is an order of magnitude lower. The different results of the experiments most likely resulted from differences in the starting genotypes; even within Mukai’s experiment, a subset of MA lines, which I argue probably resulted from a contamination event, showed much slower viability declines than did the majority of lines. Because different genotypes may show very different mutational behavior, only studies using many founding genotypes can determine the average rate and distribution of effects of mutations relevant to natural populations.

scholarly journals Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: A Complex Story

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 253 ◽  
Author(s):  
Mauricio Comas-Garcia
Keyword(s):  
Rna Viruses ◽  
Genomic Rna ◽  
Rna Packaging ◽  
Dna And Rna ◽  
Relative Contribution ◽  
Double Stranded Dna ◽  
Positive Sense ◽  
Infectious Cycle

The packaging of genomic RNA in positive-sense single-stranded RNA viruses is a key part of the viral infectious cycle, yet this step is not fully understood. Unlike double-stranded DNA and RNA viruses, this process is coupled with nucleocapsid assembly. The specificity of RNA packaging depends on multiple factors: (i) one or more packaging signals, (ii) RNA replication, (iii) translation, (iv) viral factories, and (v) the physical properties of the RNA. The relative contribution of each of these factors to packaging specificity is different for every virus. In vitro and in vivo data show that there are different packaging mechanisms that control selective packaging of the genomic RNA during nucleocapsid assembly. The goals of this article are to explain some of the key experiments that support the contribution of these factors to packaging selectivity and to draw a general scenario that could help us move towards a better understanding of this step of the viral infectious cycle.

scholarly journals Natural Infection of Alstroemeria brasiliensis with Lily Mottle Virus

Plant Disease ◽  
2000 ◽  
Vol 84 (1) ◽  
pp. 103-103 ◽  
Author(s):  
I. Bouwen ◽  
R. A. A. van der Vlugt
Keyword(s):  
Polymerase Chain Reaction Amplification ◽  
Natural Infection ◽  
Tobacco Rattle Virus ◽  
Chenopodium Quinoa ◽  
Flower Color ◽  
Systemic Vein ◽  
Leaf Chlorosis ◽  
Local Lesions ◽  
Funded Project ◽  
Reaction Amplification

During a survey for a European Union-funded project on viruses of Alstroemeria, two A. brasiliensis plants were found expressing virus-like symptoms, including leaf chlorosis with deep-green oval spots and flower color breaking. In enzyme-linked immunosorbent assays (ELISA), no positive reaction was obtained with antisera to Alstroemeria mosaic, Alstroemeria carla, Cucumber mosaic, Freesia mosaic, or Tobacco rattle virus or potyvirus-specific monoclonal antibodies (Agdia, Elkhart, IN). ELISA reactions were positive with antisera to Lily mottle (LMoV) and Rembrandt tulip breaking viruses (1). In electron microscopy preparations of A. brasiliensis, potyvirus-like particles were observed. Using sap-inoculation, the virus was transferred to a range of host species. Chenopodium quinoa, Nicotiana occidentalis accession 37B, and N. occidentalis subsp. obliqua (P1) expressed local lesions; N. clevelandii expressed local and systemic mottle; and N. benthamiana expressed local lesions, systemic vein yellowing, and leaf crinkling. Isolated total RNA from infected N. benthamiana was used for initial cDNA synthesis and polymerase chain reaction amplification with a potyvirus-specific primer set (2). The amplicon (≈670 bp) was cloned and sequenced. The sequence showed 92% homology with the corresponding region of LMoV RNA (GenBank accession no. S44147). The results confirm the infection of A. brasiliensis with LMoV. This is the first report of natural infection of Alstroemeria by LMoV. References: (1) E. L. Dekker et al. J. Gen. Virol. 74:881, 1993. (2) R. A. A. van der Vlugt et al. Phytopathology 89:148, 1999.

scholarly journals First Report of Tobacco rattle virus in Spinach in California

Plant Disease ◽  
2010 ◽  
Vol 94 (1) ◽  
pp. 125-125 ◽  
Author(s):  
S. T. Koike ◽  
T. Tian ◽  
H.-Y. Liu
Keyword(s):  
Sugar Beet ◽  
Spinacia Oleracea ◽  
Sandwich Elisa ◽  
Tobacco Rattle Virus ◽  
Chenopodium Quinoa ◽  
Mechanical Transmission ◽  
Rt Pcr ◽  
First Report ◽  
Local Lesions ◽  
Rigid Rod

In 2009 in coastal California (Santa Barbara County), commercially grown spinach (Spinacia oleracea) in two nearby fields exhibited symptoms of a previously unrecognized virus-like disease. Symptoms consisted of general chlorosis and bright yellow blotches and spots. Necrotic spots were also associated with the disease. In affected fields, disease occurred in limited, irregularly shaped patches that ranged from one to several meters in diameter. Symptomatic plants were unmarketable and these small patches of spinach were not harvested. With a transmission electron microscope, rigid, rod-shaped particles with a clear central canal were observed from plant sap of the symptomatic spinach. Analysis by a double-antibody sandwich-ELISA assay (Agdia Inc., Elkhart, IN) for Tobacco rattle virus (TRV) showed that the symptomatic plants were positive. Symptomatic spinach from the field was used for mechanical transmission to Chenopodium quinoa, C. murale, C. capitatum, spinach, and sugar beet (Beta vulgaris). All inoculated plants showed chlorotic local lesions and sugar beet showed chlorotic local lesions with rings. To further confirm the presence of TRV, reverse transcription (RT)-PCR was conducted. Total RNA was extracted from the mechanically inoculated symptomatic spinach plants using an RNeasy Plant Kit (Qiagen Inc., Valencia, CA) and used as a template in RT-PCR with forward (5′-TACATCACATCTGCCTGC-3′) and reverse (5′-CTTCATTCACACAACCCTTG-3′) primers specific to the movement protein gene from the spinach isolate of TRV (GenBank Accession No. AJ007294). Amplicons of the expected size (approximately 562 bp) were obtained. The RT-PCR products were sequenced (GenBank Accession No. GU002156) and compared with TRV sequences in GenBank to confirm the identity of the products. Sequences obtained had 96% nucleotide identity and 97% amino acid identity with TRV sequences available under the GenBank Accession Nos. FJ357571 and AJ007294. On the basis of the data from electron microscopy and serological and molecular analyses, the virus was identified as TRV. Soil samples collected from one of the fields were assayed for nematodes; however, Paratrichodorus or Trichodorus species were not recovered. To our knowledge, this is the first report of TRV in spinach in California. TRV has also been reported in spinach in England (1) and Germany (2). References: (1) A. Kurppa et al. Ann. Appl. Biol. 98:243, 1981. (2) K. Schmidt and R. Koenig. Arch. Virol. 144:503, 1999.

scholarly journals A New Ilarvirus Isolated from Grapevine in Greece

Plant Disease ◽  
2000 ◽  
Vol 84 (12) ◽  
pp. 1345-1345 ◽  
Author(s):  
S. M. Girgis ◽  
F. Bem ◽  
P. E. Kyriakopoulou ◽  
C. I. Dovas ◽  
A. P. Sklavounos ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Infected Plant ◽  
Chenopodium Quinoa ◽  
Tobacco Streak Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Streak Virus ◽  
Degenerate Primers ◽  
Severe Stunting ◽  
Local Lesions

In 1994, characteristic viruslike symptoms on grapevine were reported in the collection of the Grapevine Institute in Athens, Greece, on the hybrid Baresana × Baresana. The symptoms were sharp angular mosaic, leaf crinkle, and little leaf. The affected vines showed gradual decline and severe stunting or death. Such vines produced abortive flowers or very few berries with smaller, wrinkled, and nongerminating seeds. Serological testing, by enzyme-linked immunosorbent assay (ELISA), of the affected vines against the most common grapevine viruses Alfalfa mosaic, Arabis mosaic, Grapevine fanleaf, Grapevine fleck, Grapevine A, Rasberry ringspot, and grapevine leafroll-associated viruses gave negative results. A virus was isolated from affected grapevine young leaves by mechanical inoculation of Gomphrena globosa and single lesioned. The virus host range included G. globosa (local and systemic dark red or necrotic lesions), Chenopodium quinoa (necrotic local lesions and systemic mottle), and three tobacco cultivars (sharp necrotic local lesions, 1 to 3 mm in diameter). Pollination of C. quinoa with pollen from infected plant gave about 30% infected seedlings. The virus was purified from C. quinoa by differential centrifugation using 0.02 M phosphate buffer pH 8.0, containing 0.01 M DIECA and 0.01 M sodium thioglycolate as extraction buffers. In a purified preparation, quasisphaerical virus particles of about 29 nm were observed. Electrophoretic mobility of the viral coat protein showed a molecular weight of 30 kDa. Using purified preparations, an antiserum was obtained with a titer of 1:1024 in microprecipitin test and an optimum IgG dilution in ELISA of 1:10,000 for maximum absorption at OD405 nm Using degenerate primers designed from homologous regions in RNA-2 corresponding to a fragment of the polymerase gene of Ilarviruses, the expected 381-bp polymerase chain reaction product was obtained. This product was cloned and sequenced. Comparisons with sequence data from the homologous regions of RNA-2 of other known Ilarviruses, showed that the sequence of the above 381-bp amplicon shared 72% sequence similarity with Tobacco streak virus, 67% of Citrus variegation virus and Spinach latent virus, 66% of Asparagus virus 2 and Elm mottle virus, and 65% of Citrus leaf rugose virus. Based on the above data, it is concluded that the isolated virus is an Ilarvirus with closest similarity to Tobacco streak virus. From the relative bibliography (1–3) it appears that the virus reported here is different from Grapevine line pattern virus, a possible Ilarvirus, previously reported from Hungary. References: (1) J. Lehoczky et al. Kertgazdasag 19:61, 1987. (2) J. Lehoczky et al. Phytoparasitica 17:59, 1989. (3) J. Lehoczky et al. Phytopathol. Medit. 31:115, 1992.

scholarly journals Strain Characterization of Potato virus S Isolates from Tasmania, Australia

Plant Disease ◽  
2012 ◽  
Vol 96 (6) ◽  
pp. 813-819 ◽  
Author(s):  
Susan J. Lambert ◽  
Jason B. Scott ◽  
Sarah J. Pethybridge ◽  
Frank S. Hay
Keyword(s):  
Potato Virus ◽  
Chenopodium Quinoa ◽  
Protein Sequencing ◽  
Potato Seed ◽  
Serological Detection ◽  
Potato Virus S ◽  
Strain Characterization ◽  
Geographical Regions ◽  
Local Lesions

Potato virus S (PVS) is prevalent within potato (Solanum tuberosum) production worldwide. Traditionally, PVS has been split into two strains, Ordinary (PVSO) and Andean (PVSA), based on reaction in herbaceous indicator species such as Chenopodium quinoa. However, recent research has identified further strain designations, such as PVSO-CS (Ordinary and Chenopodium systemic). Forty-four isolates of PVS were collected from potato seed lines in different geographical regions within Tasmania, Australia. Isolates were initially characterized by reactions in C. quinoa. Nineteen isolates were characterized as PVSO, based on the development of local lesions and serological detection in inoculated leaves only. Three isolates were identified as PVSA-like, based on local lesion development in inoculated leaves, mild mottling or chlorotic spots on noninoculated leaves, and serological detection in both inoculated and noninoculated leaves. Thirteen isolates produced no symptoms, and were detected serologically in inoculated leaves only (PVSO-like). Four isolates produced no symptoms but were detected serologically in both inoculated and noninoculated leaves (PVSA-like). Five isolates produced symptoms in inoculated leaves only but were detected serologically in both inoculated and noninoculated leaves (also PVSA-like). The ability of isolates to infect tomato has also been used as a criterion to assist in PVS strain differentiation. A subsample of isolates (n = 16) was unable to infect tomato ‘Grosse Lisse’. Seventeen isolates representative of these groupings based on reactions in C. quinoa were also characterized by coat-protein sequencing. Phylogenetic comparisons suggested that all isolates were PVSO rather than PVSA. Therefore, whereas some of these PVS isolates were systemic in C. quinoa, findings from this study suggest that they were not PVSA, and that only PVSO and PVSO-CS isolates are present in Tasmania. The implications of this finding for disease management are discussed.

scholarly journals Genomic evidence for divergent co-infections of SARS-CoV-2 lineages

2021 ◽  
Author(s):  
Hang-Yu Zhou ◽  
Ye-Xiao Cheng ◽  
Lin Xu ◽  
Jia-Ying Li ◽  
Chen-Yue Tao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Rna Viruses ◽  
Average Rate ◽  
Genomic Analysis ◽  
Distribution Method ◽  
Reference Framework ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Recently, patients co-infected by two SARS-CoV-2 lineages have been sporadically reported. Concerns are raised because previous studies have demonstrated co-infection may contribute to the recombination of RNA viruses and cause severe clinic symptoms. In this study, we have estimated the compositional lineage(s), tendentiousness, and frequency of co-infection events in population from a large-scale genomic analysis for SARS-CoV-2 patients. SARS-CoV-2 lineage(s) infected in each sample have been recognized from the assignment of within-host site variations into lineage-defined feature variations by introducing a hypergeometric distribution method. Of all the 29,993 samples, 53 (~0.18%) co-infection events have been identified. Apart from 52 co-infections with two SARS-CoV-2 lineages, one sample with co-infections of three SARS-CoV-2 lineages was firstly identified. As expected, the co-infection events mainly happened in the regions where have co-existed more than two dominant SARS-CoV-2 lineages. However, co-infection of two sub-lineages in Delta lineage were detected as well. Our results provide a useful reference framework for the high throughput detecting of SARS-CoV-2 co-infection events in the Next Generation Sequencing (NGS) data. Although low in average rate, the co-infection events showed an increasing tendency with the increased diversity of SARS-CoV-2. And considering the large base of SARS-CoV-2 infections globally, co-infected patients would be a nonnegligible population. Thus, more clinical research is urgently needed on these patients.

scholarly journals First Report of Capsicum chlorosis virus Infecting Amaryllis and Blood Lily in Taiwan

Plant Disease ◽  
2009 ◽  
Vol 93 (12) ◽  
pp. 1346-1346 ◽  
Author(s):  
C. C. Chen ◽  
C. H. Huang ◽  
Y. H. Cheng ◽  
T. C. Chen ◽  
S. D. Yeh ◽  
...  
Keyword(s):  
Chenopodium Quinoa ◽  
Amino Acid Sequences ◽  
N Gene ◽  
First Report ◽  
N Protein ◽  
Calla Lily ◽  
Field Samples ◽  
Local Lesions ◽  
Plant Pathol ◽  
Capsicum Chlorosis Virus

Capsicum chlorosis virus (CaCV), a thrips-transmitted, tentative species in the genus Tospovirus, family Bunyaviridae, was first identified in solanaceous crops, but also infects several ornamental crops such as orchid (4), gloxinia (3), and calla lily (1). From 2005 to 2007, virus-like yellow ringspots were observed on the leaves of amaryllis (Hippeastrum hybridum Hort.) and blood lily (Haemanthus multiflorus Martyn.) plants cultured in screenhouses and a private garden, respectively. Three of several hundred amaryllis plants in screenhouses from two places were observed as showing yellow ringspot symptoms and one of six blood lily plants was observed as showing similar yellow ringspot symptoms. Sap extracts from symptomatic leaves were inoculated to Chenopodium quinoa Willd. and the resulting local lesions were passaged three successive times to C. quinoa for virus isolation. Using the tospovirus genus-specific primers gL3637 and gL4435c designed from the conserved region in the L RNA (2), DNA fragments of the expected size of 800 bp were amplified by reverse transcription (RT)-PCR from field samples and local lesions from C. quinoa. Extracts from the diseased plants and local lesions of C. quinoa reacted strongly with antiserum against the nucleocapsid (N) protein of CaCV in ELISA and western blotting. To confirm the identity of this virus, we amplified the N gene from three amaryllis and one blood lily source using primer pair WN2328 and WN3534 designed from the S RNA of Watermelon silver mottle virus (1), and these products were cloned and sequenced. The sequence from each virus isolate was determined from three independent clones. The nucleotide and deduced amino acid sequences of N genes for the blood lily isolate (GenBank Accession No. EF101344) and three amaryllis isolates (GenBank Accession Nos. EF101343, EF137177, and FJ185170) had identities greater than 97% with that of a CaCV isolate infecting Capsicum spp. found in Australia (GenBank Accession No. AY036057). Phylogenetic analysis using maximum parsimony showed that these sequences clustered with CaCV. These results show that the virus identified from amaryllis and blood lily that were expressing yellow ringspot symptoms are isolates of CaCV. To our knowledge, this is the first report of CaCV naturally infecting amaryllis and blood lily and it could become an important threat to ornamental production in Taiwan. References: (1) C. C. Chen et al. Plant Dis. 91:1201, 2007. (2) F. H. Chu et al. Phytopathology 91:361, 2001. (3) H. T. Hsu et al. J. Gen. Plant Pathol. 66:167, 2000. (4) Y. X. Zheng et al. Eur. J. Plant Pathol. 120:199, 2008.

scholarly journals Solanum americanum: reservoir for Potato virus Y and Cucumber mosaic virus in sweet pepper crops

2014 ◽  
Vol 40 (1) ◽  
pp. 78-80
Author(s):  
Monika Fecury Moura ◽  
Marcelo Soman ◽  
Tatiana Mituti ◽  
Marcelo Agenor Pavan ◽  
Renate Krause-Sakate
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Chenopodium Quinoa ◽  
Sweet Pepper ◽  
Virus Species ◽  
Black Nightshade ◽  
Local Lesions ◽  
Solanum Americanum

Weeds can act as important reservoirs for viruses. Solanum americanum (Black nightshade) is a common weed in Brazil and samples showing mosaic were collected from sweet pepper crops to verify the presence of viruses. One sample showed mixed infection between Cucumber mosaic virus (CMV) and Potato virus Y (PVY) and one sample showed simple infection by PVY. Both virus species were transmitted by plant extract and caused mosaic in tomato (Solanum lycopersicum cv. Santa Clara), sweet pepper (Capsicum annuum cv. Magda), Nicotiana benthamiana and N. tabaccum TNN, and local lesions on Chenopodium quinoa, C. murale and C. amaranticolor. The coat protein sequences for CMV and PVY found in S. americanum are phylogenetically more related to isolates from tomato. We conclude that S. americanum can act as a reservoir for different viruses during and between sweet pepper crop seasons.

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