scholarly journals Diminishing returns of inoculum size on the rate of a plant RNA virus evolution

2017 ◽  
Author(s):  
Rebeca Navarro ◽  
Silvia Ambrós ◽  
Fernando Martínez ◽  
Santiago F. Elena
Keyword(s):  
Evolutionary Biology ◽  
Rna Virus ◽  
Inoculum Size ◽  
The Novel ◽  
Clonal Interference ◽  
Rate Of Evolution ◽  
Rates Of Evolution ◽  
Diminishing Returns ◽  
Phenotypic Fitness ◽  
Asexual Populations

AbstractUnderstanding how genetic drift, mutation and selection interplay in determining the evolutionary fate of populations is one of the central questions of Evolutionary Biology. Theory predicts that by increasing the number of coexisting beneficial alleles in a population beyond some point does not necessarily translates into an acceleration in the rate of evolution. This diminishing-returns effect of beneficial genetic variability in microbial asexual populations is known as clonal interference. Clonal interference has been shown to operate in experimental populations of animal RNA viruses replicating in cell cultures. Here we carried out experiments to test whether a similar diminishing-returns of population size on the rate of adaptation exists for a plant RNA virus infecting real multicellular hosts. We have performed evolution experiments with tobacco etch potyvirus in two hosts, the natural and a novel one, at different inoculation sizes and estimated the rates of evolution for two phenotypic fitness-related traits. Firstly, we found that evolution proceeds faster in the novel than in the original host. Secondly, we found the predicted diminishing-returns effect of inoculum size on the rate of evolution for one of the fitness traits, but not for the other, which suggests that selection operates differently on each trait.

scholarly journals Diminishing returns of inoculum size on the rate of a plant RNA virus evolution

2017 ◽  
Vol 120 (3) ◽  
pp. 38001
Author(s):  
Rebeca Navarro ◽  
Silvia Ambrós ◽  
Fernando Martínez ◽  
Santiago F. Elena
Keyword(s):  
Rna Virus ◽  
Virus Evolution ◽  
Inoculum Size ◽  
Diminishing Returns

scholarly journals Speed of evolution in large asexual populations with diminishing returns

2015 ◽  
Vol 365 ◽  
pp. 23-31 ◽  
Author(s):  
Maria R. Fumagalli ◽  
Matteo Osella ◽  
Philippe Thomen ◽  
Francois Heslot ◽  
Marco Cosentino Lagomarsino
Keyword(s):  
Diminishing Returns ◽  
Speed Of Evolution ◽  
Asexual Populations

The life cycle and in silico elucidation of non-structural replicating proteins of HCV through a pharmacoinformatics approach

2021 ◽  
Vol 24 ◽  
Author(s):  
Rana Adnan Tahir ◽  
Sumera Mughal ◽  
Amina Nazir ◽  
Asma Noureen ◽  
Ayesha Jawad ◽  
...  
Keyword(s):  
Life Cycle ◽  
In Silico ◽  
Liver Diseases ◽  
Rna Virus ◽  
The Novel ◽  
Nonstructural Proteins ◽  
Drug Molecules ◽  
Liver Transplantations ◽  
Pharmacophore Generation ◽  
Approved Drugs

Background: Hepatitis C virus (HCV) is an enveloped and positive-stranded RNA virus that is a major causative agent of chronic liver diseases worldwide. HCV has become the main cause of liver transplantations and there is no effective drug for all hepatitis genotypes. Elucidation of life cycle and nonstructural proteins of HCV involved in viral replication are the attractive targets for the development of antiviral drugs. Methods: In this work, pharmacoinformatics approaches coupled with docking analyses were applied on HCV nonstructural proteins to identify the novel potential hits and HCV drugs. Molecular docking analyses were carried out on HCV approved drugs followed by the ligand-based pharmacophore generation to screen the antiviral libraries for novel potential hits. Results: Virtual screening technique has made known the top-ranked five novel compounds (ZINC00607900, ZINC03635748, ZINC03875543, ZINC04097464, and ZINC12503102) along with the least binding energy (-8.0 kcal/mol, -6.1 kcal/mol, -7.5 kcal/mol, -7.4 kcal/mol, and -7.3 kcal/mol respectively) and stability with non-structural proteins target. Conclusion: These promising hits exhibited better absorption and ADMET properties as compared to the selected drug molecules. These potential compounds extracted from in silico approach may be significant in drug design and development against Hepatitis and other liver diseases.

scholarly journals The Novel Agrotis ipsilon Nora Virus Confers Deleterious Effects to the Fitness of Spodoptera frugiperda (Lepidoptera: Noctuidae)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tong Li ◽  
Ruobing Guan ◽  
Yuqing Wu ◽  
Su Chen ◽  
Guohui Yuan ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
Rna Virus ◽  
Open Reading Frames ◽  
Agrotis Ipsilon ◽  
The Novel ◽  
Black Cutworm ◽  
A Genome ◽  
Nora Virus ◽  
Novel Host ◽  
Lepidoptera Noctuidae

In the present study, we identified a novel, positive-sense single-stranded RNA virus in the Chinese black cutworm, Agrotis ipsilon. It has a genome length of 11,312 nucleotides, excluding the poly(A) tails, and contains five open reading frames. The ORF2 encodes the conserved domains of RNA helicase and RNA-dependent RNA polymerase, while ORF4 and 5 encode three viral proteins. Herein, the A. ipsilon virus was clustered with a Helicoverpa armigera Nora virus and was thus provisionally named “Agrotis ipsilon Nora virus” (AINV). AINV was successfully transmitted into a novel host, Spodoptera frugiperda, through injection, causing a stable infection. This found the possibility of horizontal AINV transmission among moths belonging to the same taxonomic family. Nonetheless, AINV infection was deleterious to S. frugiperda and mainly mediated by antiviral and amino acid metabolism-related pathways. Furthermore, the infection significantly increased the S. frugiperda larval period but significantly reduced its moth eclosion rate. It suggests that AINV is probably to be a parasitic virus of S. frugiperda.

scholarly journals SARS-CoV-2 Isolation and Propagation from Turkish COVID-19 patients

2020 ◽  
Author(s):  
Cihan Tastan ◽  
Bulut Yurtsever ◽  
Gozde Sir ◽  
Derya Dilek Kancagi ◽  
Sevda Demir ◽  
...  
Keyword(s):  
Rna Virus ◽  
The Novel ◽  
Isolation And Characterization ◽  
Characterization Studies ◽  
Positive Strand Rna Virus ◽  
The Republic ◽  
Novel Coronavirus ◽  
Positive Strand Rna ◽  
Vaccine Testing ◽  
Republic Of Turkey

AbstractThe novel coronavirus pneumonia, which was named later as Coronavirus Disease 2019 (COVID-19), is caused by the Severe Acute Respiratory Syndrome Coronavirus 2, namely SARS-CoV-2. It is a positive-strand RNA virus that is the seventh coronavirus known to infect humans. The COVID-19 outbreak presents enormous challenges for global health behind the pandemic outbreak. The first diagnosed patient in Turkey has been reported by the Republic of Turkey Ministry of Health on March 11, 2020. Today, over ninety thousand cases in Turkey, and two million cases around the world have been declared. Due to the urgent need for vaccine and anti-viral drug, isolation of the virus is crucial. Here, we report one of the first isolation and characterization studies of SARS-CoV-2 from nasopharyngeal and oropharyngeal specimens of diagnosed patients in Turkey. This study provides an isolation and replication methodology, and cell culture tropism of the virus that will be available to the research communities.Article SummaryScientists have isolated virus from Turkish COVID-19 patients. The isolation, propagation, and plaque and immune response assays of the virus described here will serve in following drug discovery and vaccine testing.

scholarly journals Novel hepatitis D-like agents in vertebrates and invertebrates

2019 ◽  
Author(s):  
Wei-Shan Chang ◽  
John H.-O. Pettersson ◽  
Callum Le Lay ◽  
Mang Shi ◽  
Nathan Lo ◽  
...  
Keyword(s):  
Hepatitis Delta Virus ◽  
Evolutionary History ◽  
Rna Virus ◽  
Coiled Coil ◽  
The Novel ◽  
Leucine Zippers ◽  
Hepatitis Delta ◽  
Hepatitis D ◽  
B Virus ◽  
Delta Virus

Hepatitis delta virus (HDV) is the smallest known RNA virus and encodes a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly divergent HDV-like viruses are also present in fish, amphibians and invertebrates. Notably, the novel viruses identified here share HDV-like genomic features such as a small genome size of ~1.7kb in length, circular genomes, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human HDAgs. Notably, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV-HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the diversity and host range of HDV in non-human species, but shed light on its origin and evolutionary history.

scholarly journals Nora Virus VP4b and ORF1 Circulate in Hemolymph of Infected D. melanogaster with Coordinate Expression of Vago and Vir-1

Vaccines ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 491
Author(s):  
Amanda Macke ◽  
Wilfredo Lopez ◽  
Darby J. Carlson ◽  
Kimberly A. Carlson
Keyword(s):  
Rna Virus ◽  
Primary Site ◽  
The Novel ◽  
Qrt Pcr ◽  
Basal Expression ◽  
Virus Rna ◽  
Nora Virus ◽  
Candidate Target ◽  
The Brain ◽  
Insight Into

Study of the novel RNA virus, Nora virus, which is a persistent, picorna-like virus that replicates in the gut of Drosophila melanogaster offers insight into human innate immunity and other picorna-like viruses. Nora virus infection leads to a locomotor abnormality and upregulation of two candidate target proteins, Vago and Virus-induced RNA 1 (Vir-1). These proteins are uncharacterized in response to Nora virus. We hypothesize that Nora virus is circulating in the hemolymph of Nora virus-infected D. melanogaster, allowing for migration beyond the primary site of replication in the gut. Analysis by qRT-PCR demonstrated biphasic viral load and corresponding vago and vir-1 transcription levels, suggesting transcription of vago and vir-1 occurs in response to viral infection. However, Vir-1 is also present in virus-free D. melanogaster suggesting basal expression or alternative functions. Presence of Nora virus RNA and the Viral Protein 4b (VP4b), in hemolymph of infected D. melanogaster supports the hypothesized circulation of Nora virus in the hemolymph. The study suggests that impaired locomotor function may be due to transport of Nora virus from the gut to the brain via the hemolymph.

scholarly journals A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1120
Author(s):  
Chantelle Hooper ◽  
Partho P. Debnath ◽  
Sukumar Biswas ◽  
Ronny van Aerle ◽  
Kelly S. Bateman ◽  
...  
Keyword(s):  
Virus Assembly ◽  
Rna Virus ◽  
Macrobrachium Rosenbergii ◽  
Freshwater Prawn ◽  
The Novel ◽  
Protein Motifs ◽  
Giant Freshwater Prawn ◽  
Yellow Head Virus ◽  
Novel Virus ◽  
Mass Mortalities

Mass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of Macrobrachium rosenbergii golda virus (MrGV) suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture.

scholarly journals Does Asymmetrical Gonopodium Morphology Predict Lateralized Behavior in the Fish Xenophallus umbratilis?

2020 ◽  
Vol 8 ◽  
Author(s):  
Erik S. Johnson ◽  
Mary-Elise Nielsen ◽  
Jerald B. Johnson
Keyword(s):  
Decision Making ◽  
Evolutionary Biology ◽  
Morphological Traits ◽  
Costa Rican ◽  
The Novel ◽  
Mating Preferences ◽  
Novel Object ◽  
Symmetrical Body ◽  
Livebearing Fish ◽  
And Behavior

Why bilaterally symmetrical organisms express handedness remains an important question in evolutionary biology. In some species, anatomical asymmetries have evolved that accompany behavioral handedness, yet we know remarkably little about causal links between asymmetric morphological traits and behavior. Here, we explore if a dextral or sinistral orientation of the male intromittent organ predicts side preferences in male behaviors. Our study addresses this question in the Costa Rican livebearing fish, Xenophallus umbratilis. This fish has a bilaterally symmetrical body plan, with one exception—the male anal fin (gonopodium), used to inseminate females, terminates with a distinct left- or right-handed corkscrew morphology. We used a detour assay to test males for side biases in approach behavior when exposed to four different stimuli (predator, potential mate, novel object, empty tank control). We found that left morph males preferred using their right eye to view potential mates, predators, and the control, and that right morph males preferred to use their left eye to view potential mates and predators, and their right eye to view the control. Males of both morphs displayed no eye bias when approaching the novel object. Our results suggest that there is a strong link between behavior and gonopodium orientation, with right and left morph males responding with opposite directional behaviors when presented with the same stimuli. This presents the intriguing possibility that mating preferences—in this case constrained by gonopodial morphology—could be driving lateralized decision making in a variety of non-mating behaviors.

scholarly journals NOVEL CORONAVIRUS (2019-nCoV): DISEASE BRIEFINGS

2020 ◽  
pp. 22-27
Author(s):  
KANAAN AL-TAMEEMI ◽  
RAIAAN KABAKLI
Keyword(s):  
Public Health ◽  
Potential Risk ◽  
Rna Virus ◽  
Viral Pneumonia ◽  
The Novel ◽  
Strategic Objectives ◽  
Positive Sense ◽  
Novel Coronavirus

Coronavirus (CoV) (2019‐nCoV) is a large, enveloped, positive-sense, single-stranded RNA virus. The abnormal outbreak of 2019‐nCoV in Wuhan warns of the risk of CoV (2019‐nCoV) to public health which causes viral pneumonia outbreak. In our review, we will discuss the biology of CoVs and the potential risk of the novel CoV (2019‐nCoV) and guide us to strategic objectives for controlling the virus.

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