scholarly journals The total number and mass of SARS-CoV-2 virions

2021 ◽  
Vol 118 (25) ◽  
pp. e2024815118
Author(s):  
Ron Sender ◽  
Yinon M. Bar-On ◽  
Shmuel Gleizer ◽  
Biana Bernshtein ◽  
Avi Flamholz ◽  
...  
Keyword(s):  
Time Course ◽  
Current Knowledge ◽  
Infected Individual ◽  
Infected Person ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Bodily Fluids ◽  
Viral Mutation ◽  
Global Pandemic ◽  
Host Tissues

Quantitatively describing the time course of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection within an infected individual is important for understanding the current global pandemic and possible ways to combat it. Here we integrate the best current knowledge about the typical viral load of SARS-CoV-2 in bodily fluids and host tissues to estimate the total number and mass of SARS-CoV-2 virions in an infected person. We estimate that each infected person carries 109 to 1011 virions during peak infection, with a total mass in the range of 1 μg to 100 μg, which curiously implies that all SARS-CoV-2 virions currently circulating within human hosts have a collective mass of only 0.1 kg to 10 kg. We combine our estimates with the available literature on host immune response and viral mutation rates to demonstrate how antibodies markedly outnumber the spike proteins, and the genetic diversity of virions in an infected host covers all possible single nucleotide substitutions.

scholarly journals The total number and mass of SARS-CoV-2 virions in an infected person

2020 ◽  
Author(s):  
Ron Sender ◽  
Yinon M. Bar-On ◽  
Avi Flamholz ◽  
Shmuel Gleizer ◽  
Biana Bernsthein ◽  
...  
Keyword(s):  
Time Course ◽  
Current Knowledge ◽  
Infected Individual ◽  
Absolute Number ◽  
Host Cells ◽  
System Response ◽  
Infected Person ◽  
Bodily Fluids ◽  
Global Pandemic ◽  
Immune System Response

Quantitatively describing the time course of the SARS-CoV-2 infection within an infected individual is important for understanding the current global pandemic and possible ways to combat it. Here we integrate the best current knowledge about the abundance of potential SARS-CoV-2 host cells and typical concentrations of virions in bodily fluids to estimate the total number and mass of SARS-CoV-2 virions in an infected person. We estimate that each infected person carries 109-1011 virions during peak infection, with a total mass of about 1 μg-0.1 mg, which curiously implies that all SARS-CoV-2 virions currently in the world have a mass of only 0.1-1 kg. Knowledge of the absolute number of virions in an infected individual can put into perspective parameters of the immune system response, minimal infectious doses and limits of detection in testing.

scholarly journals Rapid evolutionary dynamics of the Pepino mosaic virus – status and future perspectives

2016 ◽  
Vol 56 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Julia Minicka ◽  
Beata Hasiów-Jaroszewska ◽  
Natasza Borodynko-Filas ◽  
Henryk Pospieszny ◽  
Inge Maria Hanssen
Keyword(s):  
Mosaic Virus ◽  
Evolutionary Dynamics ◽  
Current Knowledge ◽  
Plant Protection ◽  
Diagnostic Tools ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Pepino Mosaic Virus ◽  
Worldwide Population ◽  
Protection Strategies

AbstractPepino mosaic virus (PepMV) has emerged as an important pathogen of greenhouse tomato crops and is currently distributed worldwide. Population genetic studies have revealed a shift in the dominant PepMV genotype from European (EU) to Chilean 2 (CH2) in North America and several European countries. New genetic variants are constantly being created by mutation and recombination events. Single nucleotide substitutions in different parts of the genome were found to affect on development of symptoms resulting in new pathotypes and accumulation of viral RNA. The variability of the PepMV population has a great impact on designing specific diagnostic tools and developing efficient and durable strategies of disease control. In this paper we review the current knowledge about the PepMV population, the evolutionary dynamics of this highly infective virus, methods for its detection and plant protection strategies.

scholarly journals Newly Emerging Airborne Pollutants: Current Knowledge of Health Impact of Micro and Nanoplastics

2021 ◽  
Vol 18 (6) ◽  
pp. 2997
Author(s):  
Alessio Facciolà ◽  
Giuseppa Visalli ◽  
Marianna Pruiti Ciarello ◽  
Angela Di Pietro
Keyword(s):  
Surface Area ◽  
Current Knowledge ◽  
Oxidative Degradation ◽  
Health Impact ◽  
Outdoor Exposure ◽  
Environmental Matrices ◽  
Potential Health ◽  
Bodily Fluids

Plastics are ubiquitous persistent pollutants, forming the most representative material of the Anthropocene. In the environment, they undergo wear and tear (i.e., mechanical fragmentation, and slow photo and thermo-oxidative degradation) forming secondary microplastics (MPs). Further fragmentation of primary and secondary MPs results in nanoplastics (NPs). To assess potential health damage due to human exposure to airborne MPs and NPs, we summarize the evidence collected to date that, however, has almost completely focused on monitoring and the effects of airborne MPs. Only in vivo and in vitro studies have assessed the toxicity of NPs, and a standardized method for their analysis in environmental matrices is still missing. The main sources of indoor and outdoor exposure to these pollutants include synthetic textile fibers, rubber tires, upholstery and household furniture, and landfills. Although both MPs and NPs can reach the alveolar surface, the latter can pass into the bloodstream, overcoming the pulmonary epithelial barrier. Despite the low reactivity, the number of surface area atoms per unit mass is high in MPs and NPs, greatly enhancing the surface area for chemical reactions with bodily fluids and tissue in direct contact. This is proven in polyvinyl chloride (PVC) and flock workers, who are prone to persistent inflammatory stimulation, leading to pulmonary fibrosis or even carcinogenesis.

Single Nucleotide Substitutions Effectively Block Cas9 and Allow for Scarless Genome Editing in Caenorhabditis elegans

2021 ◽  
Author(s):  
Jeffrey C Medley ◽  
Shilpa Hebbar ◽  
Joel T Sydzyik ◽  
Anna Y. Zinovyeva
Keyword(s):  
Caenorhabditis Elegans ◽  
Genome Editing ◽  
Dna Breaks ◽  
Nucleotide Substitutions ◽  
Paternal Genome ◽  
Single Nucleotide ◽  
C Elegans ◽  
Homology Directed Repair ◽  
Maternal Genome ◽  
Guide Sequence

In Caenorhabditis elegans, germline injection of Cas9 complexes is reliably used to achieve genome editing through homology-directed repair of Cas9-generated DNA breaks. To prevent Cas9 from targeting repaired DNA, additional blocking mutations are often incorporated into homologous repair templates. Cas9 can be blocked either by mutating the PAM sequence that is essential for Cas9 activity or by mutating the guide sequence that targets Cas9 to a specific genomic location. However, it is unclear how many nucleotides within the guide sequence should be mutated, since Cas9 can recognize off-target sequences that are imperfectly paired to its guide. In this study, we examined whether single-nucleotide substitutions within the guide sequence are sufficient to block Cas9 and allow for efficient genome editing. We show that a single mismatch within the guide sequence effectively blocks Cas9 and allows for recovery of edited animals. Surprisingly, we found that a low rate of edited animals can be recovered without introducing any blocking mutations, suggesting a temporal block to Cas9 activity in C. elegans. Furthermore, we show that the maternal genome of hermaphrodite animals is preferentially edited over the paternal genome. We demonstrate that maternally provided haplotypes can be selected using balancer chromosomes and propose a method of mutant isolation that greatly reduces screening efforts post-injection. Collectively, our findings expand the repertoire of genome editing strategies in C. elegans and demonstrate that extraneous blocking mutations are not required to recover edited animals when the desired mutation is located within the guide sequence.

Spatial perception changes associated with space flight: Implications for adaptation to altered inertial environments

2003 ◽  
Vol 13 (4-6) ◽  
pp. 331-343
Author(s):  
Donald E. Parker
Keyword(s):  
Time Course ◽  
Prolonged Exposure ◽  
Spatial Perception ◽  
Current Knowledge ◽  
Landing Site ◽  
Complete Understanding ◽  
Counter Measures ◽  
Ground Support ◽  
Site Evaluation ◽  
Adaptation Processes

Preparation for extended travel by astronauts within the Solar System, including a possible manned mission to Mars, requires more complete understanding of adaptation to altered inertial environments. Improved understanding is needed to support development and evaluation of interventions to facilitate adaptations during transitions between those environments. Travel to another planet escalates the adaptive challenge because astronauts will experience prolonged exposure to microgravity before encountering a novel gravitational environment. This challenge would have to be met without ground support at the landing site. Evaluation of current adaptive status as well as intervention efficacy can be performed using perceptual, eye movement and postural measures. Due to discrepancies of adaptation magnitude and time-course among these measures, complete understanding of adaptation processes, as well as intervention evaluation, requires examination of all three. Previous research and theory that provide models for comprehending adaptation to altered inertial environments are briefly examined. Reports from astronauts of selected pre- in- and postflight self-motion illusions are described. The currently controversial tilt-translation reinterpretation hypothesis is reviewed and possible resolutions to the controversy are proposed. Finally, based on apparent gaps in our current knowledge, further research is proposed to achieve a more complete understanding of adaptation as well as to develop effective counter-measures.

scholarly journals Patterns of Gene Expression Upon Infection of Soybean Plants by Phytophthora sojae

2004 ◽  
Vol 17 (10) ◽  
pp. 1051-1062 ◽  
Author(s):  
Pat Moy ◽  
Dinah Qutob ◽  
B. Patrick Chapman ◽  
Ian Atkinson ◽  
Mark Gijzen
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Phytophthora Sojae ◽  
Gene Microarray ◽  
Pathogenesis Related ◽  
Soybean Plants ◽  
Related Proteins ◽  
Phytoalexin Biosynthesis ◽  
Host Tissues ◽  
Mixed Samples

To investigate patterns of gene expression in soybean (Glycine max) and Phytophthora sojae during an infection time course, we constructed a 4,896-gene microarray of host and pathogen cDNA transcripts. Analysis of rRNA from soybean and P. sojae was used to estimate the ratio of host and pathogen RNA present in mixed samples. Large changes in this ratio occurred between 12 and 24 h after infection, reflecting the rapid growth and proliferation of the pathogen within host tissues. From the microarray analysis, soybean genes that were identified as strongly upregulated during infection included those encoding enzymes of phytoalexin biosynthesis and defense and pathogenesis-related proteins. Expression of these genes generally peaked at 24 h after infection. Selected lipoxygenases and peroxidases were among the most strongly downregulated soybean genes during the course of infection. The number of pathogen genes expressed during infection reached a maximum at 24 h. The results show that it is possible to use a single microarray to simultaneously probe gene expression in two interacting organisms. The patterns of gene expression we observed in soybean and P. sojae support the hypothesis that the pathogen transits from biotrophy to necrotrophy between 12 and 24 h after infection.

scholarly journals An exploration of ambigrammatic sequences in narnaviruses

2019 ◽  
Author(s):  
Joseph L. DeRisi ◽  
Greg Huber ◽  
Amy Kistler ◽  
Hanna Retallack ◽  
Michael Wilkinson ◽  
...  
Keyword(s):  
De Novo ◽  
Rna Viruses ◽  
Nucleotide Substitutions ◽  
Rna Dependent Rna Polymerase ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Reverse Complement ◽  
Positive Sense ◽  
Reverse Strand ◽  
Coding Strategy

ABSTRACTNarnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ∼ 3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The > 3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.

scholarly journals A Novel Distinct Genetic Variant of Tomato Torrado Virus with Substantially Shorter RNA1-Specific 3’untranslated Region (3’UTR)

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2454
Author(s):  
Marta Budziszewska ◽  
Przemysław Wieczorek
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Untranslated Region ◽  
Genetic Variant ◽  
Sequencing Data ◽  
Sequence Analyses ◽  
Nucleotide Substitutions ◽  
Systemic Necrosis ◽  
Single Nucleotide

Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates.

scholarly journals A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

2019 ◽  
pp. 1-5
Author(s):  
Svetlana Kovalchuk ◽  
Arina Tagmazyan ◽  
Eugene Klimov
Keyword(s):  
Nucleotide Substitution ◽  
Milk Proteins ◽  
Test System ◽  
Nucleotide Polymorphisms ◽  
Dna Testing ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Selection Of

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

scholarly journals Viral Mutation Rates

2010 ◽  
Vol 84 (19) ◽  
pp. 9733-9748 ◽  
Author(s):  
Rafael Sanjuán ◽  
Miguel R. Nebot ◽  
Nicola Chirico ◽  
Louis M. Mansky ◽  
Robert Belshaw
Keyword(s):  
Mutation Rate ◽  
Rna Viruses ◽  
Experimental Testing ◽  
Mutation Rates ◽  
Cell Infection ◽  
Nucleotide Substitutions ◽  
Data Set ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Viral Mutation

ABSTRACT Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10−8 to10−6 s/n/c for DNA viruses and from 10−6 to 10−4 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut .

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