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Could someone suggest some societies/organizations etc., that fund laboratory projects in Microbiology/Infectious Diseases/Virology? I am looking for funding of a minimum of 100,000 EUR over 1-2 years.
Any suggestions would be appreciated :) Thank you in advance.
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Your title is a broad one so first put clear title project then search for projects agree with your desire and fullfill needs of funding country,institutes andcompanies
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Hi there,
after scooping the known models, would like to learn more of the impact of:
-temperature
-humidity
on the CO₂ air quality indoors with all other input factors fixed.
Is its impact calculus or are there jump diffusions and reverse changing patterns in the impact on indoor air quality?
Cherish your feedback.
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Hi there,
would like to learn more about the African Swine Fever Virus. Any recommended updated research. Cherish your insights.
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African Swine Fever (ASF) is a highly contagious and deadly swine disease that can affect both farm-raised and feral (wild) pigs. ASF doesn’t infect people, but it is readily passed from one pig to another by direct contact with bodily fluids from an infected pig. The practice of feeding uncooked food waste (that has not been appropriately heat treated) to pigs can also result in transmission of the virus if the food waste being fed to pigs contains contaminated pork products.
African Swine Fever | FDA
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Hi,
I wonder if anyone knows how to use sample release reagent from Sansure Biotech ?
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Hi,
The supplier claims that their "sample release reagent" (nucleic acid release technology), can lyse pathogens at room temperature very fast, with no need to heating, centrifuging or replacing tubes, the sample DNA/RNA can be extracted quickly through simple operations. The reagent is applied for the pretreatment of nucleic acid molecules, to release them from specimens, then the released nucleic acids can be used for clinical in vitro diagnosis or for the detection through appropriate apparatus.
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Where can I find Monkeypox sequences collected in the recent scattered outbreak, I am aware that NCBI has some sequences posted. but is there any database specificely concerned with Monkeypox
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Hello everyone,
I hope this message finds you doing well.
​I am writing to ask you a significant question about whole-virus ELISA and its procedure.
Honestly, it seems that coating a microplate with viruses is not as convenient as some papers mentioned, especially when high accuracy is needed. Now, my question is, is there any particular procedure in order to enhance the efficiency of the coating? For instance, what would we do if we tended to expose viral protein to the microplate better than before, based on your experience?
Thank you
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Use Carbonate bicarbonate buffer pH 9.6
Composed of:
1.59gm Na carbonate
2.9gm Na bicarbonate
In 1000ml DDW
addrd 1:1 to the diluted virus and incubate it at 4°C overnight and then washed
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We are hunting around for the related information about the following conclusion:
  • The 1890s were a watershed in virology, when Russian microbiologist Dmitri Ivanovski (alternative spelling Dmitrii Iwanowski or Dmitry Iwanowski or Dimitri Ivanovski or Dmitri Iwanovsky or Dmitrij Ivanovskij)(Russian: Дми́трий Ио́сифович Ивано́вский)(1864–1920) isolated the tobacco mosaic virus in 1892 and reported it to the Imperial Academy of Sciences in St. Petersburg1.
Q1: What exactly is the correct spelling?
There are at least 10 different English spellings of his name. In Ref. 2, on p. 755, the editors spelled the Russian scientist’s name as Dimitri Ivanovski2. However, most authors spelled his name as Dmitri Ivanovski in their literature3, whereas many others spelled his name as Dmitri Iwanovsky in English textbooks and documents.
Q2: What is the most accurate description of his identity?
In the same vein, he was described as a scientist/microbiologist/botanist/virologist in different documents. Which one is the best?
Q3: We need the pertinent reference of 1892.
As the Editorial (Ref. 2) remarked, “some notable achievements in microbiology have gone unrewarded by the Nobel committee.” I think, the isolation of the tobacco mosaic virus in 1892 should be a notable achievement in virology. Embarrassingly, the authors barely care about the original reference or document when recounting the ‘trivial story’.
We need help to check the information about the original reference:
  • Von Dm. Iwanowsky. Über die Mosaikkrankheit der Tabakspflanze. Bulletin Scientifique Publié Par l'Académie Impériale des Sciences de Saint-Pétersbourg. 35: 67–70 (1892).
It would be appreciated if anyone could provide the original document.
References:
1. Iwanowsky, D. V. Über die Mosaikkrankheit der Tabakspflanze (Concerning the mosaic disease of the tobacco plant). Bull. l’Académie impériale des Sci. Saint-pétersbg. 35, 67–70 (1892).
2. Editorial. A Nobel endeavour. Nat. Rev. Microbiol. 8, 755–755 (2010).
3. Lechevalier, H. Dmitri Iosifovich Ivanovski (1864-1920). Bacteriol. Rev. 36, 135–145 (1972).
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Totally agree with my colleaques suggestions
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Hi there,
looking for research about Covid transmissibility in ponds.Cherish your valued expertise.
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Hello, I work at a virology lab in Mexico and we are currently facing a pretty heavy contamination with mycoplasma on our cell cultures, thus we would be really thankful if, as the question says, you coud share some recommendations, tips or even protocols for cleaning and disinfecting incubators, biosafety cabinets and other surfaces. Thanks for your time!
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Paulina,
The recommendations for using 70% ethanol is excellent and it is effective; however, one must always keep in mind that it comes with many warnings:
: H225 - Highly flammable liquid and vapor H350 - May cause cancer
: P201 - Obtain special instructions before use P202 - Do not handle until all safety precautions have been read and understood P210 - Keep away from sparks/open flames. - No smoking P233 - Keep container tightly closed P240 - Ground/bond container and receiving equipment P241 - Use explosion-proof electrical/lighting equipment P242 - Use only non-sparking tools P243 - Take precautionary measures against static discharge P280 - Wear eye protection, protective clothing, protective gloves P303+P361+P353 - IF ON SKIN (or hair): Remove/Take off immediately all contaminated clothing. Rinse skin with water/shower P308+P313 - IF exposed or concerned: Get medical advice/attention P370+P378 - In case of fire: Use water spray for extinction P403+P235 - Store in a well-ventilated place. Keep cool P405 - Store locked up P501 - Dispose of contents/container to Collect all waste in suitable and labeled containers and dispose according to authorities having jurisdiction.
A safer disinfectant to use would be sodium hydroxide (NaOH) at a 0.8% concentration (8,000 ppm). It is not flammable. Of course, PPE should always be used.
I would suggest that you use high quality Healthcare Grade Ultra Microfiber wipers that are 12" x 12" (30.5 cm x 30.5 cm) and 36 grams per square meter (GSM). This type of wiper will provide a 7-log10 reduction of microorganisms and dis compatible with NaOH. The wiper can then be commercially laundered. If you choose to use a disposable microfiber wiper, select one that is approximately 12" x 12" (30.5 cm x 30.5 cm) and a high gram weight (12-17 grams per wipe) as that prevents the wipe from being too unwieldy yet provides sufficient bulk to hold sufficient disinfectant to be effective not not flood the surface being cleaned. Remember, NaOH is a cleaner, not a disinfectant, so it is important to use a wiper that provides the highest log reduction with the proper trap, capture, and removal properties.
Finally, with regards to using HEPA filters, I would suggest a filtration system with nano filtration capabilities and UV-C disinfection for the filtration chamber, as well as the filter. It is essential that mycoplasma be removed before it has an opportunity to form a biofilm, and email viable, at which time it is more difficult to remove and destroy. However, the recommended Healthcare Grade Ultra Microfiber will remove biofilm. Due to the production of biofilm, I would suggest replacing the filtration medium much more often that every six months if HEPA filtration is the only filtration method in use.
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Reassortment is the result of segmentation phenomena, but why do some RNA viruses develope segmentation, not all RNA but especially groups of them with consideration of the segment number variation?
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Epstein-Barr seems like one of the most successful viruses in history given that it infects a species that numbers in the billions and lives for about 70 years, and can remain with the host for life.
That said, what properties of EBV prevent it from infecting other species but allow it to target humans so effectively?
For instance, why doesn't EBV infect mice, who share a similar genome to humans?
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at present the only non-human species which can be infected with EBV is Cotton-top tamarin. Immortalized cell line from this species (B95-8) was used since 1980-s in EBV research. This is one of the few cell lines which also produces infectious virus in 2-4% of the cell population therefore it was used for virus production in research studies.
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Couldn't find any fresh publications explaining this. Also nobody usually says what strand encodes all ORFs of HBV.
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HBV genome (DNA) is organized in a highly condensed manner and all the genes are encoded within four partially overlapping open reading frames (ORFs), namely as; S (surface), C (core), P (polymerase) and X (X protein) and include 7 proteins: HBcAg, HBeAg, HBx, polymerase (pol) and the three different sizes HBsAg- the small (S), medium (M) and large (L) proteins.
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How does circular DNA benefit Epstein-Barr virus (EBV)?
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EBV circular DNA benefit establishing latent infection and long _term persistance for viral genome.the also the circular DNA infected cells may well be ignored by the immune system.the attached ref.illustrate all the request:
Annual Rview of Virology.Vol.3:359_372
Epsten_Barr virus is another herpes simplex 1
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I'm curious to learn more about virus detection.
What are reliable methods for detecting viruses inside a host?
If a virus integrates into the host genome, if given a viral sequence, is analyzing the host genome for matches reliable? In other words, is it impossible for viral genomes to change before attaching to the host genome?
If a virus doesn't integrate, is scanning for viral proteins sufficient? Presumably scanning for viral sequences is not possible as the viral genome is not exposed?
Put another way, what evasion mechanisms do viruses deploy to avoid detection?
Thanks in advance for your help!
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Kindly check the following RG link that discusses commonly used techniques for the detection and diagnosis of viruses in clinical samples.
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My understanding is that proving causation between pathogen and disease requires satisfying Koch's postulates (https://en.wikipedia.org/wiki/Koch%27s_postulates).
It is accepted that the varicella-zoster virus causes chicken pox and shingles, yet the shingles causal relationship violates the first postulate: not everyone with the virus develops shingles.
Could someone kindly explain how researchers proved the causal relationship between varicella-zoster and shingles?
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The non-uniformity of shingles occurrence does not violate Koch's first postulate since all patients with shingles exhibit active VZV. The converse (All VZV infections must cause shingles) is not necessarily required by the first postulate or even the third postulate. You can find several good examples of why the postulates still hold true for shingles/VZV in the paragraph below the list on that Wikipedia page you linked.
Causality can be established using several tests for VZV during a shingles episode including checking for anti-VZV antibodies from blood and PCR for VZV directly from shingles blisters. (https://en.wikipedia.org/wiki/Shingles#Diagnosis)
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Particularly in the context of infecting humans, what advantages would DNA viruses have over RNA viruses or vice versa?
Is it accurate to say that DNA viruses are more more dangerous because larger genomes can encode more viral proteins, allowing for more countermeasures and redundancies against host defense systems while also producing more complex proteins capable of sophisticated exploitation of host cell metabolism?
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Dear Clarence,
The most obvious advantage is the larger genome. Unlike RNA polymerases (I mention the majority of the enzymes excluding the polymerases of the order Nidovirales), DNA polymerases have proofreading activity. Consequently, the mutation rate for DNA viruses is at least 10-100 times lower than for RNA viruses. For RNA viruses, it is almost impossible to construct the genome exceeding 10 000 nucleotides. That means that RNA viruses are usually limited by 10 proteins (it is not so simple to override cellular defensive mechanisms, orchestrate your own reproduction and escape the immune system if you only have a several, or even a couple, of non-structural proteins). Double-stranded DNA viruses usually have about 100 000 nucleotides genomes, and some of them have reached even more that 2 million nucleotides (Pandoraviruses). The larger genome allows encoding the larger number of non-structural proteins. For example, herpesviruses, the typical double-stranded DNA viruses, encode from 70 to 200 proteins.
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Egypt has the highest prevalence of HCV. What is the major risk factor or history behind it?
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I have experience in phylogenetic analysis, but not virology. I would like to develop a substitution model for the mutations that occur in SARS-CoV-2, and would like feedback from virologists. A substitution model provides values for the 12 mutation rates A->C, A->G, ..., T->G at a particular site. There are lots of substitution models used in phylogenetic analysis, from the simplest Jukes-Cantor model, which says all 12 rates are equal, to one with 12 individual rates, and more complicated ones still, which take into account neighbouring nucleotides.
Here are some observed values:
A C G T
A - 52 308 68
C 58 - 18 1098
G 255 46 - 437
T 56 327 52 -
These may be mutations produced by the virus, or by host editing, and there are sequencing errors which can confuse matters. Note the large number of C->Ts and G->Ts, and high C->T/G->A and G->T/C->A ratios.
Please correct me if I am wrong, but this is how I understand the mechanisms within a cell:
Virus-mediated mutations. If the polymerase mismatches a pair like G:T instead of G:C, at a certain rate, it will do this when copying positive sense to negative sense, and negative to positive, at the same rate. (If not, why not?) Every virus genome that exits a cell must be the result of an equal number of positive-to-negative and negative-to-positive copies. This implies a symmetry among the rates like this:
A->C ~= T->G
A->G ~= T->C
A->T ~= T->A
C->A ~= G->T
C->G ~= G->C
C->T ~= G->A
For example,
C mispaired with A, A correctly paired with T produces a C->T.
G correctly paired with C, C mispaired with A produces a G->A.
Host-mediated mutations. (See refs below.) These do not have to obey the above symmetry, if they act preferentially on positive or negative sense RNA. The APOBEC proteins can cause a C->T mutations, but that would produce as many G->A mutations as C->T mutations if it acted on positive or negative sense RNA equally. So it seems it must mainly act on positive sense RNA. What would be the most likely reason for this? (I can think of various ideas, but don't know how plausible they are.)
Are there any known mechanisms (virus or host) which can produce more G->T mutations than C->A mutations?
RG project:
References:
The divergence between SARS-CoV-2 and RaTG13 might be overestimated due to the extensive RNA modification,
Yue Li, Xinai Yang, Na Wang, Haiyan Wang, Bin Yin, Xiaoping Yang& Wenqing Jiang.
Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2,
Salvatore Di Giorgio, Filippo Martignano, Maria Gabriella Torcia, Giorgio Mattiuz, Silvestro G. Conticello.
Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design,
Alan M Rice, Atahualpa Castillo Morales, Alexander T Ho, Christine Mordstein, Stefanie Mühlhausen, Samir Watson, Laura Cano, Bethan Young, Grzegorz Kudla, Laurence D. Hurst.
Rampant C to U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories,
Peter Simmonds.
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I know that Shi et al 2016 inferred hosts for novel RNA virus genomes by searching their genes across cellular genome databases, so linking them with endogenous virus elements (EVEs).
Are you aware of other methods infer hosts for RNA virus contigs?
Thank you,
Guillermo
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The answer is found in the results of this study:
Nat Commun. 2017; 8: 16054.
Published online 2017 Jun 28. doi: 10.1038/ncomms16054
PMCID: PMC5493757
PMID: 28656958
Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics
Mohammad Moniruzzaman,1 Louie L. Wurch,2 Harriet Alexander,3 Sonya T. Dyhrman,3 Christopher J. Gobler,4 and Steven W. Wilhelm
we examined metatranscriptomes from two highly productive sites on the east coast of USA—Quantuck Bay, New York, and Narragansett Bay, Rhode Island. Quantuck Bay experiences recurring ecosystem disruptive brown tide blooms caused by the pelagophyte A. anophagefferens16, which are shaped by a giant virus (AaV)7,17. Narragansett Bay is a highly productive system with seasonal diatom blooms, but a poorly described eukaryotic virus community. By employing selection for polyadenylation before sequencing, we were able to focus on active virus infections within eukaryotes. Using time-series data, we captured emergent relationships of putative virus–host pairings and their ecological dynamics. This approach also allowed us to characterize viruses with diverse nucleic acid genomes actively infecting eukaryotes. The results show that this approach could both confirm known virus–host infections (including the infection of Aureococcus by AaV) as well as identify novel virus–host interactions. These observations demonstrate that the depth of virus–host interaction in the global oceans is likely much deeper than previously anticipated, with viruses containing all forms of genetic material potentially infecting single-celled eukaryotes.
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Since temperate phages would not produce bacteria lysis, thus it can't be used in phage typing. So how to determine the hosts for temperate phages?
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Pierre Béguin is correct that temperate phages still produce plaques. Therefore determining the host for a temperate phage is no different than determining a host for a lytic phage, does it form plaques (or lyse) the host.
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I have a problem with gateway technology and LR reaction.
I Perform LR reaction with various vector concentrations but the reaction is not carryout. I  did check LR enzyme and this enzyme worked good (with control PENTR-lacZ in kit).
Various vector concentrations:
1. pad/v5/dest vector: 150 ng, pentr11/gene containing: 150 ng: total volume: 10µl
2. pad/v5/dest vector: 150 ng, pentr11/gene containing: 100 ng: total volume: 10µl
3. pad/v5/dest vector: 150 ng, pentr11/gene containing: 75 ng: total volume: 10µl
4. pad/v5/dest vector: 50ng, pentr11/gene containing: 25 ng: total volume: 5µl
PAD5/V5/DEST vector length: 36686 bp
PENTR11/GENE containing: 6.7 kb
What is your recommendation?
Please help me
Thanks
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Try with equimolar concentration of Dest vector and shuttle vector. Hope you know the formula for that.
And also, If you are relying on spectrophotometer/qubit to quantify your DNA, try to run your insert DNA on gel and estimate the DNA concentration using a molecular weight marker (gene ruler). That is because the reading from machines are sometimes not accurate and LR or BP reactions require appropriate reaction mixture to work. Hope this helps. Reply me if you need more help. Thanks!
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The motivation behind this question is to understand how researchers discover new retrotransposons in humans?
Thanks in advance for the help.
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Searching the sequenced genome is the best start before moving into wet lab work. Different software/approach are scattered around in literature.
Here is a good start:
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I'm looking for published or unpublished papers.
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Is anyone aware of a scientific answer, specifically what type of biochemical or biophysical triggers can trigger activation?
Thanks.
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endogenous retrovirus comprises up to 5–8% of the human genome, it is vertically inherited.
The majority of ERVs that occur in vertebrate genomes are ancient, inactivated by mutation, and have reached genetic fixation in their host species. For these reasons, they are extremely unlikely to have negative effects on their hosts except under unusual circumstances such as (people with schizophrenia), therefore we can suggest that some Neurological disorders lead to activation ERV
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Stability of SARS-CoV-2 varies in different body secretions, environmental conditions and surfaces. However, it is crucial to understand the viability of SARS-CoV-2 in the respiratory or GI tract for successful postmortem specimen collection.
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Vertigo is a condition that can make it feel like you or your surroundings are spinning, sometimes leading to a loss of balance, according to the U.S. National Library of Medicine.
Coronavirus 2019 or COVID-19 is a novel entity which had led to many challenges among physicians due to its rapidly evolving nature. Vertigo or dizziness has recently been described as a clinical manifestation of COVID-19.
So, Are dizziness and vertigo COVID-19 Symptoms? and why?
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First, I am not an expert in the field of Virology. Viruses manipulates host cell's translation mechanism to replicate. And also it is known that most of the plant species protects themselves against viral infection by global translational repression. Could we adopt this strategy of plants to control viral outbreaks????
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It may be easy to control viral infections attributed to DNA viruses but not RNA viruses. Its a 50/50 thing!
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hi everyone !
we are doing a Stability test of our virus by Particle Stability Thermal Release Assay (PaSTRy). We purified the virus by Optiprep gradient. To do the PASTRY assay we put 1 μg of virus and 4 μL of SYTO9 green 20X and we add PBS until 20 μL. Afterwards we heat it by Qpcr from 25 until 95 celsius degree. We should basically obtain a pic for the RNA release, but what we have obtained is very weird and we can't find an explanation (cf figure attached). we did the basic control like the dye with the buffer, optiprep with dye etc... to see the autofluorescence but all results were negative. we don't understand what could produce this hight fluorescence directly in the beginning. Thanks you very much for your futur answers !
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Just to add on as based on my experience, this could due to there i abundant free RNA outside the virus capsid, and therefore the dye will bind to these free RNA and give high background fluorescence. It comes with your sample and thats why you wont see this is neg ctrl.
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May be it will sound anecdotal, but in my country, during an outbreak of chikungunya, we have seen the lowest incidence of dengue and vice versa.
May be some ascertainment issue, may be prioritizing issues, I am not sure. But I am more interested to find out from virologic or ecological view point for an explanation it. Thanks
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In fact, such cases are observed epidemiologically, as with the spread of the Corona pandemic, epidemic influenza infections have decreased significantly...This may be due to the reasons for isolation, social distancing, wearing masks, and other health guidelines that have been applied to maintain public health, in addition to people's generally trying to maintain a healthy diet to strengthen the body's immunity. All these and other factors have affected the spread of influenza.
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The US Government Comparative Toxicogenomics database shows that Fluoride can inhibit Human immunity to viruses and pneumonia. Angiotensin I-Converting Enzyme (ACE), 2'-5'-Oligoadenylate Synthetase 1 (OAS1) and Intercellular Adhesion Molecule 1 (ICAM1) are included as susceptible epigenetic targets of the poison.
Wuhan is an area with high Fluoride exposure from atmospheric and groundwater pollution.
Are there more studies linking virus outbreaks or mutations with Fluoride?
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I recently received advice from a researcher in India stating that 9 of the 10 most severely COVID19 affected areas also suffer from endemic Fluorosis.
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RNA vaccines follow a different strategy, without using any "real" component of the virus at all. Instead, researchers aim to trick the human body into producing a specific virus component on its own. Since only this specific component is built, no complete virus can assemble itself. Nevertheless, the immune system learns to recognize the non-human components and trigger a defense reaction. So May I ask, What are your opinions about the safety and efficacy of the BNT162b2 mRNA Covid-19 Vaccine?
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I'm trying to implement a real-time RT-PCR protocol in our virology lab. I have a cell-culture virus isolate, which I intent to use as a positive control for the experiments. My question is should I dilute the isolate? I don't know the exact viral RNA quantity after extraction. Without dilution this isolate give a strong positive signal at Ct values about 17-20. However, it is known that in samples (environmental or faecal) the concentration of viruses of interest would be lower. Please help?
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Dear colleaque,all samples are tested in duplicate wells.include several"No RNA" negative controls(NTC) by adding water instead of any RNA including a positive control.
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Hi all,
As long as I know, DEAE Dextran can mediate the delivery of nucleic acid into mammalian cells during transfection process. Can DEAE Dextran also mediate the delivery/internalization of the whole virus (not only it's genetic material) to mammalian cells?
Thank you for your answer.
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Maybe. (but if you infect with the genetic material you could obtain virus?...)
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As yet, no one has found the animal that gave people Covid-19. The Center for Disease Control (CDC) points out that at this time, there is no evidence that animals play a significant role in spreading SARS-CoV-2, the virus that causes COVID-19, to people.
SARS-CoV-2 is unprecedented in its combined characteristics: its long period of asymptomatic infection, high transmissibility, significant lethality in high-risk populations, being well-adapted to human cells since its emergence, and having the ability to hijack human innate immunity and bind with high affinity to the human ACE2 receptor.
The reason why we should try hard to figure out the origin of Covid-19 is to inform our efforts to prevent another pandemic like this from happening again. This one was an unfortunate and terrible accident. We should badly want to avoid a second occurrence. We can be blamed for allowing a second one like it if we do not work together soon to find the origin. Right now it appears likely it came directly or indirectly from bats. But specifics would better help us to avoid a second pandemic disaster. Furthermore time is not our friend in finding the origin and sooner is better before information is lost. We need all countries to support a real epidemiological investigation by an unbiased team of scientists given access and authority to take the investigation where ever it leads – possibly to patient zero or to the CoV-2 animal source.
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Also, have a look at this useful link.
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There are different types of treatments/therapies practiced for curing/controlling a disease involving several medicines. Can all or some of these medicines be termed vaccines? How is a vaccine for a specific disease different from large number of other medicines being used to treat the same disease? What are the features expected to be possessed by a vaccine?
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Please allow me to ask a complementary question:
An intrant with the features described about, is it still considered as a vaccine if the features are significantly different depending to groups of people such as gender?...
or
is there a level in these features below which an intrant is not considered a vaccine any longer?
I am looking forward to reading inputs from experts as well.
With my compliments
GH
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From what I can see, many virology studies use SK-N-SH whereas neuroscience studies use SH-SY5Y. I would like to know the differences between the cell lines and their suitability for which types of study.
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Dear Jeremy!
Please You look at the following article:
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That vaccines have been produced in such a short time, makes me doubt if they will help fight this pandemic and if they will not do us more harm.
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Yes, the preliminary results coming from mass vaccination drive in Israel are very encouraging.
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For animals vaccine.
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please, anyone has idea about the optimal parameter for cultivation of BHK cells in Bioreactor ( Agitation, DO, CO2 and PH).
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The coronavirus pandemic has brought the world to a grinding halt and no doubt has altered the lives of each one of us. I think COVID-19 also has an impact on our normal research (i.e. related to our relevant field) and diverted us to work on various aspects of coronavirus to help combat the virus.
What's your opinion in this regard?
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I agree. My routine research into the environmental epidemiology of waterborne disease, and my preferred research into alcohol policy and climate policy, have been largely pushed aside in favour of research into the geospatial epidemiology of covid-19.
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HI Everyone!
I am asking to know by you, expert in cybersecurity and mathematics, if Computer virology (the one of Cohen and Andler) is still an active field of research. That research made in France at Inria at 2000-2010 . I do not see any prosecutor and I do not understand if this is a dead branch or not. I am interested in it in order to understand malware and detect behavior.
Thank you very much for your precious help!
Bye
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I'm looking for some adenoviruses which have diameters of <40 nm (not including the fibers, which can be removed). If you know of any adenoviruses fitting this description, please list them in your answer! (Note: *not* AAVs). Thanks!
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Hi Logan
My understanding (memory going back a long way in time now) is that the capsid dimensions exclude the spikes. As far as I know, all strains of Ad have capsids within the range of 70 - 100 nm.
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Hi y'all!
I'm troubleshooting some low cell yields following my fix and stain steps. I noticed that the 96-well V-bottom plates that I've been using are TC-treated. The cells are fixed almost immediately following transfer to the 96-well plate, but can fixed Vero cells still attach to the TC-treated plate? Could this possibly explain my low yields?
Should I use TC-treated or non-TC-treated V-bottom plates for IF intracellular staining? Thanks!
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Use non-TC-treated ones for better result.
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Dear professors,
I would like to discuss about immunology of COVID-19 vaccination as follows:
1. If you have received COVID-19 vaccination, which immunoglobulin (s) should be used as marker(s) for vaccination?
2. The presence of IgG represents vaccinated, isn't it ?
3. How to distinguish between the immunity from natural infection of SARS-CoV-2 and vaccination ?
Thank you very much.
Dr. Methee
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Now, in a new, non-peer-reviewed study published in the journal bioRxiv, researchers show that this decrease is related to the disappearance of a family of antibodies called immunoglobulin M, or IgM, in blood plasma. In other words, IgM antibodies play a major role in neutralizing the virus and are part of the arsenal that the immune system uses to fight
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I am doing HI Test for NDV and Avian Influenza Viruses but before going to start I first tested the serum whether any reactivity exists or not with 1% washed Chicken RBC. but I found that some serum show reactivity and even hemagglutinate the chicken RBC. My question is, that apart from heat treatment is there any other simple treatment so that to inhibit the serum hemagglutination activity because I heated it at 56 C for 30 minutes but it won't work. Please guide.
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I am not far from the protcol which include first inactivation to destroy non specific inhibitors second get rid from low concentration of agglutinins by adsorption with chicken RBC. I think the question not need the procedure Thanks
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I am looking for a recent diagnosis for chikungunya virus through computational biology techniques.
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Molecular docking
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I am looking into this research, any interesting papers relating to this would be amazing. Papers on pregnant women and infants would be great. Thank you :)
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Virology, microbiology, immunology, vaccine
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Please take a look at this useful link.
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Since the start of the Covid-19 epidemic, several apparent cases of reinfection in patients considered to be cured have caused concern. But many hypotheses can explain this phenomenon. In the state of science, nothing proves in any case that these are indeed confirmed reinfections.
Will the coronavirus epidemic never end? While laboratories are busy looking for a vaccine, a question remains unanswered today: is it possible, yes or no, to be infected again with the coronavirus? Since the start of the epidemic, several apparent cases of reinfection have caused concern, before being qualified. In China, in the province of Guangdong, 14% of infected patients officially out of business were found to be positive again in February after a virological test. In South Korea, the same test carried out on more than 260 people * was again positive * a few days later.
A situation experienced by other patients on the planet who thought they were cured, report the New York Times * and the Reuters * agency. But at no time have these apparent reinfections been scientifically authenticated. Because elements have been provided on several occasions to explain the a priori contradictory results of virological tests (PCR). First, some patients may have obtained a false negative result (a "false negative") after a nasal sample. "There are two things. On the one hand, if the viral load in the nose is very, very low, the result may be negative," notes virologist Anne Goffard.
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O yea
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Reports from Britain and South Africa of new coronavirus strains that seem to spread more easily are causing alarm, but virologists say it’s unclear if that’s the case or whether they pose any concern for vaccines or cause more severe disease.
On Saturday, Prime Minister Boris Johnson announced new restrictions because of the new strain, and several European Union countries banned or limited some flights from the U.K. to try to limit any spread.
Here’s what is known about the situation:
* Health experts in the U.K. and U.S. said the strain seems to infect more easily than others, but there is no evidence yet it is more deadly.
* Patrick Vallance, the British government’s chief scientific adviser, said that the strain “moves fast and is becoming the dominant variant,” causing over 60% of infections in London by December.
* The strain is also concerning because it has so many mutations — nearly two dozen — and some are on the spiky protein that the virus uses to attach to and infect cells. That spike is what current vaccines target.
* “I’m worried about this, for sure,” but it’s too soon to know how important it ultimately will prove to be, said Dr. Ravi Gupta, who studies viruses at the University of Cambridge in England. He and other researchers posted a report of it on a website scientists use to quickly share developments, but the paper has not been formally reviewed or published in a journal.
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Currently, there is no firm evidence that new mutant variant of SARS-CoV-2 causes a more intense illness or leads to a higher fatality rate.
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With the great interest in Virology in the world due to the COVID-19 pandemic and its related vaccine development is doing a Phd in Virology from a good institute in UK the right thing to do?
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I did mine at the UCL (Cruciform) in collaboration with the Virus Diagnostic Centre in Colindale of the Health Protection Agency (now renamed). I also worked in Cambridge, where there are several groups involved in virology, particularly that of Ian Goodfellow. I think you should check the papers that you find most exciting and see where they are done. Given Brexit, I imagine the center of power has also shifted. If One COVID vaccine is linked to Oxford, BioNtech in Mainz (Germany) doe not joke neither, so keep an eye also on the countries you like most. At the end of the day, it is not only the lab that matters but what to do after the working hours...
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Salam (Hello)!
We have prepared some new compounds with important potential to inhibit viruses.
We are interested in inhibition of Hepatetis-B/C, Nipah, Nil and coronavirus.
Who can collaborate with us in Virology?
ALLAH HAFIZ
Taibi BEN HADDA
Makkah/KSA and Oujda/Morocco
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Please, what is Nil virus?
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My specialty is quantum physics but because of the pandemium I was interested in physical methods applied to virology. Today's physics is at nanolevel manufacturing so I suppose it can solve problems with viruses too.
As far as I know to force the organism to produce antibodies one can introduce the capsid or the envelope of the virus in it. I wonder if the following method below is used to collect capsids of a virus.
Method: I know it is possible to remove the nucleus of a cell. So lets take a number of cells from a human and extract the nuclea. Then put a huge number of the viruses in a culture with the cells. The viruses will inject their the DNA (or RNA) in the cells thereby leaving their capsids outside. But the cell can not reproduce the virus because there is no nucleus. Now one can separate the human cells with the viruses's DNA from the capsids and use the capsids to create antibodies by directly injecting as a vaccine.
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This is not necessarily true that if you remove the nucleus then the cell cannot create copies of a virus. Some viruses carry with them their own replicative machinery and that being said because you've removed the nucleus doesn't mean you've removed the necessary polymerases for the virus to reproduce.
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Hello, 
My name is Ashley and I'm part of a student team consulting for a local biotech startup. Our goal is to gather insights from researchers and stakeholders in effort to advance the company in their journey to commercialize new technologies. Biodye, is a life science company specializing in unique fluoroprobes to enhance researchers capabilities, generally in the areas of cell imaging, cancer research, biosensing, virology, and immunology to name a few.
The crux of the technology is the disruptive synthetic process. Their efficient synthetic route leads to less steps, less waist, higher yields, more flexibility when adding substituents, more agile when refining R&D efforts, and an overall higher quality in most features.
Please provide email if interested.
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Following
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The scientific community has been efficient in response to the fight against COVID-19 with research in multi-dimensional fields ranging from virology to artificial intelligence. We need a list of journals/conferences that have proposed call for papers to fast-track research publications on COVID-19. If a list is available for such CFP, one can mention in answers below. Or post links to CFPs that can be compiled for a comprehensive list.
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Hi everyone,
Currently i am working to Norovirus and SARS-Cov -2 assays, I would like to know if a ph meter specific for virology exists ?
I mean that we need to test pH from several samples eventually contaminated by virus.
Or if it doesn't exist, can someone tell me how decontaminate the probe?
Except for use bleach and ethanol, because there is a porous part on the tip of the probe..
Thank you
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So there isn't any alternativ to ph paper strip in virology ?
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UVGI technology has long been known to be an effective tool to fight against airborne infectious viruses. However, lower wavelength UV light source (<240 nm) is also known to induce Ozone production from oxygen in the air. In addition, UV light is known to have carcinogenic and cataractogenic effects. UV lamps of wavelengths in far-UVC range (207 to 222 nm) and low dosage (2 mJ/sq.cm) have been studied to have an effective germicidal effect by neutralizing viruses and bacteria without adverse health effects to humans. Far UVC has emerged as a promising technology in the recent years ( https://www.nature.com/articles/s41598-018-21058-w ). While the use of wavelengths higher than 240 nm can be incorporated in enclosed systems like air purifiers and HVAC which can minimize direct skin and eye exposure of humans to UV light, far UVC has additional advantages of usability in open configuration in public places.
What are some other known real-life challenges and other important issues associated with UVGI technology to be cared for while designing systems integrating HEPA/ULPA filtration to be used in portable air purifiers, HVAC systems or upper room UVGI lamps in hospitals, commercial and residential buildings specially in the context of fighting the rapid spread of infectious viruses like the coronavirus associated with COVID-19?
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The following may have useful information
Deleted research item The research item mentioned here has been deleted
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Hey guys,
I am kinda new to virology and i find myself at the moment having to decide on a virus titer. I am doing a GFP plaque assay. I got to the point where FACS gave me the percentage of the GFP viral expression. However, i dont know how to calculate the PFU.
Anyone could help please
thanks x 10000
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hello,
if you use 96-wells plates, you can use the Spearman & Kärber algorithm (ready to use excel added. be carefull not to change the wrong parameter). Any well with GFP signal is counted as 1, even if not all cells are GFP+.
Another way is to use 6-wells plates, with a short infection time in 1mL (in serial dilution) and then use methylcellulose or agarose coating (to avoid virus diffusion via the culture medium) for X days before counting.
There you count the number of green spots (or lysis spots if your virus is aggressive enough) and you report with the dilution you used. For example, if you have 8 zones of infected cells in your 10^-6 dilution well, then you have a rought concentration of 8.10^6 infectious virus per mL in your production.
Use of duplicate is strongly advised.
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I need to know hoe we can calculate how much induction of inos is there in treated compared to control with absorbance value. Hoe to use standard curve value in exp values??
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Dear All,
What is the difference of using Griess assay or iNOs ELISA kit?
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Hi everyone,
We are synthesizing a virucidal material that will kill SARS-CoV-2 on contact.
In these preliminary stages, we want to use enveloped surrogate viruses that are the easiest to propagate and safe to handle. For example, Phi6 bacteriophage and its easily cultured host, Pseudomonas syringae.
Other CoVs (299e, OC43, etc.) and influenzas have been considered, but as I said for now we want to keep complications to a minimum.
Any advice on possible enveloped viruses to use?
Thanks,
Max Bueckert
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follow
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As I understand it the rhinovirus can spread around 3-4 feet, droplet respiratory infections generally spreading 3-6 feet. It occurred to me that personal space varies widely across cultures so I was wondering if viruses in regions which have a greater personal space standard have selected for more virulent features such as hacking coughs.
This graph is supposedly in 1/12 inches, but I believe they meant 1/12 foot. Given this, Scottish people's average social conversation distance may just be enough to prevent them from catching rhinovirus [1].
I wonder if anyone has done research on this. It would also be interesting if different strains took foot hold in regions dependent on social distance. I doubt you would be able to distinguish this likely minor variable from other factors such as population density, climate, sanitation, etc., but I thought it was an interested idea nonetheless.
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I agree with Caio Freire
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I want to isolate (preferably infectious) hepatitis C viral particles form infected patient's serum. I have reviewed some protocols which are based on PEG 8000, PEG 6000 with or without salt precipitation followed by centrifugation. Is there any optimized protocol for HCV isolation. Additionally I am interested in in-dept understanding the criteria/principles for selecting PEG type, slat concentration so that I can manipulate protocols optimized for other viruses to develop my own protocol.
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Good question
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  • Molecular biology is the study of the molecular underpinnings of the processes of replication, transcription, translation, and cell function.
  • Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules such as proteins, lipids, carbohydrates and nucleic acids.
  • Genetics is the study of how genetic differences affect organisms. Genetics attempts to predict how mutations, individual genes and genetic interactions can affect the expression of a phenotype.
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For detailed study:
1) Molecular biology by ROBERT F WEAVER
2) Molecular Biology of the Cell by Bruce Albert et al.
3) Karp's Cell and Molecular Biology by Gerald Karp, Janet Iwasa, Wallace Marshall
4) Cell and Molecular Biology Concepts and Experiments by Gerald Karp
5) Molecular Cell Biology by Harvey Lodish, Arnold Berk, Chris A. Kaiser, Monty Krieger, Anthony Bretscher, Hidde Ploegh, Angelika Amon, Kelsey C. Martin
For outlines ( simplified book):
1) Molecular and Cell Biology For Dummies by René Fester Kratz
2) Schaum's Easy Outline Molecular and Cell Biology by William Stansfield, Raul Cano, Jaime Colome
3) Study Guide to accompany Cell and Molecular Biology: Concepts and Experiments, by Gerald Karp, Nancy L. Pruitt
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Are the terms "serotype" and "subtype" interchangeable?
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Hi all,
I'm not an expert on virology, but I'm trying to look for any RNA extraction methods that are preferably bead-based, for potential integration to a liquid handling robot workflow. I know there are many automation systems from different companies on the market, but I don't want to rely on a package deal that ties everything (reagents, type of beads and the equipment) to a single company.
Any suggestions/papers?
Thanks!
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You can use oligoT magnetic beads that will pull down polyA+ RNA
But if you're isolating viral RNA from cell culture medium, the viruses are typically filtered (0.2um) and centrifuged at high speeds (in my experience) but there are commercial kits that can extract RNA just from bronchial lavage samples, but to do this they likely bind a specific complementary oligonucleotide of whichever viral RNA they are interested in to magnetic beads like Thermofisher's magmax kit.
But if your virus has a polyA tail then oligoT beads should be enough tho you will get mRNA in there too if the viruses aren't purified first.
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As the whole world is suffering with COVID19 infection; the research for vaccines are at its peak and so is the funding towards virology projects. Will it have a negative impact on funding in other research areas i.e. basic research in RNA biology, stem cells and cancer?
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I hope all government provide more support the research agencies and all researchers particularly health researches.
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A biosafety level is the level of the biocontainment precautions required to isolate dangerous biological agents in an enclosed facility. The levels of containment range from the lowest biosafety level 1 to the highest at level 4. In the United States, the Centers for Disease Control and Prevention (CDC) have specified these levels. In the European Union, the same biosafety levels are defined in a directive. Sabanci University is following the same directive in accordance with Turkish biological safety regulation.
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As the whole world is suffering with COVID19 infection; the research for vaccines are at its peak and so is the funding towards virology projects. Will it have a negative impact on funding in other research areas i.e. basic stem cell research, RNA biology and cancer?
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Dear Sourav
I agree that research for vaccines and the funding towards virology projects are surely on peak. However, for better understanding the molecular mechanisms as well as genetic background of COVID-19 disease or any other disease, basic research always play an essential part with the end goal of development of therapeutics. Research related to RNA biology, Stem cell research, Cellular and Molecular Biology, Immunology, Medicinal chemistry and drug discovery and various other research fields are few areas for research in COVID-19, prevention and treatment. It’s just that the basic science and concerned scientists for medicine is just as significant and crucial for understanding and treatment of any disease as the field specific scientist or clinician. Any research for any disease always runs simultaneously with every other field of research. For COVID-19 every other research field is equally important to be funded for better understanding of every aspect of this disease.
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Genome sequencing helps find vital information, for example the strain type, virulence, location of origin and differences between strains transmitted within the country and in other countries
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You can find a centralized database of genomes on https://www.gisaid.org/ . To access them, you have to register and it can take some time to actually obtain the info. Nevertheless, you can see the authors of the publications and contact them directly.
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... There is an urgent need for information on virus replication, immunity and infectivity in specific sites of the body. Here we report a detailed virological analysis of nine cases of COVID-19 that provides proof of active virus replication in tissues of the upper respiratory tract. Pharyngeal virus shedding was very high during the first week of symptoms, with a peak at 7.11 × 108 RNA copies per throat swab on day 4. Infectious virus was readily isolated from samples derived from the throat or lung, but not from stool samples—in spite of high concentrations of virus RNA. Blood and urine samples never yielded virus. Active replication in the throat was confirmed by the presence of viral replicative RNA intermediates in the throat samples. We consistently detected sequence-distinct virus populations in throat and lung samples from one patient, proving independent replication. The shedding of viral RNA from sputum outlasted the end of symptoms. Seroconversion occurred after 7 days in 50% of patients (and by day 14 in all patients), but was not followed by a rapid decline in viral load. COVID-19 can present as a mild illness of the upper respiratory tract. The confirmation of active virus replication in the upper respiratory tract has implications for the containment of COVID-19.
from
Wölfel, R., Corman, V.M., Guggemos, W. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020). https://doi.org/10.1038/s41586-020-2196-x
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Something interesting to follow.. nice question
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FDA has issued guidance to provide recommendations to health care providers and investigators on the administration and study of investigational convalescent plasma collected from individuals who have recovered from COVID-19 (COVID-19 convalescent plasma) during the public health emergency.
The guidance provides recommendations on the following:
  • pathways for use of investigational COVID-19 convalescent plasma
  • patient eligibility
  • collection of COVID-19 convalescent plasma, including donor eligibility and donor qualifications
  • labeling, and
  • record keeping
Because COVID-19 convalescent plasma has not yet been approved for use by FDA, it is regulated as an investigational product.  A health care provider must participate in one of the pathways described below.  FDA does not collect COVID-19 convalescent plasma or provide COVID-19 convalescent plasma.  Health care providers or acute care facilities should instead obtain COVID-19 convalescent plasma from an FDA-registered blood establishment.
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Virus latency (or viral latency) is the ability of a pathogenic virus to lie dormant (latent) within a cell, denoted as the lysogenic part of the viral life cycle. A latent viral infection is a type of persistent viral infection which is distinguished from a chronic viral infection. Latency is the phase in certain viruses' life cycles in which, after initial infection, proliferation of virus particles ceases. However, the viral genome is not fully eradicated. The result of this is that the virus can reactivate and begin producing large amounts of viral progeny (the lytic part of the viral life cycle) without the host becoming reinfected by new outside virus, and stays within the host indefinitely.
Virus latency is not to be confused with clinical latency during the incubation period when a virus is not dormant.
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No latent or reactivated SARS-CoV-2 in clinically recovered COVID-19 patients
You will note in the first article (1) that HCWs who had clinical recovery did not transmit the disease to contacts despite positive RT-PCR tests. In a study recently published (2), patients who had clinically recovered but showed positive RNA based RT-PCR tests did not transmit COVID-19 by donating plasma that was transfused to other recipients.
This indicates that SARS-CoV-2 virus latency or reactivation is more of a hype than a reality and viral RNA in clinically recovered patient is inactive viral litter or garbage, not an active virus.
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The adaptive, or acquired, immune response takes days or even weeks to become established—much longer than the innate response; however, adaptive immunity is more specific to pathogens and has memory. Adaptive immunity is an immunity that occurs after exposure to an antigen either from a pathogen or a vaccination. This part of the immune system is activated when the innate immune response is insufficient to control an infection. In fact, without information from the innate immune system, the adaptive response could not be mobilized. There are two types of adaptive responses: the cell-mediated immune response, which is carried out by T cells, and the humoral immune response, which is controlled by activated B cells and antibodies. Activated T cells and B cells that are specific to molecular structures on the pathogen proliferate and attack the invading pathogen. Their attack can kill pathogens directly or secrete antibodies that enhance the phagocytosis of pathogens and disrupt the infection. Adaptive immunity also involves a memory to provide the host with long-term protection from reinfection with the same type of pathogen; on re-exposure, this memory will facilitate an efficient and quick response.
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Please see the following PDF attachment.
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On the side, I doing some research (literature-based) on a particular treatment that may help for COVID-19 symptoms but I need someone with a stronger medical knowledge base with expertise in virology and/or immunology that would also have the time to help me co-research this. Currently running into a bit of a wall. Please PM if you or someone you know can and has the time to help. Thanks
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I am virologist, I need more details about the aspect of collaboration
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COVID- 19
Respiratory infections can be transmitted through droplets of different sizes: when the droplet particles are >5-10 μm in diameter they are referred to as respiratory droplets, and when then are <5μm in diameter, they are referred to as droplet nuclei. According to current evidence, COVID-19 virus is primarily transmitted between people through respiratory droplets and contact routes.2-7 In an analysis of 75,465 COVID-19 cases in China, airborne transmission was not reported.
Droplet transmission occurs when a person is in in close contact (within 1 m) with someone who has respiratory symptoms (e.g., coughing or sneezing) and is therefore at risk of having his/her mucosae (mouth and nose) or conjunctiva (eyes) exposed to potentially infective respiratory droplets. Transmission may also occur through fomites in the immediate environment around the infected person. Therefore, transmission of the COVID-19 virus can occur by direct contact with infected people and indirect contact with surfaces in the immediate environment or with objects used on the infected person (e.g., stethoscope or thermometer). 
Airborne transmission is different from droplet transmission as it refers to the presence of microbes within droplet nuclei, which are generally considered to be particles <5μm in diameter, can remain in the air for long periods of time and be transmitted to others over distances greater than 1 m. 
In the context of COVID-19, airborne transmission may be possible in specific circumstances and settings in which procedures or support treatments that generate aerosols are performed; i.e., endotracheal intubation, bronchoscopy, open suctioning, administration of nebulized treatment, manual ventilation before intubation, turning the patient to the prone position, disconnecting the patient from the ventilator, non-invasive positive-pressure ventilation, tracheostomy, and cardiopulmonary resuscitation. 
There is some evidence that COVID-19 infection may lead to intestinal infection and be present in faeces. However, to date only one study has cultured the COVID-19 virus from a single stool specimen.  There have been no reports of faecal−oral transmission of the COVID-19 virus to date.
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The virus is primarily spread between people during close contact, often via small droplets produced by coughing, sneezing, or talking. While these droplets are produced when breathing out, they usually fall to the ground or onto surfaces rather than remain in the air over long distances.People may also become infected by touching a contaminated surface and then touching their eyes, nose, or mouth. The virus can survive on surfaces for up to 72 hours. It is most contagious during the first three days after the onset of symptoms, although spread may be possible before symptoms appear and in later stages of the disease.
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Khem Raj Meena I agree with you. But everyone is scared again of the vaccination because of the numerous rumours around it
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Dengue fever is a disease caused by a family of viruses transmitted by infected mosquitoes. It is an acute illness of sudden onset that usually follows a benign course with symptoms such as headache, fever, exhaustion, severe muscle and joint pain, swollen lymph nodes (lymphadenopathy), and rash.
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A hospital-acquired infection (HAI), also known as a no