How to obtain virus samples?

How to obtain virus samples?

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I'm trying to observe the behavior of simple viruses in different environments. I'm just looking for simple viruses like the common cold and the flu virus nothing major. Is there a way to obtain them?

First of all, cold and flu viruses are not 'simple viruses', and they are not harmless. They kill tens to hundreds of thousands of people every year.

Secondly, this would depend highly on the risk group that the virus falls in. The NIH sets strict guidelines on who can handle infectious agents. Unfortunately, I can almost guarantee you that no one is going to give you even risk group 1 plant viruses, and they are certainly are not going to give you cold or flu viruses. Risk groups range from 1 to 4. To handle risk group 2 viruses, for example, you are expected to do so in a BSL-2 or higher laboratory, and anyone maintaining stocks of virus is going to do a hefty check of you and your 'facilities' before shipping you anything.

Furthermore, even if you did obtain the virus, you would need to store it or maintain stocks of the virus in tissue culture. Its not like you can just get an eppendorf tube of virus in saline and expect it to survive in your refrigerator at home, and its not like companies are shipping virus willy-nilly to anyone.

That being said, and at the expense of sounding self-righteous, there is really no reason for you to obtain virus particles. You should start by getting a book on virology and reading it. There is plenty of learning material both visual and written out there, and all I will say is if you don't already know how to culture virus or where to obtain it, you shouldnt be doing so, and no one is going to give it to you.

CDC Biosafety in Microbiological and Biomedical Laboratories:

WHO Laboratory Biosafety Manual:

NIH guidelines recombinant nucleic acids:

I think its great that you are interested, and it sounds like you are interested in histopathological changes caused by virus, so I have included some nice histo pictures below

Syncytia (Herpes Simplex Virus type 1)

Clearer example of syncytia

Characteristic owl-eye (Cytomegalovirus)

Distemper virus inclusion body

Coronavirus particles with 'crown' of surface glycoproteins

Budding HIV virus particles from the plasma membrane

Bacteriophage T4 escape by lysis


Rous-sarcoma virus

Tobacco mosaic virus

Specimen Collection

Whole stool is the preferred clinical specimen for laboratory diagnosis of norovirus illness. During outbreak investigations, specimens should be collected from at least 5 ill people. Ideally, stool specimens should be collected during the acute phase of illness (up to 72 hours after symptoms start) while the stool is still liquid or semisolid. The greatest amount of virus is shed during the acute phase of illness.

Norovirus can sometimes be detected in stool specimens that are collected later in the illness or after the symptoms have resolved (up to 7 to 10 days after onset). The number of specimens collected should be increased if collected after the acute phase of illness or for large or protracted outbreaks.

If the specimens are shipped to a laboratory for testing, each sample should be:

  • Clearly labelled with a unique identifier (such as specimen ID),
  • Placed in a leak-proof plastic container and sealed in a separate bag, and
  • Kept on frozen refrigerant packs in an insulated, waterproof polystyrene container.

If testing occurs within 2 to 3 days from collection for whole stool and Cary-Blair specimens, and within 2 to 3 weeks for stool specimens, samples should be refrigerated at 39°F (4°C). If testing occurs beyond these times or are to be archived, samples should be frozen ideally at -94°F (-70°C) or at -4°F (-20°C) if storage at -94°F (-70°C) is not available.

Vomitus can be collected in addition to stool specimens during an outbreak investigation. These specimens should be collected and shipped in the same way as stool specimens. Vomitus samples should always be stored frozen at -4°F (-20°C) or at -94°F (-70°C).

Serum specimens are not recommended for routine laboratory diagnosis of norovirus illness.

If feasible and warranted for special studies, acute (symptoms showing) and convalescent (recovering from symptoms)-phase serum specimens may be collected and tested for a greater than four-fold rise in IgG titer to noroviruses. Serum samples should be stored frozen at -4°F (-20°C).

  • Acute-phase serum specimens should be collected during the first 5 days after the symptoms start.
  • Convalescent-phase specimens should be collected during the third to fourth week after the symptoms start.

A new methodology for sequencing viruses

Plot showing the co-infection of the Dengue type three virus (DENV3) and the Zika virus (ZIKV) identified in one clinical subject by using the “baits” on blood samples from the patient. From the outermost circle, the plot shows the DENV3 and ZIKV viral genomes, the number of reads of a given nucleotide (amount of genomic material) and locations where the baits hybridise. Credit: PLOS Neglected Tropical Diseases

NUS scientists have developed a more efficient method to sequence the complete genomes of infectious diseases carried by mosquitoes directly from patient samples.

The Dengue, Zika and Chikungunya viruses are potentially life-threatening diseases. These viruses are transmitted to humans by the bite of an infected mosquito. The Zika virus can also be transmitted from an infected mother to her unborn fetus. Alarmingly, the distribution of these viruses and their mosquito vectors have increased dramatically in recent years, leading to an upward trend in the number of infections. Patients infected by these viruses exhibit similar symptoms, making it challenging to make a correct diagnosis.

In response to the threat posed by these viruses, a research team lead by Prof October SESSIONS from the Department of Pharmacy and the Saw Swee Hock School of Public Health, NUS has developed a more efficient method to sequence the complete viral genomes of the Dengue, Zika and Chikungunya viruses directly from patient samples (urine and blood). Complete viral genome information is important because it can provide information on the origin of the virus and its harmful effects. This information can then be used to rapidly characterize outbreaks and curb the spread of the virus within the community.

Obtaining the full genomes of viruses from patient samples is a laborious, often futile prospect that requires detailed knowledge about the virus. The main problem encountered with the direct sequencing of complete viral genomes from patient samples is that the sample contains too much human genetic material, compared to the amount of viral genomes, for this approach to work consistently. The researchers used a computational algorithm which they had developed to design "baits" that can specifically capture the viral genome, and in the process remove the non-viral part of the sample. This increases the amount of viral genomes in the sample, which results in improved sensitivity and efficiency of the genome sequencing.

Prof Sessions said, "Broad adoption of this methodology can potentially provide a more efficient way to obtain viral information from infected patients. It can be further developed into a portable, phone-sized genomic sequencer, making it accessible in the field."

What does the study involve?

The NIAID Vaccine Research Center is collecting blood samples from adults ages 18 years of age or older who are fully recovered from confirmed COVID-19 infection. Blood samples will be collected by ordinary blood drawing (phlebotomy) or by apheresis, a procedure for collecting a larger quantity of blood cells or plasma than would be possible through simple blood drawing. Participants may have only one sample collected or may be asked to undergo repeat sample collection procedures, depending upon the requirements of the research project.

Scientists develop test to detect the virus that causes COVID-19 even when it mutates

A team of scientists led by Nanyang Technological University, Singapore (NTU Singapore) has developed a diagnostic test that can detect the virus that causes COVID-19 even after it has gone through mutations.

Called the VaNGuard (Variant Nucleotide Guard) test, it makes use of a gene-editing tool known as CRISPR, which is used widely in scientific research to alter DNA sequences and modify gene function in human cells under lab conditions, and more recently, in diagnostic applications.

Since viruses have the ability to evolve over time, a diagnostic test robust against potential mutations is a crucial tool for tracking and fighting the pandemic. Over its course so far, thousands of variants of SARS-CoV-2, the virus that causes COVID-19, have arisen, including some that have spread widely in the United Kingdom, South Africa, and Brazil .

However, the genetic sequence variations in new strains may impede the ability of some diagnostic tests to detect the virus, said NTU Associate Professor Tan Meng How, who led the study.

In addition to its ability to detect SARS-CoV-2 even when it mutates, the VaNGuard test can be used on crude patient samples in a clinical setting without the need for RNA purification, and yields results in 30 minutes. This is a third of the time required for the gold standard polymerase chain reaction (PCR) test, which requires purification of RNA in a lab facility.

The team of scientists led by NTU hopes that the VaNGuard test can be deployed in settings where quickly confirming COVID-19 status of individuals is paramount.

Associate Professor Tan, who is from NTU's School of Chemical and Biomedical Engineering, said: "Viruses are very smart. They can mutate, edit, or shuffle their genetic material, meaning diagnostic tests may fail to catch them. Hence, we spent considerable effort developing a robust and sensitive test that can catch the viruses even when they change their genetic sequences. In addition, frequent testing is essential for helping to break the transmission of viruses within populations, so we have developed our tests to be rapid and affordable, making them deployable in resource-poor settings."

The findings were published in scientific journal Nature Communications on 19 March.

The research team has filed a patent for the VaNGuard test.

Moving forward, they plan to perform further experiments to further refine their diagnostic kit, obtain regulatory approval from relevant authorities, and commercialise their test in partnership with diagnostic companies.

Using a pair of "molecular scissors" to detect virus

The VaNGuard test relies on a reaction mix containing enAsCas12a, a variant of the enzyme Cas12a that acts like a pair of "molecular scissors."

The enzyme enAsCas12a is 'programmed' to target specific segments of the SARS-CoV-2 genetic material and to snip them off from the rest of its viral genome. Successfully snipping off segments is how the enzyme 'detects' the presence of the virus. The programming is done by two different molecules known as guide RNAs, which are designed to recognise specific sites on the SARS-CoV-2 genome.

The scientists decided to use two guide RNAs that recognise sequences that are extremely similar between variants of SARS-CoV-2 and that are also unique to the virus. Each guide RNA is computationally predicted to recognise over 99.5 per cent of the thousands of SARS-CoV-2 isolates that have so far been sequenced around the world.

Assoc Prof Tan explained: "Combining two or more guide RNAs with the enzyme enAsCas12a ensures that if one of the guide RNAs fails to guide it to the correct segment of the virus because of a mutation, the other guide RNA can still 'rescue' this mismatch."

So far, the made-in-NTU diagnostic platform can recognise up to two mutations within the target sites on the SARS-CoV-2 genome.

When the SARS-CoV-2 virus or one of its variants is detected in a sample, the engineered Cas12 enzyme variant enAsCas12a becomes hyper-activated and starts cutting other detectable genetic material in the sample as well, including a molecule tagged with a fluorescent dye that is added to the reaction mix.

When the molecule is cut, it starts to glow. This glow is picked up by a microplate reader, a lab instrument that can detect and quantify the light photons emitted by the molecule.

Assoc Prof Tan, who is also from the Genome Institute of Singapore at the Agency for Science, Technology and Research, Singapore (A*STAR), explained: "If the virus is present, the molecule will glow. If not, it means the virus is not present to cause the hyper-activation of the molecular scissors."

Making the VaNGuard test easy to use

To make the test easier to use once it has been approved for roll out, the scientists integrated the test into a specially treated paper strip that looks similar to a pregnancy test.

The paper strip is dipped into a tube containing the crude nasopharyngeal sample and the reaction mix. In the presence of a SARS-CoV-2 virus or its variant, two strong bands will appear on the paper strip. In the absence of the virus, only one band will appear.

The scientists validated the VaNGuard test's ability to detect SARS-CoV-2 variants by synthesising an RNA sample that has the same mutated sequence as a known SARS-CoV-2 variant.

They added different amounts of the synthesised sample to their test and observed two strong bands when the paper strip was dipped into each reaction mix. This indicates that the VaNGuard test is robust against mutated viral sequences. The scientists also developed a mobile phone app to facilitate the interpretation of the paper strips.

The VaNGuard test was developed by scientists from NTU's School of Chemical and Biomedical Engineering, School of Biological Sciences, and School of Computer Science and Engineering National University Health System and A*STAR.

Seeing viruses by both light and electron microscopy

An example of the images of viruses obtainable with cryo-CLEM. These images show pseudotyped HIV-1 particles being taken into the cell, with viral membrane as light blue, mature core as yellow, and clathrin cages as purple. Credit: Hampton et al Nat. Protocols (2016)

Advances in both light and electron microscopy are improving scientists' ability to visualize viruses such as HIV, respiratory syncytial virus (RSV), measles, influenza, and Zika in their native states. Researchers from Emory University School of Medicine and Children's Healthcare of Atlanta developed workflows for cryo-correlative light and electron microscopy (cryo-CLEM), which were published in the January 2017 issue of Nature Protocols.

Previously, many electron microscopy images of well-known viruses were obtained by studying purified virus preparations. Yet the process of purification can distort the structure of enveloped viruses, says Elizabeth R. Wright, PhD, associate professor of pediatrics at Emory University School of Medicine.

Wright and her colleagues have refined techniques for studying viruses in the context of the cells they infect. That way, they can see in detail how viruses enter and are assembled in cells, or how genetic modifications alter viral structures or processing.

"Much of what is known about how some viruses replicate in cells is really a black box at the ultrastructural level," she says. "We see ourselves as forming bridges between light and electron microscopy, and opening up new realms of biological questions."

Wright is director of Emory's Robert P. Apkarian Integrated Electron Microscopy Core and a Georgia Research Alliance Distinguished Investigator. The co-first authors of the Nature Protocols paper are postdoctoral fellows Cheri Hampton, PhD. and Joshua Strauss, PhD, and graduate students Zunlong Ke and Rebecca Dillard.

The Wright lab's work on cryo-CLEM includes collaborations with Gregory Melikyan in Emory's Department of Pediatrics, Phil Santangelo in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory, and Paul Spearman, now at Cincinnati Children's.

For this technique, virus-infected or transfected cells are grown on fragile carbon-coated gold grids and then "vitrified," meaning that they are cooled rapidly so that ice crystals do not form. Once cooled, the cells are examined by cryo-fluorescent light microscopy and cryo-electron tomography.

Extremely low temperatures (well below -150° C) are necessary for cryo-fluorescent light microscopy and cryo-electron tomography. Performing the light microscopy steps after sample vitrification prevents the cells from continuing to grow and shift in position in between live-cell light and cryo-electron microscopy. The cryo-fluorescent light microscopy is facilitated by use of a heat-insulated, short working distance ceramic objective lens, Wright says. Other technological advances that have enabled CLEM include computer software for combining data from the two imaging modes, and a variety of fluorescent proteins and probes.

With the cryo-electron tomography data, it is possible to obtain images of individual intact viruses and viral proteins at high resolution – in some cases, close to atomic resolution—via sub-volume averaging, Wright says. This approach was used in a recent Nature Communications paper on RSV, demonstrating that a live attenuated vaccine candidate resembles RSV structurally.

The cryo-CLEM technique works best with cells that can grow flat, because a standard electron beam can't penetrate cell bodies more than about 1 micron (a millionth of a meter) thick. Mammalian cells are usually several microns wide, while viruses such as HIV are around 0.1 microns across.

Potentially, the cryo-CLEM technique could be extended to study many systems including neuronal cells or bacterial biofilms, Wright says.

Scientists Describe How 1918 Influenza Virus Sample Was Exhumed In Alaska

The effort to find preserved samples of the 1918 influenza virus has been a pursuit of both historical and medical importance. The 1918 influenza pandemic was the most devastating single disease outbreak in modern history, and examining the virus that caused it may help prepare for, and possibly prevent, future pandemics. When the complete sequence of the 1918 virus was published in 2005, it represented a watershed event for influenza researchers worldwide.

In an article in the journal Antiviral Therapy, scientists at the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, narrate the story of how scientists discovered samples of the 1918 strain in fixed autopsy tissues and in the body of a woman buried in the Alaskan permafrost. The article places this discovery in the context of decades of research into the cause of pandemic influenza, and the authors detail the strange convergence of events that allowed them to recover and sequence the virus in the first place. Its genetic material is so fragile that it should not have survived for days, let alone decades.

In a mass grave in a remote Inuit village near the town of Brevig Mission, a large Inuit woman lay buried under more than six feet of ice and dirt for more than 75 years. The permafrost plus the woman's ample fat stores kept the virus in her lungs so well preserved that when a team of scientists exhumed her body in the late 1990s, they could recover enough viral RNA to sequence the 1918 strain in its entirety. This remarkable good fortune enabled these scientists to open a window onto a past pandemic--and perhaps gain a foothold for preventing a future one.

'It is alarming'

However, experts are concerned.

"It is suspicious. It is alarming. It is potentially life-threatening," said Amir Attaran, a law professor and epidemiologist at the University of Ottawa.

WATCH | Deadly viruses were sent from Canada to China, documents show:

Deadly viruses were sent from Canada to China, according to access documents

"We have a researcher who was removed by the RCMP from the highest security laboratory that Canada has for reasons that government is unwilling to disclose. The intelligence remains secret. But what we know is that before she was removed, she sent one of the deadliest viruses on Earth, and multiple varieties of it to maximize the genetic diversity and maximize what experimenters in China could do with it, to a laboratory in China that does dangerous gain of function experiments. And that has links to the Chinese military."

Gain of function experiments are when a natural pathogen is taken into the lab, made to mutate, and then assessed to see if it has become more deadly or infectious.

In Canada, gain of function experiments to create more dangerous pathogens in humans are not prohibited, but are not done because they're considered too dangerous, Attaran said.

"The Wuhan lab does them and we have now supplied them with Ebola and Nipah viruses. It does not take a genius to understand that this is an unwise decision," he said.

"I am extremely unhappy to see that the Canadian government shared that genetic material."

Attaran pointed to an Ebola study first published in December 2018, three months after Qiu began the process of exporting the viruses to China. The study involved researchers from the NML and University of Manitoba.

The lead author, Hualei Wang, is involved with the Academy of Military Medical Sciences, a Chinese military medical research institute in Beijing.

All of this has led to conspiracy theories linking the novel coronavirus responsible for COVID-19, Canada's microbiology lab, and the lab in Wuhan.

The RCMP and PHAC have consistently denied any connections between the pandemic and the virus shipments. There is no evidence linking this shipment to the spread of the coronavirus. Ebola is a filovirus and Henipa is a paramyxovirus no coronavirus samples were sent.

The ATIP documents identify for the first time exactly what was shipped to China.

The list includes two vials each of 15 strains of virus:

  • Ebola Makona (three different varieties)
  • Mayinga.
  • Kikwit.
  • Ivory Coast.
  • Bundibugyo.
  • Sudan Boniface.
  • Sudan Gulu.
  • MA-Ebov.
  • GP-Ebov.
  • GP-Sudan.
  • Hendra.
  • Nipah Malaysia.
  • Nipah Bangladesh.

PHAC said the National Microbiology Lab routinely shares samples with other public health labs.

The transfers follow strict protocols, including requirements under the Human Pathogens and Toxins Act (HPTA), the Transportation of Dangerous Goods Act, the Canadian Biosafety Standard, and standard operating procedures of the NML.

CBC News has not been provided with some of the paperwork involved with the transfer, as information was redacted under sections of the Access to Information Act dealing with international affairs, national security and other issues.

Molecular Testing (Nucleic Acid Amplification)

How are nucleic acid amplification tests performed?

Nucleic acid amplification testing requires respiratory samples from the patient because SARS-CoV-2 is a respiratory virus. Nasopharyngeal swabs are most commonly used. Lower respiratory secretions, such as sputum and bronchoalveolar lavage fluid, are also used if a patient has pneumonia or lung involvement with infection.

Samples are then processed and tested for SARS-CoV-2 RNA. The test includes extraction of RNA from the patient specimen, conversion to DNA and PCR amplification with SARS-CoV-2-specific primers.

What does nucleic acid amplification testing reveal?

What to do with a positive nucleic acid amplification test?

Is there an accuracy concern with nucleic acid amplification testing?

Novel Coronavirus SARS-CoV-2 Under the Microscope

The National Institute of Allergy and Infectious Diseases Rocky Mountain Laboratories (NIAID-RML), located in Hamilton, Montana was able to capture images of the novel coronavirus (SARS-CoV-2, previously known as 2019-nCoV) on its scanning electron microscope and transmission electron microscopes. SARS-CoV-2 causes COVID-19 disease which has resulted in a global pandemic.

This scanning electron microscope image shows SARS-CoV-2 emerging (the round gold objects) from the surface of cells cultured in a lab. SARS-CoV-2 is the virus that causes COVID-19. The virus shown was isolated from a patient in the United States. Credit: NIAID-RML.

This is a micrograph of SARS-CoV-2 virus particles that were isolated from a patient. The image was captured under a transmission electron microscope and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This is a transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient. The image was captured using a transmission electron microscope and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This image captured with a scanning electron microscope shows SARS-CoV-2 (the round magenta objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2 is the virus that causes COVID-19. The virus shown was isolated from a patient in the United States. Credit: NIAID-RML.

This transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19 isolated from a patient in the United States. Virus particles are shown emerging from the surface of cells cultured in the lab. The spikes on the outer edge of the virus particles give coronaviruses their name, crown-like. Credit: NIAID-RML.

This scanning electron microscope image shows SARS-CoV-2 (in yellow), the virus that causes COVID-19 isolated from a patient in the United States, emerging from the surface of cells (blue and pink) cultured in the lab. Credit: NIAID-RML.

A transmission electron microscope was used to capture SARS-CoV-2 virus particles isolated from a patient. The image was captured and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This scanning electron microscope image shows SARS-CoV-2 (in yellow), also known as 2019-nCoV, the virus that causes COVID-19 isolated from a patient in the United States, emerging from the surface of cells (pink) cultured in the lab. Credit: NIAID-RML.

This is a transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient. The image was captured and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This scanning electron microscope image shows SARS-CoV-2 (the round blue objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2 is the virus that causes COVID-19. The virus shown was isolated from a patient in the United States. Credit: NIAID-RML.

This transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19 isolated from a patient in the United States. Virus particles are shown emerging from the surface of cells cultured in the lab. The spikes on the outer edge of the virus particles give coronaviruses their name, crown-like. Credit: NIAID-RML.

This scanning electron microscope image shows SARS-CoV-2 (in orange), the virus that causes COVID-19 isolated from a patient in the United States emerging from the surface of cells (green) cultured in the lab. Credit: NIAID-RML.

How Can I View COVID-19 Under the Microscope?

The novel Coronavirus (SARS-CoV-2) causes COVID-19 disease and can be viewed under a scanning electron microscope or a transmission electron microscope. Viruses can not be viewed under standard light compound microscopes.

What is a Scanning Electron Microscope?

A scanning electron microscope (SEM) scans a sample with a focused electron beam and acquires images with information about the samples' topography and composition. Scanning Electron Microscopes are widely used in nanotechnology, materials research, life sciences, semiconductor, raw materials and industry.

What is a Transmission Electron Microscope?

A transmission electron microscope (TEM) uses beams of electrons transmitted through a specimen to form an image. The specimen is usually an ultra-thin section less than 100nm thick. The image is magnified and focused onto an imaging device such as a layer of photographic film.

Transmission electron microscopes are capable of imaging at a significantly higher resolution than light microscopes, due to the smaller de Broglie wavelength of electrons. This allows the TEM to capture fine detail, even as small as a single column of atoms, which is thousands of times smaller than a resolvable object seen in a light microscope.

Transmission Electron Microscopes are used in cancer research, virology, materials science, nanotechnology, paleontology, and semiconductor research.

Microscope Questions?

If you have any questions regarding scanning electron microscopes, transmission electron microscopes, or simple light microscopes contact Microscope World and we will be happy to help.

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