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The answer considers them as first formed living cells as they were precursor of life. But they had no lipid bilayer nor any cellular organization, shouldnt they be more like Viruses ,or like Prions and Viriods ??
Introduction to viruses
A virus is a tiny infectious agent that reproduces inside the cells of living hosts. When infected, the host cell is forced to rapidly produce thousands of identical copies of the original virus. Unlike most living things, viruses do not have cells that divide new viruses assemble in the infected host cell. But unlike simpler infectious agents like prions, they contain genes, which allow them to mutate and evolve. Over 4,800 species of viruses have been described in detail  out of the millions in the environment. Their origin is unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria.
Viruses are made of either two or three parts. All include genes. These genes contain the encoded biological information of the virus and are built from either DNA or RNA. All viruses are also covered with a protein coat to protect the genes. Some viruses may also have an envelope of fat-like substance that covers the protein coat, and makes them vulnerable to soap. A virus with this "viral envelope" uses it—along with specific receptors—to enter a new host cell. Viruses vary in shape from the simple helical and icosahedral to more complex structures. Viruses range in size from 20 to 300 nanometres it would take 33,000 to 500,000 of them, side by side, to stretch to 1 centimetre (0.4 in).
Viruses spread in many ways. Although many are very specific about which host species or tissue they attack, each species of virus relies on a particular method to copy itself. Plant viruses are often spread from plant to plant by insects and other organisms, known as vectors. Some viruses of humans and other animals are spread by exposure to infected bodily fluids. Viruses such as influenza are spread through the air by droplets of moisture when people cough or sneeze. Viruses such as norovirus are transmitted by the faecal–oral route, which involves the contamination of hands, food and water. Rotavirus is often spread by direct contact with infected children. The human immunodeficiency virus, HIV, is transmitted by bodily fluids transferred during sex. Others, such as the dengue virus, are spread by blood-sucking insects.
Viruses, especially those made of RNA, can mutate rapidly to give rise to new types. Hosts may have little protection against such new forms. Influenza virus, for example, changes often, so a new vaccine is needed each year. Major changes can cause pandemics, as in the 2009 swine influenza that spread to most countries. Often, these mutations take place when the virus has first infected other animal hosts. Some examples of such "zoonotic" diseases include coronavirus in bats, and influenza in pigs and birds, before those viruses were transferred to humans.
Viral infections can cause disease in humans, animals and plants. In healthy humans and animals, infections are usually eliminated by the immune system, which can provide lifetime immunity to the host for that virus. Antibiotics, which work against bacteria, have no impact, but antiviral drugs can treat life-threatening infections. Those vaccines that produce lifelong immunity can prevent some infections.
What Is a Virus?
Viruses are a bit of an enigma. They contain DNA or RNA that are found in all living things. This is packaged in a protein coat. Despite this, viruses are not usually considered living because they are not made up of cells and cannot reproduce by themselves. Instead, the virus will inject the DNA or RNA into a living cell, and the cell will make copies of the virus and assemble them so they can spread.5
Viruses vary considerably in their ability to cause disease. Many known viruses are not associated with disease at all. Others cause mild symptoms that may often go undetected. Some, like the HIV virus that causes AIDS in people, appear to have come from another species where they do not cause disease. Given our current knowledge of viruses, it is quite reasonable to believe that disease-causing viruses are descended from viruses that were once not harmful.6 It has been suggested that they have played an important role in maintaining life on Earth—somewhat similar to the way bacteria do.7 In fact, they may play a role in solving an intriguing puzzle that faces creationists.
Host range and distribution
Logic originally dictated that viruses be identified on the basis of the host they infect. This is justified in many cases but not in others, and the host range and distribution of viruses are only one criterion for their classification. It is still traditional to divide viruses into three categories: those that infect animals, plants, or bacteria.
Virtually all plant viruses are transmitted by insects or other organisms (vectors) that feed on plants. The hosts of animal viruses vary from protozoans (single-celled animal organisms) to humans. Many viruses infect either invertebrate animals or vertebrates, and some infect both. Certain viruses that cause serious diseases of animals and humans are carried by arthropods. These vector-borne viruses multiply in both the invertebrate vector and the vertebrate host.
Certain viruses are limited in their host range to the various orders of vertebrates. Some viruses appear to be adapted for growth only in ectothermic vertebrates (animals commonly referred to as cold-blooded, such as fishes and reptiles), possibly because they can reproduce only at low temperatures. Other viruses are limited in their host range to endothermic vertebrates (animals commonly referred to as warm-blooded, such as mammals).
Where Do Viruses Come From?
The origin of viruses is a hotly debated topic. It’s unclear how they first evolved. However, there are many ideas floating around out there. There are three classical hypotheses but many new ideas and discoveries challenging them.
The first one is the virus first hypothesis, and states that since viruses are so much simpler than a cell, they must have evolved first, and that ancestors of modern viruses could have provided raw material for the development of cellular life. The key data that supports this is apparent when you look at virus genes, compare them and their genetic sequence with cellular life data available in genetic databases. This will reveal a mismatch that suggests viruses aren’t a simpler version of cellular life, but are different fundamentally and might have predated cellular life altogether. This model also suggests there was an ancient virosphere from which all viruses evolved. However, some scientists dismiss this hypothesis because of one key feature. According to the classical definition of viruses, they need a host’s cell to replicate. So, how could viruses have survived before the existence of cellular life?
The second model is called the regressive hypothesis, sometimes also called the degeneracy hypothesis or reduction hypothesis. This one suggests that viruses were once small cells that parasitized larger cells, and that over time the genes not required by their parasitism were lost. The discovery of giant viruses that had similar genetic material to parasitic bacteria supported this idea. But what it can’t explain is why the tiniest of cellular parasites don’t resemble viruses at all.
The third model is escape hypothesis, or vagrancy hypothesis, and states that viruses evolved from bits of RNA or DNA that escaped from genes of larger organisms. For example, bacteriophages (viruses that infect bacteria) came from bits of bacterial genetic materials, or eukaryotic viruses are from bits of genetic material from eukaryotes like us. However, in this model, it would be expected that viral proteins would then share more qualities with their hosts, but this is largely not the case. This model also doesn’t explain the unique structure viruses have that is not seen in cells.
Some recent discoveries of giant viruses have even further complicated the question about the origin of viruses. These discoveries also challenge many of the classical definitions of what makes a virus, such as the size requirement, gene behavior, and how they replicate.
Giant viruses were first described in 2003. The first specimen was Acanthamoeba polyphaga mimivirus (APMV), isolated from an amoeba in cooling tower in England. The name “mimivirus” stands for MImicking MIcrobe virus because of the way amoebae mistake it for their typical meal of bacteria. Mimiviruses are different from viruses in that they have way more genes than other viruses, including genes with the ability to replicate and repair DNA.
The pandoravirus, discovered in 2013, is even larger than the mimivirus and has approximately 2500 genes, with 93 percent of their genes not known from any other microbe.
|Illustration: Nicole Elmer|
The pithovirus was discovered in 2013 from a Siberian dirt sample that had been frozen for 30,000 years. It’s larger than the pandoravirus, as well as some bacteria, and behaves differently than viruses when it comes to reproduction. According to the classical definition of viruses, they must have a host’s cell to reproduce and cannot do it on their own. However, the pithovirus possesses some replication machinery of its own. While it contains fewer genes than the pandoravirus, two-thirds of its proteins are unlike those of other viruses.
Tupanvirus was discovered in Brazil. It holds an almost nearly complete set of genes necessary for protein production.
The discoveries of these giant viruses and others not listed here have made some researchers suggest they lie somewhere between bacterium and viruses, and might even deserve their own branch on the Tree of Life. This would create a yet undescribed fourth domain of life aside from Bacteria, Archaea, and Eukaryotes. And in case you’re worried if these big viruses can infect us human being, rest easy. You only need to worry if you happen to be an amoeba.
In our next posting about viruses, we'll look at how they might be the most successful of earth's inhabitants.
Several observations made during the course of studies on stealth-adapted viruses are explainable by a pervasive, energy-rich, ether environment. Activation of an alternative cellular energy (ACE) pathway provides stealth virus damaged cells with a repair mechanism that is independent of the cellular immune response. ACE activation can also assist in the systemic healing of infections caused by conventional viruses such as Herpes simplex virus, Herpes zoster virus and human papillomavirus. ACE pigments convert conventional forms of physical energies into a biological cell healing energy, the nature of which is still uncertain. More recent studies suggest that ACE pigments may also capture etheric energy. In addition to cellular repair, ACE pigment activation can lead to the biogenesis of lipid-like chemical structures. ACE pigment and virus culture healing activities were also seen with several natural products, including a homeopathic formulation. A colloidal silver solution appeared to facilitate the transmission of ACE and to enhance its biosynthetic activity. These results open a window into a greater understanding of a fundamental force of nature of potential therapeutic importance.
Are Viruses Alive?
Editor's Note: This story was originally published in the December 2004 issue of Scientific American.
In an episode of the classic 1950s television comedy The Honeymooners, Brooklyn bus driver Ralph Kramden loudly explains to his wife, Alice, &ldquoYou know that I know how easy you get the virus.&rdquo Half a century ago even regular folks like the Kramdens had some knowledge of viruses&mdashas microscopic bringers of disease. Yet it is almost certain that they did not know exactly what a virus was. They were, and are, not alone.
For about 100 years, the scientifi c community has repeatedly changed its collective mind over what viruses are. First seen as poisons, then as life-forms, then biological chemicals, viruses today are thought of as being in a gray area between living and nonliving: they cannot replicate on their own but can do so in truly living cells and can also affect the behavior of their hosts profoundly. The categorization of viruses as nonliving during much of the modern era of biological science has had an unintended consequence: it has led most researchers to ignore viruses in the study of evolution. Finally, however, scientists are beginning to appreciate viruses as fundamental players in the history of life.
Coming to Terms
It is easy to see why viruses have been diffi cult to pigeonhole. They seem to vary with each lens applied to examine them. The initial interest in viruses stemmed from their association with diseases&mdashthe word &ldquovirus&rdquo has its roots in the Latin term for &ldquopoison.&rdquo In the late 19th century researchers realized that certain diseases, including rabies and foot-and-mouth, were caused by particles that seemed to behave like bacteria but were much smaller. Because they were clearly biological themselves and could be spread from one victim to another with obvious biological effects, viruses were then thought to be the simplest of all living, gene-bearing life-forms.
Their demotion to inert chemicals came after 1935, when Wendell M. Stanley and his colleagues, at what is now the Rockefeller University in New York City, crystallized a virus&mdash tobacco mosaic virus&mdashfor the fi rst time. They saw that it consisted of a package of complex biochemicals. But it lacked essential systems necessary for metabolic functions, the biochemical activity of life. Stanley shared the 1946 Nobel Prize&mdash in chemistry, not in physiology or medicine&mdashfor this work.
Further research by Stanley and others established that a virus consists of nucleic acids (DNA or RNA) enclosed in a protein coat that may also shelter viral proteins involved in infection. By that description, a virus seems more like a chemistry set than an organism. But when a virus enters a cell (called a host after infection), it is far from inactive. It sheds its coat, bares its genes and induces the cell&rsquos own replication machinery to reproduce the intruder&rsquos DNA or RNA and manufacture more viral protein based on the instructions in the viral nucleic acid. The newly created viral bits assemble and, voilà, more virus arises, which also may infect other cells.
These behaviors are what led many to think of viruses as existing at the border between chemistry and life. More poetically, virologists Marc H. V. van Regenmortel of the University of Strasbourg in France and Brian W. J. Mahy of the Centers for Disease Control and Prevention have recently said that with their dependence on host cells, viruses lead &ldquoa kind of borrowed life.&rdquo Interestingly, even though biologists long favored the view that viruses were mere boxes of chemicals, they took advantage of viral activity in host cells to determine how nucleic acids code for proteins: indeed, modern molecular biology rests on a foundation of information gained through viruses.
Molecular biologists went on to crystallize most of the essential components of cells and are today accustomed to thinking about cellular constituents&mdashfor example, ribosomes, mitochondria, membranes, DNA and proteins&mdashas either chemical machinery or the stuff that the machinery uses or produces. This exposure to multiple complex chemical structures that carry out the processes of life is probably a reason that most molecular biologists do not spend a lot of time puzzling over whether viruses are alive. For them, that exercise might seem equivalent to pondering whether those individual subcellular constituents are alive on their own. This myopic view allows them to see only how viruses co-opt cells or cause disease. The more sweeping question of viral contributions to the history of life on earth, which I will address shortly, remains for the most part unanswered and even unasked.
To Be or Not to Be
The seemingly simple question of whether or not viruses are alive, which my students often ask, has probably defi ed a simple answer all these years because it raises a fundamental issue: What exactly defi nes &ldquolife?&rdquo A precise scientifi c defi nition of life is an elusive thing, but most observers would agree that life includes certain qualities in addition to an ability to replicate. For example, a living entity is in a state bounded by birth and death. Living organisms also are thought to require a degree of biochemical autonomy, carrying on the metabolic activities that produce the molecules and energy needed to sustain the organism. This level of autonomy is essential to most definitions.
Viruses, however, parasitize essentially all biomolecular aspects of life. That is, they depend on the host cell for the raw materials and energy necessary for nucleic acid synthesis, protein synthesis, processing and transport, and all other biochemical activities that allow the virus to multiply and spread. One might then conclude that even though these processes come under viral direction, viruses are simply nonliving parasites of living metabolic systems. But a spectrum may exist between what is certainly alive and what is not.
A rock is not alive. A metabolically active sack, devoid of genetic material and the potential for propagation, is also not alive. A bacterium, though, is alive. Although it is a single cell, it can generate energy and the molecules needed to sustain itself, and it can reproduce. But what about a seed? A seed might not be considered alive. Yet it has a potential for life, and it may be destroyed. In this regard, viruses resemble seeds more than they do live cells. They have a certain potential, which can be snuffed out, but they do not attain the more autonomous state of life.
Another way to think about life is as an emergent property of a collection of certain nonliving things. Both life and consciousness are examples of emergent complex systems. They each require a critical level of complexity or interaction to achieve their respective states. A neuron by itself, or even in a network of nerves, is not conscious&mdashwhole brain complexity is needed. Yet even an intact human brain can be biologically alive but incapable of consciousness, or &ldquobrain-dead.&rdquo Similarly, neither cellular nor viral individual genes or proteins are by themselves alive. The enucleated cell is akin to the state of being braindead, in that it lacks a full critical complexity. A virus, too, fails to reach a critical complexity. So life itself is an emergent, complex state, but it is made from the same fundamental, physical building blocks that constitute a virus. Approached from this perspective, viruses, though not fully alive, may be thought of as being more than inert matter: they verge on life.
In fact, in October, French researchers announced fi ndings that illustrate afresh just how close some viruses might come. Didier Raoult and his colleagues at the University of the Mediterranean in Marseille announced that they had sequenced the genome of the largest known virus, Mimivirus, which was discovered in 1992. The virus, about the same size as a small bacterium, infects amoebae. Sequence analysis of the virus revealed numerous genes previously thought to exist only in cellular organisms. Some of these genes are involved in making the proteins encoded by the viral DNA and may make it easier for Mimivirus to co-opt host cell replication systems. As the research team noted in its report in the journal Science, the enormous complexity of the Mimivirus&rsquos genetic complement &ldquochallenges the established frontier between viruses and parasitic cellular organisms.&rdquo
Impact on Evolution
Debates over whether to label viruses as living lead naturally to another question: Is pondering the status of viruses as living or nonliving more than a philosophical exercise, the basis of a lively and heated rhetorical debate but with little real consequence? I think the issue is important, because how scientists regard this question infl uences their thinking about the mechanisms of evolution.
Viruses have their own, ancient evolutionary history, dating to the very origin of cellular life. For example, some viral- repair enzymes&mdashwhich excise and resynthesize damaged DNA, mend oxygen radical damage, and so on&mdash are unique to certain viruses and have existed almost unchanged probably for billions of years.
Nevertheless, most evolutionary biologists hold that because viruses are not alive, they are unworthy of serious consideration when trying to understand evolution. They also look on viruses as coming from host genes that somehow escaped the host and acquired a protein coat. In this view, viruses are fugitive host genes that have degenerated into parasites. And with viruses thus dismissed from the web of life, important contributions they may have made to the origin of species and the maintenance of life may go unrecognized. (Indeed, only four of the 1,205 pages of the 2002 volume The Encyclopedia of Evolution are devoted to viruses.)
Of course, evolutionary biologists do not deny that viruses have had some role in evolution. But by viewing viruses as inanimate, these investigators place them in the same category of infl uences as, say, climate change. Such external infl uences select among individuals having varied, genetically controlled traits those individuals most able to survive and thrive when faced with these challenges go on to reproduce most successfully and hence spread their genes to future generations.
But viruses directly exchange genetic information with living organisms&mdashthat is, within the web of life itself. A possible surprise to most physicians, and perhaps to most evolutionary biologists as well, is that most known viruses are persistent and innocuous, not pathogenic. They take up residence in cells, where they may remain dormant for long periods or take advantage of the cells&rsquo replication apparatus to reproduce at a slow and steady rate. These viruses have developed many clever ways to avoid detection by the host immune system&mdash essentially every step in the immune process can be altered or controlled by various genes found in one virus or another.
Furthermore, a virus genome (the entire complement of DNA or RNA) can permanently colonize its host, adding viral genes to host lineages and ultimately becoming a critical part of the host species&rsquo genome. Viruses therefore surely have effects that are faster and more direct than those of external forces that simply select among more slowly generated, internal genetic variations. The huge population of viruses, combined with their rapid rates of replication and mutation, makes them the world&rsquos leading source of genetic innovation: they constantly &ldquoinvent&rdquo new genes. And unique genes of viral origin may travel, finding their way into other organisms and contributing to evolutionary change.
Data published by the International Human Genome Sequencing Consortium indicate that somewhere between 113 and 223 genes present in bacteria and in the human genome are absent in well-studied organisms&mdashsuch as the yeast Saccharomyces cerevisiae, the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans&mdashthat lie in between those two evolutionary extremes. Some researchers thought that these organisms, which arose after bacteria but before vertebrates, simply lost the genes in question at some point in their evolutionary history. Others suggested that these genes had been transferred directly to the human lineage by invading bacteria.
My colleague Victor DeFilippis of the Vaccine and Gene Therapy Institute of the Oregon Health and Science University and I suggested a third alternative: viruses may originate genes, then colonize two different lineages&mdashfor example, bacteria and vertebrates. A gene apparently bestowed on humanity by bacteria may have been given to both by a virus.
In fact, along with other researchers, Philip Bell of Macquarie University in Sydney, Australia, and I contend that the cell nucleus itself is of viral origin. The advent of the nucleus&mdash which differentiates eukaryotes (organisms whose cells contain a true nucleus), including humans, from prokaryotes, such as bacteria&mdashcannot be satisfactorily explained solely by the gradual adaptation of prokaryotic cells until they became eukaryotic. Rather the nucleus may have evolved from a persisting large DNA virus that made a permanent home within prokaryotes. Some support for this idea comes from sequence data showing that the gene for a DNA polymerase (a DNAcopying enzyme) in the virus called T4, which infects bacteria, is closely related to other DNA polymerase genes in both eukaryotes and the viruses that infect them. Patrick Forterre of the University of Paris-Sud has also analyzed enzymes responsible for DNA replication and has concluded that the genes for such enzymes in eukaryotes probably have a viral origin.
From single-celled organisms to human populations, viruses affect all life on earth, often determining what will survive. But viruses themselves also evolve. New viruses, such as the AIDS-causing HIV-1, may be the only biological entities that researchers can actually witness come into being, providing a real-time example of evolution in action.
Viruses matter to life. They are the constantly changing boundary between the worlds of biology and biochemistry. As we continue to unravel the genomes of more and more organisms, the contributions from this dynamic and ancient gene pool should become apparent. Nobel laureate Salvador Luria mused about the viral infl uence on evolution in 1959. &ldquoMay we not feel,&rdquo he wrote, &ldquothat in the virus, in their merging with the cellular genome and reemerging from them, we observe the units and process which, in the course of evolution, have created the successful genetic patterns that underlie all living cells?&rdquo Regardless of whether or not we consider viruses to be alive, it is time to acknowledge and study them in their natural context&mdashwithin the web of life.
Two New Coronaviruses Make the Leap into Humans
May 20, 2021
S cientists have identified two new coronaviruses in humans, although neither was proven to cause illness or spread to other people. One study identified pigs as the animal host of one virus, and another study found that a coronavirus had likely stemmed from dogs, the first time a canine coronavirus has been shown to infect humans.
“This research clearly shows that more studies are desperately needed to evaluate critical questions regarding the frequency of cross-species [coronavirus] transmission and potential for human-to-human spread,” Ralph Baric, a virologist at the University of North Carolina, Chapel Hill, who was not involved in either study, tells Science.
See “A Brief History of Human Coronaviruses”
The dog study, published May 20 in Clinical Infectious Diseases, stemmed from a question Gregory Gray, an infectious disease epidemiologist at Duke University, had early in the pandemic, reports NPR. He wondered whether there were other coronaviruses already infecting people that might one day spark outbreaks, and he asked his graduate student, coauthor Leshan Xiu, to design a test that would detect not just SARS-CoV-2, but previously unknown coronaviruses as well.
The team used its diagnostic test to screen more than 300 nasal swabs taken from pneumonia patients in Malaysian Borneo in 2018. Eight patients, or 2.7 percent, showed evidence of prior exposure to a novel coronavirus, and seven were children, Science reports. For a previously undetected virus, “that’s a pretty high prevalence,” Gray tells NPR. “That’s remarkable.”
Gray sent samples of the virus to Anastasia Vlasova, an expert in animal coronaviruses at the Ohio State University, and she found that the virus was actually a chimera—portions of its genome matched a feline coronavirus, while another part was similar to a porcine coronavirus. But the majority of its genome was most similar to two coronaviruses previously isolated from dogs, and she was able to grow the virus in canine cell cultures. “Canine coronaviruses were not thought to be transmitted to people,” Vlasova tells NPR. “It’s never been reported before.”
It’s not clear if the virus, dubbed CCoV-HuPn-2018, caused the patients’ pneumonia, and it’s not yet known if the virus is capable of jumping from person to person or how an adult immune system might react if it did. “We don’t really have evidence right now that this virus can cause severe illness in adults,” Vlasova says in a press release.
She did find that the virus had a key mutation—a deletion—that isn’t found in other canine coronaviruses but is found in those that infect humans. While it warrants further study to determine if this mutation is necessary for initiating a cross-species jump, Vlasova adds that she “cannot rule out the possibility that at some point this new coronavirus will become a prevalent human pathogen. Once a coronavirus is able to infect a human, all bets are off.”
Speaking to NPR, Xumin Zhang, a virologist at the University of Arkansas for Medical Sciences, says, “As the authors are careful to say in their paper, they have not proven what’s called Koch’s postulates,” meaning they would need to infect a human with the virus in order to show that it causes pneumonia. Such an experiment would be unethical, he adds, but they could instead test more samples to see how common the virus is in pneumonia patients and then use animal models to test their hypotheses.
See “Coronavirus Closeup, 1964”
The pig study, released as a preprint on medRxiv in March and since submitted to a peer-reviewed journal, identified a new coronavirus in serum samples from three Haitian children who came to the hospital with fevers between 2014 and 2015. Researchers at the University of Florida were able to grow the virus in monkey cells, and a genomic analysis showed that it closely matched known delta-coronaviruses in pigs.
Coronaviruses parse into four groups—alpha, beta, gamma, and delta—and delta-coronaviruses were once thought to only infect birds, Science reports. But in 2012, one appeared in pigs in Hong Kong, thought to have jumped from songbirds. The same virus caused a 2014 outbreak in swine in the US, and delta-coronaviruses have since been shown to infect human cells as well.
The coronaviruses most dangerous to humans—SARS-CoV, SARS-CoV-2, and MERS-CoV—have all been betas. While delta-coronaviruses cause significant outbreaks in animals, the same has not been true in humans. Alphas, including the dog-derived coronavirus isolated in Malaysia, have also never triggered epidemics in humans, Texas A&M University virologist Benjamin Neuman tells Science, “but that doesn’t feel like much comfort in the wild world of viruses.”
Taken together, the studies suggest that coronaviruses are likely circulating in animals at higher rates than previously thought. “I think the more we look, the more we will find that these coronaviruses are crossing species everywhere,” University of Iowa virologist Stanley Perlman, who was not involved in the work, tells Science.
The goal moving forward, Gray says in the press release, will be to seek out these viruses before they cause illness in people. “We are likely missing important animal viruses that are beginning to adapt to humans,” he says, adding that places where animals and people intermingle, such as open markets or farms, might be good places to screen for “early warning[s] of a new virus which may become a future pandemic virus.”
Could Crispr Be Humanity's Next Virus Killer?
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On February 19, Tim Abbott, a PhD candidate at Stanford University’s Bioengineering Department, checked the results of an experiment that he was running as a part of a team using the gene-manipulating Crispr technology to fight coronavirus. Abbott was working out of the lab of Stanley Qi, a pioneer developing Crispr tools that can mess with cancer cells and the like to fight diseases. Using an approach the lab called PAC-MAN (Prophylactic Antiviral Crispr in huMAN cells), the idea was to attack the coronavirus by directing a Crispr torpedo at it, attacking the virus’s genetic makeup that allows it to penetrate human cells and then use the cell’s machinery to self-replicate.
What Is the Coronavirus?
In this particular experiment, he had introduced the lab’s Crispr-based system for finding and destroying SARS-Cov 2 (what scientists call the new coronavirus) into a solution containing an inert synthesized fragment of that virus. Like all Crispr systems, this one was composed of two parts: an enzyme and a strand of so-called "guide RNA." The RNA directs the enzyme, in this case, Cas-13d, to latch onto specific spots in the coronavirus's genome where it then makes a series of cuts. You can think of it like a pair of scissors programmed to scan a cookbook and chop up only the page containing the recipe for SARS-Cov-2.
After Abbott analyzed the data, he called over Marie La Russa, a research scientist managing the project, to verify what he’d seen. The coronavirus-targeted Crispr had reduced the amount of virus in the solution by 90 percent. If effectively delivered, this kill rate, they theorized, might be enough to stop the disease in a human.
That result, along with others included in a paper released last weekend—in preprint form and not yet peer-reviewed—suggests that we may be entering an era of developing new Crispr-based weapons against deadly viruses, from flus to coronaviruses. “The PAC-MAN approach,” the authors wrote, “is potentially a rapidly implementable pan-coronavirus strategy to deal with emerging pandemic strains.”
But before you spring from your isolation-in-place for a cheer, underline “potentially.” As the Stanford team readily admits, their paper is more a blueprint, or proof of concept, than an actual medical treatment ready for testing in animals or humans. The project has some serious X-factors, including the fact that they weren’t able to test PAC-MAN on the actual coronavirus. They still haven’t developed a system to get it into human cells. And, as Fyodor Urnov, a professor in UC Berkeley’s Department of Molecular and Cell Biology, points out, even if it works, there’s still a long horizon between preprint and clinical testing. “There is, frankly, zero chance that this approach can be tested in humans in the next four to six months,” says Urnov. “By analogy, if we were trying to go to the moon and come back safely, what this work shows is one can build a rocket that achieves escape velocity.”
No, it’s not a quick fix, but working on moon shots isn’t a bad idea. “We are at point in human history where every thoughtful idea should be pursued, well beyond the tools we have, which were developed in the 13th century (quarantine), the 17th century (medicines) and the 18th century (inoculation/vaccination),” says Laurie Zoloth, senior advisor to the provost at the University of Chicago for programs on social ethics. “Crispr is very new, very unproven in human disease, but it is logical that it should work.”
The gene-editing power of Crispr technology has been increasingly directed at fighting diseases, originally against genetic ones. But more recently, it’s been harnessed to fight infectious diseases, including, now, the new coronavirus. For instance, multiple teams inside and outside of academia are working on using Crispr for more effective tests. Mammoth Biosciences, a private company, claims to have developed a test for Covid-19 that cuts the result time from several hours to under 30 minutes. Sherlock Biosciences has produced a protocol that could possibly enable something that would work like a pregnancy test, giving a positive signal on a test strip.
Efforts using Crispr to actually prevent or fight coronavirus are also emerging from existing projects designed to fight influenza and other infectious viruses. In 2018, Darpa began a four-year program called Prepare. According to its call for proposals, the idea was to use genetic approaches to “generate new medical countermeasures for future use in humans.” Qi’s lab at Stanford was one of several grant recipients. In April 2019, they began working on a Crispr-based means of fighting influenza. Naturally, as the coronavirus spread earlier this year, the team took notice, and in late January they switched their focus to the virus that’s now changed the way we live.
Tackling this particular virus was a challenge. The coronavirus, says Qi, has 30,000 nucleotides, and the Crispr-powered guide RNA can only target regions of 22 nucleotides to cut. It took a lot of bioinformatics computation and experimentation to locate the best spots to attack.
The attack itself, says Qi, is a double-barreled genetic assault, affecting the target. “One effect is to decrease the concentration of the virus genome inside the human cells,” he says. “The second is to block the production of the viral proteins” that it would otherwise use to create copies of itself and overwhelm the body’s defenses.
The nature of the attack inspired its arcade moniker. ”I like videogames,” says Qi. “The Pac-Man tries to eat cookies, and it is chased by a ghost. But when it encounters a specific kind of cookie called the power cookie—in our case will be a Crispr Cas13 design—suddenly it turns itself to be so powerful. It can start eating the ghost and start cleaning up the whole battlefield.”
But before PAC-Man can try to clean up anything, the Stanford group has a lot of work to do to prove that their concept will work in actual human bodies.
The biggest caveat so far is that they didn’t use the actual SARS-Cov-2 coronavirus in the experiment. Since they could not get sufficient samples of the coronavirus—and did not have the authorization to handle the dangerous virus—Qi’s group created what they called a synthesized, non-replicating version that they felt expressed the relevant genetic characteristics to serve as a stand-in for the actual virus.
The Stanford group contends that their result matters, even without the live virus. “Using fragments of the coronavirus show that there are regions that we can target and interfere with,” says Abbott. “This won't end at just a concept—this will eventually be brought into something that's rapidly deployable.”
But other researchers say that in order to prove you can neutralize the virus, you have to use the real thing. “These viruses replicate rapidly,” says Philip Santangelo, a professor at Georgia Tech University who is part of a team (that also received one of the Darpa Prepare grants) working on a similar Crispr-based approach to fighting influenza-like outbreaks, and is now studying the coronavirus. “Their study doesn’t deal with those kinetics.”
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Another problem: There’s not yet a proven delivery system for a Crispr-based treatment for viruses. One of the continuing problems of Crispr medicine is a way to get the treatment to the right cells. The lung, where the coronavirus battle must be fought, is a particularly tricky battlefield—relatively inaccessible and full of mucus that could interfere with targeting. Qi says that while there are a number of potential options, he has yet to find the ideal way to introduce the PAC-MAN RNA to the virus. Perhaps, he suggests, someone else’s solution to this problem is already out there. “That’s one reason why we posted the paper so quickly,” he says. “Some people may have amazing delivery methods.”
Santangelo’s team at Georgia Tech, which is collaborating with several other universities, believes the answer is a nebulizer, a mist-inhaling device that allows subjects to breathe in the Crispr-based treatment. This week, in fact, they are testing the nebulizer/Crispr combo on a mouse.
Extended Data Fig. 1 Gene expression of ACE2 in an in vitro air-liquid interface (ALI) system.
Epithelial regeneration system from nasal epithelial cells was used for in vitro cultures on successive days (7, 12 and 28), resulting in different epithelial cell types along differentiation trajectory characterized in Ruiz García et al. 2019. The cultures were differentiated in Pneumacult media. Schematic illustration depicts the respective cell types in the differentiation trajectory, and the dot plot illustrates the cultured cell types along the differentiation pseudotime, along with their respective location within the epithelial layers. For gene expression results in the dot plot: the dot size represents the proportion of cells within the respective cell type expressing the gene and the dot color represents the average gene expression level within the particular cell type.
Extended Data Fig. 2 Expression and co-expression of SARS-CoV-2 entry-associated proteases in ACE2 + airway epithelial cells.
The expression of SARS-CoV-2 entry-associated proteases TMPRSS2, CTSB, and CTSL in ACE2 + cells from the Vieira Braga, Kar et al. (top) and Deprez et al. (bottom) airway epithelial datasets is shown. The color represents the expression level at the single-cell resolution and the cells are grouped based on the cell types specified.
Extended Data Fig. 3 Spearman’s correlation results from the two airway datasets are largely consistent.
a, Respiratory epithelial expression of the top 50 genes correlated with ACE2 expression based on Spearman’s correlation analysis performed on all cells within the Deprez et al. dataset. The colored gene names represent genes that are immune-associated (GO:0002376: immune system process). b, The Spearman’s correlation coefficients of gene expression with ACE2 from the Vieira Braga, Kar et al. airway epithelial dataset and the Deprez et al. airway dataset are shown in the scatter plot. The number of observations for the genes is counted in each bin, the value on the x-axis represents the Spearman’s correlation coefficients from the Vieira Braga, Kar et al. dataset, and the value on the y-axis represents the Spearman’s correlation coefficients from the Deprez et al. dataset.