Spillover: the powerful, prescient book that predicted the Covid-19 coronavirus pandemic.
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A zoonosis is an animal infection transmissible to humans.
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Infectious disease is a kind of natural mortar binding one creature to another, one species to another, within the elaborate biophysical edifices we call ecosystems.
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Smallpox could be eradicated because that virus, lacking ability to reside and reproduce anywhere but in a human body (or a carefully watched lab animal), couldn’t hide.
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The eradication campaign for poliomyelitis, unlike other well-meant and expensive global health initiatives, may succeed. Why? Because vaccinating humans by the millions is inexpensive, easy, and permanently effective, and because apart from infecting humans, the poliovirus has nowhere to hide. It’s not zoonotic.
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Polio success story
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By the cold Darwinian logic of natural selection, evolution codifies happenstance into strategy.
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To reside undetected within a reservoir host is probably easiest wherever biological diversity is high and the ecosystem is relatively undisturbed. The converse is also true: Ecological disturbance causes diseases to emerge. Shake a tree, and things fall out.
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Reservoir host = natural host
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Nearly all zoonotic diseases result from infection by one of six kinds of pathogen: viruses, bacteria, fungi, protists (a group of small, complex creatures such as amoebae, formerly but misleadingly known as protozoans), prions, and worms.
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Viruses are the most problematic. They evolve quickly, they are unaffected by antibiotics, they can be elusive, they can be versatile, they can inflict extremely high rates of fatality, and they are fiendishly simple, at least relative to other living or quasi-living creatures.
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The thing with viruses
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the percentage of sampled individuals showing some history of infection, either present or past—is called seroprevalence. It constitutes an estimate, based on finite sampling, of what the percentage throughout an entire population might be.
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Seroprevalance
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An amplifier host is a creature in which a virus or other pathogen replicates—and from which it spews—with extraordinary abundance.
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Human-caused ecological pressures and disruptions are bringing animal pathogens ever more into contact with human populations, while human technology and behavior are spreading those pathogens ever more widely and quickly.
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“Spillover” is the term used by disease ecologists (it has a different use for economists) to denote the moment when a pathogen passes from members of one species, as host, into members of another. It’s a focused event.
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spillover in the reverse direction—from humans to a nonhuman species—is known as an anthroponosis.
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their trapping and hunting efforts, plus the bounties they paid for creatures delivered alive by villagers, yielded more than fifteen hundred animals representing 117 species. There were monkeys, rats, mice, bats, mongooses, squirrels, pangolins, shrews, porcupines, duikers, birds, tortoises, and snakes. Blood was taken from each, and then snips of liver, kidney, and spleen. All these samples, deep-frozen in individual vials, were shipped back to the CDC for analysis. Could any live virus be grown from the sampled tissues? Could any Ebola antibodies be detected in blood serum? The bottom line, ...more
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The elusive Ebola
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Many factors contribute to the case fatality rate during an outbreak, including diet, economic conditions, public health in general, and the medical care available in the location where an outbreak occurs.
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Some scientists use the term “dead-end host,” as distinct from “reservoir host,” to describe humanity’s role in the lives and adventures of ebolaviruses. What the term implies is this: Outbreaks have been contained and terminated; in each situation the virus has come to a dead end, leaving no offspring. Not the virus in toto throughout its range, of course, but that lineage of virus, the one that has spilled over, betting everything on this gambit—it’s gone, kaput. It’s an evolutionary loser. It hasn’t caught hold to become an endemic disease within human populations. It hasn’t caused a huge ...more
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Ebola: An evolutionary loser
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Every spillover is like a sweepstakes ticket, bought by the pathogen, for the prize of a new and more grandiose existence. It’s a long-shot chance to transcend the dead end. To go where it hasn’t gone and be what it hasn’t been. Sometimes the bettor wins big. Think of HIV.
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Lmao
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concerning the five ebolaviruses: “Viruses of each species have genomes that6 are at least 30–40% divergent from one another, a level of diversity that presumably reflects differences in the ecologic niche they occupy and in their evolutionary history.” Towner and company suggested that some of the crucial differences between one ebolavirus and another—including the differences in lethality—might be related to where and how they live, where and how they have lived, within their reservoir hosts.
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Ebola: a multifaceted killer
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Acholi cultural knowledge dictated a program of special behaviors, some of which were quite appropriate for controlling infectious disease, whether you believed it was caused by spirits or by a virus. These behaviors included quarantining each patient in a house apart from other houses; relying on a survivor of the epidemic (if there were any) to provide care to each patient; limiting movement of people between the affected village and others; abstaining from sexual relations; not eating rotten or smoked meat; and suspending the ordinary burial practices, which would involve an open casket and ...more
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Wisdom
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another aspect of the pathology of Ebola virus disease is a phenomenon called disseminated intravascular coagulation, familiar to the medical community as DIC. It’s also known as consumptive coagulopathy (if that helps you), because it involves consumption of too much of the blood’s coagulating capacity in a misdirected way. Billy Karesh had told me about DIC as we boated down the Mambili River after our gorilla stakeout. Disseminated intravascular coagulation, he explained, is a form of pathological blood sludge, in which the normal clotting factors (coagulation proteins and platelets) are ...more
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One of the lab people at Porton Down was Geoffrey S. Platt. On November 5, 1976, in the course of an experiment, Platt filled a syringe with homogenized liver from a guinea pig that had been infected with the Sudanese virus. Presumably he intended to inject that fluid into another test animal. Something went amiss, and instead he jabbed himself in the thumb. Platt didn’t know exactly what pathogen he had just exposed himself to, but he knew it wasn’t good. The fatality rate from this unidentified virus, as he must have been aware, was upwards of 50 percent. Immediately he peeled off his ...more
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Ebola is relentless
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Did you ever consider not going back to Ebola? I asked. “No,” she said. Why do you love this work so much? “I don’t know,” she said, and began to ruminate. “I mean, why Ebola? It only kills maybe a couple hundred people a year.” That is, it hasn’t been a disease of massive global significance and, notwithstanding the lurid scenarios that some people evoke, it’s unlikely ever to become one. But she could cite its attractions in scientific terms. She took deep interest, for instance, in the fact that such a simple organism can be so potently lethal. It contains only a tiny genome, enough to ...more
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The allure of Ebola
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Ebola virus is not in your habitat. You are in its.
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Ebola is difficult to study, Leroy explained, because of the character of the virus. It strikes rarely, it progresses quickly through the course of infection, it kills or it doesn’t kill within just a few days, it affects only dozens or hundreds of people in each outbreak, and those people generally live in remote areas, far from research hospitals and medical institutes—far even from his institute, CIRMF. (It takes about two days to travel, by road and river, from Franceville to Mayibout 2.) Then the outbreak exhausts itself locally, coming to a dead end, or is successfully stanched by ...more
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What Walsh suggested—to recapitulate in simplest form—is a wave of Ebola virus sweeping across Central Africa by newly infecting some reservoir host or hosts. From its recent establishment in the host, according to Walsh, the virus spilled over, here and there, into ape and human populations. The result of that process is manifest as a sequence of human outbreaks coinciding with clusters of dead chimps and gorillas—almost as though the virus were sweeping through ape populations across Central Africa. Walsh insisted during our Libreville chat, though, that he had never proposed a continental ...more
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there’s a critical minimum size of the host population, below which it can’t persist indefinitely as an endemic, circulating infection. This is known as the critical community size (CCS), an important parameter in disease dynamics. The critical community size for measles seems to be somewhere around five hundred thousand people. That number reflects characteristics specific to the disease, such as the transmission efficiency of the virus, its virulence (as measured by the case fatality rate), and the fact that one-time exposure confers lifelong immunity. Any isolated community of less than a ...more
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On critical community size *Does not apply to zoonotic pathogens
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Although the control measures he advocated were effective toward reducing malaria in certain locales (Panama, Mauritius), in other places they failed to do much good (Sierra Leone, India) or the results were transitory. For all his honors, for all his mathematical skills, for all his combative ambition and obsessive hard work, Ronald Ross couldn’t conquer malaria, nor even provide a strategy by which such an absolute victory would eventually be won. He may have understood why: because it’s such an intricate disease, deeply entangled with human social and economic considerations as well as ...more
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Why malaria couldn't be arrested by math alone
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The four kinds of malaria to which these statements applied are caused by protists of the species Plasmodium vivax, Plasmodium falciparum, Plasmodium ovale, and Plasmodium malariae, all of them belonging to the same diverse genus, Plasmodium, which encompasses about two hundred species. Most of the others infect birds, reptiles, or nonhuman mammals. The four known for targeting humans are transmitted from person to person by Anopheles mosquitoes. These four parasites possess wondrously complicated life histories, encompassing multiple metamorphoses and different forms in series: an asexual ...more
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The malarial life cycle
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It shows evolution’s power, over great lengths of time, to produce structures, tactics, and transformations of majestic intricacy. Alternatively, anyone who favors Intelligent Design in lieu of evolution might pause to wonder why God devoted so much of His intelligence to designing malarial parasites.
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Within the Plasmodium family tree, as revealed by molecular phylogenetics over the last two decades, the four human-afflicting kinds don’t cluster on a single branch. They are each more closely related to other kinds of Plasmodium, infecting nonhuman hosts, than to one another. In the lingo of taxonomists, they are polyphyletic. What that suggests, besides the diversity of their genus, is that each of them must have made the leap to humans independently.
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Each malaria has a different origin story
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the entire genetic range of P. falciparum in humans forms “a monophyletic lineage within the gorilla P. falciparum radiation.”9 In plain talk: The human version is one twig within a gorilla branch, suggesting that it came from a single spillover. That’s one mosquito biting one infected gorilla, becoming a carrier, and then biting one human. By delivering the parasite into a new host, that second bite was enough to account for a zoonosis that still kills more than a half million people each year.
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Ek machchar insaan ko...
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dR/dt = γI merely means that the number of recovered individuals in the population, at a given moment, reflects the number of infected individuals times the average recovery rate. So much for R, the “recovered” class. The equations for S (“susceptibles”) and I (“infected”) are likewise opaque but sensible. All this became known as an SIR model. It was a handy tool for thinking about infectious outbreaks, still widely used by disease theorists.
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A look into the SIR disease model
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MacDonald got some of his field experience in Ceylon (now Sri Lanka) during the late 1930s, just after a calamitous malaria epidemic there in 1934–1935, which sickened a third of the Ceylonese populace and killed eighty thousand. The severity of the Ceylon epidemic had been surprising because the disease was familiar, at least in parts of the island, recurring as modest annual outbreaks that mostly affected young children. What happened differently in 1934–1935 was that, after a handful of years with little malaria at all, a drought increased breeding habitat for mosquitoes (standing pools in ...more
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Dayum
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The ultimate product of MacDonald’s equations was a single number, which he called the basic reproduction rate. That rate represented, in his words, “the number of infections distributed in a community13 as the direct result of the presence in it of a single primary non-immune case.” More precisely, it was the average number of secondary infections produced, at the beginning of an outbreak, when one infected individual enters a population where all individuals are nonimmune and therefore susceptible. MacDonald had identified a crucial index—fateful, determinative. If the basic reproduction ...more
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I wonder what it's like for COVID
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Wagner-Juaregg solved that problem after noting that Treponema pallidum didn’t survive in a test tube at temperatures much above 98.6 degrees Fahrenheit. Raise the blood temperature of the infected person a few degrees, he realized, and you might cook the bacterium to death. So he began inoculating patients with Plasmodium vivax. He would allow them to cycle through three or four spikes of fever, delivering potent if not terminal setbacks to the Treponema, and then dose them with quinine, bringing the plasmodium under control. “The effect was remarkable;15 the downward progression of ...more
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Killing syphilis with malaria
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Ciuca evidently felt that Plasmodium knowlesi might be a better weapon against neurosyphilis than other kinds of the parasite. He inoculated several hundred patients and, in 1937, reported fairly good success. His program of treatments continued until, almost twenty years later, a problem arose. Repeatedly passaging P. knowlesi through a series of human hosts (injecting infected blood, allowing the merozoites to multiply, and then extracting infected blood) had made Ciuca’s strain increasingly virulent—too virulent for comfort. After 170 such passages, he and his colleagues became concerned ...more
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Poison turned medicine turned poison again
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PCR amplification of DNA fragments, followed by sequencing (reading out the genetic spelling) of those fragments, plumbs far deeper than microscopy. It allows a researcher to see below the level of cellular structure to the letter-by-letter genetic code.
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Why PCR testing is better
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In the RNA molecule, which serves for translating DNA into proteins (and has other roles, as we’ll see), a different piece called uracil substitutes for thymine, and the Scrabble pieces are therefore A, C, G, and U.
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RNA has Uracine instead of Thymine
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Her husband pulled down a box and opened it. “This is our collection of blood spots,” he said with quiet pride. Borneo is off the beaten path and, I suppose, not many science journalists visit. Inside the box was a neat file of plastic envelopes, each one containing a piece of porous paper no bigger than a business card; on each card was a rusty black spot. Near the center of the dark spot, on the card I inspected closely, was a perfectly round little hole. The punched dot, missing there, had already surrendered its secrets to science. DNA confetti.
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Loved this XD
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Plasmodium knowlesi malaria, they wrote, is not a new emergent infection of humans. It has been getting into people for some while but it was overlooked. Three kinds of Asian primate serve as its reservoir hosts: the long-tailed macaque, the pig-tailed macaque, and the banded leaf monkey. Other monkeys, still unidentified, might be harboring the parasite too. Transmission from monkey to monkey (and from monkey to human) occurs by way of mosquitoes belonging to one group of closely related species, Anopheles leucosphyrus and its cousins, including Anopheles latens in Borneo. Anopheles latens is ...more
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Greed shall bring us down
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the level of human jeopardy depends on other factors besides the geographical ranges of the mosquitoes and the monkeys. It depends on whether those mosquitoes come out of the forest to bite humans, and whether people go into the forest to be bitten. It depends on whether sizable expanses of forest are left standing within that region and, if not, how the mosquitoes react. As deforestation proceeds, do the forest mosquitoes go extinct, or do they adapt? It depends on whether the parasite becomes so well established within human populations that monkey hosts are no longer necessary. It depends ...more
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Two aspects of what made SARS so threatening were its degree of infectiousness—especially within contexts of medical care—and its lethality, which was much higher than in familiar forms of pneumonia. Another ominous trait was that the new bug, whatever it might be, seemed so very good at riding airplanes.
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Novel coronavirus: "Hold my beer"
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Snake on the menu wasn’t unusual in Guangdong. It’s a province of ravenous, unsqueamish carnivores, where the list of animals considered delectable could be mistaken for the inventory of a pet store or a zoo.
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Symptoms included headache, high fever, chills, body aches, severe and persistent coughing, coughing up bloody phlegm, and progressive destruction of the lungs, which tended to stiffen and fill with fluid, causing oxygen deprivation that in some cases led to organ failure and death.
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SARS symptoms
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While R0 (that important variable introduced to disease mathematics by George MacDonald) represents the average number of secondary infections caused by each primary infection at the start of an outbreak, a superspreader is someone who dramatically exceeds the average. The presence of a superspreader in the mix, therefore, is a crucial factor in practical terms that might be overlooked by the usual math. “Population estimates of R0 can obscure5 considerable individual variation in infectiousness,” according to J. O. Lloyd-Smith and several colleagues, writing in the journal Nature, “as ...more
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On superspreaders
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Back in Singapore, health officials and government authorities cooperated to stanch further transmission. They enacted firm measures that reached far beyond the hospitals—such as enforced quarantine of possible cases, jail time and fines for quarantine breakers, closure of a large public market, school closures, daily temperature checks for cab drivers—and the outbreak was brought to an end. Singapore is an atypical city, firmly governed and orderly (that’s putting it politely), therefore especially capable of dealing with an atypical pneumonia, even one so menacing as this. On May 20, 2003, ...more
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the culturing work had established that an unknown coronavirus was present in SARS patients—some of them, anyway—but that didn’t necessarily mean it had caused the disease. To establish causality, Peiris’s team tested blood serum from SARS patients (because it would contain antibodies) against the newfound virus in culture. This was like splashing holy water at a witch. The antibodies recognized the virus and reacted strongly. Less than a month later, based on that evidence plus other confirming tests, Malik Peiris and his colleagues published a paper cautiously announcing this new coronavirus ...more
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Just the presence of the virus doesn't prove causality
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SARS-CoV has no ominous ring. In older days, the new agent would have received a more vivid, geographical moniker such as Foshan virus or Guangzhou virus, and people would have run around saying: Watch out, he’s got Guangzhou! But by 2003 everyone recognized that such labeling would be invidious, unwelcome, and bad for tourism.
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Smart
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IN A CROWDED country with 1.3 billion hungry citizens, it should be no surprise that people eat snake. It should be no surprise that there are Cantonese recipes for dog. Stir-fried cat, in such a context, seems sadly inevitable rather than shocking. But the civet cat (Paguma larvata) is not really a cat. More accurately known as the masked palm civet, it’s a member of the viverrid family, which includes the mongooses. The culinary trade in such unusual wild animals, especially within the Pearl River Delta, has less to do with limited resources, dire necessity, and ancient traditions than with ...more
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The Era of Wild Flavor
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Li’s focused specifically on bats. The team trapped animals from the wild, drew blood, took fecal and throat swabs, and then analyzed duplicate samples of the material independently at labs in China and Australia, creating a double-check on themselves that strengthened the certitude of their results. What they found was a coronavirus that, unlike Leo Poon’s, closely resembled SARS-CoV as seen in human patients. They called it SARS-like coronavirus. Their sampling showed that this SARS-like virus was especially prevalent in several bats belonging to the genus Rhinolophus, known commonly as ...more
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SARS-CoV2?
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