It’s a bacterium, admittedly, with some peculiar traits. When assaulted with antibiotics, for instance, B. burgdorferi seems to retreat into a defensive, impervious form, a sort of cystlike stage known as a “round body.” Round bodies are resistant to destruction and very difficult to detect. A patient who seems cured of Lyme disease by the standard two-to-four-week course of amoxicillin or doxycycline might still be harboring round bodies and therefore subject to relapse. Round bodies might even explain the “chronic Lyme disease” syndrome so hotly contested by suffering patients, maverick physicians, and the IDSA. Or not.
Don’t confuse the round bodies of Borrelia burgdorferi with the small form of Coxiella burnetii, the agent of Q fever, also cystlike but found adrift on the Dutch breezes, carrying infection downwind from a birthing goat. Nobody is claiming, not so far, anyway, that Lyme disease can likewise travel on the wind. Both the round bodies of B. burgdorferi and the small form of C. burnetii merely illustrate that, even in the age of antibiotics, bacteria can be sneaky and tough. These microbes remind us that you don’t have to be a virus to cause severe, intractable, mystifying outbreaks of zoonotic disease in the twenty-first century. Although it helps.
VI
GOING VIRAL
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Viruses were an invisible mystery, like dark matter and Planet X, until well into the twentieth century. They were momentously consequential but undetectable, like the neutron. Anton van Leeuwenhoek’s microbial discoveries hadn’t encompassed them, nor had the bacteriological breakthroughs of Pasteur and Koch, two hundred years later. Pasteur worked on rabies as a disease, true, and even developed a vaccine, but he never laid eyes on the rabies virus itself nor quite understood what it was. Likewise, in 1902, William C. Gorgas eliminated yellow fever from Cuba, by a program of mosquito eradication, without ever knowing just what infectious agent those mosquitoes carried. It was like a blindfolded hunter shooting ducks by the sound of their quacking. Even the influenza virus of 1918–1919, having killed up to 50 million people around the world, remained a ghostly cipher, unseen and unidentified at the time. Viruses couldn’t be viewed with an optical microscope; they couldn’t be grown in a culture of chemical nutrients; they couldn’t be captured, as bacteria could, with a porcelain filter. They could only be inferred.
Why so elusive? Because viruses are vanishingly minuscule, simple but ingenious, anomalous, economical, and in some cases fiendishly subtle. Expert opinion even divides on the conundrum of whether viruses are alive. If they aren’t, then at the very least they’re mechanistic shortcuts on the principle of life itself. They parasitize. They compete. They attack, they evade. They struggle. They obey the same basic imperatives as all living creatures—to survive, to multiply, to perpetuate their lineage—and they do it using intricate strategies shaped by Darwinian natural selection. They evolve. The viruses on Earth today are well fit for what they do because only the fittest have survived.
The word “virus” has a much longer history than the study of what we now call by that name. It comes directly from the Latin virus, a term meaning “poison, sap of plants, slimy liquid.” You can even find the Latin word rendered as “poisonous slime.” Its earliest known use in English to denote a disease-causing agent was in 1728, though for the rest of the eighteenth century, throughout the nineteenth, and for several decades beyond, there was no clear distinction between “virus” as a vague term, applicable to any infectious microbe, and the very particular group of entities we know as viral today. As late as 1940, even Macfarlane Burnet sometimes called the Q fever microbe a “virus” in casual usage, though by then he knew perfectly well it was a bacterium.
The effects of viruses were detected long before viruses themselves. Smallpox and rabies and measles were excruciatingly familiar at the clinical level for centuries, millennia, although their causal agents weren’t. Acute disease and epidemic outbreaks were understood in a variety of inventive ways—as caused by miasmal vapors and “effluvia,” by decaying matter and filth, by poverty, by the whim of God, by bad magic, by cold air or wet feet—but the recognition of infectious microbes came slowly. Around 1840, a German anatomist named Jakob Henle began to suspect the existence of noxious particles—creatures or things—that were too small to be seen with a light microscope and yet able to transmit specific diseases. Henle had no evidence, and the idea didn’t immediately take hold. In 1846, a Danish physician named Peter Panum witnessed a measles epidemic on the Faroe Islands, a remote archipelago north of Scotland, and drew some keen inferences about how the ailment seemed to pass from person to person, with a delay of about two weeks (what we’d now call an incubation period) between exposure and symptoms. Robert Koch, who had been a student of Jakob Henle’s at Göttingen, advanced beyond observation and supposition with his experimental work of the 1870s and 1880s, identifying the microbial causes of anthrax, tuberculosis, and cholera. Koch’s discoveries, along with those of Pasteur and Joseph Lister and William Roberts and John Burdon Sanderson and others, provided the empirical bases for a swirl of late-nineteenth-century ideas that commonly get lumped as “the germ theory” of disease, which marked a movement away from older notions of malign vapors, transmissible poisons, imbalanced humors, contagious putrefaction, and magic. But the germs with which Koch, Pasteur, and Lister mainly concerned themselves (apart from Pasteur’s brilliant guesswork on rabies) were bacteria.
And bacteria weren’t quite so ineffable. They could be seen with a normal microscope. They could be cultured in a Petri dish (the invention of Julius Petri, Koch’s assistant) containing a nutrient-rich medium of agar. They were bigger and easier to grasp than viruses.
The next crucial insight came from agronomy, not medicine. During the early 1890s, a Russian scientist named Dmitri Ivanofsky, in St. Petersburg, studied tobacco mosaic disease, a problem on plantations within the empire. The “mosaic” spots on the leaves led eventually to stunting and shriveling, which lowered productivity and cost growers money. Earlier work had shown that this disease was infectious—it could be transferred experimentally from one plant to another by applying sap drawn from infected leaves. Ivanofsky repeated the transmission experiment, with one added step. He put the juice through a Chamberland filter, a device made from unglazed porcelain, with tiny pores, for purifying water by screening out bacteria. Ivanofsky’s report, that “the sap of leaves infected with tobacco mosaic disease retains its infectious properties even after filtration,” constituted the first operational definition of viruses: infectious but “filterable,” meaning so small they would pass through where bacteria wouldn’t. Soon afterward, a Dutch researcher named Martinus Beijerinck arrived independently at the same result and then pushed one step farther. By diluting the filtered sap from an infected plant and using that tincture to infect another plant, Beijerinck found that the infectious stuff, whatever it was, regained its full strength even after dilution. That meant it was reproducing itself in the second plant’s living tissues, which meant in turn that it wasn’t a toxin, a poisonous excretion, of the sort that some bacteria produce. A toxin, diluted in volume, is reduced in effect—and it doesn’t spontaneously recover its strength. This stuff did. But in a container of filtered sap alone, it wouldn’t grow. It needed something else. It needed the plant.
So the cumulative work of Martinus Beijerinck, Dmitri Ivanofsky, and a few colleagues showed that tobacco mosaic disease is caused by an entity smaller than a bacterium, invisible by microscope, and capable of multiplication within—only within—living cells. That was the basic profile of a virus, though still nobody had seen one. Beijerinck guessed that the tobacco-mosaic agent was liquid and labeled it contagium vivum fluidum, a contagious living fluid. Later work, including the invention of the electron microscope in the 1930s, proved him wrong on that point. A virus is not liquid but solid: minute particles.
This was all about plants. The first animal virus discovered was the one causing foot-and-mouth disease, another sore problem to agriculture. Cattle and swine passed it to one
another, like a sneeze on the breeze, and died from it or else had to be culled. Friedrich Loeffler and Paul Froesch, at a university in northern Germany, using the same techniques of filtering and dilution as Beijerinck, proved in 1898 that the foot-and-mouth agent is also a filter-passing entity capable of replication only in living cells. Loeffler and Froesch even noted that it might be just one of a whole class of disease agents, so far undiscovered, possibly including some that infected people, causing phenomena such as smallpox. But the first viral infection recognized in humans wasn’t smallpox; it was yellow fever, in 1901. Around the time William Gorgas was solving the practical problem of yellow fever in Cuba, by killing off all those mosquitoes, Walter Reed and his little team of microbiologists showed that the causative agent was indeed mosquito-transmitted. Still, they couldn’t see it.
Scientists then began using the label “filterable virus,” which was a clumsy but more precise application of the old poisonous-slime word. Hans Zinsser, for example, in his 1934 book Rats, Lice and History, a classic chronicle of medical groping and discovery, declared himself “encouraged by the study of the so-called ‘filterable virus’ agents.” Many epidemic diseases, Zinsser wrote, “are caused by these mysterious ‘somethings’—for example, smallpox, chicken pox, measles, mumps, infantile paralysis, encephalitis, yellow fever, dengue fever, rabies, and influenza, to say nothing of a large number of the most important afflictions of the animal kingdom.” Zinsser realized, too, that some of those animal afflictions might overlap with the first category, human epidemics. He added a crucial point: “Here, as in bacterial disease, there is a lively interchange of parasites between man and the animal world.” Zinsser was a panoramic thinker as well as an acutely trained microbiologist. Eight decades ago he sensed that viruses, only lately discovered, might be among the most nefarious of zoonoses.
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The difficulty of cultivating viruses in vitro made them obscure to early researchers, elusive in the laboratory, but it was also a clue to their essence. A virus won’t grow in a medium of chemical nutrients because it can only replicate inside a living cell. In the technical parlance, it’s an “obligate intracellular parasite.” Its size is small and so is its genome, simplified down to the bare necessities for an opportunistic, dependent existence. It doesn’t contain its own reproductive machinery. It mooches. It steals.
How small is small? The average virus is about one-tenth the size of the average bacterium. In metric terms, which are how science measures them, roundish viruses range from around fifteen nanometers (that’s fifteen billionths of a meter) in diameter to around three hundred nanometers. But viruses aren’t all roundish. Some are cylindrical, some are stringy, some look like bad futuristic buildings or lunar landing modules. Whatever the shape, the interior volume is minuscule. The genomes packed within such small containers are correspondingly limited, ranging from 2,000 nucleotides up to about 1.2 million. The genome of a mouse, by contrast, is about 3 billion nucleotides. It takes three nucleotide bases to specify an amino acid and on average about 250 amino acids to make a protein (though some proteins are much larger). Making proteins is what genes do; everything else in a cell or a virus results from secondary reactions. So a genome of just two thousand code letters, or even thirteen thousand (as for the influenzas) or thirty thousand (the SARS virus), is a very sketchy set of engineering specs. Even with such a small genome, though, coding for just eight or ten proteins, a virus can be wily and effective.
Viruses face four basic challenges: how to get from one host to another, how to penetrate a cell within that host, how to commandeer the cell’s equipment and resources for producing multiple copies of itself, and how to get back out—out of the cell, out of the host, on to the next. A virus’s structure and genetic capabilities are shaped parsimoniously to those tasks.
Sir Peter Medawar, an eminent British biologist who received a Nobel Prize the same year as Macfarlane Burnet, defined a virus as “a piece of bad news wrapped up in a protein.” The “bad news” Medawar had in mind is the genetic material, which so often (but not always) inflicts damage on the host creature while exploiting its cells for refuge and reproduction. The protein wrap is known as a capsid. The capsid serves two purposes: It protects the viral innards when they need protection and it helps the virus lever its way into cells. The individual viral unit, one particle, standing intact outside a cell, is called a virion. The capsid also defines the exterior shape of a virus. Virions of Ebola and Marburg, for instance, are long filaments, which is why they’ve been placed in a group known as filoviruses. Other viruses have particles that are spherical, or ovoid, or helical, or icosahedral (twenty-sided, like a soccer ball designed by Buckminster Fuller). HIV-1 particles are globular. Rabies virions are shaped like bullets. A plate of Ebola virions mixed with Hendra virions would resemble capellini in a light sauce of capers.
Many viruses are wrapped with an additional layer, known as an envelope, comprising not only protein but also lipid molecules drawn from the host cell—in some cases, pulled from the wall of the cell when the virion made its exit. Across the outer surface of the envelope, the virion may be festooned with a large number of spiky molecular protuberances, like the detonator stubs on an old-fashioned naval mine. Those spikes serve a crucial function. They’re specific to each kind of virus, with a keylike structure that fits molecular locks on the outer surface of a target cell; they allow the virion to attach itself, docking like one spaceship to another, and they open the way in. The specificity of the spikes not only constrains which kinds of host a given virus can infect but also which sorts of cell—nerve cells, stomach cells, cells of the respiratory lining—the virus can most effectively penetrate, and therefore what sort of disease it may cause. Useful as they are to a virus, though, the spikes also represent points of vulnerability. They are the primary targets of immune response by an infected host. Antibodies, produced by white blood cells, are molecules that glom onto the spikes and prevent a virion from grabbing a cell.
The capsid shouldn’t be mistaken for a cell wall or a cell membrane. It’s merely analogous. Viruses, from the beginning of virology, have been defined in the negative (not captured by a filter, not cultivable in chemical nutrients, not quite alive), and the most fundamental negative axiom is that a virion is not a cell. It doesn’t function the way a cell functions; it doesn’t share the same capacities or frailties. That’s reflected in the fact that viruses are impervious to antibiotics—chemicals valued for their ability to kill bacteria (which are cells) or at least impede their growth. Penicillin works by preventing bacteria from building their cell walls. So do its synthetic alternatives, such as amoxicillin. Tetracycline works by interfering with the internal metabolic processes by which bacteria manufacture new proteins for cell growth and replication. Viruses, lacking cell walls, lacking internal metabolic processes, are oblivious to the effects of such killer drugs.
Inside the viral capsid is usually nothing but genetic material, the set of instructions for creating new virions on the same pattern. Those instructions can only be implemented when they’re inserted into the works of a living cell. The material itself may be either DNA or RNA, depending on the family of virus. Both types of molecule are capable of recording and expressing information, though each has its advantages and its drawbacks. Herpesviruses, poxviruses, and papillomaviruses contain DNA; so do half a dozen viral families you’ve never heard of, such as the iridoviruses, the baculoviruses, and the hepadnaviruses (one of which causes hepatitis B). Others, including filoviruses, retroviruses (most notoriously, HIV-1), coronaviruses (SARS-CoV), and the families encompassing measles, mumps, Hendra, Nipah, yellow fever, dengue, West Nile, rabies, Machupo, Junin, Lassa, chikungunya, all the hantaviruses, all the influenzas, and the common cold viruses, store their genetic information in the form of RNA.
The different attributes of DNA and RNA account for one of the most crucial differences among viruses: rate of mutation. DNA is a double-stranded molecule, the famed double helix, and bec
ause its two strands fit together by way of those very specific relationships between pairs of nucleotide bases (adenine linking only with thymine, cytosine only with guanine), it generally repairs mistakes in the placement of bases as it replicates itself. This repair work is performed by DNA polymerase, the enzyme that helps catalyze construction of new DNA from single strands. If an adenine is mistakenly set in place to become linked with a guanine (not its correct partner), the polymerase recognizes that mistake, backtracks by one pair, fixes the mismatch, and then moves on. So the rate of mutation in most DNA viruses is relatively low. RNA viruses, coded by a single-strand molecule with no such corrective arrangement, no such buddy-buddy system, no such proofreading polymerase, sustain rates of mutation that may be thousands of times higher. (For the record, there’s also a smaller group of DNA viruses that code their genetics on single strands of DNA and suffer high mutation rates, as in RNA. And there’s a little group of double-stranded RNA viruses. To every rule, an exception. But we’re going to ignore those minor anomalies because this stuff is already complicated enough.) The basic point is so important I’ll repeat it: RNA viruses mutate profligately.
Mutation supplies new genetic variation. Variation is the raw material upon which natural selection operates. Most mutations are harmful, causing crucial dysfunctions and bringing the mutant forms to an evolutionary dead end. But occasionally a mutation happens to be useful and adaptive. And the more mutations occurring, the greater chance that good ones will turn up. (More mutations also mean more chance of harmful ones, lethal to the virus; this puts a cap on the maximum sustainable mutation rate.) RNA viruses therefore evolve quicker than perhaps any other class of organism on Earth. It’s what makes them so volatile, unpredictable, and pesky.
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