Internet videos are not the only things going viral

Shalin Hai-Jew

By A Contributor

Carl Zimmer’s “A Planet of Viruses” captures an elusive topic memorably with its succinct descriptions of the discoveries of various viruses and their roles in human lives (and the life of the planet).

The book opens with the discovery of the Cave of Crystals in the Sierra de Naica mountain range southeast of Chihuahua in Mexico. Hot mineral-filled waters filled the cave and were maintained at stable temperature of 136 degrees by volcanic activity, which resulted in the formation of gypsum crystals growing in structures up to 36 feet long and weighing as much as 55 tons each. The cave was untouched for an estimated 26 million years, and was cut off from the biology of the outside world. Yet, when the cave waters were tested for the presence of viruses, they were plentifully present, with two hundred million viruses in each drop.

“Just about wherever scientists look — deep within the earth, on grains of sand blown off of the Sahara Desert, under mile-thick layers of Antarctic ice — they find viruses,” writes Zimmer.

Whether people are healthy or ill, they carry “viral menageries” in their bodies; in their lungs alone, there are on average 174 species of viruses (and only 10% of those species bear “close kinship” to any virus ever found, with 90% as-yet unknown).

Virology, even though it has existed since the late 1800s, is still in its infancy, with scientists discovering viruses “faster than they can make sense of them.” Viruses are protein shells containing a few genes; they replicate by injecting their genes and proteins into a host cell, which they induce into producing new copies of themselves.

A majority of viruses (and other microbial life forms) serve critical ecological functions in the world (such as creating oxygen and consuming carbon dioxide); however, people are mostly concerned about the viruses that cause human, animal, and plant diseases.

Zimmer highlights a handful of viruses in this thin volume. He describes rhinoviruses which lead to colds, noting that every human being on average will spend a year of his or her life “sick with colds.” With only 10 genes a piece, rhinoviruses have an outsized impact because of the human body’s outsized immune response, which is experienced as discomfort.

Rhinoviruses evolve quickly to adapt to the human defenses, which learn to recognize various strains of rhinoviruses. In response, these have evolved variations that can get past the human body’s antibody defenses. Scientists have been focusing on a “stretch of genetic material in rhinoviruses that folds into a loop shaped like a clover leaf” that is responsible for speeding up the rate of host cell copying of the rhinovirus genes to “stop every cold virus on Earth.”

There is debate on whether trying to eradicate rhinoviruses from the human population is advisable. Some suggest that children who get sick with relatively harmless viruses and bacteria may be protected from immune disorders (such as allergies and Crohn’s Disease) when they get older. They may train the body to avoid overreacting to minor triggers and focus on actual serious microbial assaults.

People are also very familiar with the influenza virus, which afflicts humanity annually, causing 36,000 deaths in the U.S. and a quarter to a half million deaths worldwide. The common flu virus is transmitted by people’s coughs and sneezes. When people breathe in virus-laden droplets or touch infected surfaces (and then touch their own eyes, noses or mouths), they pick up the virus and often become ill. Those who are very young, very old, or immune-compromised are at special risk.

Influenza viruses not only cause run-of-the-mill illnesses, but flu viruses that are especially virulent have decimated massive populations of humanity. The 1918 flu pandemic resulted in 50 million to 130 million dead. Scientists do not yet understand why some mutations of influenza viruses are so deadly.

All human influenza viruses come from birds. “Birds carry all known strains of human influenza viruses, along with a vast diversity of other flu viruses that don’t infect humans. Many birds carry the flu without getting sick. Rather than infecting their airways, flu viruses typically infect the guts of birds; the viruses are then shed in bird droppings. Healthy birds become infected by ingesting virus-laden water,” he writes.

Mutations of flu viruses have jumped the species barrier and become a human virus. A recent outbreak of the H5N1 avian flu had the earmarks of a potential pandemic and put the world on alert in 2003 - 2004. While the virus can transmit from birds to people, so far, H5N1 has not been able to transmit from human-to-human. How it evolves is as-yet unknown.

When a flu virus enters a host, it may invade a cell that is already harboring a flu virus. The viruses then reproduce inside the cell with new offspring carrying genetic material from both viruses through reassortment. This gene swapping means that the mutated virus has new characteristics and capabilities.

In 2009, the emergence of the Human/Swine 2009 H1N1 was of such serious concern that the World Health Organization called it a pandemic. This was a triple reassortant from avian, swine, and human strains of influenza.

The human papillomavirus (HPV), so-named because of “buds” of tumors it creates on infected animals’ heads and skin, is a common sexually transmitted disease. Some 60 percent of males and females carry antibodies for HPV, which shows that they have had the infection at one time. An estimated 270,000 women die each year from cervical cancer caused by HPV infection. This cancer is the third leading cause of death in women, surpassed only by breast cancer and lung cancer. In one man with an immune over-reaction, HPV caused uncontrolled wart growth. This virus itself, which has been deeply studied, uses complex mechanisms to manipulate infected cells to its interests.

There is a vaccine available to defend against the two most common strains of HPV, which account for 70 percent of all cases of cervical cancer. There are other HPV strains in circulation, which suggests the continuing importance of avoiding promiscuous sexual behaviors and unsafe sex.

Bacteriophages are viruses that target bacteria. These viruses, in an electron microscope, feature boxlike shells “sitting atop a set of what looked like spider legs.” Different phage species focus on particular bacteria. For a time in American medicine, bacteriophages were used to combat human disease, but with the success of antibiotics in the 1930s onwards, the focus turned to those medicines. Doctors themselves were uneasy about using live viruses in medicine.

Researchers have been able to engineer existing phages to be much more lethal against harmful bacteria, and they have been able to go through genetic codes to create phages that “can kill in new ways,” writes Zimmer. He gives an example of an engineered phage that wiped out 99.997 percent of the E. coli in a biofilm, “a kill rate that’s about a hundred times better than ordinary phages.”

The ocean, which was thought to be free of viruses, does indeed contain viruses. Marine viruses are highly infectious: “They invade a new microbe host ten trillion times a second, and every day they kill about half of all bacteria in the world’s oceans. Their lethal efficiency keeps their hosts in check, and we humans often benefit from their deadliness.” Marine viruses genetically match very little that is known.

Of 1.8 million viral marine genes, only 10% of them showed any match to any gene from any microbe known. The rest were totally new to science. Fortunately, only a minute fraction of those can infect people.

The discovery of endogenous retroviruses (viruses that insert their DNA into the host cell’s DNA and replicate along with the host cell division) has highlighted both their risks and their criticality in biological functions. Free-living retroviruses can be highly dangerous to human health, but even when they are endogenous, they are still dangerous because mutations can allow them to become free-living viruses that can cause new infections and even cancer. Their integrations with a host’s genetic code may enable it to turn on or turn off various genetic functions.

The human immunodeficiency virus (HIV) is a simian virus that mutated and started infecting people. It is spread between people through the exchange of bodily fluids through unprotected sex, contaminated blood products, the sharing of contaminated needles, and from mother to unborn child. Since HIV-AIDS came to the world’s awareness in the early 1980s, it has led to 40 million deaths worldwide, and some 35 million people are currently infected. While scientists have been pursuing a range of therapies, many of the drug regimens have harmful side effects (and have bred some drug-resistant strains), and the fast mutations of HIV have dampened hope for an effective vaccine.

West Nile virus (WNV) is transferred from infected birds to people through certain species of mosquitoes, which serve as disease vectors. Some 150 American bird species have been found to carry West Nile virus. This pathogen has found a sufficient fit in the U.S. ecology to suggest that it may become established and endemic. People who are infected with WNV may suffer permanent neurological effects. Sometimes, WNV infection results in death. There is no current treatment or cure.

Smallpox, which has ostensibly been eradicated from humanity, has remained worrisome for its potential as a biological warfare agent.

In the past 3,000 years, smallpox may have killed more people than any other disease on Earth, the author notes. Infection with smallpox resulted in the deaths of a third of those infected; others were scabbed with permanent scars.

People today no longer have smallpox immunities. The idea was to have two remaining samples of smallpox put in deep storage in Novosibirsk in Russia and at the US Centers for Disease Control and Prevention in Atlanta, Georgia.

However, during Soviet rule, smallpox stocks were sent to various labs to be weaponized to put on ICBM warheads. Some suspect that ex-Soviet virologists may have sold some to other governments or even terrorist organizations.

Further, even if the actual biological samples are destroyed, humanity already has the genetic sequencing. They have the technology to synthesize the smallpox genome from scratch; in other words, they can manufacture smallpox.

“Synthesizing viruses is not the stuff of science fiction; scientists have already manufactured the genetic material of other viruses, like polio and the deadly 1918 influenza, and have used it to generate full-blown viruses,” Zimmer writes.

The recently discovered mimivirus is an unusually large one which was first mistaken for a bacterium. This virus has been found in the lungs of those with pneumonia, but it’s as-yet unclear it leads to pneumonia or whether it just colonizes people with pneumonia.

The existence of mimivirus has sparked debate about what viruses are.

Long thought not to be “alive” but mere strands of genetic material, viruses are now being considered just another form of life. “Trying to find a moment in time when such RNA-life abruptly became ‘alive’ just distracts us from the gradual transition to life as we know it,” he writes.

Humans, with their 20,000 genes, have viral history interwoven into their genetics. While people may think of their genomes as their “ultimate identity,” research into virus genetics suggests that people’s genes are a mish-mash, cobbled by evolution. “It’s as if the world was filled with hybrid monsters, with clear lines of identity blurred away,” he writes, applying the ever-present cultural overlays to the science.

Wild gene-swapping is not just a factor of microbial life forms but affects the human genome as well. Many segments of the human genome have segments that resemble retroviruses.

Shalin Hai-Jew works for Kansas State University. She lives in Manhattan.

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