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2013

A Catalog for all the World’s Viruses?
New York Times, September 5, 2013
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Viruses have a knack for ambush. Time and again, they have struck our species without warning, producing new diseases. H.I.V. burst on the scene in the early 1980s, and it took years for scientists to figure out that it had evolved from a chimpanzee virus in the early 1900s. In 2003, a previously unknown bat virus in China began to cause SARS in humans. Today we are in the midst of yet another ambush, as a new virus called MERS is infecting people, mostly in in Saudi Arabia. Scientists have yet to definitively pin down its origin, although preliminary evidence points to another species of bat.

We might be able to take away this element of surprise if we had a catalog of all the viruses lurking in mammals. As soon as a mysterious epidemic broke out, scientists could turn to the catalog to figure out where the virus came from, potentially gaining some crucial clues to the virus’s biology. But few scientists have ventured to build such a catalog, perhaps because there seemed to be such a vast number of viruses to contend with.

“No one’s really been addressing this question, even though it seems like such a fundamental one,” said Simon J. Anthony, an associate research scientist at Columbia University and a researcher at EcoHealth Alliance, a New York-based scientific research organization.

In a new study published in the journal mBio, Dr. Anthony and his colleagues have taken an initial step toward such a catalog by exhaustively searching for all the viruses that infect a single species of mammal — a bat known as the Indian Flying Fox. They found 55 viruses, 50 of which are new to science.

That’s a lot of viruses, but Dr. Anthony and his colleagues argue that it nonetheless should be possible to make a catalog of most viruses in mammals for about $1.4 billion.

Indian Flying Foxes carry Nipah virus, which has been causing human outbreaks since 1999. In recent years, researchers from EcoHealth Alliance have traveled across Bangladesh to survey the bat population for the virus.

The scientists ended up with a huge collection of samples from the animals — both throat swabs and urine samples from more than 1,000 bats. Dr. Anthony and his colleagues decided to take advantage of this rare opportunity and search the samples for every possible mammal virus.

“We said, ‘let’s focus on the viruses and not the diseases,’ ” said Dr. Anthony.

To carry out this search, the scientists developed probes that could latch onto genetic material from all known families of mammal viruses. They then used the probes to fish out virus genes from the samples, which they could then decipher.

The more bats the scientists studied, the more viruses they found — but only up to a point. By the time they were on their 500th bat, they tended to find viruses that were already on their list. And after 1,000 bats, adding a new virus to the list became a rare event. The fact that their search slowed down so much meant that there probably weren’t a vast number of other viruses waiting to be found.

Their catalog of 55 viruses makes for a sobering read. The vast majority of them have gone unknown till now. And 10 of the viruses belong to the same family as Nipah. “We have no idea if any of them are any threat to human health,” said Dr. Anthony.

But the study is also encouraging for scientists who would like a virus catalog. If the other 5,485 known species of mammals have a similar level of virus diversity, Dr. Anthony and his colleagues estimate that they would have at least 320,000 viruses in total. They believe it would only take about 500 animals per species to identify 85 percent of all mammal viruses.

“This is a very impressive piece of work,” said Linfa Wang of Duke-NUS Graduate Medical School in Singapore, who was not involved in the work.

But Dr. Wang and other experts cautioned that it is only a rough approximation of virus diversity in mammals. A search for viruses in saliva or urine may miss some species of viruses that lurk elsewhere, like in the spleen or kidneys.

Vincent Racaniello of Columbia University also pointed out that the presence of a short genetic fragment of a virus is not proof that it actively infects an animal. That sort of certainty would require finding evidence that the viruses are replicating. “In such a broad survey of viruses in a bat, it’s very hard to obtain this evidence,” he said.

It’s also not clear whether the Indian Flying Fox is a typical mammal when it comes to virus diversity. “The headline number of at least 320,000 viruses to be discovered should be taken with caution,” said Andrew Rambaut, of the University of Edinburgh.

Dr. Anthony agreed. “The number is almost certainly wrong,” he said.

To move toward the true number, he and his colleagues are expanding their search, looking now at a species of monkey in Bangladesh and another bat species in Mexico.

They’re also investigating whether any of the viruses they’ve found in Indian Flying Foxes has already spilled over into humans without anyone noticing.

But Pablo R. Murcia of the University of Glasgow points out that a virus catalog would be useful for more than just medicine. Viruses from wild animals can also wipe out livestock, potentially endangering food supplies.

“This adds another layer of potential burden that we need to keep in mind,” said Dr. Murcia.

Copyright 2013 The New York Times Company. Reproduced with permission.
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