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We are all Russian nesting dolls: Our intestines house many bacteria, which house many viruses. These so-called bacteriophages are likely as important for our health as the bacteria they live in. (Lisa Brown for NPR)

Globe-Trotting Virus Hides Inside People's Gut Bacteria

by Michaeleen Doucleff
Jul 24, 2014

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New viruses are dime a dozen.

Every few months, we hear about a newly discovered flu virus that's jumped from birds to people somewhere in the world. And the number of viruses identified in bats is "extraordinary and appears to increase almost daily," scientists wrote last year in the journal PLOS Pathogens.

But a virus that has been quietly hiding inside millions of people on three continents — and never noticed before? That doesn't come along often.

Scientists at San Diego State University have discovered what may be the most common and abundant virus in the human gut. And yet, the tiny critter, called crAssphage (oh yes, there's a story behind that name), has eluded researchers' radar for decades.

Here's the cool part: The virus doesn't just hang out in our intestines naked and alone, scientists report Thursday in the journal Nature Communications. Instead, the virus takes up residence inside gut bacteria — specifically inside Bacteroides, a group of microbes that have been linked to obesity and diabetes.

So the system is almost like a Russian nesting doll: The virus lives inside the bacterium, which lives inside our gut.

The new virus doesn't make us sick, but it may be involved in controlling weight through its effect on Bacteroides. "We suspect this virus is very important in regulating the number of these bacteria [the Bacteroides] in the intestine," says computational biologist Robert Edwards, who led the study.

Edwards and his colleagues found the virus in fecal samples from people across the U.S., Europe, Korea and Japan. "But we think the virus is likely found worldwide," he tells Goats and Soda. "We've basically found it in every population we've looked at. If we tested Africans, we think we'd find it in them, too."

Scientists are just starting to learn about all the organisms that live in and on the human body. Collectively, they're called the human microbiome. And there's no question they're important for our health.

So far, most studies have focused on the gut's bacteria — not other microbes there. These bacteria are known to help regulate everything from our weight and immunity to heart health and behavior. One study even found that changes in gut bacteria cause malnutrition in young children in Malawi.

But during all this discussion of microbiomes, there have been billions of tiny elephants in the room: Viruses.

Some scientists estimate that there are a hundred times more virus particles than human cells in the human body (and 10 times more viruses than bacteria). But no one ever talks about viruses. Why? Because they are extremely difficult to study.

The number of viruses known to infect people is remarkably small. And the number known to hang out in our bodies for a long time is even smaller. For instance, there are herpes viruses, which cause painful, recurring blisters. Adenoviruses can set up recurring respiratory infections in people, and papillomavirus causes cervical cancer.

And hepatitis viruses and HIV can silently hide in the body for years.

Beyond these common pathogens, however, the list quickly peters out, although DNA surveys suggest that humans have thousands of viral species in and on us. Most of them likely coexist within our gut in peace and harmony.

To start putting a name and function to some of these quieter organisms, Edwards and his colleagues dug deep into sequencing data from the Human Microbiome Project.

They noticed that a few genes from the same virus kept popping up over and over again. So they painstakingly stitched together the virus' genome inside the computer.

Then the team used that genetic code to search for the virus in fecal samples from people in Europe, Korea and Japan. To their surprise, the virus was strikingly common. It occurred in 75 percent of the 466 samples they analyzed.

And the virus was abundant. About a quarter of the viral genes in the samples belong to crAssphage.

"Given the virus' abundance and how widespread it is, it is probably going to be very important for understanding the ecology of the human gut," says microbiologist Jonathan Eisen, of the University of California, Davis. "And it likely infects a group of organisms [the Bacteroides] thought to be really important for health."

Eisen, who wasn't involved with the study, calls the new virus "really cool" and "worth learning more about." But he says it's too soon to say if it's truly a global virus.

"The samples searched so far have reasonable diversity — they're not just from white men in New England," Eisen says, "But we haven't sampled all of human diversity."

"We desperately need an organized systematic effort to gather information about viruses," Eisen says. He proposes something like the Human Microbiome Project, but for viruses that directly infect humans and viruses that infect the bacteria of the human microbiome.

That point brings us back to the new virus' strange name: crAssphage.

The "phage" part, Edwards says, comes from the name of viruses that infect bacteria — the so-called bacteriophages. And the first part, "crAss," comes from the computational tool that the scientists used to find the virus (Cross Assembly). But we couldn't help but notice the name also brings to mind where the scientists found the virus.

"Oh no, we never thought of that," Edwards says with a chuckle. "We would never be crass."

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Barbed-wire fence surrounding a military area is pictured in the forest near Stare Kiejkuty village, close to Szczytno in northeastern Poland. The CIA ran a secret jail on Polish soil, the European Court of Human Rights ruled Thursday. (Reuters /Landov)

European Court Rules Against Poland In CIA 'Black Sites' Case

by Krishnadev Calamur
Jul 24, 2014

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The European Court of Human Rights ruled today that Poland broke the European human rights convention by allowing the CIA to imprison and torture two terrorism suspects in secret prisons on its soil.

"The Court found that Poland had cooperated in the preparation and execution of the CIA rendition, secret detention and interrogation operations on its territory and it ought to have known that by enabling the CIA to detain the applicants on its territory, it was exposing them to a serious risk of treatment contrary to the Convention," the Strasbourg, France-based court said in a statement.

And, it said, "the treatment to which the applicants had been subjected by the CIA during their detention in Poland had amounted to torture."

The Associated Press says the ruling marks the first time any court has passed judgment on the Bush administration's program of extraordinary rendition.

The court ordered Poland to pay Abd al-Rahim al-Nashiri, a Saudi national, $135,000; and Zayn al-Abidin Muhammad Husayn, a Palestinian also known as Abu Zubaydah, $175,000.

Nashiri was charged with allegedly masterminded the deadly attack on the USS Cole in 2000. Abu Zubaydah hasn't formally been charged. Both men are now imprisoned at Guantanamo Bay, but their lawyers had said that between 2002 and 2003 they were held at secret prisons, or "black sites," in Poland. Here's more from The Wall Street Journal:

"Both Messrs. Zubaydah and Nashiri say they were taken to Poland on the same secret rendition plane in Dec. 2002, after having been captured in Pakistan and Dubai, respectively. CIA documents show that the two men were subject to "enhanced interrogation techniques," including waterboarding, during their detention at Stare Kiejkuty, a Polish military base that was first used by the German intelligence service in World War II."

The European court's decision can be appealed, and a spokesman for the Polish Foreign Ministry was quoted in The Journal saying, "We have three months to file an appeal so there is ample time for thorough work of our lawyers. Our concerns over the case were made clear during the proceedings."

But Amrit Singh, a lawyer for Nashiri who works at the Open Society Justice Initiative, said the "ruling is of landmark significance."

In 2012, the European Court of Human Rights ruled against Macedonia in another case involving rendition.

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An employee looks at a Russian foreign passport at the U.S. Embassy in Moscow. (ITAR-TASS/Landov)

U.S. Database Glitch Delays Passport, Visa Processing

Jul 24, 2014

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The U.S. State Department's global database for processing visas and passports is experiencing problems that could cause delays for millions of people around the world who are awaiting travel documents.

The Associated Press writes:

"Unspecified glitches in the department's Consular Consolidated Database have resulted in "significant performance issues, including outages" in the processing of applications for passports, visas and reports of Americans born abroad since Saturday, spokeswoman Marie Harf said. She said the problem is worldwide and not specific to any particular country, citizenship document, or visa category."

"'We apologize to applicants and recognize this may cause hardship to applicants waiting on visas and passports. We are working to correct the issue as quickly as possible,' she said."

U.S. official said about 50,000 applications were affected in one country alone.

According to AP: "The database is the State Department's system of record and is used to approve, record and print visas and other documents to ensure that national security checks are conducted on applicants."

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The same bacterium that ravaged medieval Europe as the "Black Death" still occasionally reemerges. (Bettmann/CORBIS)

Shades Of The Middle Ages: The Plague Popped Up In China And Colorado

by Rae Ellen Bichell
Jul 24, 2014

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Health officials examine rats for signs of bubonic plague in New Orleans, 1914.

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The plague isn't just something you read about in medieval history books.

This past week, five cases were reported: four in Colorado and one in China.

The Colorado residents were diagnosed after coming into contact with an infected dog.

According to Chinese officials, parts of a city in northern China were quarantined for nine days, and 151 people were put under close observation, after a man died of the disease last Wednesday. He was reportedly infected after handling a dead Himalayan marmot, a chubby rodent with a history of carrying the bacterium that causes the plague.

What's remarkable is that the disease has remained essentially the same over all those years and in all those places. Anthropologists have found that the strain of bacteria in medieval skeletons from Europe to be almost identical to the one circulating today.

Once known as the Black Death for the dark patches caused by bleeding under the skin, the plague swept Europe 700 years ago, killing a third of the population — an estimated 25 million. It wiped out millions in China and Hong Kong in the late 1800s before people put two and two together and started targeting rat populations.

Centuries later, the plague periodically pops up in countries across the globe.

The painful infection is caused by Yersinia pestis, a bacterium that dwells in fleas. The bacteria will hook onto the lining of the flea's gut and stomach, and grow into a film that can clog the insect's digestive passage. The next time the flea goes for a blood meal, it pukes into whatever animal it feeds on (usually a rodent), spreading the bacteria.

Once the rodent is infected, the bacterium can then spread to the wild carnivores that eat it, or to pets and people that come in contact with it.

The plague can persist in rodent populations, especially wild ones, for a long time without affecting humans.

But it can reemerge. Ken Gage, who studies vector-borne diseases at the Centers for Disease Control and Prevention, says temperature and humidity can change flea behavior, regulate how comfortable the bacteria are inside their hosts, and allow rodent populations to mushroom.

"The rodent densities have to get above a certain level," he says, "And when that happens, the likelihood of a rapid plague spread among the rodents goes up pretty dramatically."

As their rodent hosts die off, the fleas seek new hosts — typically the next animal to peer down the burrow hole.

"What we see in the west here is, the fleas will crawl up to the entrance of the burrow and wait for a host to come by," Gage explains. "If they get on another rodent that they can live on, then they've been successful. But they can also jump on humans, or on dogs or coyotes or cats, which aren't the right hosts, but unfortunately those animals can be bitten by the fleas and get plague."

Sometimes, that new host can transport the fleas a few miles away and spread them to other animals.

In the U.S., which sees between one and 17 human cases a year, the plague tends to surface in rural areas, often near plague-perfect settings: semi-arid forests and grasslands populated by everything from squirrels and rats to voles and rabbits. Cases can occur when people, or their pets, get within flea-jump range. Four Colorado residents were diagnosed last week after coming into contact with an infected dog.

There are three forms of the plague. The first, bubonic, happens when the bacterium infects the skin where a person has been bitten, causing a swollen lymph node, or "bubo," the hallmark bumps in medieval images of the disease. If the bacterium enters the bloodstream, that's septicemic plague. And if the infection gets into the lungs, at which point it's called pneumonic plague, it can spread from person to person in the droplets of a cough.

The World Health Organization considers pneumonic plague to be among the deadliest infectious diseases. It's that form that a man in northern China reportedly died of and that infected people in Colorado.

Gage says the Chinese quarantine was one way to handle the situation.

"Here in the U.S., what we would do is identify the person, try to figure out where they've been, who they've had contact with in the last few days," he says. That includes anyone who got within six feet of the patient — close enough to get coughed on.

As with most bacterial infections, antibiotics can treat it. But medics have to catch the symptoms early on.

In the U.S., infections tend to happen in the west, fanning out from San Francisco, where the disease may have made its first landing on American soil around 1900.

"One thing you have in the western U.S. is a good variety of rodent species that are susceptible to plague, and they have fleas that can transmit the disease," says Gage. "That's the key element."

But he's not too worried about the disease.

"I don't think we'll see another pandemic," Gage says, "Because we know the organism and we know how to treat it. We know how to do some flea control. We can break the cycle, at least as far as involvement with humans."

Indeed outbreaks in Libya in 2009, the Democratic Republic of the Congo in 2005, and Algeria in 2003 were contained.

The bacteria may still be host-hopping around the globe, but modern medicine has prevented the plague from getting anywhere near the disastrous levels it reached in the Middle Ages, described in one Scottish account from the 14th century:

"So great a plague has never been heard of from the beginning of the world to the present day .... At God's command, moreover, the damage was done by an extraordinary and novel form of death .... This sickness befell people everywhere, but especially the middling and lower classes, rarely the great. It generated such horror that children did not dare to visit their dying parents, nor parents their children, but fled for fear of contagion as if from leprosy or a serpent."

That's a plague scenario you'll likely see only in history books.

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Palestinian children, wounded in a July 24 Israeli strike on a compound housing a U.N. school in Beit Hanoun, in the northern Gaza Strip, lay on the floor of an emergency room at the Kamal Adwan hospital in Beit Lahiya. Israeli tank shells hit the compound, killing more than a dozen people and wounding dozens more who were seeking shelter from fierce clashes on the streets outside. (AP)

Israeli Artillery Hits U.N.-Run School In Gaza

Jul 24, 2014

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Displaced Palestinian children from Beit Hanoun in the northern Gaza Strip stand behind the window of a classroom July 23 at a UN school where displaced families took refuge after fleeing heavy fighting in the Gaza Strip.

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A United Nations-run school sheltering civilians in Gaza has been hit by Israeli artillery, the U.N. says. More than a dozen people have been killed, according to Palestinian officials.

Reuters quotes Chris Gunness, a spokesman for the UN Relief and Works Agency, the main U.N. agency in Gaza, as confirming that the shelter in Beit Hanoun was hit.

The Associated Press reports that "Gaza health official Ashraf al-Kidra says the dead and injured in the school compound were among hundreds of people seeking shelter from heavy fighting in the area."

Reuters says:

"Laila Al-Shinbari, a woman who was at school when it was shelled, told Reuters families had gathered in the courtyard expecting to be evacuated shortly in a Red Cross convoy.

" 'All of us sat in one place when suddenly four shells landed on our heads ... Bodies were on the ground, (there was) blood and screams. My son is dead and all my relatives are wounded including my other kids,' she wept."

In 16 days of an Israeli offensive in Gaza, more than 700 Palestinians and 30 Israelis have been killed. Israel launched the ground operation in response to cross-border rocket attacks by Hamas.

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