May 22, 2009 / 3:58 PM / 11 years ago

Genes of new flu virus show it's not so new

WASHINGTON (Reuters) - The most complete analysis yet of the new H1N1 swine flu virus shows it must have been circulating undetected for years, most likely in pigs, researchers said on Friday.

People wear medical masks while walking past a hospital in Taipei May 22, 2009. REUTERS/Pichi Chuang

They said pigs are clearly a potential source of human pandemics.

“The results of the study show the global need for more systematic surveillance of influenza viruses in pigs,” Dr. Nancy Cox, chief of the influenza division at the U.S. Centers for Disease Control and Prevention, told reporters in a telephone briefing.

The report by Cox and international team of researchers in the journal Science said the virus “might have been circulating undetected among swine herds somewhere in the world.”

The researchers confirmed the odd mixture of human, pig and bird genes in the new virus, which has infected more than 11,000 people in 42 countries, and killed 86. The World Health Organization is poised to declare a full pandemic of the virus, which so far causes mostly mild disease in people.

The researchers said it is likely other odd mixtures are infecting pigs but simply have not yet been seen. They sequenced the genetic codes of 70 different samples of the new virus from the United States and Mexico.

“We can actually determine where each of the genes ... originated,” Cox said.

The new virus is a mixture of mixtures — it includes part of a so-called triple reassortant virus first seen in 1998 that contains elements of human, bird and swine strains.

It also includes bits from so-called Eurasian strains of flu, including a segment most closely related to a sample from a patient in Hong Kong infected with a swine flu in 1999.


How this particular new mixture arose is still a mystery, the researcher said.

“Several scenarios exist, including reassortment in Asia or the Americas, for the events that have lead to the genesis of the novel A(H1N1) virus,” they wrote.

It is possible another animal acted as the so-called reservoir, which means an animal that can be infected by a pathogen but does not get sick from it. Cox noted that researchers only recently learned, for instance, that cats, from lions to house cats, can be infected with H5N1 avian flu.

“We do know that our veterinary colleagues at USDA (the U.S. Department of Agriculture) and elsewhere in the world are now looking to see if samples in freezers from pigs or other animals that might provide the missing link,” Cox said.

“If we can determine the origin we can also take measures to ensure that the virus doesn’t reemerge in a slightly different form,” she said.

The researchers said they do not know how this particular virus acquired the ability to infect people. It does not have the usual mutations that allow animal viruses to jump into people and then to pass easily from one person to another.

Flu experts get worried when viruses go straight from animals to people. Usually they do not pass any further than one person — for example the feared H5N1 avian influenza virus that has infected 429 people and killed 262 of them rarely passes from person to person.

But all three recent pandemics — in 1918, 1957 and 1968 — occurred when a new avian flu virus started infecting people.

So far sampling of the new H1N1 virus shows very little genetic mutation — a sample from a patient in Mexico is virtually identical to samples from various U.S. states and other countries.

This “indicates that this virus may have been introduced into humans in sort of a single event,” Cox said. Or if more than one person was infected directly from an animal or other source, they were infected with genetically identical viruses.

Editing by Eric Beech and Vicki Allen

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