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Swine Flu Genes Went Undetected for Years: Report
Date:5/22/2009

Sequencing of virus' genome should make finding a vaccine easier, CDC says

FRIDAY, May 22 (HealthDay News) -- Many of the genes that make up the new H1N1 swine flu virus have been circulating undetected in pigs for more than a decade, researchers reported Friday.

Scientists at the U.S. Centers for Disease Control and Prevention and elsewhere sequenced the genomes of more than 50 samples of the swine flu strain and found it is distantly connected to its closest viral relatives.

The researchers also found that the new H1N1 strain lacks genes that -- in other influenza A strains -- confer ease of transmission and virulence.

At at teleconference Friday, CDC officials discussed the findings, released early in the journal Science because of the broad interest in this new strain of swine flu.

"From our analysis we have confirmed that the novel H1N1virus likely originated from pigs, based on data that each of the genetic components of this virus are most closely related to corresponding influenza virus genes identified from swine influenza viruses," said Dr. Nancy Cox, chief of CDC's Influenza Division.

However, this new virus is not similar to seasonal H1N1 viruses, she said. In their analysis of 70 samples of the new H1N1 virus from the United States and Mexico, the researchers found minor genetic differences, but consider the virus to be basically homogeneous, Cox noted.

Knowing the genetic make up of the virus makes it easier to come up with a candidate vaccine, Cox said. "We see much less variation among these new H1N1 viruses than we do for typical seasonal influenza viruses," she said.

Sequencing the virus' genetic code is also important for planning the public health response, including knowing which antiviral medications will be effective and which won't, Cox said.

And, Cox added, "We can take measures to be sure that the virus doesn't reemerge in a slightly different form."

In the future, scientists will need to keep a closer eye on pig populations to spot similar emerging flu viruses, the researchers said in the Science paper.

In the United States, most cases of the swine flu continue to be no worse than seasonal flu. Testing has found that the swine flu virus remains susceptible to two common antiviral drugs, Tamiflu and Relenza, according to the CDC.

While the new swine flu only seems to cause relatively mild infection, experts worry that, if the virus mutates, people would have limited immunity to it. The CDC is concerned that, as the H1N1 virus moves into the Southern Hemisphere, where the flu season is just getting under way, it could mutate and return in a more virulent form in the Northern Hemisphere next fall.

On Thursday, U.S. health officials said that, while many states are still reporting new cases of infection, there seems to be an overall decline in visits to doctors and hospitals by people with the disease, indicating that the outbreak might be subsiding.

"At the national level, we're seeing that the percent of visits [to doctors and hospitals] for influenza-like illness is starting to turn down," Dr. Anne Schuchat, the CDC's interim deputy director for science and public health program, said during a teleconference. "That's a good sign. It's consistent with the idea that the worst may be over."

The CDC reported on Wednesday that some older people may have partial immunity to the new H1N1 swine flu virus because of possible exposure to another H1N1 flu strain circulating prior to 1957. So far, 64 percent of cases of swine flu infection in the United States have been among people aged 5 to 24, while only 1 percent involves people over 65, officials said.

On Friday, the CDC was reporting 6,552 U.S. cases of swine flu in 48 states, including nine deaths, although health officials said the death toll could be as high as 10.

The World Health Organization on Friday was reporting 11,168 diagnosed cases in 42 countries, including 86 deaths, mostly in Mexico, believed to be the source of the outbreak.

Mexico City on Thursday lowered its swine flu alert level from yellow to green after no new infections had been reported for a week, the Associated Press reported.

U.S. Human Cases of H1N1 Flu Infection
(As of May 22, 2009, 11:00 AM ET)
States # of
confirmed and
probable cases
Deaths
Alabama
66
 
Arkansas
3
 
Arizona
520
2 deaths
California
553
 
Colorado
59
 
Connecticut
81
 
Delaware
94
 
Florida
129
 
Georgia
27
 
Hawaii
33
 
Idaho
18
 
Illinois
877
 
Indiana
106
 
Iowa
71
 
Kansas
34
 
Kentucky**
22
 
Louisiana
86
 
Maine
9
 
Maryland
41
 
Massachusetts
197
 
Michigan
176
 
Minnesota
39
 
Mississippi
7
 
Missouri
24
1 deaths
Montana
10
 
Nebraska
29
 
Nevada
32
 
New Hampshire
23
 
New Jersey
47
 
New Mexico
97
 
New York
327
1 deaths
North Carolina
12
 
North Dakota
5
 
Ohio
14
 
Oklahoma
50
 
Oregon
101
 
Pennsylvania
73
 
Rhode Island
9
 
South Carolina
36
 
South Dakota
4
 
Tennessee
89
 
Texas
900
3 deaths
Utah
122
1 deaths
Vermont
2
 
Virginia
25
 
Washington
494
1 death
Washington, D.C.
13
 
Wisconsin
766
 
TOTAL*(48)
6,552 cases
9 deaths
*includes the District of Columbia
**One case is resident of Ky. but hospitalized in Ga.

Source: U.S. Centers for Disease Control and Prevention

More information

For more on swine flu, visit the U.S. Centers for Disease Control and Prevention.



SOURCES: May 22, 2009, teleconference with Nancy Cox, Ph.D., chief of U.S. Centers for Disease Control and Prevention's Influenza Division; May 21, 2009, teleconference with Anne Schuchat, M.D., interim deputy director for science and public health program, U.S. Centers for Disease Control and Prevention; Associated Press


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