20 June 2009

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cdc-flu-fuzz.htm      CDC Fuzzes H1N1 Pandemic Reports                 June 18, 2009

James Atkinson (www.tscm.com) sends:

More fuzzed up numbers being published by the CDC

Note the 20% increase over last week, even though the CDC falsely claims the numbers are dropping in Press Briefings and Announcements (when these charts show they are lying).

Also note that several states with rampant infection did not report numbers for this week which skews the overall numbers.

Pay heed to the 7-10% numbers mentioned in the following articles.

But (as per Dr. Jernigan) 7% of the population = 21,560,963 (or, in other words a doctor who specializes in this sort of outbreak at the CDC says that 1000 times the confirmed number may be actually sick with influenza symptoms). Daniel Jernigan, MD, MPH, is the deputy director of the Influenza Division at the National Center for Immunization and Respiratory Diseases at the CDC.

This is why the CDC needs to be reporting statistics on a DAILY basis, and be reporting them in a Zip code level basis to the public. While it is important to publish the data on a zip coded bases (which is already in a DB at the CDC) they also need to include how many people presented with Flu like symptoms, and many came up with Influenza, and then the type and sub-strain of influenza.

-jma

http://www.medscape.com/viewarticle/704581

From Medscape Medical News
Influenza-Like Symptoms Being Reported in Large Numbers in Affected Areas
Emma Hitt, PhD

June 18, 2009 — About 7% of the population in areas highly affected by H1N1 virus are reporting influenza-like symptoms, a spokesperson for the US Centers for Disease Control and Prevention (CDC) said during a press briefing today.

Daniel Jernigan, MD, MPH, deputy director of the Influenza Division at the National Center for Immunization and Respiratory Diseases at the CDC, provided an update about the H1N1 pandemic, stating that the United States will likely continue to have flu activity through this summer and probably until the start of the fall flu season.

According to Dr. Jernigan, approximately 89% of flu cases currently being confirmed by the CDC are of the novel H1N1 strain. The number of cases varies significantly from region to region, with northeastern states continuing to see the highest numbers, especially New York and Massachusetts.

Likely an Underestimate

The number of lab-confirmed cases in the United States is now estimated at more than 17,800, which includes around 1600 hospitalizations and 44 deaths.

"These numbers are likely an underestimate of the number of cases that are out there," Dr. Jernigan said. "The amount of disease in the areas that are having activity with H1N1 is perhaps around 7% of the population reporting symptoms due to influenza-like illness."

Antivirals — that is, neuraminidase inhibitors such as oseltamivir and zanamivir — still appear to be effective against H1N1. "We are recommending that [antivirals] be used in high-risk patients that are sick and also in those that are being hospitalized in those that have severe illness," he said.

According to Dr. Jernigan, asthma, diabetes, and heart disease are the most predominant underlying conditions in hospitalized patients.

"About 70% or so [of hospitalized patients] have some kind of underlying disease," Dr. Jernigan told Medscape Infectious Diseases during the call. "The most predominant [underlying condition] is asthma, [with] the second being diabetes." He added that immunocompromised status — either through cancer chemotherapy or immunocompromising conditions — is present in about 13% of the patients, as is chronic underlying heart disease.

H1N1 in Healthcare Providers

H1N1 influenza infection among healthcare personnel was also discussed during the briefing. Michael Bell, MD, associate director for infection control in the Division of Healthcare and Quality Promotion of the CDC's National Center for Preparedness, Detection, and Control of Infectious Diseases, discussed a report in the June 19 issue of the CDC's Morbidity and Mortality Weekly Report.

The report, which describes H1N1 influenza cases among healthcare personnel detected up until May 13, 2009, includes detailed information about 26 patients. None of the patients with the H1N1 virus died or required intensive care during hospitalization, Dr. Bell said. Half of them had exposure within the general community or from unknown causes, and the remaining half probably contracted the disease within the healthcare setting.

According to the report, "most of the probable or possible patient-to-[healthcare provider] transmissions ... occurred in situations where the use of [personal protective equipment] was not in accordance with CDC recommendations."

Dr. Bell pointed out that they are beginning to see "a pattern of healthcare personnel to healthcare personnel transmission in some of these additional clusters, which is also concerning because it gets to the issue of people showing up for work sick." He added that healthcare personnel should stay home if they are sick and that healthcare facilities need to have appropriate sick leave policies.

However, the report states that healthcare personnel do not appear to be "overrepresented among reported cases of persons infected with novel influenza A (H1N1) virus in the United States."

According to Dr. Bell, there is currently no routine recommendation for healthcare workers to receive antiviral medication. "Probably the most important thing is that infectious patients be identified at the front door," Dr. Bell said. "Consistent application of precaution is important to make sure that there isn't occupational exposure."

Current recommendations to prevent H1N1 spread include using a single patient room for infected individuals and having infectious patients cover their cough. Healthcare personnel are advised to use respirators, gloves, gowns, and eye protection while they are in patients' rooms. In addition, careful attention to hand hygiene is also recommended.

Morb Mortal Wkly Rep. 2009;58(23):641–645.

Authors and Disclosures
Journalist
Emma Hitt, PhD
Emma Hitt is a freelance editor and writer for Medscape.

Disclosure: Emma Hitt, PhD, has disclosed no relevant financial relationships.

http://www.healthnewsblog.com/tags/daniel-jernigan

CDC: 50,000 People May Have Swine Flu
Posted on May 15, 2009

WebMD reports that Daniel Jernigan, MD, PhD, deputy director of the CDC's influenza division says that more than 100,000 Americans probably have the flu and of these at least half probably have swine flu. This means there are probably 50,000 or more people with the H1N1 swine flu virus.

Jernigan noted that the 4,700 confirmed or probable cases of swine flu reported to CDC represent a gross underestimate. When asked how many actual cases there were, Jernigan noted that 7% to 10% of the U.S. population -- up to 30 million people -- get the seasonal flu each year.

"So with the amount of activity we are seeing now, it is a little hard to know what that means in terms of making an estimate now of the total number of people with flu out in the community," Jernigan said. "But if I had to make an estimate, I would say ... probably upwards of maybe 100,000."

The WebMD article also says that flu cases are going up at a time of year when they generally decrease.

At a time when flu season should be ending or over, the CDC's flu season indicators are going up instead of down. As of May 9, 22 states had widespread or regional flu.

WebMD says that flu/pneumonia deaths for the week ending May 9th were 7.2% of all deaths. This is just under the "epidemic threshold" of 7.4% of all deaths. WebMD also reports that 173 people been hospitalized with H1N1 so far and most of them have been very young, between 5-24 years old.

http://www.wired.com/wiredscience/2009/05/disease-hunters-add-swine-flu-genome-to-arsenal

Wired Science News for Your Neurons Disease Hunters Add Swine Flu Genome to Arsenal
By Alexis Madrigal May 22, 2009 | 3:15 pm |

The genetic portrait of the novel swine flu strain that’s still spreading around the globe has been completed, but some mysteries remain.

A huge international team of scientists sequenced the partial or full genomes of 51 samples of the virus from the United States and Mexico. While many genetic clues about the new H1N1 strain have trickled out, a new paper assembles the best working knowledge of the flu’s origins.

As reported by Wired Science, the new virus combines genes from two swine flu viruses that first emerged in 1998. It’s still unclear how the disease made the jump into humans — either directly from pigs or through an intermediate host — and the molecular basis for how it spreads.

“Many of the molecular markers predicted to be associated with adaptation to a human host or to the generation of a pandemic virus, such as in 1918 H1N1 or highly pathogenic H5N1, have not been identified in the 2009 H1N1 viruses characterized here,” the researchers write in Science.

The Centers for Disease Control estimate that 100,000 people in the United States have now contracted swine flu. The good news is the disease is not highly virulent. It’s only caused 300 hospitalizations and fewer than 10 deaths. It also turns out that it might be easier to come up with a vaccine for swine flu, because it’s genetically homogenous, unlike the motley crew of seasonal flus. But in a press conference Friday, CDC officials warned that now that the flu is in humans, it could mutate faster than it had in swine, like standard human seasonal flu does.

“We do expect that now that these viruses have been introduced into humans that they’ll evolve at the same rate that other seasonal influenza viruses mutate,” said Nancy Cox, chief of the influenza division at the National Center for Immunization and Respiratory Diseases.

That could mean trouble later this year, if the virus re-emerges in a more virulent form during the standard winter flu season.

Anne Schuchat of the Science and Public Health Program at the CDC also called for increased swine-disease surveillance and smart husbandry practices to reduce the chance that the disease will jump again into humans.

“There are controls like good agricultural and good farming practices that can lead to recognition when there are ill animals and ways of taking care of the animals that reduce the chance that viruses will resist or swap around,” she said.

Both statements seemed directed at large-scale pig farms, which as Bob Martin, former executive director of the Pew Commission on Industrial Animal Farm Production, told Wired.com “are super-incubators for viruses.” They’ve come under criticism

http://www.wired.com/wiredscience/2009/05/swineflufarm/

Swine Flu Ancestor Born on U.S. Factory Farms
By Brandon Keim May 1, 2009 | 4:29 pm |

Scientists have traced the genetic lineage of the new H1N1 swine flu to a strain that emerged in 1998 in U.S. factory farms, where it spread and mutated at an alarming rate. Experts warned then that a pocket of the virus would someday evolve to infect humans, perhaps setting off a global pandemic.

The new findings challenge recent protests by pork industry leaders and U.S., Mexican and United Nations agriculture officials that industrial farms shouldn’t be implicated in the new swine flu, which has killed up to 176 people and on Thursday was declared an imminent pandemic by the World Health Organization.

“Industrial farms are super-incubators for viruses,” said Bob Martin, former executive director of the Pew Commission on Industrial Animal Farm Production, and a long-time critic of the so-called “contained animal feeding operations.”

As Wired.com reported on Tuesday, geneticists studying the composition of viruses taken from swine flu victims described it as the product of a DNA swap between North American and Eurasian swine flu strains.

On Wednesday, Columbia University biomedical informaticist Raul Rabadan added new information on the virus’ family history in a posting to ProMed, a public health mailing list. His description paralleled that of other researchers who had analyzed the new strains, but with an extra bit of detail. Six of the genes in swine flu looked to be descended from “H1N2 and H3N2 swine viruses isolated since 1998.”

Experts contacted by Wired.com agreed with Rabadan’s analysis. For researchers who track the evolution of influenza viruses, the news was chilling.

H3N2 — the letters denote specific gene variants that code for replication-enhancing enzymes — is the name of a hybrid first identified in North Carolina in 1998, the tail end of a decade which saw the state’s hog production rise from two million to 10 million, even as the number of farms dropped. H3N2 originated in a relatively benign swine flu strain first identified in 1918, but had absorbed new genes from bird and human flus.

These new genes provided replication advantages that allowed the hybrid to permeate densely packed pig farms whose inhabitants were routinely shipped across the United States. That rapid replication rate also increased the chances of strains evolving in ways that allowed them to evade hog immune systems.

Within a year, exposures topped 90 percent in several heartland states. A retrospective news account in Science said that “after years of stability, the North American swine flu virus had jumped on an evolutionary fast track.”

At the genetic level, the years that followed remain a mystery — hog flus are poorly monitored, compared to human influenza. But eventually an H3N2 spawn merged with a strain of Eurasian pig flu, producing the swine flu variant that’s now infecting humans.

At an environmental level, the conditions which shaped H3N2 and H1N2 evolution, and increased the variants’ chances of taking a human-contagious form, are well understood. High-density animal production facilities came to dominate the U.S. pork industry during the late 20th century, and have been adopted around the world. Inside them, pigs are packed so tightly that they cannot turn, and literally stand in their own waste.

Diseases travel rapidly through such immunologically stressed populations, and travel with the animals as they are shuttled throughout the United States between birth and slaughter. That provides ample opportunity for strains to mingle and recombine. An ever-escalating array of industry-developed vaccines confer short-term protection, but at the expense of provoking flu to evolve in unpredictable ways.

The Pew commission concluded that this system created an “increased chance for a strain to emerge that can infect and spread in humans.” Scientists and public health experts have said the same thing for years, in even starker terms.

In 2003, the American Public Health Association called for a ban on contained animal feeding operations. One year later, St. Jude’s Children’s Hospital virologist Richard Webby, one of the original chroniclers of H3N2’s emergence, called the U.S. swine population “an increasingly important reservoir of viruses with human pandemic potential.” United States Department of Agriculture researcher Amy Vincent reportedly said that vaccine-driven evolution created a “potential for pandemic influenza emergence in North America.”

Officials and the pork industry argued this week that a direct link hadn’t been found to pigs, and that the new flu strain had yet to be found in farm animals or workers, both in the United States and at a giant hog factory near the outbreak’s epicenter in La Gloria, Mexico. Owned by a subsidiary of Smithfield Foods, the largest U.S. pork producer and a notorious polluter, the factory processes one million hogs each year.

As of now, neither swine flu nor its close relatives have been found anywhere. But “that probably says more about the lack of sampling in pig flu than anything else,” said Andrew Rambaut, a University of Edinburgh viral geneticist who has studied swine flu. “We don’t sample nearly the complete diversity of pig flu around the world. Most outbreaks go unstudied.”

On Thursday, Reuters called concern with “evil factory farms in Mexico” one of many “wild theories,” on a par with a conspiracy between Al Qaeda and Mexican drug cartels. Indeed, the location may yet prove coincidental. But absence of evidence at the factory and elsewhere is not evidence of absence.

The new swine flu could have emerged in a myriad number of ways, passing between any number of birds and pigs and people, at locations across North America, during its evolutionary journey. It may well prove impossible to pinpoint exactly where it first emerged or became infectious to people. But most of its genes are almost certainly part of a North American industrial virus lineage long expected to produce pandemic variants like this one.

“We haven’t found evidence of infected pigs,” said Ian Lipkin, a Columbia University epidemiologist and member of the World Health Organization’s surveillance network. “But even if we never find that smoking pig, we can surmise that this is probably where it came from.”

The circumstances “are certainly enough to warrant asking questions,” said Lipkin. “The question, then, is how deeply do you want to look to try to find the evidence?”

H1N1-2009.06.20.2009.pdf

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