Did new flu emerge from a pig farm?

From ANIMAL PEOPLE, May 2009:
MEXICO CITY–Rumors swept the world
during the last week of April 2009 that a newly
detected H1N1 flu virus variant suspected of
killing as many as 149 Mexicans might have
evolved at a factory-style pig farm at Perote,
in Vera Cruz state on the Gulf of Mexico. As
ANIMAL PEOPLE went to press on the night of April
28, however, little medical or veterinary
evidence supported the hypothesis that the
disease is of factory farm origin, and some
evidence seemed to refute it.
Among the first 1,995 suspected Mexican
cases of the new flu strain, only 27 were
laboratory-confirmed. Lab-confirmed human cases
had occurred in 19 other nations, including 64
cases in the U.S., but no deaths were reported
outside of Mexico.
Bloggers and news media usually called
the virus “swine flu,” but although it contained
genetic material of swine origin, nothing linked
it to recent swine infections.
The Perote farm belongs to the Mexican
firm Granjas Carroll, a half-owned subsidiary of
Smithfield Inc., the world’s largest pork
producer. Smithfield spokesperson Keira Ullrich
told media that an internal investigation had
found no clinical signs or symptoms of swine
influenza in animals and employees at any of its
Mexican facilities. A United Nations’ Food &
Agriculture Organiz-ation team reportedly reached
Pecote on April 28 to seek independent
confirmation.

“We deny completely that the influenza
virus affecting Mexico originated in pigs because
it has been scientifically demonstrated that this
is not possible,” claimed the Mexican National
Organization of Pig Production and Producers.
That was an exaggeration, but at press
time the case for factory farm involvement
appeared to rest on the coincidence that the
earliest identified case of the new H1N1 virus
variant was detected in 5-year-old Edgar
Hernandez, who lives near the Granjas Carroll
pig farm.
Hernandez fell ill on April 2, Mexican
health secretary Jose Angel Cordova told media.
Many other Perote residents fell ill at about the
same time, but “Only one sample from the group,
that belonging to the boy, was preserved,”
reported Tracy Wilkinson and Cecilia Sanchez of
the Los Angeles Times. “It was retested after
other cases of the new strain were confirmed
elsewhere in the country, Cordova said. The boy
had the same disease. It is unknown how many
more of the hundreds of people who fell sick in
Perote also were infected by the strain.”
“In Perote,” Wilkinson and Sanchez
found, “residents of the hamlet known as La
Gloria have complained since mid-March that the
pig farm was tainting their water and causing
respiratory infections. In one demonstration in
early April, they carried signs with pictures of
pigs crossed out with an X and the word
‘peligro’–danger. Residents told reporters at
the time that more than half the town’s 3,000
inhabitants were sick, and that three children
under age two had died.
“Local health officials mobilized when
the outbreak was first reported,” Wilkinson and
Sanchez reported, “but they gave a different
account: The infection may have started with a
migrant farmer who returned from work in the U.S.
and gave the disease to his wife, who in turn
passed it to other women in the community.”
“La Gloria was not alone in experiencing
a fierce flu outbreak in recent weeks,” noted
Marc Lacey of The New York Times. “Public health
officials in other parts of Mexico said they had
noticed an unusual spike in cases in the
beginning of April, when the normal flu season
would usually end.”
Door-to-door census taker Maria Adela
Gutierrez, 39, of Oaxaca, capital city of
Oaxaca state, on April 13 became the first
confirmed fatality from the new H1N1 strain.

James Wilson, MD

Most reports associating the Perote pig
farm with the H1N1 outbreak, including two
widely distributed columns by Grist food editor
Tom Philpot, referenced a biosurveillance web
site and blog posted by James M. Wilson V, M.D.,
of Seattle.
Wilson has done biosurveillance for the
U.S. armed forces, the USDA, NASA, and the
Centers for Disease Control and Prevention,
among other agencies, and is cofounder of the
Veratect Corporation, which “provides animal and
human infectious disease event detection and
tracking globally,” says his online biographical
page.
But Wilson was more cautious than many of
the people who used his material.
“One key myth I wish to dispel,” Wilson
updated on April 27, “is the claim that there
was any credible link to a pig farm. Such claims
must be verified through solid epidemiological
investigation.”
Wilson on April 24 posted a “Swine Flu in
Mexico” timeline that began with a March 30
report that “a 47-year-old attorney was
hospitalized in a coma at Ottawa General Hospital
following a recent trip to Mexico.”
On April 27 Wilson acknowledged that this
case “tested negative according to Canadian
officials,” and that there was therefore no
reason to link it to H1N1.
On April 2, the timeline continued,
“Local media source Imagen del Golfo reported
that [Vera Cruz] state health officials recorded
a 15% increase in disease over an unspecified
period in the highland areas of Vera Cruz, which
includes La Gloria. The increase was primarily
due to higher levels of upper respiratory disease
and gastroenteritis. Specifically, officials
noted an increase in pneumonia and bronchial
pneumonia. Health officials attributed the
increase to seasonal climate changes.”
On April 6, recounted Wilson’s timeline,
“Local health officials declared a health alert
due to a respiratory disease outbreak in La
Gloria. Sources characterized the event as a
‘strange’ outbreak of acute respiratory
infection, which led to bronchial pneumonia in
some pediatric cases. Health officials recorded
400 cases who sought medical treatment in La
Gloria, population 3,000; officials indicated
that 60% of the town’s population had been
affected. No precise timeframe was provided,
but sources reported that a local official had
been seeking health assistance for the town since
February. Residents claimed that three pediatric
cases, all under two years of age, died from
the outbreak,” as Wilkinson and Sanchez of the
Los Angeles Times confirmed.
“However,” Wilson continued, “health
officials stated that there was no direct link
between the pediatric deaths and the outbreak;
they stated the three fatal cases were ‘isolated’
and ‘not related’ to each other.”

Flu or biting flies?

Continued the April 6 timeline entry,
“Residents believed the outbreak was caused by
contamination from pig breeding farms operated by
Granjas Carroll. According to residents, the
company denied responsibility and attributed the
cases to ‘flu.'” This was apparently the first
mention of flu in connection with the La Gloria
disease outbreak.
“However,” the timeline added, “a
municipal health official stated that preliminary
investigations indicated that the disease vector
was a type of fly that reproduces in pig waste,
and that the outbreak was linked to the pig
farms. It was unclear whether health officials
had identified a suspected pathogen responsible
for this outbreak.”
Many insect-borne diseases produce
flu-like symptoms, including the ricketsial and
malarial disease families–but the ricketsial
diseases are caused by bacteria, and the
malarial diseases by protozoan parasites.
On April 27, Wilson posted that his
timeline mention of flu “was simply to flag an
event as worthy of closer scrutiny and higher
awareness, as there was absolutely no proof of
true involvement of this company in the outbreak.
A proper epidemiological investigation is
required to prove such links.”
Meanwhile, added the April 6 Wilson
timeline entry, “A health cordon was established
around La Gloria. Officials launched a spraying
and cleaning operation that targeted the fly
suspected to be the disease vector. State health
officials also implemented a vaccination campaign
against influenza, although sources noted
physicians ruled out influenza as the cause of
the outbreak. Finally, officials announced an
epidemiological investigation that focused on any
cases exhibiting symptoms since March 10.”
Ten days later, on April 16, wrote
Wilson, “Veratect reported the Oaxaca Health
Department indicated that an unspecified number
of atypical pneumonia cases were detected at the
Hospital Civil Aurelio Valdivieso in Reforma,
Oaxaca State, Mexico. No information was
provided about symptoms or treatment for the
cases. NSS Oaxaca reported that rumors were
circulating that human coronavirus was spreading
at the hospital; sources did not provide any
response to these statements from the hospital or
health officials. Laboratory samples were sent
to Mexico City for analysis. According to NSS
Oaxaca, health officials intensified preventive
measures aimed at mitigating further spread of
the disease.”

Why “swine flu”?

Explained ProMED animal disease moderator
Peter Cowen on April 25, “The H1N1 virus is
called ‘swine flu’ because of the outbreak of the
1918 virus that caused significant mortality in
both swine and human populations. The virus
probably has a wild bird origin,” as all
influenzas have evolved from avian diseases.
“Influenza viruses regularly circulate in
swine populations,” Cowen continued. “Swine flu
viruses have been known to infect humans, [but] it appears as if no exposure to swine has
occurred among people who have come down with the
current novel H1N1 virus. Since we know nothing
of how this particular virus has gotten into the
human population, but there apparently is no
history of swine exposure, it probably makes
more sense epidemiologically to refer to this
simply as an H1N1 influenza.
“Unfortunately,” Cowen concluded, “the
name ‘swine flu’ will imply a simple transmission
between swine and people, when in reality its
origin and epidemiology are likely to be much
more complex.”
Elaborated fellow ProMED animal disease
moderator Arnon Shimshony, “Swine influenza in
senso stricto,” unlike the common use in
connection with the H1N1 virus afflicting humans,
“is an animal disease, caused by a specific
porcine virus. Swine influenza viruses are very
contagious, mainly affecting pigs, but can
sporadically cause disease in turkeys and humans.
Such an interspecies infection, when occurring,
is not followed by further spread in the affected
populations,” who become dead end hosts.
“The current influenza virus spreads
readily among humans without any known
involvement of, or contact with pigs,”
Shimshony emphasized. Thus, regardless of
origin, “The causative virus can persist among
humans independent of animal involvement.”

Genetic link

Assistant professor Raul Rabadan, PhD.
of the Department of Biomedical Informatics at
Columbia University on April 28 shared with
ProMed members the strongest medical hint before
ANIMAL PEOPLE went to press that the H1N1
outbreak might be associated with pig farming.
But Rabadan’s finding did not point directly
toward factory pig farming, or even to pig
farming per se.
“My group and I are analyzing the recent
sequences from the isolates in Texas and
California of swine H1N1 deposited in the
National Center for Biotechnology Inform-ation,”
Rabadan posted. “Preliminary analysis using all
the sequences in public databases suggests that
all segments are of swine origin,” contrary to
earlier reports that the new H1N1 virus included
elements from human and avian viruses. Rabadan’s
team found the parts of the new virus “related to
Asian/European swine and the rest to North
American swine. There is also an interesting
substratification between these groups,” Rabadan
observed, “suggesting a multiple reassortment.”
Rabadan’s findings pointed toward the new
H1N1 virus originating in pigs. However, the
mix of Asian/European swine and North American
swine virus segments may point toward hybridized
boars, commonly raised for hunting and the
restaurant trade– and feral in much of North
America–rather than factory-farmed pig breeds.
However, reminded the British
Department of Food, Agriculture, and Rural
Affairs later in the day, “The virus has not
been isolated from pigs, and there have been no
reports of unusual disease in pig herds.
“H1N1 and H3N2 swine flu viruses are
endemic among pigs in many countries and
something that the industry deals with
routinely,” DEFRA continued. “Outbreaks among
pigs normally occur in late fall and winter.
U.S. studies have shown that between 30% and 50%
of the pig population have been exposed to H1N1
infection at some time. Mexico does not
routinely report swine influenza,” DEFRA noted,
“so there is some uncertainty regarding the
situation in that country.”
However, DEFRA concluded, “We consider
there is a negligible likelihood of introducing
human influenza strain H1N1 to the U.K. by the
legal import of pigs or pig products from North
America. There is no evidence that meat or other
products would be contaminated with known strains
of virus.”
Commented the Office International des
Epizooties [World Organization for Animal Health] in a parallel statement, “The virus has not been
isolated in animals to date. Therefore, it is
not justified to name this disease swine
influenza. Urgent scientific research must be
started in order to know the susceptibility of
animals to this new virus,” the OIE said, “and
if relevant to implement biosecurity measures,
including possible vaccination to protect
susceptible animals.”

Mixing vessels

Speaking before Rabadan released his
genetic findings, OIE director general Bernard
Vallat told Agence France-Presse that the new
H1N1 virus contains an avian strain of American
origin, and American swine strain and an
apparent Asian swine strain, and an American
human strain. But even with that mix, Vallat
explained, “There is no proof that this virus,
currently circulating among humans, really is of
animal origin. There is no element to support
this.”
Both pigs and humans are influenza
“mixing vessels,” within whom different flu
strains can meet, incubate, and mutate.
Regardless of the medical evidence,
animal advocates seized upon the H1N1 outbreak as
an opportunity to expose and denounce aspects of
factory farming other than disease transmission.
Posted Michigan activist Eileen Liska,
“What intensive confinement factory farming has
done to the animals, in terms of the cruelty
involved, the drugs used to offset the disease
and stress caused to the animals by how they are
overcrowded and not allowed to meet their basic
behavioral needs, etcetra, is going to come
back to haunt us until we change our ways, and
that doesn’t even include the human side effects
from eating meat filled with antibiotics and
hormones.”
“For more than 23 years we have warned
that cramming thousands of animals into factory
farms is not only bad for the animals,” said
Farm Sanctuary cofounder Gene Baur. “These
stressful, filthy, disease-ridden confines are
also bad for humans. Animals packed by the
thousands in unnatural conditions suffer
immensely and these unhealthy, overcrowded
operations are a breeding ground for
disease–swine flu, avian flu, e-coli,
salmonella, mad cow diseaseŠFactory farms are a
prescription for disaster.”
Baur mentioned pending federal
legislation which, if passed, “would eliminate
the use of sub-therapeutic antibiotics on factory
farms.”
This measure is favored by most of the
human health community as well as animal
advocates, since heavy use of antibiotics in
farming is tending to increase the capacity of
infectious bacteria to resist antibiotic
treatment.