swine flu

Recombinomics Commentary 22:50
March 27, 2012 The CDC has released five sets of H3N2 from recent collections in Maryland.  All five sequences were generated directly from the clinical samples, strongly suggesting that all five were linked to the recent death cluster. 

Three of the samples (A/Maryland/04/2012, A/Maryland/05/2012, A/Maryland/06/2012) were from March 5 collections, the date of death for two of the siblings.  The other two, A/Maryland/08/2012 and A/Maryland/09/2012, were from collections on February 21 and February 20 respectively.  Although the ages and gender of the index case and three children involved in the Maryland death cluster have been cited in media reports, the CDC withheld the age and gender for all five sequences. 

Thus, the assignment of each of the five samples was not possible from the public data released by the CDC.  However, all five H3 sequences were virtually identical and related to the drift variant, A/Brisbane/299/2011, which has S199A, as noted for prior sequences designated as low reactors by the CDC. 

A reassortant of A/Brisbane/299/2011 (designated A/Brisbane/299/2011 X-215) has been generated as a potential H3N2 vaccine target because it is a variant that produces a low reaction when tested against the current vaccine, which is directed against A/Perth/16/2009.

Thus, the sequence data confirmed that the Maryland cluster were from a drift variant and were unlikely to react well with the current vaccine, in contrast to the CDC comments and internet rumor.

Sad news out of Maryland, and a reminder of how devastating MRSA, methicillin-resistant Staphylococcus aureus, can be when it combines with flu infection. According to the Maryland Department of Health and Mental Hygiene, the Washington Post and ProMED, five members of a family have fallen ill and three have died from MRSA pneumonia that took hold in lungs inflamed by flu infection.

The dead are Ruth Blake, 81, and her children Lowell, 58, and Vanessa, 56. Another child, Elaine, also fell ill and was hospitalized, and Ruth Blake’s sister has been hospitalized also. They had all contracted one of the seasonal flu strains circulating this year: H3N2. According to the Post, Ruth Blake was vaccinated against flu this season; her children were not. The assumption is that both flu and MRSA spread from the mother to the children.

 From the Post:

Calvert health officials said in a statement Wednesday that the cases were isolated to a single family and that “there are currently no other affected individuals.” Local health-care providers, they said, are not reporting any significant increase in patients with flulike symptoms.

David Rogers, the county’s health officer, said health officials suspect that Blake also had the flu and then suffered a serious lung infection that turned into pneumonia.

“In older people, that can often be fatal,” he said.

Blake had a flu shot, he said. None of the others were vaccinated.

What’s unusual, he said, is that the infection spread from the mother to three children, probably at her bedside. Most likely, the mother’s coughing spread the virulent organisms into the air, and her caregivers, two of whom also had the flu, breathed them in and became infected, he said. (Byline: Annys Shin and Lena H. Sun)

MRSA pneumonia is fast-acting and lethal; it is often called “necrotizing pneumonia” for the way it simply kills lung tissue. Exactly why it has that effect is still disputed — MRSA has so many cellular toxins at its disposal that there could be a number of culprits — but there is no dispute that it is a very serious disease.

MRSA post-flu pneumonia isn’t well-understood because it has been a concern only recently. The first cases to alert the United States this might be a problem were in Baltimore in the flu season of 2003-04. The four patients were all seen at Johns Hopkins University Medical Center, and physicians there wrote the cases up afterward. Over two months, there was a 31-year-old woman who was in the hospital for four weeks; MRSA ate holes in her lung, the largest of which was 1 by 1.5 inches. Two other women, 20 and 33 years old, were each hospitalized for three months. The 20-year-old’s heart stopped, and her blood clotting grew so disordered that doctors had to amputate one leg below her knee; the 33-year-old lost both lower legs. The fourth patient was a 52-year-old man, a two-pack-a-day smoker, who died.

Other reports came into the Centers for Disease Control and Prevention over the course of that flu season. When the CDC counted up the following summer, there had been 15 cases of severe MRSA pneumonia in 9 states. Four of them died. CDC personnel wrote another article warning of the dangers of MRSA and flu two years later, after clusters of cases in Louisiana and Georgia during the 2006-07 flu season. They said: “Secondary S. aureus pneumonia is a potentially catastrophic complication of influenza… MRSA [community-acquired pneumonia] often affects young, otherwise healthy persons and can be rapidly fatal.”

Pneumonia that follows on flu is a seriously under-appreciated danger of flu infection: An analysis from 2010 points out that, in 2007, there were 457 deaths from flu in the US and 52,847 deaths from post-flu pneumonia. There is no reliable way to protect yourself against MRSA, since there is no vaccine, and the bacterium can live on the skin undetected for an unpredictable period of time. Hypothetically, if you prevent flu infection you lessen the likelihood of this pneumonia occurring — but as the mother’s case illustrates, flu vaccine doesn’t confer perfect protection, especially not in the elderly whose immune systems are not robust enough to begin with.

It’s a very sad story, and another illustration of how perilous and destructive MRSA can be.

http://www.wired.com/wiredscience/2012/03/flu-mrsa-pneumonia/

Recombinomics Commentary 18:45
March 7, 2012

"State health officials say today that lab tests confirm that two of the members of a Calvert County family who died early this week of severe respiratory illness had Influenza H3, a strain of the flu that has been going around this season".

The above comments confirm the Recombinomics commentary published this morning on the H3 sero-type of the HA from the fatal Calvert County, Maryland cluster.  However it is unlikely to be the “strain” of flu that has been going around this season. 

Recombinomics called the Calvert County Health Department as well as the Maryland Department of Health and Mental Hygiene, and the US CDC to get a clarification on the testing that led to the report that the influenza A was seasonal flu, since the CDC has reported an explosion of H3N2 low reactors in the week 7 and week 8 FluView reports.  The antigen characterization data indicated an new H3 had replaced the H3N2 strain that had been circulating earlier this season.

The CDC did not comment on this explosion and therefore it was unclear if the low reactors were a drift variant of the current seasonal H3N2 vaccine target, Perth/16, or were widespread H3N2v, which would also generate a low reactor result.

Moreover, the CDC PCR test distributed to state labs can identify H3N2v under ideal conditions, but most confirmed H3N2v cases gave negative, inconclusive, or seasonal H3 results, and H3N2v was confirmed by CDC sequencing.

The cluster in Maryland was determined to be H3 by the Maryland state lab, which was used for this morning’s announcement by Calvert County.  Media at the Maryland state lab suggested I e-mail the specific testing questions, and also noted that the best source of information would be the CDC, who had already been asked via cell phone and e-mail about testing and the relationship between the H3 result generated by the Maryland state lab and the low reactors reported by the CDC, which may be H3N2v.

As of this commentary, neither agency has responded to the e-mailed questions, and the relationship between the H3 in the death cluster, the low reactors reported by the CDC, and H3N2v remains unclear, but the likelihood that the H3 “strain” in the Maryland death cluster matches the seasonal H3N2 dominant in the US in 2011 and early 2012 is extremely small.

Recombinomics Commentary 16:30
March 7, 2012

"Initial testing of two of four family members in Lusby, three of whom have died, suggests that that the serious lung infection suffered by all four was a complication of seasonal flu. A fourth family member remains hospitalized at Washington Hospital Center and is improving".

The above comments from the latest update from the Calvert County Health Department website indicate the Calvert County, Maryland death cluster was linked to seasonal influenza.  A call to the health department indicates the state lab obtained an H3 serotype.  However, it remains unclear if the H3 is Perth/16-like and recognized by the current H3N2 vaccine or a "low reactor” as described in the week 8 FluView.

Moreover, it remains unclear if this is a Perth/16 variant or an H3N2v which gives and H3 positive on the CDC PCR test.  H3N2v has D225G, which is associated with patients coughing up blood.

More detail on the PCR testing and sequences from the CDC would be useful

Recombinomics Commentary 17:30
March 6, 2012

"The first patient, an 83-year-old woman, became sick on Feb. 23. Three of her children, a son and two daughters all in their 50s, arrived on Feb. 28 to take care of her.

The mother died on March 1. One daughter, 56, and her son, 58, both died on Monday while a third daughter, 51, remains at Wash Hospital Center in critical condition".

The above comments describe a death cluster in Calvert County, Maryland.  Anecdotal reports also describe a fifth victim, the funeral director who had contact with the bodies.  These reports also indicate fatal cases were coughing up blood and the funeral director was hospitalized with breathing difficulties.

More information on testing would be useful.

Friday, 02/17/2012 22:32

The avian influenza virus was genetically engineered into the new virus is highly virulent, contagious and resistant to vaccines. While Vietnam does not have A/H5N1 flu vaccine on humans

While bird flu continues to spread to many provinces, the deadly virus have been many changes detrimental to the prevention and treatment measures in poultry. More worrying when the death rate from influenza A/H5N1 in humans is 100% of cases are detected.

Resistant virus vaccine

On 17-2, Hoang Van Nam, Director of Animal Health authority (Ministry of Agriculture - Rural Development), said from the beginning of this year has 11 local detection of avian influenza including Thanh Hoa, Quang Tri, Soc Trang, Ha Nam, Hai Duong, Thai Nguyen, Kien Giang, Bac Giang, Ha Tinh and Hai Phong and Quang Nam.

Not yet quarantined poultry still be comfortable buying and selling, slaughtering in Hanoi

There were nearly 20,000 birds, mostly ducks to be destroyed. The bird flu is complicated, spread in all 3 regions. If loose slaughtering operations management, transportation and trade of poultry, the risk of widespread outbreaks is huge.

Risk of spreading bird flu, today (18-2) National Steering Committee for prevention of avian influenza will have an emergency meeting to discuss measures to cope. Meanwhile, Mr. Diep Kinh Tan on 17-2, Deputy Minister of Agriculture - Rural Development, said it had written to the Prime Minister requests the State budget of 13 billion contract to buy 50 million doses of H5N1 vaccine Re-vaccination strains fifth round of 1-2012 for timely enclosure, stamping out.

According to Tan, 2012 is expected to need 327 million doses of vaccine given to poultry, but due to bird flu virus in the northern provinces with the change, the vaccine strain H5N1 Re-5 protection levels households is not high. Meanwhile, in the southern provinces, not bird flu virus is modified to use H5N1 vaccines imported from China, so immediate permission to import 50 million doses.

The risk to humans is very large

According to experts, the bird flu virus may be genetically caused the surveillance becomes more difficult. Department of Animal Health representative said before, there are 3 branches Vietnam H5N1 virus has been detected. A branch in the south, north branch and the branch 2.3.4 7 capable of highly infectious.

However, recently in the northern provinces, discovered a new bird flu virus branch, symbol 2.3.2 branch. More worryingly, had discovered the virus 2.3.2 branch into 2 groups. With a group of old virus, vaccine against bird flu meets only 75%, while the new virus, vaccines are currently using does not work. Therefore, the risk of spreading the virus in poultry and humans is very large. What is more dangerous than professional bodies continue on raising waterfowl flocks, sold in many places but no signs or symptoms but still carry the virus H5N1.

Dr. Nguyen Hong Ha, deputy director of Tropical Diseases Hospital Central, concerned with the weather hot and humid climate are favorable for growing influenza virus. Moreover, with the normal seasonal flu viruses such as influenza B, H1N1, H3N1, H5N1 ... the risk is present, the virus strains combine or mutate to create new influenza virus virulent more dangerous is huge. Currently, flu vaccines are being used in Vietnam is just common flu as influenza A (H3N1, H3N2, H1N1) and there is no vaccine against A/H5N1 flu in humans.
100% mortality rate

According to Dr. Tran Thanh Duong, deputy director of the Department of Preventive Health (MOH), A/H5N1 flu spread from birds, waterfowl infected with influenza A/H5N1 virus to humans is strongly virulent virus, the mortality rate very high. At this point, the rate of death from influenza A/H5N1 in humans is 100% of cases were detected. Two cases were patients who died despite antiviral treatment.

http://nld.com.vn/20120217102740382p0c1002/virus-h5n1-bien-doi-vacxin-bat-luc.htm

 This is a two-year-old girl, in Duoc, Long An and is now cured. For years, our country has recorded cases of infection with influenza virus A (H3N2) in humans, also known as regular seasonal flu, while flu patients is derived from pigs.

Recombinomics Commentary 13:15
February 15, 2012

The national flu monitoring system detected this case in April 2011. A two-year-old female baby in Long An province contracted the disease and was treated successfully at the Children’s Hospital No 1. in HCM City. The A/H3N2 flu virus she had originated from pigs.

The test results of the HCMC Pasteur Institute were confirmed on January 10, 2012, by the WHO laboratory at the US Centres for Disease Control and Prevention (CDC).

The above comments provide additional clarity on the dates surrounding the confirmed H3N2v case in Vietnam, but still leave many questions unanswered.  It is likely that this case was initially classified as seasonal H3N2 in 2011.  The H3N2v cluster in Iowa in November led to an alert issued by WHO, largely because the three confirmed cases had no swine exposure.  That alert was followed by a media report in Vietnam that described the US cases and increased surveillance in Vietnam.  Those reports incorrectly described the US H3N2v cases as H3N1.
Last week media reports in Vietnam again issued a warning about H3N2v cases, but only provided detail on the cases in the United States and again described the cases as H3N1, and a follow-up report claimed no H3N2v cases in Vietnam in 2012 (carefully parsed to avoid acknowledgement of the 2011 case).

Today, reports from Vietnam described the above case (age, gender, and location) and the English language reports clearly indicated this was a 2011 case that was confirmed over a month ago by the US CDC.

This raises several important questions, which have not been answered. None of the reports have cited a swine exposure by the confirmed case.  Similarly, the CDC has not released the sequences at GISAID, as was done for the 2011 variant cases in the United States (H3N2v, H1N2v, H1N1v).  Moreover, WHO has not announced the confirmed case, in spite of lab confirmation by a WHO regional center, although it is unclear if the WHO has announced this case at its password protected site.
Thus, a month after confirmation, all of the above questions remain unanswered by public data, although the sequence would clearly distinguish between a linkage to Asian or North American swine lineages.

The lack of transparency by WHO and the CDC continues to increase pandemic concerns.

Recombinomics Commentary 09:15
February 15, 2012

As reported by the National Influenza Center - Pasteur Institute of Ho. Ho Chi Minh, influenza surveillance system key southern countries found cases of A/H3N2 flu originated from pigs.

This is a new 2-year-old female patients in Duoc, Long An influenza have been treated at Children's Hospital 1 and then cured. Samples of these patients have been tested in a laboratory at the CDC standard WHO official - the United States and has been confirmed.

Yang said, this is the first case reported in Vietnam A/H3N2 flu originated from pigs. This slight movement of cases and no evidence of transmission from person to person.

The above translation describe the first case (2F) of H3N2v in Vietnam (Duoc, Long An).  In contrast to earlier reports, which described similar cases in the United States, this report describes a PCR confirmed case in the Mekong Delta region in southern Vietnam.

As noted earlier, there are 6 sets of public sequences from H3N2v in swine, isolated in 2010 (A/swine/Binh Duong/03_06/2010, A/swine/Binh Duong/03_08/2010, A/swine/Binh Duong/03_09/2010, A/swine/Binh Duong/03_10/2010, A/swine/Binh Duong/03_13/2010, A/swine/Binh Duong/03_14/2010). All six isolates are closely related and have human H3 and N2 genes, with swine internal genes that are generally more closely related to H3N2v swine sequences in Asia (South Korea and Hong Kong).

However, Hong Kong has released 3 sets of sequences from Guangxi and Hong Kong (A/swine/Guangxi/NS2783/2010, A/swine/Hong Kong/2503/2011, A/swine/Hong Kong/NS2439/2011) , which have similar H3 and N2 human genes surrounding six internal genes from H1N1pdm09. In the United States, all 12 of the H3N2v sequences in humans in 2011 have an H1N1pdm09 M gene. Prior H3N2v cases in the United States have PB1 E618D, which is not in the swine isolates from Vietnam, but is in the new sequences from Hong Kong and China, since E618D is in virtually all H1N1pdm09 PB1 sequences.

The above report does not cite swine contact, so the origin of the infection is far from clear.  H3N2v in Vietnam is readily distinguished from H3N2v in the United States.

Information on the constellation of genes in the case in Vietnam would be useful.

By NOBUYA SAWA / Staff Writer

Face masks are being seen everywhere in Japan at the peak of flu season, as the number of patients is increasing at the fastest pace in 10 years.

The number of patients who sought treatment at medical institutions subject to a survey stood at 42.62 on average in the latest week from Jan. 30 to Feb. 5. That was the highest at this time of the year since 2002.

The total number of flu patients in Japan is estimated to be about 2.11 million.

Starting this month, the number of patients who have contracted different types of flu strains is also increasing.

This influenza season features the spread of a Type A Hong Kong flu for the first time in five seasons. About 90 percent of patients were contracting that type of virus until January. From this month, however, patients that are suffering from a Type B influenza are also increasing in some areas.

“Antibodies that were gained as a result of infection are maintained for certain periods. As time passes, however, their effects wane. As a Type A Hong Kong flu is spreading after a long interval, people may have lost their immunities,” said Hideki Hasegawa, director of the Department of Pathology at National Institute of Infectious Diseases (NIID).

Because of the various types of strains, there is a growing fear that the current flu season will be a long-lasting one.

In the Tokyo metropolitan area, until mid-January, the number of patients was relatively small. In recent weeks, however, it has increased sharply there. In addition, the number of patients has been hovering at high levels in the Tokai and Shikoku regions since early January.

According to an announcement from the NIID, the number of patients per medical institution stood at 35.95 on a national average in the previous week from Jan. 23-29.

In the latest week, however, the figure jumped to 50.94 in Saitama Prefecture, 50.84 in Chiba Prefecture, 45.20 in Tokyo and 48.86 in Kanagawa Prefecture.

In the Kinki region, the corresponding figures were hovering around 40 in the latest week, almost the same as that in the previous week. For example, it stood at 44.81 in Osaka Prefecture and 42.46 in Hyogo Prefecture.

In the previous week, prefectures with the largest numbers of patients per medical institution were Fukui, Kochi and Aichi. In all of the three prefectures, their figures dropped to 64.41, 54.21 and 47.38 respectively in the latest week. However, the figures were still at high levels.

In Chugoku and Kyushu regions, high levels also continued in the latest week with the number of patients at 51.64 in Yamaguchi Prefecture, 55.36 in Miyazaki Prefecture and 45.67 in Oita Prefecture.

The number of flu patients is also increasing in areas affected by the Great East Japan Earthquake. In Iwate Prefecture, the number increased from 45.52 in the previous week to 58.98 in the latest week, the second highest in Japan following Fukui Prefecture.

http://ajw.asahi.com/article/behind_news/social_affairs/AJ201202110005

Recombinomics Commentary 16:00
January 6, 2012 HHS has contracted with pharmaceutical companies Novartis and Sanofi Pasteur to develop investigational lots of the vaccine. Novartis will produce its supply using cell-culture technology at its plant in Holly Springs, North Carolina, and Sanofi Pasteur will grow the vaccine in chicken eggs (a slower method of production) at its plant in Swiftwater, Pennsylvania.

The influenza virus being targeted is a variant of the A(H3N2) virus found in pigs.

The above comments describe preparations for spring clinical trials for an H3N2v pandemic vaccine.  These developments are not a surprise.  In August the CDC released sequences of vaccine constructs of A/Minnesota/11/2010, which was followed by a WHO September 29, 2011 report on vaccines, showing that the sera against the above target was effective against the first H3N2pdm11 isolate, A/Indiana/08/2011.
 
Although December media reports cited the creation of a seed vaccine, the real drivers for the clinical trials were the H3N2pdm11 cluster at the daycare center in Iowa, followed by the trH3N2 sustained cluster in the daycare center in Mineral County, West Virginia (which has a novel N2 which has acquired seasonal polymorphisms via recombination.

The West Virginia cluster was alarming, with 23/70 contacts of the index case exhibiting ILI (influenza-like illness), which led to a CDC request to all states to increase surveillance, especially in children.  Multiple states issued advisories or alerts, including Marin County, California, which also cited a new H3N2v case in a Napa county resident in its week 50 report.

Today the CDC published the December 23 early release MMWR, which described the West Virginia cluster, which made it clear that transmission was sustained for a month at the daycare center, but failed to note that 23 contacts had ILI.  In December the CDC also held a 50 state conference call.

An explosion of H3N2v cases and clusters is expected this month.

Recombinomics Commentary 05:00
January 5, 2012 More recently, investigation of a case in West Virginia has identified a possible outbreak, with 23 out of 70 contacts of the case reporting ILI; all have recovered.

The above comments are in the California Department of Public Health December 15 H3N2v advisory.  The West Virginia cluster was described in the CDC early release MMWR, but the 23 ILI cases were not mentioned.  Instead the report said there were several contacts of the index case, A/West Virginia/06/2011, which initially tested as negative.  trH3N2 was isolated from a contact, A/West Virginia/07/2011, which initially tested as inconclusive and was reported as an influenza A case.  The partial sequence of HA and NA were virtually identical to the index case, and both had a novel N2 that was easily distinguished from the first 10 cases in 2011 (H3N2pdm11).

Thus, the vast majority of cases at the day care center were not reported, and the two confirmed cases had serious testing issues.  The numbers cited in the California advisory indicate the attack rate was high, and the transmission was sustained for almost a month, but the CDC maintains that there is no sustained or community transmission of H3N2v.  None of the cluster members have reported contact with swine.

A pediatric case in Napa County, California has also tested positive for trH3N2 and is under investigation.  Anecdotal reports indicate ILI is widespread in pediatric cases in northern California, but most are mild and not tested.  As seen in the West Virginia cluster, testing is a serious issue, allowing the trH3n2 to silently spread.

An explosion of cases and clusters is expected this month.

January 4, 2012 — Taking no chances, the US Centers for Disease Control and Prevention (CDC) is laying the groundwork for a possible vaccine against a novel strain of a swine influenza virus that has surfaced in 5 states and sickened 12 individuals, mostly children, since July 2011, an agency official told Medscape Medical News Tuesday.

The strain, designated A(H3N2)v, is a variant of the A(H3N2) virus that circulates among humans on a seasonal basis. What makes it a variant is a gene from the pandemic 2009 influenza A(H1N1) virus that codes for matrix proteins found in the viral shell.

In Indiana, Pennsylvania, and Maine, the virus appeared to have spread from pigs to humans, according to the CDC. In Iowa and West Virginia, however, the evidence suggests limited human-to-human transmission. In general, the novel virus is no more severe than ordinary seasonal influenza, and all the people infected with it have recovered.
The CDC is encouraging public health agencies and clinicians to collect more nasopharyngeal swabs from patients presenting influenza-like illness for testing to determine whether the novel virus may be spreading on a sustained basis.
CDC spokesperson Thomas Skinner told Medscape Medical News that the agency already has prepared a "seed virus" obtained from A(H3N2)v specimens that drug manufacturers can use to develop a vaccine if needed. Preparing a seed virus involves genetically manipulating specimens to incorporate preferred features.
Because the new virus is different enough from the seasonal viruses now in circulation, the seasonal influenza vaccine for 2011-2012 "is not expected to provide significant protection" against the newcomer, according to a Morbidity and Mortality Weekly Report that the CDC published on December 23. The trivalent seasonal vaccine is formulated to protect against the 2009 pandemic virus, the regular A(H3N2) virus, and an influenza B strain.
CDC Could Be Preparing for 2012-2013 Influenza Season
So far, the evidence does not suggest that the A(H3N2)v strain is spreading freely through communities, which would create the need for a vaccine. The bug could fizzle out, according to Christine Layton, PhD, MPH, a public health researcher and influenza pandemic expert at RTI International in Research Triangle Park, North Carolina.
"There have been past instances where a novel virus comes up and then goes back down," Dr. Layton told Medscape Medical News. "There may be something about the virus that [prevents] sustained human-to-human transmission."
If the A(H3N2)v virus ever takes off, she said, drug manufacturers would have a tough time turning out a corresponding monovalent vaccine "at the drop of a hat." Influenza vaccines are still mass-produced, for the most part, by being grown in chicken eggs. Together with testing and licensing a vaccine, this process easily can last 3 to 4 months.
A more likely scenario, said Dr. Layton, would be incorporating an A(H3N2)v strain in the trivalent seasonal vaccine for 2012-2013, assuming the novel virus becomes that much of a threat. Each February or so, an advisory panel of the US Food and Drug Administration (FDA) recommends 3 strains of influenza that should make up the seasonal vaccine for the coming fall on the basis of what it expects to see circulating then. The CDC then develops the seed viruses for these 3 strains, which the FDA distributes to vaccine makers. 

http://www.medscape.com/viewarticle/756348

CDC confirms two human infections with novel influenza viruses

December 9, 2011 -- CDC has confirmed two cases of human infection with two different novel influenza A viruses in different states. Both patients have fully recovered. While the viruses infecting both patients have been found in U.S. swine and some of the prior human infections with these viruses have been associated with direct or close swine contact, there are no reports of direct or close contact with swine prior to illness onset in either of these cases. Laboratory testing at CDC has confirmed that both novel viruses are susceptible to the antiviral medications oseltamivir (Tamiflu®) and zanamivir (Relenza®).

West Virginia
One case of human infection with a novel influenza virus was reported by West Virginia and involves infection of a child with the novel influenza A (H3N2) virus with genes from swine, human, and avian lineages with the M gene from the 2009 H1N1 virus that was first identified in August 2011. Ten prior human infections with this virus in four other states have been confirmed. These occurred in Indiana (2), Pennsylvania (3), Maine (2), and Iowa (3).

These novel influenza A (H3N2) viruses are substantially different from currently circulating seasonal (human) influenza A (H3N2) viruses, but are distantly related to human influenza viruses that circulated among people in the 1990s. For that reason, some adults may have some residual immunity against this virus. This might help explain why 10 of the 11 cases that have been detected have occurred in children.

Most human infections with viruses that circulate in swine (but not humans) have been associated with swine exposure, but limited human-to-human transmission associated with these viruses is thought to have occurred as well, most recently in Iowa. While an investigation is ongoing in West Virginia, no direct or indirect contact with swine has been reported, implying that limited human-to-human transmission of this virus may have occurred again.

No ongoing community transmission of this virus has been detected in the United States. However, CDC is taking this situation very seriously. Surveillance surrounding reported cases is being further enhanced and, as a precaution, a vaccine virus has been developed and provided to manufacturers for them to begin vaccine production should that become necessary.

Minnesota
The other case of novel influenza A virus infection was reported by Minnesota, and is associated with a different influenza virus; an influenza A (H1N2) virus that circulates in swine  in the United States, but does not normally infect or cause illness in humans. This case also was in a child. This is only the second case of human infection with this novel influenza A (H1N2) virus reported to CDC since novel influenza virus infections became nationally notifiable in 2007. The first such case was identified in Michigan in 2007. By some characteristics, this H1N2 virus is close to human influenza A (H1N1) viruses called “A/New Caledonia /20/99-like,” which circulated and caused illness among people as recently as 2007. As a result, people who were exposed to A/New Caledonia/20/99-like viruses may have some existing immune protection against the virus detected in Minnesota. Again, no direct or indirect contact with swine has been reported with this case, implying that limited human-to-human transmission may have occurred in this instance as well.

Detection of Swine Influenza Infections in Humans
Human infections with novel influenza A viruses normally found in swine are rare events. Recently, however, the frequency of such detections has increased. This could be occurring for a number of reasons, including one or more of the following factors: First, laboratory methods for testing for these viruses in the United States were improved following the 2009 H1N1 pandemic. These improvements may be resulting in viruses being identified now that would have gone undetected previously. Second, this could be due to increased surveillance in the United States for influenza at this time of year. CDC has requested that states analyze, and then send, their first influenza virus specimens of the season for seasonal influenza surveillance purposes. This practice, coupled with very low levels of seasonal flu activity at this time, could mean that sporadic novel influenza infections are more likely to be tested. Third, it is possible that the increased frequency of detection of novel influenza viruses with swine origins identified by CDC represents a true increase in the number of such cases, possibly occurring from exposure to infected swine  or through subsequent, limited human-to-human transmission.

The novel influenza A (H1N2) virus identified in Minnesota is known to circulate in U.S. swine herds. While the prevalence of the novel influenza A H3N2 virus with the 2009 H1N1 M gene in swine is unknown, the virus has been detected in U.S. swine through the United States Department of Agriculture’s swine influenza surveillance program.

In response to recent human infections with novel influenza viruses, CDC would like to convey the following information:

1. 1. CDC recommends an annual seasonal flu vaccine to protect against seasonal influenza viruses; however, a seasonal flu vaccine is unlikely to protect against flu viruses that normally circulate in swine.
2. There are two FDA–cleared drugs that are expected to be effective in treating illness associated with these viruses. The antiviral drugs oseltamivir and zanamivir – which are used to treat infection with human seasonal influenza viruses – also have shown activity against influenza viruses from swine. (For more information about influenza antiviral medications, please see www.cdc.gov/flu/antivirals/whatyoushould.htm )
3. Influenza has not been shown to be transmissible to people through eating properly handled and prepared pork (pig meat) or other products derived from pigs. For more information about the proper handling and preparation of pork, visit the USDA website fact sheet “Fresh Pork From Farm to Table.”

At this time, CDC recommends the following:

1. People who experience flu symptoms following direct or close contact with swine and who require medical attention (see below) should mention this exposure to their doctor or health care provider. (A list of flu symptoms is available at www.cdc.gov/flu/about/disease/symptoms.htm.)
2. For people who have NOT had exposure to swine and develop ILI, CDC’s recommendations for seeking treatment are the same as they are for seasonal influenza.
   1. If you have symptoms of flu and are very sick or worried about your illness contact your health care provider.
   2. Certain people are at greater risk of serious flu-related complications (including young children, elderly persons, pregnant women and people with certain long-term medical conditions) and this is true both for seasonal flu and novel  flu virus infections. (For a full list of people at higher risk of flu related complications, see www.cdc.gov/flu/about/disease/high_risk.htm.) 
   3. If these people develop ILI, it’s best for them to contact their doctor. (The majority of recent novel influenza A (H3N2) cases have been in children.)
   4. Your doctor may prescribe antiviral drugs that can treat the flu. These drugs work better for treatment the sooner they are started.

More information about swine influenza and links to all previous reports related cases of novel influenza A (H3N2) viruses infections are available on the CDC swine influenza website at www.cdc.gov/flu/swineflu/index.htm.

Source: http://www.cdc.gov/media/haveyouheard/stories/novel_influenza.html

by Agencies

04:45 AM Nov 28, 2011

//

WASHINGTON - Flu experts are gearing up their response planning, after an odd new flu virus has been detected, a senior official of the World Health Organization (WHO) said.

The virus is currently jumping from pigs to people in parts of the United States, and experts are "figuring out what needs to be done if the virus continues to spread and a global response is required", Dr Keiji Fukuda, assistant director-general for Health Security and Environment, was quoted as saying by The Toronto Star.

The virus is influenza A of the H3N2 subtype, a distant cousin of H3N2 viruses that circulate in humans.

Since the virus was first spotted in July, 10 cases have been confirmed in Maine, Indiana, Pennsylvania and Iowa.

All the victims were children under 10, with an exception - a 58-year-old adult.

Flu expert Malik Peiris, chairman of the Department of Microbiology at the University of Hong Kong, said exposure to contemporary H3N2 viruses might provide some protection against these swine viruses.

"It is important to see the serological data to see how much vulnerability or susceptibility there is in the human population," he was quoted by the paper.

The WHO's desire to be ready without causing alarm comes after its failure to communicate uncertainties about the H1N1 swine flu pandemic in 2009.

Critics said the WHO had created panic about the swine flu virus, which turned out to be moderate in its effect, and caused governments to stockpile vaccines that went unused.

http://www.todayonline.com/World/EDC111128-0000016/New-flu-virus-has-WHO-gearing-up-to-respond

Some of the media reports above reference the current flu vaccine as a good preventative measure for trH3N2. This is not true. That strain is not included in this year's trivalent flu shot.

Recombinomics Commentary 17:30
November 26, 2011
 "We have received disturbing information on the WHO alert system that the U.S. two people the virus H3N2: a seven-month child in Illinois and 46-year-old man in Pennsylvania, "- told Interfax Rospotrebnadzor head Gennady Onishchenko.
 
The WHO wants to be ready to make recommendations and issue guidance to countries if the need arises — though Fukuda stressed at this point it is far from certain there will be that need.

"We're very aware that we don't want to over-play or under-play. We're trying to get that right," says Fukuda, a leading influenza expert.

"(We're) trying to make sure that we're ready to move quickly, if we have to move quickly, but also trying not to raise alarm bells."

The desire to be prepared without raising alarm is a legacy of the 2009 H1N1 pandemic. The WHO was heavily criticized in Europe for declaring that event a pandemic when the outbreak turned out to be far milder than originally feared.

But what exactly the agency — and the world — might need to prepare for now is very unclear. With the public relations problems of the 2009 outbreak fresh in the minds of health officials, no one is using the "p" word these days.

Yet in some respects the parallels to 2009 are striking.

The above comments are from the response to the WHO pager alert (in blue), issued almost exactly one year ago, and the latest media report (in red) of current WHO pandemic plans.

The alert issued in November, 2010 cited two trH3N2 isolates (A/Wisconsin/12/2010 and A/Pennsylvania/14/2010), but WHO and the CDC were probably aware of a third case (A/Pennsylvania/40/2010) who developed symptoms less than a week prior to the Wisconsin case (cited as an Illinois cases in the alert).

If the WHO and CDC didn’t know about the second Pennsylvania case when the alert was issued, within days they knew of that case, as well as a case from Minnesota (A/Minnesota/11/2010) and symptomatic contacts.  When the CDC released the sequences from these cases, there was clear cause for concern, as seen in slide 7 from the CDC (Nancy Cox) presentation in February, 2011 (at the FDA vaccine advisory committee meeting). 

The H3 sequences from cases in Wisconsin, Pennsylvania, and Minnesota were clustering, indicating the H3 for all three cases were remarkably similar and distinct from trH3N2 swine isolates.  Moreover, the sequences from the Wisconsin case and the Pennsylvania case that was not mentioned in the alert, were virtually identical, creating striking parallels between the trH3N2 data and the initial cases in southern California at the start of the H1N1 pandemic in 2009.

However, the absence of the sequences from the second case allowed the CDC to offer assurances that there was no human transmission because of sequence differences between the two cases in the alert, which were isolated 6 weeks apart.  The announcement of the second case in Pennsylvania was delayed until February 5, because the case was initially classified as seasonal H3N2, but sequence data showed that the case was clearly trH3N2.  That sequence was used in slides 7 and 8 in the CDC February 25, 2011 presentation, but the sequence was not released until Sunday, April 17, 2011 at GISAID without comment.
As seen in slides 7 and 8, the PA/40/2010 sequence was virtually identical to WI/12/2010 and this identity extended to all 8 gene segments.  Moreover the two cases developed symptoms within a week of each other, even though they were not epidemiologically linked.  Thus, the only significant difference between the trH3N2 matches in 2010 and the trH1N1 matches in 2009 was the claim of “swine exposure” for the trH3N2 cases.

However, this “exposure” was listed in the CDC slide as a “visit to a local animal fair”.  Since the Wisconsin case was only seven months old at the time, the extent of “contact” was likely limited, and no trH3N2 was reported at any of the swine at the fair.  Similarly, the Pennsylvania case (3F) was only 3 years of age, and swine contact at the fair was also likely limited, and no trH3N2 matching the human cases has been reported from either state.  Similarly, the other case from Pennsylvania (PA/14/2010) had no reported exposure to swine, although he lived in a rural area (and closely related sequences to this case were subsequently identified in Pennsylvania swine).

Thus, the red flag raised over a year ago in the WHO pager alert signaled the start of a series of events which left little doubt that the trH3N2 had begun in 2010, and gained significant speed in 2011.  In week 21 of 2011 trH3N2 was lab confirmed (serologically) in the daughter of the Minnesota case and her lack of swine exposure led to the CDC concession that the case represented limited human to human transmission.

This concession was made again for the first 2011 trH3N2 case (A/Indiana/08/2011), who also had no swine contact.  However, the caretaker of the patient had swine exposure, so the case was said to have “indirect swine exposure” even though the caretaker and swine were asymptomatic and not trH3N2 was identified in either case.

Similarly, the first 2011 case from Pennsylvania (A/Pennsylvania/09/2010) also visited an agricultural fair (Washington county) but no symptomatic swine was identified at the fair, which included the market hogs exhibited by the second Pennsylvania case.  The third case also visited the fair and a friend who exhibited swine, but there was no evidence that any of the three cases were infected by trH3N2 in swine at the fair, and the sequences from the 2nd and 3rd Pennsylvania case (A/Pennsylvania/10/2011 and A/Pennsylvania/11/2011) were virtually identical to the Indiana case.

Thus, the matches between cases that were not epidemiologically linked as seen in late 2010, was repeated in the initial cases in 2011, although this sequence had evolved from the 2010 sequences by acquiring an NA gene matching the other Pennsylvania case (PA/14/2010) and an M gene segment from 2011.

This constellation and lineage has now been found in all 2011 human cases, including the Iowa cluster, which had no swine contact and involved three confirmed cases and two symptomatic family members of the index case.

Thus, the “swine exposure’ link, which generated the more advanced testing at the CDC required to confirm trH3N2, was absent from the Iowa cluster, leaving little doubt that the novel trH3N2 was spreading in humans and was orders of magnitude higher than the ten confirmed cases from four states (Indiana, Pennsylvania, Maine, Iowa) as well as one novel trH3N2 swine isolate from New York, A/swine/NY/A01104005/2011.

Consequently, WHO is planning for the trH3N2 pandemic, without using the “P” word.

Currently, the CDC is watching the development of a novel strain of influenza A H3N2 identified as S-OtrH3N2 [Swine-Origin, triple reassortant (H3N2)]. Triple reassortant H3N2 was first identified in pigs in 1998 (link) and a few years later found to be endemic in pigs and turkey populations in the USA with evidence of interspecies transmission (link). The first reported possible human case of trH3N2 was a farm worker from Ontario Canada in 2005 (link).

Since 2009 there have been sporadic scattered human cases in the USA, most from apparent interspecies transmission.

2009-2010 Influenza Season

http://www.cdc.gov/mmwr/preview/mmwr...cid=mm5929a2_w

2010-2011 Influenza Season

http://www.cdc.gov/mmwr/preview/mmwr...cid=mm6021a5_w

2011-2012 Influenza Season

Since July 2011, 10 additional human trH3N2 cases have been reported in the USA, all carrying the M gene from the pH1N1 virus. The virus is now officially referred to as S-OtrH3N2. The first seven of these 10 cases appear to have resulted from interspecies jump from swine to humans on different occasions.

http://www.cdc.gov/mmwr/preview/mmwr...m60d1123a1.htm

Of these seven cases 2 are from Indiana, 2 from Maine, and 3 from Pennsylvania.

Indiana (2):
1. http://www.cdc.gov/mmwr/preview/mmwr...cid=mm6035a6_w
2. http://www.in.gov/isdh/files/Week43-2011.pdf

Maine (2) : http://www.maine.gov/tools/whatsnew/...id=318365&an=2

Pennsylvania (3)
1. http://www.cdc.gov/mmwr/preview/mmwr...cid=mm6035a6_w
2. http://www.cdc.gov/media/haveyouhear...b_testing.html
3. http://www.cdc.gov/media/haveyouhear...b_testing.html

Human to Human Transmission – Iowa

Yesterday, The CDC published an MMWR report on three new S-OtrH3N2 human infections from Iowa (link). These three reported cases are all children who attended the same day care center. The staggered onset dates suggests that one of the children infected the others. And none of the children were reported to have contact with swine. In addition, another sibling and parent of the children also exhibited ILI symptoms but were not tested. These 5 individuals perhaps represent the first reported human cluster of S-OtrH3N2 infection resulting from human-to-human (H2H) transmission. These cases represent intraspecies transmission of S-OtrH3N2; the threat of this novel virus as a pandemic virus has increased.

Discussion and Implications

So far, human infections with S-OtrH3N2 have not resulted in any deaths, but several of the cases have been hospitalized. Children under 10 years are the most commonly infected individuals, suggesting that previous exposure to earlier strains of H3N2 may provide some cross-protective immunity. The ultimate virulence of this novel strain as it continues to infect human is unknown. The CDC has already developed and submitted a sample strain of this virus for potential inclusion into future influenza vaccines (link).

http://www.flutrackers.com/forum/showthread.php?t=177008

Recombinomics Commentary 22:45
November 23, 2011
 Prior to the three cases in Iowa, most human infections with this virus were associated with exposure to swine. In Iowa, however, no swine exposure has been identified. At this time, it appears that unsustained human-to-human transmission may have occurred.

The above comments are from the November 22 “Have You Heard?”, a CDC backgrounder for the media.  The latest Iowa cluster leaves little doubt that the novel trH3N2 with the H1N1pdm09 M gene is transmitting in a sustained manner.  The CDC maintains its “unsustained” claim by limiting testing.

Since the trH3N2 virus has a human H3 and N2, it frequently tests positive for seasonal H3N2.  This mis-classification can be corrected in the newly approved CDC PCR test, which has two swine genes from H1N1pdm09, but low abundant RNA samples can test negative for these markers to produce a false positive for seasonal H3N2, as was reported for a case from 2010 (A/Pennsylvanai/40/2010), as well as the second case from Maine (A/Maine/07/2011).  Therefore sequencing is required to conclusively classify the H3N2 positive case as seasonal H3N2 or trH3N2.

The CDC has released 14 sequences collected from adolescent samples that were influenza A positive since July 20, 2011.  9 of the 10 confirmed trH3N2 cases in 2011 were from patients aged 1-9.  Thus, only 5 seasonal H3N2 sequences have been identified in public sequences which include the patients age and gender, as updated below.  trH3N2 cases are in bold.

As seen below, 64.2% of the US cases were trH3N2, and the percentage for those under 10 years-of-age is 75%.  Moreover, for cases in the four states where trH3N2 has been detected, 90% of the cases have been trH3N2 confirmed (all have the H1N1pdm09 M gene and all eight gene segments are from the same lineages). 

Other than the 9 cases from children, one novel trH3N2 case was from an adult, A/Indiana/10/2011, and one case was identified in swine, A/swine/NY/A01104005/2011 .

Thus, trH3N2 is common and transmitting, and cases will explode if the CDC begins serious testing, including sequencing of influenza A positive samples from children under 10 years of age.

A/Iowa/09/2011                11/14 2M
A/Iowa/08/2011                11/14 1M
A/Iowa/07/2011                11/14 3F
A/Maine/07/2011              10/24 8M
A/Maine/06/2011              10/10 8M
A/Indiana/09/2011             10/03 1M
A/Washington/17/2011      09/14 10F
A/Pennsylvania/10/2011 08/26 9F
A/Florida/24/2011               08/25 1M
A/Pennsylvania/11/2011 08/25 9F
A/Pennsylvania/09/2011 08/20 2F
A/Louisiana/06/2011          08/16 13F
A/Florida/20/2011               08/05 8M
A/Indiana/08/2011              07/27 2M

Three children in Iowa have come down with a new type of flu virus previously linked to pigs, but this time the bug appears to have been spread by people.

The children, who live in rural Webster and Hamilton counties, did not become seriously ill, said Dr. Patricia Quinlisk, medical director for the Iowa Department of Public Health. But the detection of the virus known as swine-origin A/H3N2 in patients who hadn't had contact with animals raises concerns about potentially greater spread of a new type of flu.

"We have pretty good evidence of person-to-person spread," Quinlisk said. "None of the children or anyone around them had exposure to swine, turkeys or other sources."

Officials with the Centers for Disease Control and Prevention had previously detected seven cases of people with the new H3N2 virus that appears to have acquired a gene that may make it more transmissible from H1N1, the flu that sparked the so-called swine flu pandemic in 2009. Flu viruses often swap genetic parts. Officials say the new virus was probably formed when a pig became infected with the H3N2 virus and the H1N1 virus at the same time.

The new bug has components of human, avian, H1N1 and swine flu viruses, all mixed together in what scientists call a recombinant virus.

The first new H3N2 case was identified in a child in Indiana in July, and has been followed by cases in Pennsylvania, Maine and, now, Iowa.

In the previous cases, however, the patients either had direct exposure with pigs, or exposure to a person who'd been around pigs. In the new cases, it appears that one of the children transmitted the flu to the other two, and none of them had any animal exposure, Quinlisk said. She declined to identify the children or their ages, saying only they were younger than 18. No further cases have been identified in the past week, she said.

The Iowa cases are nothing to panic about, health officials emphasized. The H3N2 flu causes symptoms similar to the regular seasonal flu, including fever, cough, fatigue, body aches and loss of appetite. 

"People need to be most concerned about the regular, everyday seasonal flu," Quinlisk said.

But Iowa health officials are now testing samples of people with flu-like illness to detect further spread of the new bug. And CDC officials have asked states across the country to be vigilant in looking for it, said Dr. Joe Bresee, the agency's influenza and epidemiology branch chief.

The current seasonal flu vaccine being offered by doctors and clinics was not developed to protect against the H3N2 virus. It contains some antigens similar to a flu virus that circulated in the 1990s, so some people who had the flu then or were vaccinated could have some immunity, but it's not clear how much, Quinlisk said. The Iowa children apparently had not been vaccinated, she added.

With the new cases, CDC officials have confirmed 31 cases in the U.S. of the new swine-origin virus since 2005, including 10 with the H3N2 virus that carries the M gene from the 2009 H1N1 virus.

The best prevention for the new flu, as with any flu, is to wash hands frequently, cover coughs and sneezes and limit spread of germs by staying home when you're sick, health officials said.

http://vitals.msnbc.msn.com/_news/2011/11/23/8977636-new-flu-virus-in-three-iowa-kids-raises-concern-about-wider-spread

Recombinomics Commentary 14:00
November 23, 2011
Iowa has increased flu surveillance state-wide. And Cox said the CDC has asked bordering states to enhance their surveillance efforts as well.

The three children attended a small day-care together. They live in adjacent counties, Webster and Hamilton, in the centre of the state.
One became sick first and appears to have infected the other two. Quinlisk said it's not clear how the first child got infected.

Another child who is a contact of the first child was ill with what may have been influenza prior to the first child's infection, she said. But by the time laboratories had confirmed the cases, that other child had recovered.

The above comments on the trH3N2 cluster in Iowa leaves little doubt that the novel virus has spread across the United States, yet the CDC continues to deny the extent of the spread and is increasing surveillance in “bordering states”.

The trH3N2 has already been confirmed in children in Indiana, Pennsylvania, Maine, and now Iowa, in addition to a pig in New York.  Surveillance remains abysmal in spite of rates of 100% in confirmed cases in children in Maine and Pennsylvania, and 50% in Indiana.  All seven of the prior isolates match in all 8 gene segments, which also match the swine isolate in New York, signaling a jump from human back to swine.

The CDC has maintained a “swine exposure” narrative, leading to a request for samples with “swine exposure” when the first two cases were announced in the early release MMWR.  The denial of human transmission was maintained in the Maine CDC advisory claiming that all prior 2011 cases had a swine exposure, which was not true for the case in Indiana, and the cases in Pennsylvania had limited exposure to asymptomatic swine at a state fair (and only one had direct contact).  Moreover, the Maine state epidemiologist claim “no thought” of human transmission, and these agency claims were propagated by media and ProMED reports, and remarkably, this narrative on swine exposure is still be propagated by CIDRAP in its report in the Iowa cluster.
The upcoming MMWR on the cluster in Iowa should demand an increased surveillance throughout the country to get a true estimate of the extent of spread and the number of hospitalized cases.

The silent spread of a trH3N2 pandemic two years after the trH1N1 pandemic raises serious concerns about influenza surveillance in the United States and worldwide.