HEALTH 1/25-2/1/10 Weekly Bird & Other Flu Thread:Police aid bird culling teams in India

Link to last weeks thread:

1/17-1/24/10 Weekly Bird & Other Flu Thread:Spike in H1N1 D225G Cases in Spain

http://www.timebomb2000.com/vb/showthread.php?t=352953

Please See:

Confirmed cases of Swine Flu and maps
http://www.timebomb2000.com/vb/showthread.php?t=330689

Comprehensive Flu Thread, Latest reports, States, Countries, Closings.

http://www.timebomb2000.com/vb/showthread.php?t=330395

Useful Links:

Avian Influenza (Bird Flu)
http://www.cdc.gov/flu/avian/gen-info/facts.htm

Johns Hopkins on influenza:
http://www.iom.edu/Object.File/Master/33/450/Rashid Chotani.pdf

National Avian Influenza Surveillance Information:
http://wildlifedisease.nbii.gov/ai/

CDC
http://www.cdc.gov/flu/avian/index.htm

WHO
http://www.who.int/csr/disease/avian_influenza/en/index.html

CIDRAP
http://www.cidrap.umn.edu/

Official U.S. Government Web site
http://www.pandemicflu.gov/

FAO
http://www.fao.org/ag/againfo/subjects/en/health/diseases-cards/special_avian.html

Public Health Agency of Canada
http://www.phac-aspc.gc.ca/influenza/avian_qa_e.html

European Union
http://ec.europa.eu/dgs/health_consumer/dyna/influenza/country_en.htm

The World Bank
http://web.worldbank.org/WBSITE/EXT...68427~piPK:64168435~theSitePK:1793593,00.html

Police aid bird culling teams in flu-hit areas​

http://timesofindia.indiatimes.com/...eams-in-flu-hit-areas/articleshow/5490242.cms

BEHRAMPORE: After meeting with stiff resistance from villagers, the Murshidabad district administration, on Friday, took the help of police to forcefully cull poultry in the bird flu-affected areas of Khargram.

Khargram BDO Kalyan Kumar Das and Kandi SDO Utpal Bhadra went to Sherpur and Nagar villages with a large police backup and oversaw the culling operations. Birds were forcefully seized from villagers who tried to resist the culling teams.

"We have decided to forcefully cull birds from villagers who refuse to co-operate with us. In those cases, no compensation will be given," said Murshidabad DM Parwez Ahmed Siddiquie. "A large number of flu-affected birds are alive, as locals aren't handing them over hoping that the birds would get cured. We haven't got the desired success in culling ducks, too. If we keep even a single bird alive in the affected areas, there is a probability of an outbreak next year too. If the administration remains inactive, the virus might also spread to the human body. So, we had to take a stern decision."

Khargram panchayat samiti sabhapati Abul Kashem said, "About 45 culling teams have been working for the past week in seven gram panchayat areas. By this time, the culling operation should have ideally got over but so far, we have culled only 55,000 birds."

Villagers were also seen demonstrating against the district administration's move at several places.

The Khargram sabhapati said that very few people had handed over ducks. "Villagers are handing over hens, since they have started getting compensation on the spot. But they aren't handing over ducks. Seeing this resistance, there was no option for the district administration other than forceful culling," he said.

Barwan panchayat samiti sabhapati Krishnendu Roy said: "Last year, many people of my block didn't get the one-time grant of Rs 500 from the government. So, there is some unwillingness to hand over birds to the culling teams. Culling operations have also begun in some parts of Kalyanpur-I gram panchayat from Friday."

He said there is an urgent need to revise the compensation. "There's not much difference in the rates for big and medium-sized birds. So, people are mostly only handing over the medium-sized birds, keeping the full-grown birds with them. We have appealed to the government and district administration to revise the compensation rates," Roy said.

Bird flu affects Gazipur farm, 531 chickens culled​

http://www.thedailystar.net/newDesign/latest_news.php?nid=21840

Some 531 chickens were culled at a poultry farm in Gazipur on Monday in presence of the district livestock officer after it was affected by bird flu virus H5N1.

The Field Disease Investigation Laboratory at Jaypurhat on Sunday confirmed that the virus affected Lata Poultry farm at Khetlal Upazila.

Earlier this month, Yati Poultry Farm in the same upazila was affected with the virus.

The district livestock authorities culled some 932 chickens and 183 eggs to contain the spread of the virus within 12 hours of confirmation.

Talking to The Daily Star, Jaypurhat District Livestock Officer Dr Shahidul Islam said the newly affected farm was less than half a kilometre away from the previous one where H1N1 virus was confirmed on January 5.

"The virus broke out due to lack of bio-security maintenance. Both the farms are situated adjacent to the dwelling place and people are coming in contact with the farms frequently," he said.

The last outbreak was experienced in the country in August 2009 in Bogra. But it was not a massive one, said sources at the Institute of Epidemiology, Disease Control and Research (IEDCR).

Bird flu killed at least 287 people affecting 467 worldwide since it began to ravage poultry stocks in Asia in late 2003. World Health Organisation has counted the fatality at more than 60 percent.

Widespread D225G/N In Fatal Ukraine Cases​

http://www.recombinomics.com/News/01251001/D225GN_Ukraine_Widespread.html

Mill Hill released 32 HA sequences at GISAID. 28 were from Ukraine and were from autopsy lung. These were collected between the end of October through mid-November. 10 of the Ukraine samples had D225G and D225N. Three had D225N and one was mixed for D225N. Four has D225G and three more were mixed for D225G. Thus, 21/28 had D225G, D225N, or both.

The widespread detection of D225G and D225N in these samples support earlier data which had D225G, D225N, or both in 8 of 8 fatal cases. Although the new sequences include the first sequences from clear fatal cases in Ukraine lacking the position 225 changes, the vast majority of samples had the changes, and for regions in western Ukraine, like Lviv, all samples had 225 changes.

The large number of cases with both D225G and D225N (including one sample from the Azores), greatly reduces the likelihood that these are random copy errors, which appears to be the WHO working hypothesis. Similarly, the high concentration of these changes in fatal cases again supports transmission. Earlier 22 sequences were released, from patients that were not likely to be fatal, and only one had D225G (as a mixture).

The vast majority of the new sequences are also mixture, either because samples had D225G and D225N, or had one or the other along with wild type. These combinations may facilitate spread by allowing for infections in both the upper respiratory tract as well as the lower respiratory tract.

Moreover, a pair sample from a patient in Kathmandu had D225G (as a mixture) in the nasal sample, while the throat sample had a wild type RBD. Similarly, the fatal samples in Ukraine were from multiple oblasts and represented multiple sub-clades. Most sub-clades had at least one sample lacking the RBD change, further supporting acquistion of the position 225 chnages via recombination.

The current series of sequences did not have excessive copy errors, and analysis of this clade in Russia demonstrates that all samples have PB2 K340N, reducing the likelihood that the PB2 change has any direct impact on the changes at position 225. K340N is in samples lacking position 225 changes and other clades which lack K349N have position 225 changes. K340N at this time appears to just be a marker for the dominant clade in Ukraine (and much of eastern Russia).

The high frequency of 225 changes in Ukraine is of concern because recent media reports indicate an uptick in cases in eastern Ukraine, especially in Donetsk (see map), where schools are closing again. Donetsk has recorded the largest number of fatalities, and the rate this month is about 4 fold higher that 2009, raising concerns that position 225 changes are on the rise.

Sequences from these recent cases would be useful.

H1N1 School Closings in Donetsk Ukraine​

http://www.recombinomics.com/News/01251002/H1N1_Donetsk_School.html

With regard to the incidence of seasonal flu and SARS, the incidence rate in the region has reached the epidemic threshold (53.2%), noted in the SES. And the most disease-prone age group - children of school age.

In connection with the elevated incidence of acute respiratory suspended the educational process in 5 schools and one boarding schools, 78 classes of 27 schools and three groups in three pre-school educational institutions

The above translation describes the closing of schools in Donetsk, Ukraine (see map) because the incidence of influenza/ARI has reached the epidemic threshold. This level was reached in most regions of Ukraine earlier, but the latest report lists 4 oblast above the epidemic threshold, with 4 more approaching the threshold. The other 19 regions, including Donetsk are below, and in a relatively safe zone. Donetsk has been a concern because of the dramatic rise in fatalities. The total of 162 to date is well above Lviv, which has 105. The rise in Donetsk has been recent. At the end of 2009 there were 91 deaths and 329,281. This month the number of deaths has almost doubled to 162, which the number of cases has only increased about 20%. Thus, instead of just under one in 4000 cases dying, the rate this month is closer to 1 in 1000. This rate increase of almost four fold raises concerns that D225G/N are becoming more common in eastern Ukraine.

Today Mill Hill released 28 HA sequences from autopsy lung samples, and 21 had D225G, D225N, or both. Of the 30 cases with D225G/N, 29 were from fatal cases. This high fatality rate raises concerns that an increase in D225G/N levels will lead to a pronounced increase in severe or fatal H1N1 cases and reports of school closings in Donetsk due to a rise in cases raises concerns that the number of fatalities will significantly increase in the near term.

Cirebon, West Java ::: Forty-year-old extension worker treated as bird flu suspect​

http://birdflucorner.wordpress.com/...extension-worker-treated-as-bird-flu-suspect/

Cirebon – A resident of Kelurahan Tukmudal, Keamatan Sumber, Kabupaten Cirebon, with initial Dur (41), had been stated as bird flu suspect since Thursday (21/1). Until Monday (25/1), Dur is still being treated at isolation unit Ruang X of Gunungjati regional hospital.

Patient had high fever and nausea at the time of admission. Patient, who is an agriculture and livestock extension worker for government, was reported to have had contact with numbers of suddenly died chickens.

Vice Director of Medical Service and Treatment of Gunungjati hospital, Lucya Agung, said patient was treated at isolation unit until confirmation test issued by laboratory of Ministry of Health.

“We expect to receive the result on Wednesday. We cannot conclude anything before receiving the result,” said Lucya.

“Patient doesn’t show specific bird flu symptoms, but because he had contact with sick chickens, he should be isolated,” added Lucya.

Source: Indonesia local newspaper, Pikiran Rakyat.

http://www.pikiran-rakyat.com/index.php?mib=news.detail&id=123747

Nation focuses on combating bird flu epidemic​

http://english.vovnews.vn/Home/Nation-focuses-on-combating-bird-flu-epidemic/20101/112145.vov

After announcing a new bird flu outbreak on January 25, the central city of Ha Tinh has implemented measures to contain the epidemic.

The City’s Veterinary Department has vaccinated more than 14,000 poultry in the commune of Thach Han. It has also set up 23 checkpoints to prevent illegal transportation of birds and has vaccinated 50,000 poultry in the districts of Cam Xuyen, Ky Anh, Can Loc, Thach Ha and Loc Ha.

In northern Quang Ninh province, around 1,100 poultry were also infected. Local authorities have taken measures to quickly control the spread of the epidemic and illegal transportation of diseased poultry in the province, especially in those areas bordering with China.

Quang Ninh has scheduled vaccinations for more than 3.7 million poultry in 2010.

Bird flu again ​

http://www.thedailystar.net/newDesign/news-details.php?nid=123507

The bird flu virus H1N1 struck again on Sunday at Lata Poultry Farm under Khetlal upazila in Joypurhat.

The Field Disease Investigation Laboratory in the district confirmed the infection while district and upazila livestock officers culled some 531 hens there.

Earlier on January 5, the Yati Poultry Farm -- less than half a kilometre away from the new one -- was affected with the virus. The district livestock authorities culled some 932 chickens and destroyed 183 eggs to contain the virus's spread that time.

Joypurhat District Livestock Officer Dr Shahidul Islam said, "Slack maintenance of bio-security would be the cause of the spreading and the authority would observe both the farms and the people involved with culling for a month."

Last year, infection was detected for the last time in the country in August in Bogra. But it was not a massive one, said the Institute of Epidemiology, Disease Control and Research, Dhaka sources adding that the prevalence of H1N1 virus was lower last year comparing to that of the previous years.

They stressed the need for strict maintenance of the precautions by the poultry workers and the bio-security in the city markets, which are more vulnerable places.

Bird flu killed at least 287 people affecting 467 worldwide since it started ravaging poultry sector in Asia in the late 2003.

H1N1 Duke Death Cluster With H274Y and D225G/N​

http://www.recombinomics.com/News/01261001/Duke_H274Y_D225GN.html

In the USA outbreak, which involved four severely immuno-compromised patients, cases occurred in a two-week period between mid-October and early November. Three of the four cases were fatal, but the role of H1N1 infection in contributing to these deaths is uncertain.

The above comments describe a fatal H1N1 cluster with H274Y at Duke Medical Center. Although the outbreak was in October / November, it was not announced until December. Fatal clusters of H1N1 cases, especially with H274Y are cause for concern. The clustering of deaths raised concerns that the patients had D225G and/or D225N, which has been linked to fatal cases. In Ukraine D225G, D225N or both have been found in 30 patients and 29 were fatal.

The CDC has released sequences (at GISAID) from the above cluster, which had H274Y. One HA sequence, A/North Carolina/39/2009, had D225G (as a mixture with wild type). Another sequence, A/North Carolina/42/2009, had D225N (as a mixture with wild type), raising concerns of coupling of H274Y with receptor binding domain changes, which was a precursor to the fixing of H274Y in H1N1 seasonal flu through hitchhiking and recombination.

NOTE: A third sequence, A/North Carolina/49/2009, has D225G (and H274Y). It is likely that the three sequences with D225G/N were from the three fatal cases.

Although WHO issued a December 2 update on the cluster, there was no mention of the receptor binding domain changes. The D225G report in the WHO Weekly Epidemiological Record mentions three instances of D225G with H274Y. This combination has been reported in France and in Illinois in the United States. The cluster at Duke Medical Center would represent a third example, but this example was in the context of another patient with D225N and H274Y transmission, and it seems likely that the two examples of D225G/N were in the three fatal cases at the medical center.

The increasing appearance of D225G/N in fatal cases, including the high frequencies in Ukraine and Russia continue to cause for concern.

D225G In First 2010 H1N1 Sequence​

http://www.recombinomics.com/News/01271001/D225G_2010.html

The State Research Center of Virology and Biotechnology Vector in Novosibirsk, Russia has released the first 2010 H1N1 sequence, A/Karasuk/01/2010, of the 2009//2010 pandemic, which has D225G, matching the events in the 1918/1919 pandemic where the first 1919 H1N1 sequence, A/London/1/1919, also had D225G.

The presence of D225G in the Karasuk isolate was not a surprise. Recent sequences from nearby Tomsk also had D225G, which has been linked to fatal cases in Russia. Many of these sequences are related to sequences in Ukraine, where 29 of the 30 isolates with D225G/D225N have been from fatal cases. Moreover, many of these new sequences were released in January and late December from November/December cases.

The rise in cases with D225G/N have been a concern, which has increased by the recently released sequences from Ukraine, as well as sequences from a Tamiflu resistant fatal outbreak at Duke Medical center which also involved D225G/N.

In Ukraine, schools have been closed in Donetsk, the oblast with the largest number of fatalities, raising concerns that a new wave will have a higher frequency of D225G.

One of the early isolates from Ukraine was found to be a low reactor and the only non-synonymous HA change was D225G, raising concerns that the polymorphism will be selected in upcoming outbreaks

Bird Flu Discovered at Kibbutz​

http://www.israelnationalnews.com/News/Flash.aspx/179376

An outbreak of bird flu was discovered Tuesday night at a henhouse in Kibbutz Ein Shemer. The disease was found in a henhouse containing about 43,000 hens. Agriculture Ministry workers began Tuesday night marking off the birds to be culled. All agricultural production in the area has been shut down until further notice.

HPAI Virus Detected in Israel Birds​

http://www.thepoultrysite.com/poultrynews/19382/hpai-virus-detected-in-israel-birds

ISRAEL - The Israeli veterinary authorities have reported a new outbreak of highly pathogenic avian influenza (HPAI) H5N1 virus in the country.

The World Organisation for Animal Health (OIE) received an immediate notification on 26 January. The outbreak was first confirmed in birds on the same date.

The cause of the outbreak has still not been determined. 700 cases were detected at a farm in Haifa. According to the OIE, there have been 700 cases and 43000 birds have been found susceptible to the disease. The farm has three poultry houses that contain 43,000 heavy breeder pullets aged 16 weeks. These poultry houses are in a farm under extremely high biosecurity. Clinical signs occurred in only one house.

Two tests - pathogen isolation by egg inoculation and polymerase chain reaction (PCR) - confirmed the presence of the virus.

Bird flu reappears in two provinces of Vietnam ​

http://english.people.com.cn/90001/90777/90851/6879816.html

The Vietnam's national committee on bird flu prevention and control said here on Tuesday that bird flu has reappeared in two provinces of Vietnam with nearly 4,000 poultry infected with the disease.

The announcement was made at a regular meeting of the committee to review its tasks in dealing with the bird flu disease.

In the country's Mekong Delta province of Ca Mau, there have been 3,000 chickens, ducks and swans found infected with bird flu in two districts of the province.

In the central Ha Tinh province, about 658 chickens and ducks have acquired the H5N1 virus and become ill or died. All these poultry have not been injected with vaccines, according to the committee.

The committee said local authorities are currently adopting measures to prevent the spread of the disease.

Karanganyar, Central Java ::: Patient presumably dies of bird flu​

http://birdflucorner.wordpress.com/...ral-java-patient-presumably-dies-of-bird-flu/

Karanganyar – A resident of RT 03/ RW XVI Dukuh Josari Desa Wonorejo Jatiyoso, Wardi, 22 years old, presumably died of bird flu or avian influenza (AI) infection on Thursday (21/1).

Investigation of local newspaper Espos mentioned victim had high fever and lung infection. Head of Disease Control and Environment Health, Health Service of Kabupaten Karanganyar, Fatkhul Munir, confirmed the information above.

Fatkhul assumed victim had contracted bird flu virus in Cirebon. He had been sick when he returned back to Karanganyar, and finally died after had been admitted to hospital.

“Report mentioned victim had high fever and lung damage. Wardi also had contact history with birds,” said Fatkhul.

Source: Indonesia local newspaper, Solo Pos. http://www.solopos.com/2010/karanganyar/diduga-suspect-ai-warga-jatiyoso-meninggal-13002

D225G/N H1N1 Clustering Raises Concerns​

http://www.recombinomics.com/News/01271002/D225GN_Clusters.html

The changes have been found since April 2009, but have not been associated with temporal or geographical clustering, strongly suggesting the mutation of these viruses has occurred sporadically as opposed to emergence and sustained transmission of a variant virus.

The above comments, from Friday’s WER, are a restatement of the December 28 WHO announcement on D225G, which were similar comments by the ECDC, which was also on December 28.

However, sequences from Ukraine had already been made public, and those sequences clearly demonstrated temporal and geographic clustering. The initial series was published by Mill Hill, a WHO regional center. 10 HA sequences were released. Nine were from western Ukraine and were the same clade, and D225G was found in the four fatal cases. All western Ukraine samples were collected on Oct 27-28 and the four fatal sequences signal clustering. These sequences were public a day after WHO announced that there were no significant genetic changes in the Ukraine sequences. However, the clustering I fatal cases was obvious, which prompted Norway to look at samples and they found 3 examples of D225G. Two were fatal and the third was severe, leading to Norway issuing an alert, which was followed by a WHO announcement on the “Norway” mutation (which was called insignificant two days earlier when found in Ukraine.

The fatal Ukraine sequences also included a rare marker on one of the sequences. This marker was only found in two pandemic H1N1 sequences at Genbank, and both were from New York and had D225N, providing a genetic link between D225G and D225N. This linkage was strengthened by two fatal Ukraine sequences released by the CDC, another WHO regional center, who found D225N in the two samples. In addition, the CDC released a partial PB2 sequences on five isolates (which included three of the mild cases in the Mill Hill release) and all five had F340N, adding further confirmation that the sequences from western Ukraine were all from the same clade.

The association between D225G and D225N was further established by addition sequences from lung samples in an around Kiev, which had both D225G and D225N in samples from the same patients. Thus, prior to the December 28 comments by WHO and ECDC, there was clear clustering in time and space of D225G/N in Ukraine.

The Ukraine clustering was expanded by additional sequences from neighboring countries. When Mill Hill released the two fatal Ukraine cases with D225G/N, they also released a sequence from Moldova which also had D225G and D225N from a sample collected within a day of the first reported H1N1 fatality in Moldova. In addition, multiple labs in Russia were releasing sequences from fatal cases with D225G/N, including sequences from the same clade and collected at the same time (November), increasing the number of sequences which were collected at the same time and in the same general area. These sequences were released at the end of 2009 and beginning of 2010, well in advance of Friday’s WER, which did not include updates in concepts of cases.

More sequences from Ukraine were released on Monday. 28 HA sequences from autopsy lung had 21 examples of D225G/N. 11 of the 21 had both D225G and D225N and the recent data brought the number of cases with D225G/N in Ukraine to 30, and 29 were from fatal cases.

Thus, the absence of clustering cited above is false, but the Ukraine is not the only area where D225G is clustering in time and space. Sequences released from the fatal outbreak at Duke Medical Center were released. These sequences had also been generated by the CDC, and followed a December 2 announcement on the death cluster. The three fatal cases were part of a cluster of 4 patients who were Tamiflu resistant. The sequences from those patients showed that all had a rare polymorphism, supporting patient to patient transmission, and three of the sequences with these markers also had D225G/N. Since these samples were collected in October and announced December 2, the transmission data was also available to the authors of the December 28 WHO report.

The North Carolina cluster involved a different clade and was at different location, but it was the movement of these polymorphisms from genetic background to genetic background that led to the prediction that the Ukraine sequences would have D225G/N.

This movement from one genetic background to another had been documented in the oseltamivir resistances cases in H1N1 seasonal flu. H274Y had jumped from one genetic background to another in patients who were not taking Tamiflu. This jumping was a product of hitchhiking and homologous recombination.. Additional polymorphisms from clade 2C jumped to clade 2B which led to the fixing of H274Y in seasonal flu. These data thoroughly discounted the WHO mantra on “random mutations” by the same excuse was used to claim that the D225G and D225N in Ukraine was spontaneous and did not transmit, which has also been thoroughly discounted by the recent data from Ukraine and North Carolina.

Thus, the reliance on “random mutations” to explain data that is clearly not generated by random mutations continues to be hazardous to the world’s health.

Fujian H5N1 In Israel?
​

http://www.recombinomics.com/News/01271003/H5N1_Israel_Fujian.html

The Health Ministry said Tuesday that the strain of bird flu discovered earlier would not infect humans.

The above comments from the Israeli Ministry of Health raise concerns that the H5N1 outbreak reported to the OIE is the Fujian strain of H5N1 (clade 2.3.2).

Clade 2.3.2 has been found previously in wild birds in Asia. It frequently appears at this time of year in wild birds in Hong Kong, but in 2008 it was found in South Korea, Japan, and Russia in the spring. The finding of the strain in whooper swans in Japan raised concerns that the H5N1 would spread to Mongolia and Russia over the summer.

Those concerns were realized when an outbreak of H5N1 in wild birds at Uves Lake in Mongolia on the border with Russia produced clade 2.3.2 sequences. The presence of clade 2.3.2 in wild birds in Russia and Mongolia led to concern that the Fujian strain would then spread to Europe, the Middle East, and Africa, as had happened to the Uvs Lake strain of the Qinghai Strain (clade 2.2.3).

The comments by the Health Ministry in Israel were remarkably similar to comments from South Korea when a soldier culler exhibited bird flu symptoms and was H5 positive. The Fujian strain was responsible for most human H5N1 cases in China. However, at the time the human Fujian cases had been clade 2.3.4. There was little reason to assume that clade 2.3.2 wouldn’t infect humans because human cases had been reported for clade 1 as well as clade 2.1, 2.2, and 2.3. Therefore, it was likely that all sub-clades of 2.3 would be able to infect humans. In South Korea the H5 virus was not isolated, so a formal report to WHO was not made and South Korea remains free of human H5N1 cases. However, in early 2009 China did report a human infection involving clade 2.3.2. However, this distinction between 2.3.2 and 2.3.4 was not widely reported, so the Israeli health ministry may still be assuming that the South Koreans comments on human infections by clade 2.3.2 may still be accurate.

However, clade 2.3.2 has produced at least one human infection in China, and clade 2.3.2 has never been reported outside of Asia. Thus, release of the sequences from the H5N1 outbreak in Israel would be useful.

Spike In Severe H1N1 in Memphis Tennessee Children​

http://www.recombinomics.com/News/01271004/H1N1_TN_ICU.html

Doctors at Le Bonheur Children's Medical Center are on high alert tonight after a spike in the number of children with flu-like symptoms. Right now, they believe all cases to be the novel H1N1 swine flu virus.

"Over the past 3 weeks or so, we've had about 17 or 18 admissions to Le Bonheur with confirmed influenza. I should say that we believe all or almost all of these will prove to be the novel H1N1 influenza virus."

Infectious disease doctors believe its the only virus circulating in significant amounts in the community right now.

"I think 7 of the 17 or 18 have been admitted to the ICU. So that's a bit of a shift of what we saw before."

The above comments describe an increase in sever H1N1 cases in children in Tennessee. The Children’s Medical Center (see map) had seen high numbers of patients in the fall, which led to the use of tents to cover the overload. The current spike is well below earlier levels, but the frequency of cases admitted to the ICU is higher.

The increase in severe cases represents the concerns linked to the H1N1 evolution and increased reports of D225G/N, which have been tightly associated with severe and fatal cases. In the fall, the number of exposed to H1N1 was high, leading to protective immunity and a sharp decline in cases. However, there current is virtually no seasonal influenza A in circulation in the United States, but the traditional flu season is beginning, whicj will likely lead to emergence of a new swine H1N1 strain. Mill Hill has reported a Ukraine isolate with D225G as a low reactor, raising concerns that immunity generated bu infection with wild type H1N1 or protection from the H1N1 killed vaccine will select for D225G/N variants, leading to a higher frequency of severe or fatal cases.

Consequently, the increase of ICU cases in Tennessee children is cause for concern.

H1N1 Fatality Rate in Memphis Children Raises Concerns
​

http://www.recombinomics.com/News/01271005/H1N1_TN_CFR.html

A 12-year-old has died of complications from the H1N1 flu, officials at Le Bonheur Children's Medical Center said Wednesday.

"Le Bonheur Children's confirms the death of a 12-year-old male resulting from complications of H1N1," a hospital spokesperson said in a written statement. "This is the fifth H1N1 death at Le Bonheur since we began tracking in September 2009."

It is the second time this week the hospital has announced a death from the virus. Le Bonheur confirmed the death of a 14-year-old patient from the virus Monday.

In a news conference Tuesday, Dr. Keith English, one of Le Bonheur's leading pediatricians, said there is no reason to be alarmed, but he does not want people to think the H1N1 threat is over.

The above comments describe the H1N1 deaths of two children in Memphis (see map). The hospital had announced a spike in severe cases. 17 patients had been admitted this month, and 7 went to the ICU. Two of those patients have died. The ratio of hospitalized to ICU to deaths is markedly different this month than last fall, when thousands of children were seen and about 340 were admitted. 30-40 went to the ICU and 3 died. Thus, the death of 2 of the 17 admitted or of the 7 in the ICU is at a much higher rate and raises concerns that the H1N1 circulating this year will be more virulent due to increases in D225G/N, which is being reported in multiple locations worldwide, including a Tamiflu resistant fatal cluster at Duke Medical Center.

The flu season in the US traditionally peaks in February or March, so the increases seen in Memphis may represent the start of a dramatic rise in severe and fatal cases. Seasonal H1N1 and H3N2 have virtually disappeared in much of the northern hemisphere including the United States, so pandemic H1N1 variants will likely emerge in the next few weeks.

Sequence data on the H1N1 from these two fatal cases would be useful.

400 people put on medication in bird flu-hit areas of West Bengal​

http://timesofindia.indiatimes.com/...-areas-of-West-Bengal/articleshow/5506499.cms

NEW DELHI: At least 409 people have been put on medication in bird flu-hit areas of West Bengal, health authorities said on
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Monday.

In the last few years, the country has not registered any case of human transmission of bird flu but there is always a possibility of human infection among the high risk groups.

"A total of 409 poultry workers, cullers, veterinary surgeons involved in culling operations have been put on chemoprophylaxis," a health ministry official said.

However, the ministry said that there is no cause for alarm and the state administration has adequate stock of medicine and personal protective equipments.

The outbreak of avian influenza was notified in Murshidabad district of West Bengal Jan 14. Since then, officials said, it has spread to several areas of the district.

"Containment measures have been initiated as per the contingency plan. Culling of birds has started and so far 116,824 birds have been culled and 11,409 eggs have been destroyed," the official added.

Karanganyar, Central Java ::: Officials collect bird
samples from deceased bird flu suspect’s neighborhood​

http://birdflucorner.wordpress.com/...from-deceased-bird-flu-suspects-neighborhood/

Karanganyar – Livestock and Fishery Service of Kabupaten Karanganyar conducted investigation to chicken samples such as cloacal and throat swab of birds in Desa Wonorejo, Jatiyoso, regarding to the death of bird flu suspect patient named WD, 22 years old.

Head of Animal Health Division, Saptawan Hadiputra mentioned officials had collected about 25 chicken samples to be subjected for laboratory test, since they did not find any bird flu evidence by field investigation.

Victim is a meatball seller (meatball is bakso in Bahasa Indonesia. Typically, sellers are circulating with their cart to get costumers. -adm-), and suggested to have caught infection around his place in Cirebon. For this evidence, Livestock and Fishery Service of Kabupaten Karanganyar, Central Java, had contacted its counterpart in Kabupaten Cirebon, West Java for more investigation.

Wd, resident of Desa Wonorejo, Jatiyoso, possibly died of bird flu infection on Wednesday (20/1). Patient finally died after refused to be transferred from Wonogiri regional hospital to Dr Moewardi regional hospital to get medical treatment.

Source: Indonesia local newspaper, Solo Pos. http://www.solopos.com/2010/karanganyar/suspect-ai-di-jatiyoso-pemkab-ambil-sampel-unggas-13224

Hundreds of chickens die of bird flu​

http://www.antara.co.id/en/news/1264672913/hundreds-of-chickens-die-of-bird-flu

Jambi (ANTARA News) - Hundreds of chickens have died of bird flu (Avian Indluenza) at Teluk Kuali village, Tebo Ulu sub district, Tebo District, Jambi Province, a local official said here on Thursday.

The death of the chickens was reported last Tuesday (Jan. 26), according to Muhsin, head of the Tebo district animal husbandry and fishery office.

"According to the results of laboratory tests, the dead chickens had been infected with the H5N1 virus that causes Avian Influenza," he said.(*)

D225G/N In Fatal H1N1 in Chernihiv Ukraine
​

http://www.recombinomics.com/News/01281001/D225GN_Chern.html

Mill Hill released five more HA sequences (at GISAID) from autopsy lung patients in Chernihiv (see map), and four had D225G. Three were mixtures with wild type and one was a mixture with D225N. All four were most closely related to earlier isolates from Ukraine, as well as isolates from Russia. The five new sequences raise the number of autopsy tissues sequenced to 41 and 33 had D225G/N, clearly demonstrating strong clustering in time, space, and phylogeny.

However, the sequences were from multiple sub-clades which included sequences lacking D225G/N, indicating the sequences with D225G/N required multiple independent introductions, as was seen with H275Y in seasonal and pandemic H1N1. These large number of introductions of the same polymorphisms in the same area over a short time frame is most easily explained by recombination, and is inconsistent with sporadic, spontaneous, or random mutations, as postulated by WHO and consultants. They are once again surprised by the actual data, which renders the tired old paradigm of random mutation untenable.

However, while the WHO bases actions and policies on the obsolete tenet of random mutation, the striking association between D225G/N acquisitions and fatal outcomes becomes more ominous. The reported frequency is highest in Ukraine and adjacent countries, but the release of sequences from the fatal and transmissible Tamiflu resistant infections at Duke Medical Center highlights the speed at which the polymorphism can span the globe, which raises concerns that the wild type and D225E changes which have been dominant, will be replaced by D225G/N, leading to much more severe illness and deaths.

In the eastern oblast on Donetsk, schools are closing as the H1N1 infections spread. Daily Ministry of Health reports for the country have yet to be released this week, raising concerns that information flow from Ukraine will slow or cease. This month the case fatality rate in Donetsk has increased almost four fold, raising concerns that the level of D225G/N is on the rise.

Similarly, reports of more severe and lethal infections in Memphis have recently surfaced. A high frequency of admitted children are moving into the ICU and dying, putting the hospital on high alert and encouraging vaccinations.

These recent events in Donetsk and Memphis raise concerns that a more deadly H1N1 wave has begun.

Independent H1N1 D225G Introductions In California
​

http://www.recombinomics.com/News/01291001/D225G_CA.html

CVI released 50 full sequences at Genbank and almost all were from California. Included was one sample with D225A, A/California/VRDL31/2009, (as mixture with wild type) as well as two D225G and 8 D225E. These sequences were from isolates collected over the summer and early fall. The two isolates with D225G are distinct from each other and the many recent examples from Ukraine and Russia, representing two additional independent introductions.

A/California/VRDL27/2009 has four recently acquire polymorphisms, including A716G, which codes for D225G. The other three polymorphisms are in a California isolate, A/California/VDLR20/2009 and a Texas isolate, A/Texas/45101424/2009.

The first polymorphism, C437T, is in several other pandemic H1N1 sequences and many swine (see list here). Another polymorphism, A1280A is widespread and in Ukraine, Russia, and Norway isolates with D225G (see list here). The third polymorphism, G1360A is only in the three pandemic H1N1 sequences (see list here), which are the ones listed above. The Texas isolate only has the three polymorphisms listed above, so the California isolate is the Texas sequence plus D225G, representing an independent acquisition. Like most of the polymorphism, the other California sequence is the Texas sequences plus two other polymorphisms that are share with additional sets of pandemic isolates.

In contrast, the other California sequence, A/California/VDLR7/2209, with D225G has a different set of polymorphisms. One, G79A, is in other California sequences (see list here) but not those sequences described above. The second polymorphism, T598C, codes for S185P and is also in an isolate from Ankara (see list here). The second California isolate is a second independent isolate acquisition of D225G, which is not linked to the other California sequence or the sequences in Russia and Ukraine.

The Russian and Ukraine sequences follow the same pattern, but at a much higher frequency. There are examples of the same genetic background with wild type, D225G, D225N, or both new acquisitions. Similarly the same polymorphism (D225G or D225N) is on multiple related but distinct backgrounds which includes isolate with a wild type HA receptor binding domain, which again requires separate independent acquisitions in the same are over a short time frame. All of the Ukraine sequences were collected in late October or early November. This clustering in time and space of related but distinct sequences that have acquired the same polymorphisms at position 225 are inconsistent with a random mutation mechanism, and is easily explained by recombination moving the polymorphism from one genetic background to another as was described for H274Y in seasonal H1N1 or a synonymous NA polymorphism, A743G ,in the H5N1 NA clade 2.2 sequence.

Similarly, the D225G polymorphism (A716G) has been added on D225E genetic backgrounds (with T717A and othere D225E markers), including the most recently released D225E sequence from Japan, A/Yamaguchi/247/2009, released today by NIID at GISAID, and earlier isolates in Europe.

The movement of polymorphisms from one genetic background to another via recombination is common, and readily explains the explosion of D225G on multiple H1N1 genetic backgrounds from fatal cases.

H1N1 D225E Converted to D225G in Japan
​

http://www.recombinomics.com/News/01291002/D225G_Japan.html

NIID recently released two HA sequences at GISAID. One, A/YAMAGUCHI/247/2009, has A716G, which codes for D225G, but it also has T717A, which codes for D225E, as well as additional markers for D225E. Thus, D225G has been appended to a D225E genetic background resulting in conversion to D225G.

Although D225G has been reported appended to a D225E background in Europe, the sequence in Japan has C940T, which defines a D225E sub-clade that is largely in the United States and Japan (see list of Genbank sequences here). In addition to the sequences at Genbank, C940T is also in D225E sequences at GISAID, including A/Tennessee/17/2009 and A/Shiga/43/2009. Like the Hong Kong sequence in the list linked above, the Tennessee and Shiga sequences have H274Y, supporting the spread of H274Y in the United States and Japan. Like the position 225 changes, H274Y also jumps from one genetic background to another, but as was seen in the cluster on the train in Vietnam, or the fatal cases at Duke Medical Center, isolates with these newly acquired changes (like D225G and/or H274Y), transmit and create clusters that are linked in time, space, and phylogeny.

This type of clustering is most dramatic in Ukraine, where 33 sequences collected in late October or early November have D225G, D225N, or both on identical or closely related sequences. However, the presence of sequences with wild type receptor binding domain changes indicates sequences with the changes require multiple independent events which are consistent with homologous recombination as was seen during the fixing of H274Y in seasonal H1N1.

These data invalidate the WHO working hypothesis that these changes are spontaneous events generated by recent and repeated copy errors, a paradigm that was thoroughly discounted by the fixing of H274Y.

The clinging of WHO to this outdated paradigm continues to be hazardous to the world’s health.

Moreover, the replacement of D225E, which is widespread in Europe, by D225G raises concerns that D225G/N will become more common in upcoming waves, since Mill Hill has designated H1N1 with D225G as a “low reactor”, and the reduced activity with reference sera directed against D225, signals potential selection of D225G.

Spike In US Pneumonia and Influenza Deaths
​

http://www.recombinomics.com/News/01291003/Week3_PI.html

The CDC Week 3 influenza report has been released and once again there were no reported cases of seasonal influenza A. 2 cases of influenza B were reported and the vast majority of cases (98%) were pandemic H1N1, indicating seasonal influenza A has been crowded out in the US. The frequency of influenza detection has risen slightly and is at the highest level since week 50, signaling the end of the fall wave and the beginning of a winter wave. However, although the detection rate rose slightly, the P&I deaths spiked higher and are now well above the epidemic threshold and as high as it has been since the peak of the 2008/2009 season.

This dramatic jump in deaths raises concerns that the current H1N1 is more virulent and lethal than the H1N1 circulating in the fall. The early appearance of that virus dramatically increased the P&I, which then declined as the H1N1 levels declined. However, the current jump is well ahead of such a corresponding jump in H1N1, which would support a more lethal H1N1.

Recent reports from Tennessee have described a higher frequency of children with H1N1 entering the ICU as well as a higher percentage dying. These results are early, but mimic the increase in case fatality rate in eastern Ukraine in association with the release of sequences from Oct/Nov which had a strong association of D225G/N with fatal cases, who had significant lung damage.

The low number of positives in the US may reflect a sampling problem. Most tested samples have been from hospitalized patients, but the fatal and severe cases frequently are associated with a rapid movement of virus to the lungs and a high false negative rate. A high false negative rate would keep lab confirmed cases artificially low and preclude aggressive antiviral treatment. Similarly the increase in H274Y may also impact treatments involving Tamiflu.

Since most H1N1 fatalities have been young adults, an age distribution on fatal cases would be useful.

Pekanbaru, Riau ::: Two babies suspected of having bird flu​

http://birdflucorner.wordpress.com/

Pekanbaru – Arifin Achmad regional hospital in Pekanbaru received two more bird flu (H5N1) suspect patients from Kabupaten Indragiri Hulu, Riau Province.

Those patients were AN, six months old, and YL, three years and six months old. They both referred to Arifin Achmad hospital on Thursday afternoon and evening.

Both patients were neighbors, resided in Kecamatan Kelayang, Indragiri Hulu. They had contact history with dead chickens.

Patients are now under intensive treatment.

Wawan, AN’s parent said his child had been treated for two days at home, but the fever was increasing up to 38℃ so that he rushed the six-month-old to Indrasari hospital in Rengat. The baby was treated for two hours in that hospital before then transferred to Arifin Achmad hospital because doctors suspected bird flu infection.

Meanwhile, Iwan, uncle of YL stated similar information. Before been admitted to Arifin Achmad hospital, YL’s parents mentioned that their son was playing with quail two days before development of fever. He also mentioned that many backyard chickens around YL’s resident died of unknown cause. However, people took it as a usual event.

In mean time, officials have not done any control action, neither examining surrounding people’s health status nor disinfecting suspected area, even though at the end of last year the area was stated as bird flu endemic.

At the end of December 2009, Arifin Achmad hospital received two bird flu patients from Kabupaten Indragiri Hulu, where one of them, Ananda (8) resident of Dusun Tuo Pelang, Kecamatan Kelayang had died.

Another victim, An Nisha (4), resident of Desa Bongkal Malang, Kecamatan Simpang Kelayang had been recovered after received intensive treatment.

Source: Indonesia news office. ANTARA. http://www.antara.co.id/berita/1264706689/rsud-pekanbaru-kembali-terima-pasien-diduga-flu-burung

Bird flu alert in Balasore​

http://www.expressbuzz.com/edition/story.aspx?Title=Bird+flu+alert+in+Balasore&artid=00nzFMGEniA=

BALASORE: The outbreak of bird flu in Murshidabad district of neighbouring West Bengal has spread panic among the poultry farmers in Balasore district. While the border villages in Balasore and Mayurbhanj have been put on alert, Chief District Veterinary Officers (CDVOs) of both the districts have been asked to inspect chicken farms and hatcheries.

Alert has been sounded in 120 villages in both the districts and local elected representatives have been asked to inform the veterinary officials in case of death of birds due to any disease.

Even as officials claim no incidence of bird flu has been reported in the State so far, the Animal Husbandry Department has started inspecting farms in both the districts. The firm owners have been asked to vaccinate the birds and the veterinary officials have started vaccination in some areas. Altogether 20 teams have been formed for the purpose.

‘’We have collected 125 blood samples and 80 swab samples of chickens. In the first phase no virus has been found in about 40 test reports. Still we are on alert and a control room has been opened round the clock to create awareness among people and farm owners about the disease,’’ CDVO of Balasore, Dolagobinda Nayak said.

‘’So far we have vaccinated nearly 6,000 birds in Balasore district. The inspecting teams have been asked to complete the vaccination within a week. If they suspect flu virus in birds, the owners will be instructed to kill the whole lot in the hatchery,’’ he added.

Veterinary department sources said bird flu spreads through air and the government cannot take any risk.

‘’Both organised and unorganised sectors will be checked during the drive.

However, more stress will be given to farms situated in the bordering villages.

The areas put on alert include Kuliana, Rasagobindapur, Sarasakana, Morada in Mayurbhanj and Jaleswar and Bhogarai in Balasore,’’ said RK Dutta, a veterinary expert.

Reports said, Balasore district has 332 poultry farms (small and big). But no case of bird flu has yet been reported from the district, which is the third largest producer of poultry products in the State. Berhampur and Sundargarh are two other producers of poultry products.

South Jakarta ::: Official conducts operation of healthy chicken transport​

http://birdflucorner.wordpress.com/...nduct-operation-of-healthy-chicken-transport/

Kebayoran Lama – Livestock and Fishery Sub-service of South Jakarta stopped about 17 from 26 units of truck to transport chicken meat from outside Jakarta. Those chicken meat trucks could not show animal health certificate.

This action, Healthy Chicken Transport Operation (Operasi Transportasi Ayam Sehat/OTAS), was carried out at Jl. Raya Kebayoran Lama and Jl. Ciledug Raya, Kebayoran Lama, in particular to trucks carrying chicken carcass to be delivered to traditional markets, said official of Livvestock and Fishery Service, South Jakarta, Chaidir Taufik.

Total bird carcasses loaded in those 26 units of trucks were about 19,180 chickens and 800 ducks, which were coming from Subang, Bogor, Serpong and Sukabumi.

OTAS action was done to anticipate bird flu outbreak in Jakarta, in particular South Jakarta.

Chaidir also mentioned, OTAS action was done regarding to the death of bird flu suspect patient, Nurlalila, a resident of Jl. Pengadegan Barat V, on 26 January 2010 in Pasar Rebo hospital.

Information mentioned that victim brought four chickens from Cibitung Tangerang on the former month. One chicken was slaughtered and then victim developed sickness at the following days. Victim was then treated and tested positive bird flu infection. The remaining three chickens were returned back to Cibitung.

Source: Indonesia local newspaper, Pos Kota. http://www.poskota.co.id/metro/jaksel-metro/2010/01/29/tak-bawa-skkh-truk-ayam-kena-razia

Mystery Spike In US Pneumonia and Influenza Deaths​

http://www.recombinomics.com/News/01311001/Week3_PI_Mystery.html

Deaths from pneumonia and influenza across the country rose sharply in the weekly flu report released Friday by the Centers for Disease Control and Prevention, but a spokesman for the agency called it merely “a blip we’re checking out.”

Lyn Finelli, the disease centers’ chief flu epidemiologist, said most of the deaths were from pneumonia and were among the elderly. It was possible, she said, that some cities had delayed reporting deaths over the holidays, which would make later data look artificially high.

The above comments, from Donald McNeil’s NY Times piece really do not address the dramatic spike in P&I deaths reported in this week’s CDC flu report. The composite underlying data is available in MMWR weekly reportable diseases section, which indicates that cities with incomplete data are list as unavailable across the board (P&I deaths as well as all other deaths). Thus, missing data from a small number of cities would have a minimal impact on regional or national rates.

The data in the three most recent reports do show that the region (West North-Central) with the highest rate (12.2%) is markedly higher than each of the prior two weeks (8.3%). Other regions with double digit rates in week 3 are the Pacific, with steady increases from 9.1% to 10.6% to 11.0%, as well as New England, which was high for all three weeks (11.1%, 9.2%, 10,7%). South Atlantic, where reported flu levels are highest, had increases from 4.9% in week 1 to 7.0 and 6.8% in the two most recent weeks. Cities with high rates in week 3 include Bridgeport, CT (25.0%), Peoria, IL (21.1%), St Paul, MN (19.0%), and Glendale, CA (17.3%).

Thus, the high rates are widespread and higher than the peak levels in the fall, as well as peak levels for all season since 2005/2006, except 2007/2008, when the peak week broke 9%. However, even in that year, the week 3 rate was 7.1%. Thus, it is not clear why week 3 in 2010 would be more impacted by holiday anomalies than any other recent season, all of which had rates well below the 8.1% in 2010.

Moreover, the highest rates in the prior years were linked to peak levels of seasonal flu, and this season there is no seasonal flu. Over 99% of flu this season has been pandemic H1N1, and although reported levels have been declining, the P&I deaths are spiking to strikingly high levels.

The above CDC explanations do not address the size of the peak and the relationship to reported H1N1 levels, and raise concerns of serious undercounts,. Many hospitals continue to use the rapid tests, which in some instances only detect 10% of pandemic H1N1 infected individuals. The virus quickly moves to the lower respiratory tract in severe cases, and many media reports describe fatal cases that were first confirmed at autopsy.

Thus, the current testing methodologies may significantly under-represent pandemic H1N1 cases, and the true level may correspond to the current strikingly high spike in P&I deaths. The current MMWR tables break down total deaths by age, but the P&I deaths are listed as a composite number. An age breakdown of the P&I deaths in the 122 cities would be useful.

The above CDC explanations, as well as their “thought to” qualifier on the explanation in the week 3 report, raise serious questions that have not been credibly addressed.

D225G/N H1N1 Linkage by Recombination in Australia US China
​

http://www.recombinomics.com/News/01311002/D225GN_Australia_US_China.html

JCVI has released a series of full sequences at Genbank. Although most were from California, three sequences were from Australia, including A/Australia/6/2009. This sequence begins with two polymorphisms that are found in Australian sequences with D225G or D225N. The third polymorphism is Y233H, which is in the Duke death cluster in North Carolina, which has D225G and D225N. The fourth polymorphism is in the China cluster in Zhejian province, which also has D225G. Thus, the Australia HA sequence has polymorphisms which link together three distinct sub-clades with D225G and D225N, providing compelling evidence for movement of these polymorphisms by homologous recombination.

Although each of these sub-clades contains D225G, D225N, or both, prior to the release of the Australian sequence the sub-clades were unlinked, other than the common changes at position 225. The Australian sub-clade had two polymorphisms that were found in Australian sequences, but the sequences with the position 225 diverged, and one series had A/VICTORIA/2125/2009 with D225N and A/SYDNEY/2503/2009 with D225G, while the other branch had SYDNEY/2501/2009 with D225N. The Australian/6 sequence has both of these polymorphism (A208G and T519C) – see list here and here.

The third polymorphism in Australia 6 is T739C, which codes for Y233H. This polymorphism is found in isolates from the cluster of patients at Duke Medical Center who also had H274Y. In this group there were two sequences with D225G and one with D225N (see list here).

The fourth polymorphism is in the cluster of sequences from Zhejian Province in China. All three sequences have D225G (see list here).

Thus, the one sequence in Australian has polymorphisms found in three distinct sub-lades with clusters of sequences with D225G and/or D225N providing a mechanism of recombination for movement of D225G and D225N from one sub-clade to another. Frequent jumping from one genetic background has been described in the above sub-clades as well as the sub-clade found in Ukraine, Russia, and Norway. Interestingly, the CDC just released another sequence (at GISAID) from North Carolina with D225G (A/North Carolina/53/2009) which is in the Ukraine sub-clade.

Thus, these sub-clades with D225G and D225N are becoming increasingly widespread, which facilitates further jumps, as was seen for H274Y in H1N1 seasonal flu and is being repeated in H1N1 pandemic flu.

The use of homologous recombination allows the polymorphisms to jump from one genetic background to the next, facilitating rapid evolution to escape immune responses generated by prior infections or vaccinations.

Ukraine H1N1 D225G in North Carolina​

http://www.recombinomics.com/News/02011001/D225G_NC.html

The CDC has released another series of H1N1 sequences at GISAID. Included was A/North Carolina/53/2009 which has D225G. Details on this patient were not provided, but the sample was collected in mid-October when there was an H1N1 outbreak at Duke Medical Center. At least four patients had H1N1 with H274Y. Those sequences were also released at GISAID and 5 sequences had H274Y as well as the HA marker Y233H. In addition, three of the sequences had D225G or D225N. At least three of the patients died, so it is likely that some or all had D225G/N, as well as H274Y.

NC/53 did not have these markers, but it had D225G as well as the marker found in Ukraine (and Russia and Norway), A1281G. Thus, NC/53 provides a link between D225G in Ukraine, Norway, and Russia and D225G in North Carolina. However, sequences from Australia also provide linkages because it has markers found in Australia isolates with D225G and D225N, but also has Y233H, which was in the H1N1 from the hospitalized patients. The Australian sequence also had a regional marker that defines the cluster of D225G sequences in Zhejiang, China, providing linkages between Sydney Australia, Raleigh-Durham. North Carolina, and Zhejiang, China.

Moreover, in North Carolina D225G was on at least two different sub-clades, which is also true for D225G/N in Australia. Similarly, in Ukraine D225G/N was on multiple sub-clades in multiple combinations requiring multiple introductions, all of which is most easily explained by homologous recombination.

Thus, the rapid movement of D225G/N like the movement of H274Y in seasonal H1N1 as well as pandemic H1N1 highlights the central role of recombination in the rapid evolution of influenza.

The failure of WHO and consultants to recognize this very common mechanism of influenza evolution continues to be hazardous to the world’s health.

Severe H1N1 Cases in North Carolina Raise Concerns
​

http://www.recombinomics.com/News/02011002/NC_Severe.html

n the past two weeks, five patents were admitted to UNC Hospital with H1N1, Weber said. Of those patients, three required intensive care.

The above comments raise concerns of more severe H1N1 in North Carolina. The above data follows similar reports for H1N1 in children in Memphis. During the first 3 weeks of January 17-18 patients were admitted to the Le Bonheur Children’s hospital and at least seven required intensive care and at least two died. Concerns were expressed by physicians at the hospital, which has also happened in North Carolina. Moreover, Friday's week 3 influenza report had a sharp spike in pneumonia and influenza deaths, and the cause remains a mystery.

North Carolina is of particular concern because of an outbreak at Duke Medical Center in the adjacent Raleigh / Durham region. Last October at least four patients had H1N1 with H274Y. Recently released sequences at GISAID included five sequences from North Carolina with H274Y and the rare HA marker Y233H. Moreover, 3 of the HA sequences had D225G or D225N, suggesting they came from the three fatal cases. Moreover, an additional North Carolina was just released and it also had D225G and was also collected in October. However, this isolate did not have H274Y or the rare HA marker, but did have an HA marker which matched the sub-clade seen in Ukraine.

Thus, the presence of D225G/N in multiple cases and sub-clades raises concerns that a new wave in North Carolina would have more severe or fatal cases.

Release of sequence data from the recent North Carolina cases would be useful.

Pekanbaru, Riau ::: Prevalence increases up to six hundred percent​

http://birdflucorner.wordpress.com/...evalence-increases-up-to-six-hundred-percent/

Pekanbaru – About 2,751 chickens had died of bird flu virus within previous month in Riau. This has folded the number of bird flu cases in chicken by 600 percent compare to number at same period of last year outbreak, 441 chickens.

Head of Livestock Service of Riau Province, Patrianov said massive chickens deaths had been reported from six municipals/cities in Riau: Kampar 1,995 chickens; Siak 351, Indragiri Hilir 234, Indragiri Hulu 128, Rokan Hulu 22, and Pekanbaru 14. The shift of rainy season had influenced the replication of the virus. Several areas in Riau were still drowned by flood which had increased the rate of virus spread, added Patrianov.

In the days of flood, people had trouble to diminish or bury dead chickens, so they preferred to dispose the chicken’s body to flowing water or puddle around their residences.

According to Patrianov, most severe bird flu attack in Riau had occurred in broiler chickens in Kabupaten Kampar with total case up to 1,900. Remaining cases were reported in backyard chickens that reared by locals.

Indragiri Hulu has been the most susceptible area of bird flu transmission from birds to human. At the end of 2009, an 8-year-old boy from Kecamatan Kelayang had died of bird flu virus. Within the former month, three more children from the same sub-districts (kecamatan) were suspected of having bird flu infection, named Julian Iman Jaya (3.5 years old), Annisa (4.5 years old) and Rafli (6.5 months old). They have been treated at Arifin Achmad regional hospital since the former few days to a week.

Source: Indonesia national newspaper, Media Indonesia. http://www.mediaindonesia.com/read/2010/02/01/120505/126/101/Flu-Burung-Renggut-2.751-Ayam

Over 10,000 ducks die in Cambodia​

http://english.eastday.com/e/100201/u1a4994311.html

The Cambodian government said on Monday that more than 10,000 ducks have died and some 30,000 others are being sick in the country's southern province of Takeo.

Kao Phal, director of animal production department of agriculture ministry said that samples of the dead ducks being examined and the results will be known Tuesday or the day after.

He said that those dead ducks were reported happening a few days ago and now some 30,000 others are being sick.

Kao Phal said while sample testing is being examined, he could not tell what the cause to the deaths of the ducks was.

However, he said no report of any disease or death of human lives, but at the same time precaution to villagers is strictly advised by the government health concerning authorities.

According to Kao Sophal, the case is happening in Prey Khla village, Rominh Commune, Koh Andeth district in Takeo province, some 90 km south of Phnom Penh.

Cambodia, in the past and present, has had reports on the bird flu and influenza A/H1N1.

Widespread High Frequencies of H1N1 D225E In Italy
​

http://www.recombinomics.com/News/02011003/D225E_Italy.html

Recently released sequences by the Universita Politecnica in Ancona, Italy and Fondazione IRCCS Policlinico San Matteo in Pavia, Italy have a high level of D225E, in the absence of D225G or D225N. In the Ancona series, 13 of 16 isolates collected over the summer had D225E. 10 more recent isolates did not have receptor binding domain changes.

In contrast, samples from Pavia and Milano, collected between July and November had high frequencies of D225E throughout the collection period, with D225E in 45 of the 77 HA sequences. Thus, 58 out of 103 HA sequences had D225E and none had D225G or D225N, demonstrating a clustering in time and space for D225E.

Moreover, the D225E was found in multiple sub-clades. In Pavia 11 of the 13 sequences with D225E also had C940T, a polymorphism associated with D225E isolates. In contrast C940T was only found in 10 of the D225E sequences from Pavia and Milan, even though the HA genetic region was covered in the vast majority of the 45 D225E isolates (see list here).

This concentration of D225E sequences is not limited to Italy. D225E is also common in Spain (where C940T is rarely found). In addition, recently released sequences collected in July and August in the UK also have a high frequency of D225E, and a much lower frequency of D225G/N.

These frequencies are in sharp contrast to Ukraine, where D225G and D225N are common in tissues collected from fatal cases. Moreover, none of the sequences from Ukraine have D225E. Thus, this clustering of position 225 polymorphisms in time and space contradicts the WHO working hypothesis that D225G/N polymorphisms are spontaneous and sporadic and are due to copy errors.

The clustering, and requirement for multiple independent introductions over a short time period, are much more easily explained by homologous recombination than random mutation, as was seen in the fixing of H274Y in seasonal H1N1, and is being repeated for pandemic H1N1.

These data support homologous recombination as the driving force between these rapid changes and movement of position 225 polymorphisms from one pandemic H1N1 sub-clade to another, and strongly discount the role of copy errors in rapid influenza evolution.

Link to next weeks thread:

2/3-2/10/10 Bird, Other Flu Weekly Thread:Recombination Driving H1N1 D225G and H274Y

http://www.timebomb2000.com/vb/showthread.php?t=354159