THE BIRD FLU REPORT

[dothedd]

DECEMBER 15, 2013

Wild birds thought to be source of Portugal H7N9? - The Poultry Site Read more »http://www.thepoultrysite.com/poultrynews/30832/weekly-overview-start-of-a-new-bird-flu-season - afludiary.blogspot.fr/2013/12/guangdong-health-department-reports-new.html

Avian Flu Diary: Guangdong Health Department Reports A New H7N9 Case Read more » 

Portugese H7N9 farm in Bird Migration Flyway (No China Link Yet) Read more »

H7N9 before 2013 in Wild Birds - An overview Read more »

Bird flu: X-rayed - spectroscopyNOW.com Read more »

H7N9 in Europe before April China outbreak - mostly Spain Read more »

Summary of avian influenza activity in Europe 2006-9, H7 noted, but not H7N9 Read more »

Multiyear surveillance of avian influenza in wild birds in Portugal (background briefing) Read more »

Portugal plays down China bird flu ban - The Portugal News Read more »

Portugese Family Being Watched over H7N9 (h/t @potrblog). Read more »

Portugese H7N9 detected during routine checks is different to Chinese strains Read more »

Peak Season In Beijing for H3N2 Read more »

Questions about H7N9 Tests Debated in Hong Kong (Google Translate for English Text Read more »

More on the H7 low path avian influenza in Portugal Read more »

More to read:
Low path. H7 flu found in Portugese birds
454% Influenza Increase prior to Hong Kong H7N9 outbreak
A word about the H7N9 influenza — Laurie Garrett
Pandemics - Coming to an Airport Near You
Avian Flu Diary: Science: The Hidden Geometry of Complex, Network-Driven Contagion Phenomena

[dothedd]

How Influenza Pandemics Occur

This video from the National Institute of Allergy and Infectious Diseases discusses the causes of influenza pandemics. When 2 different influenza A viruses infect a single animal, the narrator explains, they can combine to form a new virus to which people have limited immunity. There were 3 influenza pandemics during the 20th century, in 1918, 1957, and 1968. The first pandemic of the 21st century, the H1N1 pandemic of 2009, is thought to have occurred due to 2 viruses circulating in pigs that created a new virus capable of infecting people. - See more at: www.pharmacytimes.com/videos/How-Influenza-Pandemics-Occur#sthash.M6a5UKSX.dpuf

www.pharmacytimes.com/videos/How-Influenza-Pandemics-Occur

[dothedd]

SORRY I DON'T HAVE TIME TO GO INTO DETAIL AS USUAL, HOWEVER  BELOW ARE LINKS THAT GIVES CURRENT INFO....

www.google.com/#q=bird+flu+news+2013&revid=582339992


TEXAS:
www.search.ask.com/web?p2=%5EAKD%5EOSJ000%5EYY%5EUS&gct=&o=APN10450&tpid=ORJ-V7&itbv=12.6.0.11&doi=2013-11-05&apn_uid=668BB3D1-C9DD-4A4D-9A90-A7CE21F785D7&apn_ptnrs=AKD&apn_dtid=%5EOSJ000%5EYY%5EUS&apn_dbr=cr_30.0.1599.101&psv=&trgb=CR&q=H1N1+IN+tEXAS

[dothedd]

GREAT RESOURCE: 
www.cidrap.umn.edu/

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A MUST READ:

www.cidrap.umn.edu/news-perspective/2013/12/consumer-reports-finds-bacteria-common-chicken-breasts

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I INTEND TO PRINT THE INFO ON THE LINK BELOW AND KEEP A COPY IN MY KITCHEN....

www.cdc.gov/salmonella/heidelberg-10-13/advice-consumers.html

HAPPY NEW YEAR!

[dothedd]

Your daily flu news

Avian Influenza

SGGP English Edition- Vietnam on Alert for H7N9 Virus Read more »

H5N8 Avian Influenza Poultry outbreak confirmed Yonhap, January 17 2014, 
Post-exposure antiviral chemoprophylaxis of close contacts of a patient with confirmed H7N9 virus infection and/or high risk poultry/environmental exposures. Read more »

Prevalence and control of H7 avian influenza viruses in birds and humans. Read more »
H7N9 Low-Path Avian Flu Virus Detected in Chinese Poultry Markets - ThePoultrySite.com Read more »

Serological responses following A H7N9 virus infection. Read more »

Virus-Specific Antibody Secreting Cell, Memory B-cell, and Sero-Antibody Responses in the Human Influenza Challenge Model. Read more »

CHP notified of eight additional human cases of avian influenza A(H7N9) in Mainland Read more »


H7N9 hospitalizes 6 more in China | CIDRAP Read more »

Hong Kong and Mainland to launch H7 avian influenza serological test next Friday Read more »

Low Possibility of Avian Flu Outbreak: Ministry of Agriculture Read more »

Bird flu cloud looms over Chinese New Year celebrations Read more »

Risk Assessment of H2N2 Influenza Viruses from the Avian Reservoir Read more »

Emergence in China of human disease due to avian influenza A(H10N8) – Cause for concern? Read more »

More to read:
City reports fifth bird flu case - Shanghai
China reports 4th H7N9 bird flu death of 2014 | GlobalPost
Combustion By-Products and Their Health Effects— will not help China flu fight
Wave Of H7N9 Cases Shows Bird Flu Demands Constant Vigilance
Four New Cases of Human Infection with H7N9 Virus are Reported to WHO

[dothedd]

January 27, 2014

Avian Influenza

Pace of H7N9 cases in China continues unabated - CIDRAP Read more »
Beijing reports human H7N9 bird flu case - Xinhua Read more »

Five new H7N9 cases confirmed in Guangdong, Zhejiang, Jiangsu - WantChinaTimes Read more »

Chinese VP stresses coordinated efforts to prevent, control H7N9 - Global Times Read more »
No proof of constant H7N9 human-to-human transmission: health authority - Xinhua Read more »

Human Antibody Responses to Avian Influenza H7N9 Read more »

Divergent H7 immunogens offer protection from H7N9 challenge. Read more »
Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A H7N9 virus. Read more »

Immunogenetics: Ethnic differences in sensitivity to H7N9 virus. Read more »

Avian Influenza A H7N9 Virus Infection in Pregnant Woman, China, 2013. Read more »
Immunity status against H7N9 and other avian influenza viruses in high-risk groups and general population in India. Read more »

[Diagnosis, treatment and prevention of infectious diseases. Topics: I. Countermeasures against epidemic infectious diseases; 2. High pathogenic avian influenza, including A H7N9 infection]. Read more »

Random Analytics: H7N9 by Employment/Zhejiang Age Pyramid (to 26 Jan 2014) | Random Analytics Read more »

Poultry traders count cost as markets close | Shanghai Daily Read more »

H5N1: Mexico: H1N1 deaths in January equal all of 2013 Read more »

H5N1: China: A second case of H10N8 reported Read more »

Avian Flu Diary: CDC: Testing Recommendations For Suspected Cases of H7N9/H5N1 in The United States Read more »

Hangzhou closes live poultry markets to combat bird flu Read more »

Eleven new H7N9 cases include one in Beijing | CIDRAP Read more »

More to read:
Alberta ex-Beijing H5N1 Has RBD Change D225R
Possible Role of Songbirds and Parakeets in Transmission of Influenza A(H7N9) Virus to Humans - Volume 20, Number 3—March 2014 - Emerging Infectious Disease journal - CDC
Shanghai reports 8th H7N9 case this year: Shanghaiist
Guangdong Province confirmed two new cases of human infection with A H7N9 bird flu virus DoH, January 24 2014, edited
China reports 10 additional H7N9 cases - Healio

[dothedd]

www.who.int/influenza/human_animal_interface/influenza_h7n9/en/index.html

Eleven new H7N9 cases include one in Beijing
Filed Under: AVIAN INFLUENZA (BIRD FLU); H7N9 AVIAN INFLUENZA Jan 24, 2014

The latest H7N9 cases include one in Beijing, shown here, which had not had a case since the first H7N9 wave last spring.
As China headed into a week of Lunar New Year travel and celebrations, it reported 11 new H7N9 avian influenza infections today, including the first one in Beijing since the first wave last spring.

At least 45 infections have been reported this week, a level that tops the busiest week of the outbreak's first wave last spring.

In an outbreak that seems to be heavily driven by human contact with live poultry or their environments, health officials have aired concerns that holiday rituals that involve market-bird purchases and slaughter in people's homes, as well as crowded travel conditions, could amplify the numbers of infected people.

The surge in H7N9 activity in China, as well as other recent high-profile infectious disease events, is triggering preparedness activities and threat assessments in other countries, including the United States, other Asian nations, and Europe.

Cases swell second-wave total
The patient from Beijing is a man who got sick and was hospitalized after he bought pigeons and ate them, Xinhua, China's state news agency, reported. His infection is the first reported in the city since late May.

His case may also signal widening circulation of the virus, because the city is several hundred miles north of the main outbreak areas in eastern and southern China. Only three other infections have been reported by Beijing, and one was in an asymptomatic child.

The other 10 cases were announced today by authorities in three provinces: Fujian, Guangdong, and Zhejiang. According to statements in Chinese translated and posted by Avian Flu Diary, an infectious-disease news blog, the patients include a 46-year-old woman from Fujian province who is being treated in an isolation unit, as well as a 52-year-old man and a 58-year-old woman from Guangdong who are both hospitalized in critical condition.

Seven of the cases are patients from Zhejiang, the hardest-hit province. All are adults, ranging in age from 23 to 82. Five are women and two are men. All of them are hospitalized, five in critical condition and two listed as severe.

Of 85 cases reported in China so far this year, Zhejiang has recorded 43, more than any other province. Authorities in its capital city of Hangzhou announced the suspension of live poultry trading in the main urban areas, starting today, Xinhua reported.

Earlier this month, Shanghai announced that it would temporarily shutter live bird markets starting Jan 31 to curb the spread of the virus. During the first wave of H7N9 infections in the spring, health officials credited poultry market closures with easing the number of new human cases.

The burst of new cases today raises the outbreak total to 238, according to a case list compiled by the FluTrackers infectious disease message board. The unofficial number of deaths stands at 57.

Countries boost preparedness, make assessments
In other developments the US Centers for Disease Control and Prevention (CDC) yesterday revised its interim recommendations for addressing H7N9 in healthcare settings to include H5N1 avian influenza.

Michael Jhung, MD, MPH, a medical epidemiologist in the CDC's influenza division, told CIDRAP News that the content is the same as H7N9 infection control recommendations first released last April, but in light of the recent H5N1 case in a Canadian woman who had traveled to China, the CDC wanted to create a more general document so providers will have information on both viruses.

Efforts are under way to combine H7N9 and H5N1 guidance when appropriate, such as recommendations for treatment and prophylaxis, Jhung said.

In another preparedness effort involving H7N9, the CDC has held joint exercises with Vietnam in case H7N9 or a novel coronavirus surfaces there, according to a Jan 22 blog post written by Lauren Anderson, a global health fellow who worked on the project, which started last spring. Vietnam shares a border with China, and the countries have a robust trading relationship that includes poultry and other commodities.

Anderson wrote that the exercise tested the health ministry's response capacities, which included analyzing the threat at labs and surveillance systems and launching efforts to prevent the virus from spreading. "The scenario was just a practice drill but may be all too real with the H7N9 virus infecting people and poultry in neighboring China," she wrote.

Meanwhile, the European Centre for Disease Prevention and Control (ECDC) weighed in on the surge of new H7N9 cases in China in its latest weekly communicable disease threat assessment. It noted that between the week of Jan 17 and Jan 24, 37 new cases were reported by local authorities and that 90 sporadic cases have been reported since October.

The ECDC said the continued and increasing transmission of a novel reassortant avian flu virus that can cause severe disease in humans in one of the world's most densely populated countries raises pandemic concerns, but so far the event represents a local but widespread zoonotic outbreak with sporadic spillover to humans who have close contact with the animal reservoir.

The rise in cases since October suggests that the reservoir persists and the transmission pattern may be seasonal, the ECDC wrote.

Canada's recent detection of a fatal H5N1 infection in a traveler returning from China underscores the point that imported H7N9 cases might also be seen in Europe, but the threat of the disease spreading to humans is still considered low, the group noted.

[dothedd]

Analysis of new H7N9 wave warns of co-infection threat
Filed Under: H7N9 AVIAN INFLUENZA
CIDRAP News | Jan 28, 2014

Chinese street scene

Though ongoing H7N9 influenza activity in China—with eight new cases reported today—is mainly a zoonotic event, its parallel rise with seasonal flu poses a virus reassortment threat, according to a new assessment today from European health officials.

Activities surrounding Chinese New Year on Jan 31 will put humans in the crosshairs of both H7N9 and seasonal flu strains, according to the European Centre for Disease Prevention and Control (ECDC) in a comprehensive look at China's second wave of disease activity and its first update since May 2013.

Three Chinese provinces reported H7N9 cases today: four from Zhejiang, three from Guangdong, and one from Jiangsu.

Factors could intensify flu threat
The ECDC said the outbreak in China remains localized, with the virus mainly transmitted sporadically to humans who have close contact with the animal reservoir, presumably live poultry. Though the H7N9 virus doesn't appear to have the capacity for efficient human-to-human spread, new reassortants with seasonal flu strains could arm it with the ability to transmit more easily, a situation that bears close monitoring, the organization added.

Seasonal flu activity is at high levels and still increasing in China, with all three strains circulating, the World Health Organization (WHO) said yesterday in its global flu update. In southern China the dominant strains are H3N2 and the 2009 H1N1 virus, while the northern part is seeing mainly 2009 H1N1.

Brisk seasonal flu activity is occurring alongside rapidly accumulating H7N9 cases in the eastern and southern provinces. Last spring China's surveillance system picked up at least one coinfection case, that of a 15-year-old boy who recovered after he was sick with both H7N9 and H3N2.

"Hundreds of millions of Chinese are returning to their villages over the festive season in what is believed to be the world's largest annual human migration," ECDC said in its risk assessment.

Considering the spread of H5N1 avian influenza across geographic borders, it's surprising that neighboring Asian countries haven't detected more H7N9 cases, the agency said, urging countries to be on guard for imported cases.

It echoed a joint WHO-China inspection team's conclusion last spring that a cross-sector effort will be needed to reduce H7N9's threat. ECDC noted that there may be a role for a poultry H7N9 vaccine in affected parts of China, and it warned that the virus could threaten the country's food supply if it becomes highly pathogenic.

H7N9 vaccine developments
The ECDC's report reviewed the latest clinical findings, lab tools for detections, and vaccine developments. It said six clinical trials using different variants of H7N9 candidate vaccine strains have been registered with ClinicalTrials.gov and that initial results have been reported for two of them: a virus-like particle vaccine from Novavax and a cell-culture adjuvanted vaccine from Novartis.

Two phase 1 studies are enrolling participants, one supported by the US National Institute of Allergy and Infectious Diseases (NIAID) and one by GlaxoSmithKline, the ECDC said. Other studies, done with NIAID support, will test "mix-and-match" approaches that pair unadjuvanted candidate vaccines with other companies' adjuvants.

Few details are known about China's H7N9 vaccine development plans, but a report today from Xinhua, China's state news service, said one developed by Hualan Biological Engineering, Inc., has passed initial evaluation by regulators in Henan province, but it's not clear when China's Food and Drug Administration will clear it for production.

Provinces report eight new cases
In the latest outbreak developments today, the eight new cases pushed the outbreak total to 260, according to a case list compiled by FluTrackers infectious disease message board. The cases also edged the number of cases in the outbreak's second wave to 124, putting it within close shooting range of the 136 cases recorded after the virus first emerged last spring.

According to provincial health ministry statements translated and posted by the Avian Flu Diary (AFD) infectious disease blog, the patients are all adults and are hospitalized with their infections. Patients from Zhejiang province include a 43-year-old woman and a 57-year-old man with mild illnesses, an 81-year-old man in critical condition, and a 63-year old woman in critical condition.

Jiangsu province reported a 53-year-old man who is in serious condition, and Guangdong province reported three cases from Shenzhen involving a 43-year-old woman who is in stable condition and two women ages 31 and 41 who are listed as critical.

Elsewhere, health officials in Hong Kong today said no illnesses have been detected in people who had contact with infected chickens imported from Guangdong province. H7N9 test findings in the birds yesterday triggered the 3-week closure of Hong Kong's wholesale poultry market and the culling of 20,000 birds to curb the spread of the virus.

The Centre for Health Protection (CHP) said in a statement that the driver who brought the imported birds to Hong Kong is under hospital observation, is asymptomatic, and has tested negative for the virus. It added that 95 other contacts, including 49 people who helped cull the birds, are also being monitored. One market inspection officer had nonspecific symptoms but tested negative for the virus.

Hong Kong's government today said culling operations had been completed and that 22,604 birds were destroyed. They included 16,984 chickens, 2,898 silky fowls, 1,080 pheasants, and 1,642 pigeons.


www.cidrap.umn.edu/news-perspective/2014/01/analysis-new-h7n9-wave-warns-coinfection-threat

See on above link....

Jan 27 ECDC H7N9 risk assessment update

Jan 27 WHO global flu update

Jun 14, 2013, CIDRAP News scan "H7N9-H3N2 coinfection reported in Chinese teen"

FluTrackers human H7N9 case list

Jan 28 Xinhua story

Jan 28 AFD post

Jan 28 CHP statement

Jan 28 Hong Kong government statement on poultry culling

[dothedd]

Flu pandemic was a scourge in Burlington in 1918

Burlington Coffin Company around 1918
Historian Walter Boyd says that during the Spanish flu pandemic in 1918 the only business that thrived in the area was the Burlington Coffin Co.

Courtesy of Don Bolden
By Walter Boyd / Special to the Times-News
Published: Tuesday, February 4, 2014 at 16:57 PM.

Since it was founded as Company Shops in 1856, Burlington and its residents have endured periodic epidemics of diseases such as smallpox, cholera, typhoid fever, and diphtheria. But nothing they had endured in the past prepared them for the unusually deadly strain of avian influenza (“bird flu”) which came to town 96 years ago.


The new flu strain was first discovered at an Army post in Kansas in early 1918. But since the United States was embroiled in World War I at the time, reports of the outbreak were censored to prevent panic and to preserve morale among both soldiers and civilians. The other nations involved in the war did the same. Therefore, most people first heard about the flu from reports from neutral Spain, which led to it being called the “Spanish flu.”

The massive American troop movements to France spread the flu there, and within months it had permeated every corner of the globe — even remote Pacific islands and Arctic regions. An estimated 500 million people contracted the flu, and between 50 and 100 million people are estimated to have died, making it one of the worst natural disasters in human history.

What made the Spanish flu different from previous flu epidemics is that it disproportionately took the lives of young, healthy adults, whereas previous epidemics had usually taken the lives of the very young and elderly. Modern researchers have concluded that this was possibly due to what is known as a “cytokine storm,” an overstimulation of the immune system, causing a massive invasion of leukocytes (white blood cells) into lung tissue, which caused the lungs to fill with fluid. Consequently, those with the strongest immune systems were more likely to die from the flu, while those with weaker immune systems, i.e., children and the elderly, could more easily fight it off.

A new and particularly virulent strain of the Spanish flu first appeared in August 1918, and arrived in Alamance County about a month later. By the end of September, there were more than 100 cases among students at Elon. The gymnasium in Alumni Building (also known as “Old North Dormitory”) was converted into a makeshift hospital. Two students died. One was Modesto Lopez of Cuba, who succumbed Oct. 11, 1918. His body was not shipped home but was instead buried in Elon’s Magnolia Cemetery.

On Oct. 23, the Alamance County Board of Health banned all public gatherings, indoors and out, until Nov. 30. People were prohibited from going in and out of homes where someone had the flu unless they were nurses or on some errand of mercy or necessity. Those who had the flu were barred from leaving their homes unless a physician cleared them. For those brave enough to venture outside, nearly everyone wore a face mask, and no one shook hands.

Classes at Burlington Graded School were canceled for weeks, and the school’s main building on Broad Street was converted into an emergency hospital because the beds at Rainey Hospital were filled to overflowing. A portion of Aurora Mills on East Webb Avenue was turned into a laundry to wash the bed linens used at the high school infirmary.

Determining how many died in Burlington during the epidemic is difficult since most physicians simply listed “pneumonia” as the cause of death on death certificates. But at least 29 people in town died of the flu during October, an average of one per day. It is suspected that the actual toll was much higher.

Most businesses in Burlington suffered from a lack of customers during the fall of 1918. About the only one that profited from the Spanish flu was the Burlington Coffin Co. on Maple Avenue. There were so many orders that it couldn’t keep up with them. People reported that coffins were stacked “like cordwood” at the freight depot.

By January 1919, the flu had disappeared from Burlington almost as suddenly as it had come, although the pandemic continued into 1920 in other parts of the world. A severe outbreak of another strain of deadly flu hit Burlington 10 years later, from November 1928 to January 1929, but it was not as severe as the Spanish flu. However, schools and businesses were closed for weeks as a precaution.

[dothedd]

Avian flu variant stalks Egypt
Date:
February 7, 2014
Source:
Arizona State University
Summary:
A new study tracks the spread of an H5N1 variant in Egypt -- a country recently identified as a major epicenter for the virus. In results researchers track the spread of H5N1 cases using a technique known as phylogeography.

Since its first identification in Asia, highly pathogenic avian influenza -- H5N1 -- has caused significant alarm in the scientific community. While the virus' primary target is birds -- tens of millions have already died from it -- it is capable of infecting mammals, including humans, causing serious illness and a frightening rate of mortality.


In a new study, Matthew Scotch, a researcher at Arizona State University's Biodesign Institute, tracks the spread of an H5N1 variant in Egypt -- a country recently identified as a major epicenter for the virus. In results recently appearing in the journal BMC Genomics, Scotch tracks the spread of H5N1 cases using a technique known as phylogeography.
 
The authors hope that studies of this kind will significantly enhance efforts by public health officials to identify viral outbreaks, limit their spread, coordinate vaccination efforts, reduce mortality and better inform the public of risks.

"Egypt represents an epicenter for H5N1 and there are new variants that have emerged since it was first discovered there in 2006, "Scotch says. "We used phylogeography and influenza genome sequences to model diffusion and evolution of the virus."

Phylogeography was born out of the fields of biogeography and phylogenetics or molecular evolution. By combining viral sequence data and geographical information over time, as well as evaluating features associated with viral carriers, researchers can better understand how viruses spread across a landscape through animal and human populations.

Phylogeography has already been established as a powerful technique for investigating viral dispersal for human diseases, including dengue fever, rabies, influenza and HIV. Recent application of phylogeographic methods to the study of avian influenza promises to significantly improve fine-grained mapping of viral origin and spread.

Avian flu H5N1 is a form of influenza A -- an RNA virus -- first identified in Hong Kong in 1997. The initial cases of H5N1 were apparently not transmitted efficiently among birds. In 2002 however, new isolates of H5N1 appeared, causing acute disease in ducks, resulting in neurological dysfunction and death.

Infected birds transmit H5N1 to one another through nasal secretions, saliva, feces and blood. Other animals, including humans, may become infected with the virus through direct contact with avian bodily fluids or through contaminated surfaces.

Human cases of H5N1 often result from contact with infected poultry, particularly in live bird markets and farms, which are believed to be major reservoirs for the virus. Avian H5N1 however, is also carried by migratory species of birds, which further spread H5N1 to other parts of the world.

In 2004, researchers discovered that H5N1 is a more potent pathogen than originally assumed, attacking waterfowl, chickens, crows, pigeons and ducks, as well as mammals, yielding a high mortality rate. Avian flu is now considered a significant global health threat, with the very real prospect of an international pandemic, causing widespread fatality.

Indeed, the mortality rate in humans contracting H5N1 has been estimated to be around 60 percent, making it more lethal for infected individuals than Spanish influenza -- a genetically similar strain that killed 50-100 million people worldwide during the pandemic of 1918.

Currently, H5N1 is not highly transmissible to humans from birds and has a very low rate of human-to-human transmission, (though around a half dozen cases have been reported). Should a small number of mutations render H5N1 more easily transmissible among humans, the conditions for a deadly pandemic will have been met.

In addition to mutations, mixed forms of influenza virus -- known as reassortant strains -- can occur when a single individual is infected with two versions of a given virus and they exchange genes. An H5N1 reassortant could render avian influenza readily transmissible between human hosts.

In the new study, a particular variant of H5N1, labeled 2.2.1.1, was observed in Egypt. There, avian flu has already killed thousands of birds and caused 173 human cases, of which 63 have been fatal as of December 10th, 2013, according to the World Health Organization. These are the highest case numbers for H5N1 outside of Asia. As in the case of Asian H5N1, experts associate most human infections in Egypt with exposure to diseased poultry, particularly at live bird markets.

In their attempts to identify the origin and spread of the virus in Egypt, researchers made use of a new software platform created by Professor Scotch. Known as ZooPhy, the program enables the phylogeographic analysis of H5N1 spread.

The avian influenza virus H5N1 takes its name from two kinds of spikes adorning the viral surface, hemagglutinin (HA) and neuraminidase (NA). Influenza viruses of Type A or Type B use hemagglutinin to attach to cell surface receptors, allowing viral infection of the cell. Neuraminidase later acts to remove these receptors from infected cells, allowing newly synthesized viruses particles to escape and infect other cells.

(There are 17 different types of hemagglutinin, from H1 to H17 and nine different types of neuraminidase, from N1 to N9 among influenza A viruses. Each virus has one type of H (such as H5) and one type of N (such as N1).)

Through the analysis of 226 HA and 92 NA sequences, Scotch and his colleagues used a phylogeographic approach to trace the preponderance and transmission routes of H5N1 in Egypt. Phylogeography is a particularly fruitful approach for animal-to-human (or zoonotic) RNA viruses, due to short genomic sequences and rapid rates of evolution.

The group's findings revealed a geographic spread of the 2.2.1.1 viral form of H5N1 across Egypt's four primary areas: Cairo, Nile Delta, Canal and Upper Egypt. Statistical analysis suggests the northern governorate of Ash Sharqiyah as the point of origin for the spread of H5N1, however, the mathematical association is too weak to claim certainty. Analysis also implied that the strongest transmission routes for H5N1 were from Ash Sharqiyah to Al Gharbiyah and Al Fayyum to Al Qalyubiyah.

Most of the identified routes of transmission appeared in the densely populated Delta region of Egypt. The Al Qalybiyah governate in particular appears to be a popular area for viral transition, though dispersion to and from this region remains uncertain, requiring further research. The study also noted considerable viral diversity over a limited time frame -- perhaps an evasive response to a country-wide poultry vaccination program.

"This has significant public health implications for the rest of the world," Scotch says. "It is important to focus on variant clades in order to better understand how this virus has evolved and which governorates are propograting its spread."

The authors are further developing the ZooPhy software's graphical interface. The tool requires no specialized knowledge of phylogeography or bioinformatics, making it convenient for field use by public health officials. By zeroing in on trade routes, migration patterns and highways of viral transmission, health authorities can conserve limited resources, applying them where they can be most effective.

Story Source:
The above story is based on materials provided by Arizona State University. The original article was written by Richard Harth. Note: Materials may be edited for content and length.
Journal Reference:
Matthew Scotch, Changjiang Mei, Yilma J Makonnen, Julio Pinto, AbdelHakim Ali, Sally Vegso, Michael Kane, Indra Sarkar, Peter Rabinowitz. Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt. BMC Genomics, 2013; 14 (1): 871 DOI: 10.1186/1471-2164-14-871

www.sciencedaily.com/releases/2014/02/140207094052.htm