Saturday, February 25, 2017

Egypt: Conflicting Media Reports Of An Avian Flu Fatality In Fayoum


Since official confirmation of avian flu infections from Egypt's Ministry of Health are often delayed (sometimes for weeks), we are forced to use local media reports to try to monitor the situation there.  

The MOH's website, which has been badly neglected (and often offline) over the past few years, has been recently revamped - but a site search for avian flu `(انفلونزا الطيور) returns no results.
They may be still adding content, so hopefully that will change.

After a record-setting 2015, where Egypt reported 136 H5N1 cases (39 deaths), 2016 saw only 10 cases (and 3 deaths) reported.  The reasons behind this welcomed drop are not clear, but it should be noted that several studies have suggested that the majority of avian flu cases are never identified and reported (see EID Journal: H5N1 In Egypt).

Today we have several Arabic media reports today of a supposedly fatal case of avian flu (subtype not provided, but probably H5N1) in Fayoum, and at least one report from the Fayoum health department stating they had not received an official report.

Two reports then, the first from

Governor of Fayoum: Veterinary Medicine called for an urgent report on the death of a patient with bird flu
Saturday, February 25, 2017 14:36

Governor of Fayoum: Veterinary Medicine called for an urgent report on the death of a patient with bird flu Dr. Jamal Sami governor of Fayoum

Dr. Jamal Sami governor of Fayoum, said in a special statement for the "seventh day," he demanded of Veterinary Medicine and the Department of Health to maintain an urgent report on the incident and the death of infected citizens of bird flu on Saturday, and procedures that have been followed for Immunization and eliminate the epicenter of the disease.

The Undersecretary of the Ministry of Health in Fayoum, Dr. Hisham El Shenawy, announced the death of the first cases of bird flu in 2017, hospital diets to someone named Ocharf.a.m (48 years - factor) from the village of "compromise" Senoras Center, pointing out that he was booked Status General Hospital suffering from symptoms of a cold and high temperature, and was transferred to a hospital in Fayoum chest and took samples from him and sent to labs central Cairo, which has proven results bird flu, was transferred to the Abbasid Fever, where he died.

The second story, comes from

Fayoum Health»: We have not received a report on the death of a patient bird flu

Saturday 25 / February / 2017 - 13:57
File photo File photo Taha al - Banna

Dr. Hisham Shenawi, Undersecretary of the Ministry of Health in Fayoum, said he had not yet received a report on the death of «Ashraf Abdul Baki Mukhaimar» (48 years old) , who died of his injuries bird flu, according to the statements of Veterinary Medicine Department in the governorate.

The victim was hit by a rise in temperature and shortness of breath, and went to the Chest Hospital and was detained by three days, pulling him to the doctors a sample was sent to the analysis of the Ministry of Health which confirmed a positive case coefficient, was transferred to the Abbasid Hospital and pronounced dead there.

His body was flown to his home village on Friday night, and sent the Veterinary Medicine Department of the Committee for the sterilization of the area around the poultry farm , which was dealing with.

 Hopefully they will get this sorted out, and reported to the WHO, in short order.


Iran: Media Reports Of H5N8's Spread


In their most recent  OIE filing (Feb 13th), Iran reported 30 outbreaks of HPAI H5N8 since it first appeared last November, resulting in the loss of just over a million birds.  According to the accompanying map, outbreaks were spread across 11 provinces in the northern half of the country.

A week earlier, however - (see H5N8 & H5N1: Murmurs From The Middle East)  - we were seeing state media (IRNA) reports that the real losses were closer to 6 million birds.

As with China, getting reliable outbreak information from the Middle East can be difficult, although Iran has been a bit more forthcoming than some of its neighbors.  The official silence from Egypt - which has been the biggest hotbed of avian flu in the Mid East for a decade - is deafening (note: since H5N1 was declared endemic in 2008, they are no longer required to file weekly OIE reports).

Overnight the Iranian and Persian Language press have been filled with reports of H5N8 avian flu spreading - depending on the source - to either 15 or 21 provinces. 

While stressing that no human infections have been reported, warnings are going out to the public to avoid contact with wild birds or migratory birds (living or dead), to stop using local poultry products “until further notice.”, and to only consume chickens and eggs that have certification from the Iran Veterinary Organization or the Ministry of Agriculture.

This English language report from Iran's PRESSTV.    

Birds infected with flu seen in 15 Iranian provinces: Health Ministry official

Sat Feb 25, 2017 8:54AM

Iran’s Ministry of Health has detected flu in birds in 15 Iranian provinces and has prohibited the use of local poultry products nationwide.

Mahmood Soroush, the head of the ministry’s Center for Communicable Disease Control, told Iran’s IRNA news agency on Saturday that the avian flu, most common form of which is the H5N8 strain, had infected birds in more than 15 Iranian provinces.

Soroush said it had already been detected in many countries, especially in the region spanning between Siberia and the Horn of Africa.
A view of the building of Iran’s Ministry of Health, Treatment and Medical Education in the capital, Tehran

He said the ministry had issued three statements warning about contamination even close to urban areas, particularly near lagoons, and demanding people to avoid touching any kind of birds.

“We seriously urge people to avoid touching dead birds or even living migratory ones,” the official said.
The Iranian Health Ministry is taking different measures concerning education, vaccination, and the distribution of medication in affected areas, Soroush added.

He stressed that people should use only chickens and eggs that have certification from the Iran Veterinary Organization or the Ministry of Agriculture and avoid using local poultry products “until further notice.”

‘No human cases of bird flu’

Those who have fever following physical contact with birds should promptly refer to medical centers, the official pointed out. He said, however, that no cases of human infection had been detected in Iran.

“So far, we haven’t had even a single case of human infection with bird flu or anything like it, but preventative measures such as vaccination, distribution of medication, and sampling from at-risk individuals continue,” he added.

The H5N8 strain of bird flu is deadly for poultry, but has not been detected in humans. The virus has spread across Europe and the Middle East since late last year and led to the culling of hundreds of thousands of poultry.

I was unable to find any official statement on the Iranian MOH website (, but I'll continue to check.
Other Persian language media reports (see Influenza is still going / 21 provinces were involved) put the number of affected provinces considerably higher, and indicate the price of eggs has risen sharply in recent weeks. 

The OIE's WAHIS mapping tool shows where outbreaks have been reported around the world  - and despite media reports suggesting widespread activity - notifications from the Middle East (and points east, for that matter) since January 1st are few and far between.

While a lack of reports can be comforting - as with China, parts of South East Asia, and much of Africa - no avian flu news isn't necessarily good avian flu news.

Friday, February 24, 2017

France: MOA Announces 38 Additional H5N8 Farm Outbreaks


The number of farms affected by the HPAI H5N8 virus continues to rise rapidly in France, with 38 new outbreaks and 13 new detections in wild birds reported since last Tuesday. This is an increase of 141 cases over the past 21 days (see Feb 3rd's 200th H5N8 Outbreak In Poultry Farms Over Past 60 Days).

Earlier this week officials announced plans to completely cull the duck population in Landes, the hardest hit region of southern France (France Expands Preemptive Culling As H5N8 Outbreaks Exceed 300), in an attempt to halt the spread of the virus. 

According to the latest report by France's ESA (Epidemiosurveillance Santé Animale) - dated Februrary 21st - the tallys so far this fall's HPAI H5Nx epizootic across Europe:
The total number of outbreaks and cases of HPAI reported continues to increase and is now to 1779 including 965 in wild birds (72 species affected), 777 livestock and 37 in the avifauna captive.

Based on those numbers, France accounts for roughly 40% of the farm-related outbreaks in Europe this winter.  The latest update from the French MOA follows:

H5N8 avian influenza: monitoring the spread of the virus in farms and wildlife

24/02/2017 avian influenza
© Pascal Xicluna / Min.Agri.Fr

In France

Situation at February 24, 2017: 341 H5N8 outbreaks in farms and 41 cases in wildlife confirmed and communicated.

Learn more about the epidemiological surveillance Animal Health platform .
List of homes in the departments

  • Country: 183
  • Tarn : 8
  • Gers : 94
  • Lot-et-Garonne: 9
  • Hautes-Pyrénées: 25
  • Pyrénées-Atlantiques: 16
  • Aveyron : 2
  • Deux-Sèvres: 3
  • Lot: 1
 List of cases in wildlife
  • Pas-de-Calais: 1
  • Haute-Savoie: 2
  • Tarn : 2
  • Manche: 1
  • Ain : 17
  • Lot-et-Garonne: 2
  • Country: 3
  • Gers : 7
  • Loire-Atlantique: 1
  • Pyrénées-Atlantiques: 3
  • Vosges: 2

China: NHFPC Announces 35 New H7N9 Cases Over Past 11 Days


With the ever present caveat that we are pretty much dependent upon whatever information the Chinese government chooses to divulge, today their NHFPC (National Health & Family Planning Commission) has announced an apparent slowdown in the number of H7N9 cases over the past 11 days.
This comes after three days of very high profile meetings with the Chinese Premier, the MOA, and the NHFPC (see here, here, and here), all vowing to contain the epidemic.
The dissident press, located outside of Mainland China, continues to insist that cases are being concealed, and that the outbreak is far from under control. Claims that are almost impossible to verify.
They cite the upcoming `two sessions' - the very high profile annual meetings of the National People’s Congress (NPC) and the National Committee of the People’s Political Consultative Congress (CPPCC) which are held in early March - as reasons for slow-rolling the numbers. 
Slowdown or not, 35 cases in 11 days is still an elevated number.  And once poultry markets re-open, those numbers could easily spike again.  Cases generally peak during January-February, but usually continue into April and May, so a lull now is no guarantee the epidemic is waning.

This from the NHFPC.

Do a good job to further strengthen joint prevention and control of H7N9 epidemic prevention and control measures implemented to stabilize
Published: 2017-02-24

  February 22, Comrade Premier Li Keqiang chaired a State Council executive meeting of the deployment H7N9 epidemic prevention and control work. The meeting pointed out that this year China H7N9 outbreak came earlier compared with previous years, the number of cases increases. Local and relevant departments in accordance with the State Council deployed effectively conduct joint prevention and control. The meeting urged all localities and departments concerned to continue to do H7N9 epidemic joint prevention and control, open and transparent timely release of authoritative information on the epidemic, strengthen epidemic source control, do the monitoring and early warning and treatment of cases, the implementation of "large-scale farming, centralized slaughtering, cold chain transport, ice listed fresh "new model, and effectively protect people's health and safety.

  Deal with H7N9 joint prevention and control mechanism to conscientiously implement the State Council executive meeting, to further strengthen the H7N9 outbreak in accordance with joint prevention and control video conference agreed that matters, since February 23, the National Health and Family Planning Commission, the Ministry of Agriculture, SAIC, food and drug regulation Administration, FDA joint Steering group composed of seven, focusing on epidemic prevention and control of provinces to carry out supervision, to further promote the implementation of the measures. Recently, the National Health and Family Planning Commission, the Ministry of Agriculture, Industry and Commerce Administration, Food and Drug Administration of the four departments will jointly issued a circular calling for the spirit of the State Council meeting to further strengthen and transporting live poultry farms supervision, strict implementation of live poultry markets were closed, disinfection and quarantine system, or detection of pathogen detection of cases of cities and counties to close the live bird markets as soon as possible to take measures such as culling according to regulations. At the same time, severely crack down on illegal transport, management, slaughter and other acts. 

At present, all related to epidemic prevention and control work is solid and orderly progress, the early momentum of rapid increase epidemic has been effectively curbed. February 13, 2017 - 2 23, the Mainland of China reported a total of 11 days cases of 35 cases of H7N9, which killed seven people, the epidemic has stabilized.

  Experts believe that the current H7N9 outbreak in a highly circulated, H7N9 virus transmission is still by birds to humans, contact with infected birds or exposure to live poultry market is an important risk factor for human infection. Experts predict that the most recent period, it is possible to continue our sporadic cases occur H7N9. Experts suggest that the public in their daily lives should avoid contact with dead birds, avoid direct contact with live poultry category; quarantine certificates should be purchased fresh, live and frozen poultry and poultry-related products; attention to food hygiene, food processing to do Health cooked separately; improve self-protection awareness, found that fever and respiratory symptoms should wear a mask, doctor as soon as possible.

Eurosurveillance: Emergence Of A Novel Subclade Of Seasonal A/H3N2 - London

Credit NIAID


Twice each year (February & September) influenza experts from around the world meet (often electronically) to discuss recent developments in human and animal influenza viruses, and to decide on the composition of the next influenza season’s flu vaccine.  Vaccine strains must be selected for two A strains (H1N1 & H3N2) and two B strains (Victoria & Yamagata Lineage)

NIAID has a terrific 3-minute video that shows how influenza viruses drift over time, and why the flu shot must be frequently updated, which you can view at this link.

Due to the time it takes to manufacture and distribute a vaccine, these decisions must be made six months in advance, so the composition of next fall's flu vaccine is expected soon.

While we talk about 2 primary influenza A subtypes (H1N1 & H3N2) - in truth there are multiple variations of each subtype in circulation at any given time. Usually, one of these versions is dominant, but these evolving strains are constantly playing a viral game of `king of the mountain’, and the balance of power can shift quickly.

In the fall of 2014, a late arriving `drifted' H3N2 virus practically negated that year's flu vaccine's effectiveness (see CDC HAN Advisory On `Drifted’ H3N2 Seasonal Flu Virus).

Since 2009 seven distinct genetic groups have been defined for H3N2While all belong to clade 3C, they are divided into three subdivisions; 3C.1 , 3C.2, and 3C.3, with last November's ECDC Influenza Virus Characterization Report stating:

In 2014 three new subclades emerged, one in subdivision 3C.2, 3C.2a, and two in 3C.3, 3C.3a and 3C.3b , with subclade 3C.2a viruses dominating in recent months.

Yesterday's edition of  the Journal Eurosurveillance adds yet another layer of complexity to this already diverse field of H3N2 viruses. A new subclade of H3N2 - proposed as 3C.2a2 - has recently appeared in London. 

While more studies are needed - and the future spread or dominance of subclade 3C.2a2 is far from assured  - there are concerns that the current H3N2 vaccine may offer sub-optimal protection against this new strain.

Eurosurveillance, Volume 22, Issue 8, 23 February 2017
Rapid communication
Emergence of a novel subclade of influenza A(H3N2) virus in London, December 2016 to January 2017

H Harvala 1 2 , D Frampton 2 , P Grant 1 , J Raffle 2 , RB Ferns 2 3 , Z Kozlakidis 2 , P Kellam 4 , D Pillay 2 , A Hayward 5 , E Nastouli 1 3 6 , For the ICONIC Consortium 7

Correspondence: Eleni Nastouli (, Heli Harvala (

Citation style for this article: Harvala H, Frampton D, Grant P, Raffle J, Ferns RB, Kozlakidis Z, Kellam P, Pillay D, Hayward A, Nastouli E, For the ICONIC Consortium. Emergence of a novel subclade of influenza A(H3N2) virus in London, December 2016 to January 2017. Euro Surveill. 2017;22(8):pii=30466. DOI:
Received:13 February 2017; Accepted:23 February 2017

We report the molecular investigations of a large influenza A(H3N2) outbreak, in a season characterised by sharp increase in influenza admissions since December 2016. Analysis of haemagglutinin (HA) sequences demonstrated co-circulation of multiple clades (3C.3a, 3C.2a and 3C.2a1). Most variants fell into a novel subclade (proposed as 3C.2a2); they possessed four unique amino acid substitutions in the HA protein and loss of a potential glycosylation site. These changes potentially modify the H3N2 strain antigenicity.

The ongoing influenza season started early in eleven European Union countries, including England, on week 46 of 2016 [1]. The majority of reported infections have been caused by clade 3C.2a or 3C.2a1 influenza A(H3N2) viruses. The clade 3C.2a contains the current vaccine strain A/Hong Kong/4801/2014, and the first few viruses within the more recently emerged subclade 3C.2a1 were earlier shown to be antigenically matched with the vaccine component [2]. However, evidence for suboptimal vaccine effectiveness (VE) against laboratory-confirmed influenza A infection in people over 65 years-old was obtained in the first studies from Finland [3] and Sweden [4].

An outbreak of influenza A(H3N2) was first notified in our London centre on 30 December 2016. The outbreak coincided with unusually high ongoing circulation of respiratory syncytial virus (RSV) (Figure 1), and affected both patients and staff in the acute medical unit (AMU).

While infection control precautions were intensified, it resulted in multiple bay closures. We suspected that the sharp increase in the number of influenza A(H3N2) infections may have been caused by the emergence of a new genetic variant of H3N2, a hypothesis investigated through next generation sequencing (NGS) of influenza A(H3N2) strains.



In our centre in London, the early start and higher intensity of the 2016/17 influenza A(H3N2) virus epidemic mirrored that of the season 2014/15 where the subtype H3N2 also predominated. During the 2014/15 season, most influenza A(H3N2) infections in Europe were shown to be caused by antigenically drifted virus variants within the new genetic subgroup 3C.2a [8]. Our genetic analysis of London A(H3N2) viruses demonstrates ongoing co-circulation of drifted variants from multiple subclades (3C.3a, 3C.2a1 and proposed 3C.2a2). 

Four or more substitutions in two or more antibody binding sites are predicted to give an antigenically different virus [9] as in our case. Although we did not observe mutations in the seven positions suggested as being responsible for major transition clusters [10], position 144 is at the flank of the RBS, and additionally recognised as antigenic [11].

Although not necessarily determining major antigenic drift, the alterations of N-linked glycosylation sites are likely to contribute to more complex conformational changes in the HA due to gain or loss of glycosylation and can thus facilitate immune escape [12]. Furthermore, any amino acid changes in the 140–146 region of HA have been shown to be characteristic for antigenically distinct viruses of epidemic significance [9,13,14]. The amino acid substitution S144K in the emerging subclade 3C.2a2 viruses together with the loss of an N-linked glycosylation site (N122D) shows potential for antigenic drift that warrants further monitoring during this ongoing season. A limitation of our study was the lack of detailed vaccination data.

Our findings in London of the rapid emergence of genetically drifted influenza A(H3N2) viruses underscore the potential for such strains to spread rapidly in hospital environments among patients and staff. Characterising emerging strains of influenza by next generation sequencing adds to the local and national monitoring of influenza trends. Further studies are needed to investigate the antigenic effects of substitutions occurring within the newly described subclade.

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WHO H7N9 Risk Assessment - Feb 2017


Yesterday the World Health Organization released a new Influenza at the human-animal interface report - one that reflects information provided by the Chinese government through February 14th of this year.  As new cases continue to be announced - and others are presumably in the `pipeline' - case totals increase almost daily.
As the chart above illustrates, H7N9 cases this winter have already exceeded anything we've seen to date, and China's winter epidemic season typically has a couple of more months to run.
The cases reported reflect the `sickest of the sick' - those ill enough to require hospitalization - and so we really don't have a good handle on how many mild or moderate cases there may be.  The assumption is that number is substantial (see Beneath The H7N9 Pyramid).

Despite this abrupt increase in cases, we've seen no evidence of sustained or efficient human-to-human transmission of the virus.  Clusters have been small, and infrequently reported.  For cases where information is known, the vast majority appear to have had recent close contact with live poultry. 
Today's report does not address the recent HPAI variant viruses detected in both Taiwan and Guangdong Province (see Two H7N9 `Variants' Isolated From Human Cases) in January, as this report was compiled prior to those announcements.  So far, we've not seen any indication that these genetic changes increase the health risk to humans.

Today's report also details two swine origin H1N1 infections in Europe, and contains a line listing of H7N9 cases.   Follow the link to read the full report.

Influenza at the human-animal interface
Summary and assessment, 17 January to 14 February 2017

  • New infections1: Since the previous update, new human infections with influenza A(H7N9) andA(H1N1)v viruses were reported.
  • Risk assessment: The overall public health risk from currently known influenza viruses at thehuman-animal interface has not changed, and the likelihood of sustained human-to-humantransmission of these viruses remains low. Further human infections with viruses of animalorigin are expected.
  • IHR compliance: All human infections caused by a new influenza subtype are required to be reported under the International Health Regulations (IHR, 2005).2 This includes any animal andnon-circulating seasonal influenza viruses. Information from these notifications is critical toinform risk assessments for influenza at the human-animal interface.

Avian Influenza Viruses

Avian influenza A(H5) viruses

Current situation:

Since the last update, no new laboratory-confirmed human cases of influenza A(H5) virus infection were reported to WHO. Influenza A(H5) subtype viruses have the potential to cause disease in humans and thus far, no human cases, other than those with influenza A(H5N1) and A(H5N6) viruses, have been reported to WHO. According to reports received by the World Organisation for Animal Health (OIE), various influenza A(H5) subtypes continue to be detected in birds in West Africa, Europe and Asia. There have also been numerous detections of influenza A(H5N8) viruses in wild birds and domestic poultry in several countries in Africa, Asia and Europe since June 2016. For more information on the background and public health risk of these viruses, please see the WHO assessment of risk associated with influenza A(H5N8) virus here.

Avian influenza A(H7N9) viruses

Current situation:

During this reporting period, 305 laboratory-confirmed human cases of influenza A(H7N9) virus infection were reported to WHO from China. Case details are presented in the table in the Annex of this document. For additional details on these cases and public health interventions, see the Disease Outbreak News, and for analysis of recent scientific information on the A(H7N9) influenza virus, please see a recent WHO publication here.

1 For epidemiological and virological features of human infections with animal influenza viruses not reported in this assessment, see the yearly report on human cases of influenza at the human-animal interface published in the Weekly Epidemiological Record.
2 World Health Organization. Case definitions for the four diseases requiring notification in all
circumstances under the International Health Regulations (2005).

As of 14 February 2017, a total of 1223 laboratory-confirmed cases of human infection with avian influenza A(H7N9) viruses, including at least 380 deaths3, have been reported to WHO (Figure 2). According to reports received by the Food and Agriculture Organization (FAO) on surveillance activities for avian influenza A(H7N9) viruses in China4, positives among virological samples continue to be detected mainly from live bird markets, vendors and some commercial or breeding farms.

Risk Assessment:

1. What is the likelihood that additional human cases of infection with avian influenza A(H7N9) viruses will occur? Most human cases are exposed to the A(H7N9) virus through contact with infected poultry or contaminated environments, including live poultry markets. Since the virus continues to be detected in animals and environments, further human cases can be expected. Additional sporadic human cases of influenza A(H7N9) in other provinces in China that have not
yet reported human cases are also expected.

2. What is the likelihood of human-to-human transmission of avian influenza A(H7N9) viruses? Even though small clusters of cases have been reported, including those involving healthcare workers, current epidemiological and virological evidence suggests that this virus has not acquired the ability of sustained transmission among humans, thus the likelihood is low.

3 Total number of fatal cases is published on a monthly basis by China National Health and Family Planning Commission.
4 Food and Agriculture Organization. H7N9 situation update.

3. What is the risk of international spread of avian influenza A(H7N9) virus by travellers? Should infected individuals from affected areas travel internationally, their infection may be detected in another country during travel or after arrival. If this were to occur, further community level spread is considered unlikely as this virus has not acquired the ability to transmit easily among humans.
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