Tuesday, March 20, 2018

South Africa: Media Reports Of Another Penguin Colony Hit By H5N8


Almost a month ago, in South Africa: Endangered African Penguins Hit By H5N8, we saw reports of H5N8 activity in six penguin colonies - producing both morbidity and mortality among the endangered birds - along the shores of the Western Cape.
Although outbreaks in commercial flocks have dropped dramatically since November of last year, reports of H5N8 in wild birds - particularly shore birds - has continued throughout their summer.
Today local media is reporting of a fresh outbreak at the Table Mountain National Park in Simon's Town, just south of Cape Town.   So far, South Africa's Department of Agriculture (DAFF) hasn't posted anything on their website. 

What we do have is this representative report from IOL

Avian Flu outbreak confirmed at Cape Town's Boulders penguin colony

20 March 2018, 3:08pm / Staff Reporter

Cape Town - The Table Mountain National Park has confirmed there is an outbreak of avian flu (bird flu) at the Boulders penguin colony in Simons Town.

"Table Mountain management would like to alert the public that several cases of bird flu in the penguin colony at Boulders have been confirmed by state veterinary services," TMNP spokesperson Merle Collins said.

"It is reiterated that this virus is a very low risk to humans, but is a real threat to domestic poultry. This strain of avian influenza virus (H5N8 strain) has been detected in a range of wild seabirds e.g. swift, sandwich and common terns, African penguins and gannets.

"The park is monitoring the situation closely and has now implemented the following precautions:

  • With the exception of visitors on Boulders Beach boardwalk, nobody may access the main breeding colony.
  • In instances where staff need to go off boardwalks to collect injured birds or hats, camera lens, caps etc dropped by visitors they will limit their access to essential work and then sterilise their boots afterwards - gum boots have been issued and are easier to clean than the normal boot.
  • Monitoring routes used for moult/nest counts have been reviewed to ensure that staff and Penguin monitors do not walk through the main breeding colony.
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While penguins are are flightless birds and not long-distance vectors of avian flu -  other seabirds in the area are not - and could potentially spread the virus both locally, and globally via migratory flyways (see map below).

HPAI H5N8 arrived in South Africa for the first time last June, and rapidly spread to dozens of poultry farms, forcing the culling of millions of birds.  With fall's arrival in the Southern Hemisphere concerns over a repeat this winter are very real.

WHO Reports 3 H9N2 Cases In China (2017-2018)


Although avian flu reports have been in unusually short supply this winter from China - with only 1 H5N6 human infection, and 3 H7N9 cases - we learn from the latest (March 2nd)  WHO Influenza at the human - animal interface report of 3 new H9N2 infections between late December and the middle of February.


All three cases were described as `mild', and 2 of the 3 had recent exposure to poultry.  In 2017, China reported 5 cases, while the year before, China reported 7 cases and Egypt reported 1 (see FluTrackers Global Cumulative H9N2 Partial Case List 1998-2017).
Over the past 2 decades just over 3 dozen human H9N2 infections have been recorded in 3 countries (China, Egypt & Bangladesh). That number is undoubtedly both under diagnosed and underreported as the virus is endemic in poultry across Asia, the Middle East, and has recently moved into Africa.
A 2014 seroprevalence study, found antibodies against H9N2 ranged from 5.9% to 7.5% among poultry exposed individuals in Egypt, suggesting human infection is far more common than the official tallys would suggest.
On the positive side, H9N2 infection in humans has generally been mild, and no human-to-human spread has been detected.  
H9N2 is viewed as having some pandemic potential (see CDC IRAT SCORE), and so several candidate vaccines have been developed over the years.

The avian H9N2 virus occupies a special spot in our bird flu coverage because - while (until recently) only seen as an LPAI (low pathogenic) virus in poultry - its internal genes routinely make up the backbone of many of the HPAI viruses that pose the greatest risks to both poultry, and human health.

In the past, we’ve looked at this propensity of the H9N2 virus to reassort with other avian flu viruses (see PNAS: Reassortment Of H1N1 And H9N2 Avian viruses & PNAS: Reassortment Potential Of Avian H9N2) which have shown the H9N2 capable of producing `biologically fit’ and highly pathogenic reassortant viruses.
Nearly 4 years ago, in PLoS Path: Genetics, Receptor Binding, and Transmissibility Of Avian H9N2 researchers found evidence of Chinese H9N2 viruses binding preferentially to alpha 2,6 receptor cells -  the type commonly found in the human upper respiratory tract - rather than to alpha 2,3 receptor cells.
Five weeks ago, in A Curious OIE Notification From Ghana: HPAI H9N2?, we saw what appears to have been the first detection of an HPAI (Highly Pathogenic) H9N2 virus in West Africa.

While we are still awaiting clarification and detailed analysis of this HPAI strain, this is a reminder that avian flu viruses are perfectly capable of changing on a dime, and are quite capable of throwing us curve balls.

mBio: The Gathering Storm: Is Untreatable Typhoid Fever on the Way?


Roughly three weeks ago a team of British and Pakistani researchers published a study in the American Society For Microbiology Journal mBio - which detailed the first large outbreak of extensively drug-resistant (XDR) typhoid - which emerged in the Sindh region of Pakistan (includes Karachi & Hyderbad) in late  2016.

You can read the full paper at the link below, or read CIDRAP's excellent summary of Feb 20th (see Study: XDR typhoid in Pakistan carries added resistance genes).

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins 
Elizabeth J. Klemma, Sadia Shakoorb, Andrew J. Pagea, Farah Naz Qamarb, Kim Judgea, Dania K. Saeedb, Vanessa K. Wongc, Timothy J. Dallmand, Satheesh Naird, Stephen Bakere,f,g, Ghazala Shaheenb, Shahida Qureshib, Mohammad Tahir Yousafzaib, Muhammad Khalid Saleemb, Zahra Hasanb, Gordon Dougana,c, Rumina Hasanb
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Although XDR, this particular strain of Typhoid is not yet completely resistant; it remains susceptible to oral azithromycin.  Other strains in Southeast Asia have already shown resistance to azithromycin, leading to concerns that susceptibility to this last oral antibiotic may eventually fall.

While we've been watching the inroads made by a growing array of antibiotic resistant organisms around the globe for years, for the most part, human infections have been sporadic, and thus far, very few `pan-resistant' infections have emerged.

The past couple of years, however, we've seen an increase in the number and variety of resistant organisms, many exhibiting even broader resistance than before.  A few recent blogs include:

Global AMR Threat: Centrally Approved & Unapproved Antibiotic Formulations Sold In India
WHO: First Global Antimicrobial Surveillance System (GLASS) Report
MMWR: Fatal Pan-Drug Resistant CRE - Nevada 2016
mBio: 1st Colistin & Carbapenem Resistant E. Coli Infection In A U.S. Patient
And last fall CIDRAP reported on a Hypervirulent, highly resistant Klebsiella identified in China, one which a week later was described as New Klebsiella strains 'worst-case scenario,' experts say.
Of particular concern, the enzymes that convey antibiotic resistance can be carried by a plasmid – a snippet of portable DNA  - that can be horizontally transferred to other types of bacteria (see Study: Adaptation Of Plasmids To New Bacterial Species). 
This provides bacteria with a great advantage, as resistance need not develop independently in individual pathogens; it can be shared and passed along to other organisms.
If we're in a war against antibiotic resistance, then the news from the front isn't good.
Salmonella Typhi, the causative agent of Typhoid Fever, is a bacterium that has no known natural reservoir outside of humans. It is usually acquired via the fecal-oral route, often by consuming food or drink that has been handled by someone who is shedding the Salmonella Typhi bacteria.

While still common in some developing countries, Typhoid fever is rarely seen anymore in the United States. The CDC’s Typhoid Fever FAQ states the U.S. sees only about 400 cases of Typhoid each year, of which 3/4ths are brought into this country via international travel.   
Today mBio carries a commentary on last month's study, which the authors describe as `momentous'.  I've only included the abstract, so you'll want to follow the link and read it in its entirety.
When you return, I'll have a postscript.
The Gathering Storm: Is Untreatable Typhoid Fever on the Way?
Myron M. Levinea, Raphael Simona


Klemm et al. (mBio 9:e00105-18, 2018, https://doi.org/10.1128/mBio.00105-18) present comprehensive antibiotic sensitivity patterns and genomic sequence data on Salmonella enterica serovar Typhi blood culture isolates from typhoid fever cases during an epidemic in Pakistan. Microbiologic and genomic data pinpoint the identities and locations of the antimicrobial resistance genes and the outbreak strain’s lineage.
They propose that Salmonella enterica serovar Typhi be added to the list of bacterial pathogens of public health importance that have become extensively drug resistant (XDR). This paper portends possible dire scenarios for typhoid fever control if XDR strains disseminate globally. Since the outbreak strain is of the H58 haplotype, known for its ability to spread worldwide and displace endemic S. Typhi, this concern is well-founded. 
The report of Klemm et al. forewarns the global community to address control of typhoid fever more aggressively through prevention, should therapeutic options disappear. This Commentary frames the Klemm et al. findings within a historic perspective.
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Once a major scourge around the world, deaths from Typhoid Fever have declined greatly since the chlorination of water supplies in industrialized nations began early in the last century, along with the development of effective antibiotic treatments. 

While modern sanitation methods - at least in industrialized nations - may limit the impact of AMR (antimicrobial resistant) Typhoid, the reality is this is just one of a growing array of AMR threats in the wings.
Short of a 1918-style (or worse) pandemic, the rise of antibiotic (and anti-fungal) resistant organisms is likely the greatest public health threat we will face in the next couple of decades.
While I cover AMR topics from time to time, I can heartily recommend CIDRAP's Antimicrobial Stewardship Project as the best place to learn about this looming global threat of AMR.

You'll also want to check out the CIDRAP-ASP Youtube Channel, which has more than 20 hours of lectures and webinars on Antimicrobial stewardship.

Saudi MOH Announces 1 MERS-CoV Case

UPDATED: My thanks to Crof who picked up 2 additional cases posted by the Saudi MOH (also dated the 20th), after I posted this morning's report
The secondary household contact in Jeddah is the second one reported from that city in the last week (see here).  A primary case in nearby Medinah is of note since this is the primary destination for religious pilgrims undertaking Umrah.


After a very spotty month of reporting in February (15 of 28 days), daily MERS updates from the Saudi MOH stabilized late last month, and while often delayed by several days, reports were posted for every day in the first two weeks of March.

As the report list from the MOH (below) shows, reporting has become a bit erratic again over the past week, with only 3 or the last 6 days posted.  While linked, the report of the 16th takes us to a blank page.

Although we are missing reports for the 18th and 19th, today the MOH is reporting a single case from Riyadh, that of a 43 y.o. male in critical condition with a history of recent camel exposure.


Exactly what is behind this recent erratic reporting from the MOH is unclear, but based on other sources (see WHO EMRO MERS-CoV Report - Feb 2018), the number and type of MERS cases in KSA appears to be normal, with 23 cases reported to the WHO in February, and 25 cases in January. 

Unknown are the number of mild, asymptomatic, or misdiagnosed cases in the community (see EID Journal: Estimation of Severe MERS Cases in the Middle East, 2012–2016) - but for now, we aren't seeing any signs of increased transmission of the virus on the Arabian Peninsula.

Sunday, March 18, 2018

Arch. Virology: Co-circulation Of Multiple Genotypes of H7N9 in Eastern China, 2016-2017


While day-to-day reporting on H7N9 (and H5N6) avian flu activity from mainland China has suffered in recent years (at least compared to 2013-14), we continue to get a remarkable flow of quality studies published by Chinese scientists in international journals. 
One of the most remarkable findings we've seen, again and again, is just how much diversity there is in the H7N9 virus. 
Last year a new LPAI Yangtze River Delta lineage became dominant, and a mutated HPAI H7N9 virus emerged in Guangdong Province and began to spread (see MMWR: Increase in Human Infections with Avian Influenza A(H7N9).

H7N9 viruses have also proven themselves to be very promiscuous, reassorting easily with other avian flu viruses, producing numerous new hybrid viruses (genotypes).

Add in a myriad of smaller (although often significant) amino acid changes and the reality is we really don't know how many genetically distinct H7N9 threats there really are in the wild  - we only know that number is large - and getting larger over time.
While most of these variants carry no real evolutionary advantage over the others - and some are likely less biologically fit and doomed to failure - the more variants in circulation, the greater the chances that one will eventually hit the genetic lottery and become a pandemic strain. 
We've a new study (alas, behind a pay wall) published this week in the Archives of Virology that illustrates just how diverse H7N9 has become in Eastern China, with 18 different genotypes identified out of just 41 samples taken in Jiangsu Province.

Equally important, all 41 samples carried the HA G186V and Q226L/I amino acid substitutions, which are linked to switching the virus from binding preferentially to avian (a2,3) receptor cells to mammalian (a2,6) receptor cells.  Some past blogs on these changes include:
PLoS Pathogens: Three Mutations Switch H7N9 To Human-type Receptor Specificity

Sci. Repts: Adaptation of H7N9 in Primary Human Airway Epithelial cells

Eurosurveillance: Genetic Tuning Of Avian H7N9 During Interspecies Transmission
Last year, in Eurosurveillance: Preliminary Epidemiology & Analysis Of Jiangsu's 5th H7N9 Wave, we looked at the study referenced in the opening paragraph of the abstract below. 

Co-circulation of multiple genotypes of influenza A (H7N9) viruses in eastern China, 2016-2017

Xian Qi Email author, Xiaofei An, Yongjun Jiao, Huiyan Yu, Ke Xu, Lunbiao Cui, Shenjiao Wang, Fei Deng, Xiang Huo, Haodi Huang, Qigang Dai, Changjun Bao Email author

First Online: 14 March 2018


Five epidemic waves of human infection with influenza A (H7N9) virus have emerged in China since spring 2013. We previously described the epidemiological characterization of the fifth wave in Jiangsu province.
In this study, 41 H7N9 viruses from patients and live-poultry markets were isolated and sequenced to further elucidate the genetic features of viruses of the fifth wave in Jiangsu province.
Phylogenetic analysis revealed substantial genetic diversity in the internal genes, and 18 genotypes were identified from the 41 H7N9 virus strains. Furthermore, our data revealed that 41 isolates from Jiangsu contained the G186V and Q226L/I mutations in their haemagglutinin (HA) protein, which may increase the ability of these viruses to bind the human receptor. 

Four basic amino acid insertions were not observed in the HA cleavage sites of 167 H7N9 viruses from Jiangsu, which revealed that highly pathogenic avian influenza (HPAI) H7N9 viruses did not spread to Jiangsu province in the fifth wave. 

These findings revealed that multiple genotypes of H7N9 viruses co-circulated in the fifth wave in Jiangsu province, which indicated that the viruses have undergone ongoing evolution with genetic mutation and reassortment. Our study highlights the need to constantly monitor the evolution of H7N9 viruses and reinforce systematic influenza surveillance of humans, birds, and pigs in China.

Despite the surprising lull in H7N9 activity this winter in China, it (or more accurately, `they') remain atop the CDC's Influenza Risk Assessment Tool (IRAT) ranking list of 14 novel flu subtypes/strains that circulate in non-human hosts and are believed to possess some degree of pandemic potential.

H5 Avian Flu Resurfaces At 3 Poultry Farms In South Korea


Avian flu activity this winter has been remarkably subdued in places - like China and South Korea - where in recent years it has flourished.  Remarkably China has only reported three H7N9 cases, and 1 H5N6 case since October. 
Some of this is likely due to China's massive H7+H5 vaccination campaign launched last summer, and the extremely strict bio-security measures taken in South Korea prior to their hosting the Winter Olympics in February.
But part of it is likely due to a newly reassorted H5N6 virus arriving in South Korea this winter - similar to the one now in Europe - which, so far at least - hasn't proven to be as virulent as last year's strain.

In recent weeks - possibly due to the spring northbound bird migration -  we've started to see renewed activity across Europe (see here, here, and here), in Japan (here), and today we learn that at least three large farms in South Korea have been hit in South Korea.
According to the Korean Times (see Bird Flu confirmed at farms in Gyeonggi and South Chungcheong) more than 1.2 million birds have been culled this weekend in affected and surrounding farms and a nationwide 48 hour transport ban on all domestic poultry was ordered on Saturday.
A couple of admittedly syntax-challenged (translated) press releases from South Korea's Ministry of Agriculture (MAFRA) follow:

Pyeongtaek game hens (chickens) AI issued a global economic decision-temporarily move the stop command of the shaft occurs (3.16, deployment)

2018.03.16 23:55:37

Pyeongtaek game hens ( chickens ) AI of the shaft occurs doctor

Match triggered a global temporary stop command to move

- 3 Mon 17 days 00 am to 24 stops moving for a time in Japan and disinfection carried out -

Agriculture, Forestry, Animal Husbandry and Food is 3.16 ( Fri ) Match Pyeongtaek material laying hens ( chickens ) farms in AI inspection results according to the physician shaft occurs H5 antigen , in the same farm minute yangdoen economic Yangzhou material laying hens ( chickens ) Simple inspection of the farms results confirm the positive as , before the game stations temporarily for the stop moving the command was issued .

❍ The date and time that the move 3 0.16 ( Fri ) held Livestock Defense Council ( written hearing ) Based on the results 3.17 ( Sat ) 00 am to 3.17 ( Sat ) 24 pm 24 hours during the being carried out ,

❍ temporarily move to stop Applies the national animal quarantine when integrated system (KAHIS) to about registered 10 thousand places - a .

     * Poultry farms 3,960 points , it slaughterhouses 11 positions , feed mills 102 positions , vehicle 6725 Lighthouse

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Gyeonggi, Chungnam, etc., and a nationwide (excluding Jeju), and the National Association for the Protection of hygiene and the suspension of the temporary move command
    2018.03.17 19:32:41

The Ministry of Agriculture and Livestock farming (the lower farming food) is the ' 18.3.16 ', according to a series of four AI pseudo-axes in the Yangzhou, the province and the 18.3.17, the Asan spawning farm in Chungcheongnam-do, has issued an AI blocking hygiene enhancement action and a pause command to stop nationwide (excluding Jeju).

Anyway is a major preventive measures to prevent the removal of the national spawning system in ① (however, it is taken out upon approval in the admission of livestock Hygiene), ② of the Emergency video conference held by the Ministry of Agriculture, the Deputy Secretary of state (', ③ held the national and Municipalities video conference on the adjustment of the Secretary (' 18.3.18 09:00), ④ nationwide (excluding Jeju-do), and a temporary move to stop command.

The Ministry of Agriculture, the whole country (excluding Jeju), the reason for the suspension of the move, the four-axis doctor on a recent spawning farm, and the mechanics of the vehicle visited by the farmers ․, the facility is distributed nationwide, 

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