Sunday, July 21, 2019

Saudi MOH Reports 4th MERS Case For Epi Week 29


For the second month in a row (see last month's WHO EMRO MERS-CoV Summary - May, 2019) the WHO's monthly MERS Outbreak Summary - which is normally published around the 10th of the month - is running late.  Last month it appeared on the 18th, while this month it is running even later, and has yet to show. 
Delays and interruptions in MERS reporting from KSA have been fairly common - last summer they went more than 2 months without an update (see The Saudi MOH Breaks Their Silence On MERS-CoV) - and only rarely do we get an explanation.
While reported MERS activity has slowed, we do have a 4th case reported (yesterday) for Epi Week 29, making it the busiest month since early June.

Once again it is a primary case (M,58), with unknown exposure, this time in the southern city of Najran.

We are now less than 3 weeks from the start of the Hajj, when roughly 2 million religious pilgrims from all over the world will make the journey to the holy cities of Mecca and Medina.

Six years ago, in MERS, Mass Gatherings & Public Health, we looked at some of the immense challenges that Saudi Arabia faces each year with the Hajj.  

Emergence of medicine for mass gatherings: lessons from the Hajj

Prof Ziad A Memish MD , Gwen M Stephens MD, Prof Robert Steffen MD , Qanta A Ahmed MD
Within the immediate vicinity of the Hajj, there are 141 primary health-care centres and 24 hospitals with a total capacity of 4964 beds including 547 beds for critical care. The latest emergency management medical systems were installed in 136 health-care centres and staffed with 17 609 specialised personnel. More than 15 000 doctors and nurses provide services, all at no charge.
In 2015's EID Journal: ARI’s In Travelers Returning From The Middle East, researchers found respiratory infections are the most commonly reported illness among religious pilgrims. This study also found that:
`Pneumonia is the leading cause of hospitalization at Hajj, accounting for approximately 20% of diagnoses on admission.’
This sort of `viral noise' can make it difficult to identify and isolate those infected with MERS (see BMC Inf. Dis.: Clinical Management Of Suspected MERS-CoV Cases).

While we've been lucky in the past, with no large MERS outbreaks linked to the Hajj or Ramadan, the possibility of seeing one or more infected pilgrims returning home while silently carrying the virus remains a yearly concern.

NHC Watching The Tropics


Although the NHC only gives it a low (20%) chance of development over the next 5 days -  and the latest GFS and EURO model runs don't `see' it yet - this is the time of year when storm formation often occurs close in to land (see July Tropical Climatology), which can allow only limited time to prepare.

This morning's tropical outlook advises interests in the Central and Northern Bahamas, along with the southern Florida peninsula and the Florida Keys to monitor the progress of this system.


Tropical Weather Outlook 
NWS National Hurricane Center Miami FL 

200 AM EDT Sun Jul 21 2019 For the North Atlantic...Caribbean Sea and the Gulf of Mexico:
1. A tropical wave located about 300 miles east of the Central Bahamas is producing disorganized showers and a few thunderstorms. Although environmental conditions are currently unfavorable for development, they are expected to become a little more conducive over the next few days while the disturbance moves westward at 10 to 15 mph. Interests in the Central and Northwest Bahamas, and the southern Florida peninsula and the Florida Keys should monitor the progress of this system. 
* Formation chance through 48 hours...low...10 percent.
* Formation chance through 5 days...low...20 percent. 
Forecaster Stewart

If you live anywhere where in `hurricane country' and haven't done so already,  now is a good time to visit NOAA's Weather-Ready Nation  2019's Hurricane Preparedness week web page, and decide what you need to do now to keep you, your family, and your property safe during the coming tropical season.
While this blog, and many other internet sources, will cover this year's hurricane season your primary source of forecast information should always be the National Hurricane Center in Miami, Florida. 
These are the real experts, and the only ones you should rely on to track and forecast the storm.
If you are on Twitter, you should also follow @FEMA, @NHC_Atlantic, @NHC_Pacific and @ReadyGov and of course take direction from your local Emergency Management Office.  

For some recent blogs on preparing for hurricanes - and other major disasters - you may wish to revisit:

CDC EPIC: Hurricane Preparedness Webinar
What Lies Beneath (the flood waters)
7 Days Without A Disaster Kit Makes One Weak
Preparedness: Some Emergency Power Solutions

CDC Yellow Book 2020 Edition Now Online


Every two years the CDC updates and publishes their `Yellow Book’,  a reference for those who advise international travelers about health risks.  As international travel increases, so do the chances that travelers will contract and transport diseases from one area of the globe to another.  

Which means that doctors just about anywhere in the world are faced with advising patients on how to avoid (or worse, must diagnose when they return) rarely seen or unusual diseases like Chikungunya, Zika, Dengue, and Cholera.  
While written primarily for Health Care providers, the Yellow Book is a tremendously valuable resource for all, and I confess I use it often as a reference for this blog. You find it chock full of maps, charts, and advice and information on everything from Amebiasis to Zika, and scores of infectious diseases in-between.  
For those who will refer to it often, a hard copy is available from the Oxford University Press.  You can also order a copy from online booksellers such as Amazon and Barnes & Noble. 
But for casual users, or those on a budget, the full text of the the 2018 Yellow Book is now available online on the CDC's website.  They describe what's new in this new edition:

About the Yellow Book

CDC's Yellow Book (Health Information for International Travel) is published every two years as a resource for health professionals providing care to international travelers. The fully revised and updated CDC Yellow Book 2020 compiles the US government’s most current travel health guidelines, including pretravel vaccine recommendations, destination-specific health advice, and easy-to-reference maps, tables, and charts.

The 2020 Yellow Book includes important travel medicine updates:
  • Recommendations for providing travel health care remotely via telemedicine
  • Discussion of legal issues facing clinicians providing travel health care
  • Cutting-edge rapid diagnostic tests for infectious diseases
  • Introduction of new FDA-approved antimalarial drugs
  • Road traffic safety advice for travelers
  • Recommendations for treating infectious diseases in the face of increasing antimicrobial resistance

Not to be out done, the FDA also publishes a less frequently updated `Bad Bug Book' (last updated in 2012) - which you can download as a PDF -  more formally known as:

Foodborne Pathogenic Microorganisms and Natural Toxins Handbook

 Download the Bad Bug Book 2nd Edition in PDF (2.6MB)

The Bad Bug Book 2nd Edition, released in 2012, provides current information about the major known agents that cause foodborne illness.

Each chapter in this book is about a pathogen—a bacterium, virus, or parasite—or a natural toxin that can contaminate food and cause illness. The book contains scientific and technical information about the major pathogens that cause these kinds of illnesses.
A separate “consumer box” in each chapter provides non-technical information, in everyday language. The boxes describe plainly what can make you sick and, more important, how to prevent it.
The information provided in this handbook is abbreviated and general in nature, and is intended for practical use. It is not intended to be a comprehensive scientific or clinical reference.
The Bad Bug Book is published by the Center for Food Safety and Applied Nutrition (CFSAN) of the Food and Drug Administration (FDA), U.S. Department of Health and Human Services.

Saturday, July 20, 2019

Iowa Announces Enhanced Biosecurity For Swine Exhibitors At State Fair
How ASF Spreads


Each summer and fall for nearly a decade we've seen sporadic cases of human infection with swine variant influenza which appear to jump from pigs to humans primarily at state and county fairs (see chart below). 

Swine Variant Human Cases : 2010-2018  - Credit CDC
While cases are likely severely under-counted, over the past 15 years we've seen more than 460 confirmed human infections with these swine-origin flu viruses, with 2/3rds of those reported in 2012.

The CDC's general risk assessment of these swine variant (H1N1v, H1N2v, H3N2v) viruses reads:

CDC Assessment

Sporadic infections and even localized outbreaks among people with variant influenza viruses may occur. All influenza viruses have the capacity to change and it’s possible that variant viruses may change such that they infect people easily and spread easily from person-to-person. The Centers for Disease Control and Prevention (CDC) continues to monitor closely for variant influenza virus infections and will report cases of H3N2v and other variant influenza viruses weekly in FluView and on the case count tables on this website
Seven weeks ago we saw the first reported case of 2019 (see CDC FluView Week 21: 1 Novel (H1N1v) Flu Infection - Michigan)- in an adult > 65 years of age who, a bit unusually, reported no recent contact with live pigs.

While it is too soon to know how much of an impact swine variant flu will have this summer, there is another swine disease that has agricultural interests on edge this summer; African Swine Fever.
And while ASF doesn't infect humans, should it arrive here it could devastate North America's swine industry, much as it already has in Eastern Europe, China, and more recently, Southeast Asia
Nine weeks ago, in USDA Enhances Domestic ASF Surveillance Efforts, we looked at plans for enhanced testing and surveillance for ASF in American pigs, in hopes of detecting - and stamping out - any infections as early as possible.

The USDA also recently released a 28-page ASF response plan, in the event  the virus turns up on American soil.

Early detection and eradication of the virus are key, and so the health of pigs being exhibited at county and state fairs this year are under even greater scrutiny than before.
Three weeks ago we saw the Pennsylvania Ag Dept.: Announce New Rules For Swine Exhibits Due to ASF Threat.
Yesterday, Iowa's Department of Agriculture and Land Stewardship announced their own biosecurity rules for the Iowa State Fair which will open for 11 days starting on August 8th.
Iowa Department of Agriculture and Iowa State Fair Announce Enhanced Biosecurity Requirements for Swine Livestock Exhibitors

DES MOINES, Iowa (July 19, 2019) — Iowa Secretary of Agriculture Mike Naig, State Veterinarian Dr. Jeff Kaisand, and Iowa State Fair officials today announced new animal health inspection requirements for swine exhibitors at the 2019 Iowa State Fair.
  1. All swine must be individually inspected and identified on a Certificate of Veterinary Inspection that was completed within seven (7) days of the Iowa State Fair.
  2. A veterinarian will inspect all swine upon arrival at the Iowa State Fairgrounds before they are unloaded from the truck or mixed with other livestock on-site.
These additional exhibition requirements were developed with input from veterinarians and other third-party experts. They are designed to promote biosecurity and animal health as African Swine Fever (ASF) continues to spread across China and other parts of Asia and Europe.

“We are working with other state and federal agencies and industry partners to monitor the ASF situation and educate producers about biosecurity,” said Secretary Naig. “While the disease does not pose a human health or food safety threat, it would be detrimental to Iowa’s pork industry and the state’s economy. That’s why we’re implementing additional biosecurity measures for all swine exhibitors at this year’s Fair.”

While African Swine Fever is top of mind, the Department of Agriculture stresses the importance of following proper biosecurity protocols — with all species of animals — every day to protect Iowa’s livestock.

“All exhibitors are encouraged to practice good biosecurity both at the show and at home on the farm,” said Dr. Kaisand. “When exhibitors return home from the Fair, they should disinfect their equipment, isolate animals that traveled to the show from the rest of the herd, and monitor for signs of illness.”

Protecting the health of Iowa’s livestock and the state’s ag-based economy are top priorities for the Department of Agriculture and Fair organizers.

“We value Iowa’s largest industry, agriculture, and recognize the importance of comprehensive biosecurity practices,” said Gary Slater, CEO and Fair Manager. “We work in partnership with IDALS and our state veterinarians to maintain the highest standards for our livestock exhibitors and the animals they bring to show at the Fair.”
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While the arrival of ASF to North America is far from inevitable, it wouldn't be without precedent. Foreign Animal Dieases (FADs) - such as such as highly pathogenic avian influenza (HPAI), Virulent Newcastle disease (vND), and foot-and-mouth disease (FMD) - have in the past, and remain a constant threat.  

Six years ago we saw the arrival of another, far less dangerous porcine virus - PEDV - which is believed to have originated from China (see mBio: PEDV - Porcine Epidemic Diarrhea Virus – An Emerging Coronavirus).
Of course, we aren't always on the receiving end.
In January of this year China saw the first arrival of the Fall Armyworm,  a highly destructive crop pest native to North & South America (see Update: Fall Armyworm Now in 15 of China’s Provinces). In June they were reported in Taiwan, and Japan reported their first occurrence in early July.
One of the realities of our highly mobile and interconnected 21st century is the ease by which both human and agricultural diseases can spread.  Oceans and extended travel times no longer protect us as they once did.
While we tend to worry most about human diseases, agricultural diseases - like bird flu, swine fever, and FMD - can inflict crippling economic blows.
Add in crop failures due to increasing climate instability, and you have the ingredients for seeing increased food insecurity - and political instability - around the globe.
And that can have can have every bit as much impact on human health as a pandemic.

Friday, July 19, 2019

Virginia DOH Warns Residents of Increase in Respiratory Illnesses



We've been following the outbreak of an as-yet-unidentified respiratory illness at a Virginia Long Term Care Facility over the past week (see Virginia: (Jul 16th) Update On Outbreak Of Respiratory Illness At An LTC); one that has hospitalized at least 23 residents, killing two.

Today the Virginia Department of Health published the following press release citing an unusually high number of summer respiratory illnesses across the state from a variety of causes.

Virginia Department of Health Warns Residents of Increase in Respiratory Illnesses
July 19, 2019

For More Information Contact
Lorrie Andrew-Spear – 703-530-2627 –

Virginia Department of Health Warns Residents of Increase in Respiratory Illnesses
Anyone Experiencing Difficulty Breathing Should Seek Medical Care

(Richmond, Va.) – Since the end of flu season in May, the Virginia Department of Health has received increased reports of respiratory (breathing) illness across the Commonwealth greater than observed in previous summers. Most of the reports have occurred among older adults and those with chronic medical conditions in assisted living and long-term care facilities.
The reports involve different regions of the state and different diseases, including pertussis (whooping cough), influenza, Haemophilus influenzae infection, Legionnaire’s disease, and pneumonia caused by rhinovirus or human metapneumovirus.

“A variety of germs cause respiratory illness, some with increased activity in summer months” said State Health Commissioner M. Norman Oliver, MD, MA. “We encourage everyone to take steps to minimize the severity and prevent spreading illness to others.”

Dr. Oliver continued, “To avoid getting sick and spreading germs to others, it is important to wash hands thoroughly with soap and water, especially after coughing or sneezing. To help prevent the spread of germs, avoid close contact with people who are sick. Anyone who is sick should stay home, except when seeking medical care. If you develop difficulty breathing or shortness of breath, immediately seek medical care.”

Certain groups are especially vulnerable for developing severe respiratory illness, including young children, adults 65 years or older, those with chronic medical conditions (such as asthma, chronic obstructive pulmonary disease, and heart conditions) and those with weakened immune systems.

It is worth noting that the Southwest Nebraska Public Health Department (SWNPHD) issued an alert two days ago due to an unseasonal increase in influenza B cases as well.
A reminder of the importance of practicing good flu hygiene all year round, not just during the traditional winter flu season.  
Meanwhile, the cause of the Fairfax LTLF (Greenspring) outbreak remains under investigation, as does another, smaller outbreak at a different facility (Heatherwood), which is not currently believed connected.

This from the Fairfax County Health Department:
Outbreak Investigation at Assisted Living Facility in Springfield 
Update: July 19, 2019

The Fairfax County Health Department continues to monitor and work with Greenspring to institute appropriate prevention measures to stop further illnesses and those actions are having a positive result. In the assisted living and skilled nursing areas (Garden Ridge), there have been no illnesses reported for the last few days and residents who have been ill are recovering.

In the independent living section of Greenspring, which includes approximately 1,700 residents and is located in separate buildings from Garden Ridge, there is no outbreak of respiratory illness. While there is some illness in the independent living section, it is not considered to be an unexpected or unusual number of ill residents. Some illness is to be expected in a community of this size for older residents.

Because of the outbreak in the assisted living and skilled nursing sections, Greenspring has instituted enhanced surveillance for illness in the independent living areas. Infection control measures, implemented in the independent area out of abundance of caution, include temporarily stopping group activities, other than dining, and screening residents for illness as they arrive at the dining rooms. Residents have been informed of the respiratory illness in the Garden Ridge area by robo calls and on the internal website and have been asked to self-report any symptoms to the facility administration.
Independent living residents have been asked to not visit the Garden Ridge section, and to self-isolate if they are ill. Extra cleaning of high-touch surfaces and communal areas is in place.

Additional laboratory testing from CDC has not identified a specific cause for the increase in respiratory illness. Test results showed several bacteria that are known to colonize the nose and throat and may not be the cause of infection. In addition, several specimens were positive for rhinovirus, the cause of the common cold.

We will continue to monitor the situation and support the facility in its efforts to prevent further illness.
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UK DEFRA: Updated Outbreak Assessment (#02) African Swine fever in Europe


While the arrival of African Swine Fever in China last summer - and its subsequent spread across Southeast Asia - has been the big ASF story of late, the virus appeared in the Republic of Georgia in 2007 (see African Swine Fever Virus Isolate, Georgia, 2007), possibly brought in by ASFV contaminated feed products.
Within 6 months of its arrival, the virus was detected in the Russian Federation (cite), and by 2014 had been detected in 4 EU countries.
Over the past couple of years we've seen the ASF virus increase its rate of spread across Eastern Europe and much of Russia. 
Last September the virus was found in wild boar in Belgium - signifying a westward jump of more than 500 km (see OIE Notification: African Swine Fever Jumps To Belgium) - raising the stakes for all of western Europe.
While ASF doesn't pose a direct threat to human health, its continued spread in Asia and Eastern Europe poses an existential threat to their pork industry, as the virus is often 100% fatal in pigs, and no vaccine is currently available.

Below we have the UK's latest DEFRA (Department for Environment, Food and Rural Affairs) update on ASF activity in Eastern Europe.  After reporting a slowdown in cases earlier this spring, DEFRA now reports a substantial jump in detections which began in June.

I've only included some excerpts from the full report, so follow the link to read it in its entirety.

Updated Outbreak Assessment #02
African Swine fever in Europe (Eastern Europe & Belgium)

18 July 2019
Ref: VITT/1200 ASF in Europe (Eastern Europe & Belgium)

Disease report

Since our last report on the 25 th June 2019, there have been new outbreaks of ASF in domestic pigs in Eastern Europe, and further cases in wild boar in both Eastern Europe and Belgium.
The numbers of outbreaks in domestic pigs (backyard and commercial) since January 2019 are summarised in Table 1 for each affected country.

Generally, there has continued to be low number of outbreaks reported in domestic pigs since January 2019, though there have been notable increases observed in Romania (205) and Bulgaria (15). Other reports in July to date are restricted to Poland (11), Lithuania (5), Latvia (1), Russia (3) and Ukraine (5). The largest number of outbreaks in domestic pigs each month continues to be in Romania, mainly in backyard pig small-holdings, though since our last report on the 25 th of June, there have been an additional 281 outbreaks in small commercial holdings.
The number of cases in wild boar continues to be high in Poland, with 114 cases in June and 65 in July so far, while cases in Hungary appear to be continuing a downward trend (Table 2). Generally, the number of reported cases in wild boar in Eastern Europe has been decreasing through 2019, though further monitoring is required to confirm if this indicates a trend or is simply due to seasonality, as this does not match the recent increase observed in outbreaks in domestic pigs.
There have been no new large geographical jumps so far in 2019, and increased numbers of ASF-positive domestic pigs may be related to local spread or increased surveillance activities. The last significant jump of ASF within Europe was the emergence of ASF in Belgium in September 2018, where there have been 825 cases of ASF in wild boar (reports of ASF in wild boar to 16/07/2019 (Wallonie, 2019).
In June 2019, as part of their routine activities, port authorities in Northern Ireland seized a total of 300 kg of meat and dairy products illegally brought into NI by passengers during the month. A sample of one of these seizures; a sausage originating from Asia, was tested at the Agri-Food and Biosciences Institute (AFBI), resulting in the detection of ASF virus DNA fragments.
Though the presence of ASF DNA does not necessarily mean that the meat was infectious, it further underlines the potential risk to the UK from pork and pork products being brought illegally into the country by international air passengers.
Situation assessment
Eastern Europe is continuing to report outbreaks of ASF in domestic pigs, although this appears to be restricted to the south-east countries in the region; namely Ukraine, and Romania, with a small number of outbreaks reported in Bulgaria, Lithuania, Latvia, Poland and Russia. However, while control efforts may be reducing incidence in domestic pigs (with the exception of Romania and Bulgaria), the wild boar population represents a significant reservoir in Eastern Europe which may hinder eradication, and serve as a source for further geographic jumps, along with the potential for arthropod vectors of disease to contribute.


There has been an increase in the number of outbreaks reported in domestic pigs in Eastern Europe in June compared to recent months, indicating that the disease is still present across much of the region, with large numbers of cases in wild boar continuing. Given the ongoing situation in Eastern Europe, continued reports of ASF in wild boar in Belgium, as well as the ongoing disease situation in South East Asia, the risk therefore remains at medium for the entry of contaminated or infected products into UK.

The risk of exposure to the pig population in the UK is still highly dependent on the level of biosecurity on individual pig premises but is still considered to be low, although the situation is being kept under review.
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