Monday, October 21, 2019

Saudi MOH Reports 4th MERS Case For Epi Week 42

Recent Saudi MERS Weekly Totals


The Saudi MOH has reported their 4th MERS case for Epi Week 42, making this the busiest reporting week since mid-July.  While only 4 cases were reported during the month of September, so far October has seen 10 cases identified.
This morning's case, posted sometime late yesterday on the MOH site, is dated October 19th, and involves a 70 y.o. male, listed as a `primary case', with unknown camel contact.

This is the second case reported from Khamis Mushait  - which lies in the far southwest of the country - in less than a week (see Oct 13th report) The first involved a 26 y.o. female, again with unknown camel contact.
Although details in these reports are sparse, both are both listed as `primary' with unknown camel contact. The assumption is they are not epidemiologically linked, and are therefore community acquired cases.
They could have been infected via an environmental contamination (including from local camel products), or perhaps from exposure to a mildly ill or asymptomatic carrier of the virus in the community.
Since the initial signs of MERS infection are often similar to a cold or the flu, differentiating who is - and who isn't - infected can be a extremely difficult, even for doctors used to seeing cases (see Evaluation of a Visual Triage for the Screening of MERS-CoV Patients). 

And while the jury is still out on how much of an infection risk an asymptomatic MERS patient poses, in recent years we've seen increasing evidence suggesting transmission to others is possible. Last December, we looked at:

Asymptomatic Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection: Extent and implications for infection control: A systematic review
Jaffar A.Al-Tawfiq abc Philippe Gautretd

The proportion of asymptomatic MERS cases were detected with increasing frequency as the disease progressed overtime. Those patients were less likely to have comorbid disease and may contribute to the transmission of the virus.

While we've seen a number of large healthcare and household chains of transmission (see Ziad Memish: Two MERS-CoV Hospital Super Spreading Studies), the extent and importance of community chains of transmission remains largely unquantified.

The concern is, as chains of MERS infection increase, so do the number of opportunities for the virus to better adapt to human hosts.  And that, over time, could increase its transmissibility. 
While MERS-CoV hasn't managed to spread the way that SARS did 16 years ago, we've seen studies (see A Pandemic Risk Assessment Of MERS-CoV In Saudi Arabia) suggesting the virus doesn't have all that far to evolve before it could pose a genuine global threat. 
Last year, in the WHO List Of Blueprint Priority Diseases, the World Health Organization listed MERS-CoV listed among the 8 disease threats in need of urgent accelerated research and development.

Sunday, October 20, 2019

The JHCHS #Event201 (Fictional) CAPS Pandemic Scenario

Photo Credit CDC EID Journal


On Friday, Johns Hopkins Center For Health Security (JHCHS) - in concert with the World Economic Forum and the Bill & Melinda Gates Foundation - hosted a half-day table top pandemic exercise (#Event201) in NYC, parts of which were live streamed on the Internet to a couple of hundred people that participated in their own moderated discussions.
Despite some early hiccups in the video feeds (which were resolved quickly), this online discussion was both lively, and informative.
Although opinions over priorities differed, the primary take-away I think was there are no easy solutions in a pandemic. Everything desperately needed is heavily interconnected - essential services (food, water, power, security), healthcare, and vaccine development - and if you shortchange one, you can easily derail the others. 
I look forward to seeing the full exercise when it is released. 
But in the meantime, I thought we'd take a look at the fictional pandemic virus created for use in this week's exercise - CAPS (Coronavirus Acute Pulmonary Syndrome) - and just how plausible a threat this type of virus might be.

Unlike last year's Clade X exercise - which envisioned a genetically altered Nipah virus (spliced onto a parainfluenza backbone) - the fictionalized CAPS virus is a naturally occurring coronavirus (not unlike SARS or MERS) which  originated in bats, but was hosted by, and emerged from pigs.

The JHCHS Ecent 201 scenario reads:

The Event 201 scenario

Event 201 simulates an outbreak of a novel zoonotic coronavirus transmitted from bats to pigs to people that eventually becomes efficiently transmissible from person to person, leading to a severe pandemic. The pathogen and the disease it causes are modeled largely on SARS, but it is more transmissible in the community setting by people with mild symptoms.

The disease starts in pig farms in Brazil, quietly and slowly at first, but then it starts to spread more rapidly in healthcare settings. When it starts to spread efficiently from person to person in the low-income, densely packed neighborhoods of some of the megacities in South America, the epidemic explodes. It is first exported by air travel to Portugal, the United States, and China and then to many other countries. Although at first some countries are able to control it, it continues to spread and be reintroduced, and eventually no country can maintain control.

There is no possibility of a vaccine being available in the first year. There is a fictional antiviral drug that can help the sick but not significantly limit spread of the disease.

Since the whole human population is susceptible, during the initial months of the pandemic, the cumulative number of cases increases exponentially, doubling every week. And as the cases and deaths accumulate, the economic and societal consequences become increasingly severe.

The scenario ends at the 18-month point, with 65 million deaths. The pandemic is beginning to slow due to the decreasing number of susceptible people. The pandemic will continue at some rate until there is an effective vaccine or until 80-90 % of the global population has been exposed. From that point on, it is likely to be an endemic childhood disease.
They fleshed out this fictional pathogen even further in a document called CAPS: The Pathogen and Clinical Syndrome (PDF), including:
  • Approximately 50% of CAPS cases require hospitalization, many of them in an intensive care unit (ICU).
  • The CAPS fatality rate in hospitalized patients is about 14%.
  • The overall case fatality rate (CFR) is 7%.
  • The average R 0 is 1.74.
  • The incubation period ranges from 5 to 7 days.
Essentially, something a bit more transmissible, but comparable in severity to the 2003 SARS epidemic - but not as deadly as the current, albeit highly scattered outbreaks of MERS we've seen over the past 7 years.
The choice of pigs as intermediary hosts is highly plausible. There are already several porcine coronaviruses circulating in pigs, which has raised concerns over their ability to further expand their host range (see SECD: Another Emerging Coronavirus Threat).

Two years ago, in EID Journal: A New Bat-HKU2–like Coronavirus in Swine, China, 2017, we saw a study that described the recent discovery of a new HKU2-like coronavirus in Chinese pigs showing symptoms of PED, which had tested negative for the usual suspects.
HKU2 is one of a number of coronaviruses discovered in the wild (in this case, in Horseshoe bats) by Hong Kong researchers in the years immediately following the SARS epidemic.
As pigs are physiologically fairly close to humans (if that bothers you, think how the pig feels), we watch porcine adapted viruses with particular interest. Even more so when they are descendant from bats, which tends to up the ante (see Curr. Opinion Virology: Viruses In Bats & Potential Spillover To Animals And Humans).
A non-influenza pandemic virus - such as envisioned by Clade X and Event 201 - complicates the pandemic response immensely. 
When graded on the curve, we're pretty good at creating, and manufacturing influenza vaccines. Producing an emergency influenza pandemic vaccine in quantity within the first year - while fraught with difficulties (see Pandemic Flu Vaccines: Easier Said Than Done) - is at least technically possible.

But scientists have been trying to create a SARS coronavirus vaccine for 15 years, and a MERS-CoV vaccine for the past 7 years, and so far no safe and effective vaccine has been created. 
We might get lucky, and a breakthrough could happen, but it is doubtful. 
At this point, I would remind my readers that nearly every `pandemic Plan' drafted by U.S. states (and many nations) over the past 15 years envisions a less  than 2% fatality rate, the availability of effective antivirals, and a vaccine being produced starting after about 6 months.

Like generals always planning to fight the last war, we seem fixed on the notion that the next pandemic will be very much like the last two (2009 and 1968), which paled in comparison to 1918. 
Once again, we could get lucky.  But at some point, that luck will run out. 
While the outcome at 18 months in this pandemic scenario (65 million deaths) is horrific, it isn't the worst case scenario. And it isn't clear from the exercise materials how many collateral deaths - those not directly related to virus - would occur. 
But what is clear is we are far from being ready to deal with a severe pandemic. Even one half as bad as the one depicted in Event 201.
Just over a decade ago, then Secretary of HHS Michael O. Leavitt famously said:
"Any community that fails to prepare with the expectation that somehow the federal government will come to their rescue at the last moment will be tragically disappointed."
Hopefully pandemic exercises like Event 201 and Clade X will help convince business, government, and community leaders to revive our long-neglected pandemic preparedness programs before the clock runs out again. 

For more on the Event 2001 Table top exercise, you may wish to visit their resources page:
Communication in a pandemic (PDF)
Event 201 Model (PDF)
Finance in a pandemic (PDF)
Medical countermeasures (PDF)

Saturday, October 19, 2019

More Reports of Pig and Poultry Die Offs In Indonesia


Indonesia - once the world's hotbed for avian flu - has reported very little bird flu activity over the past few years, as the local strains of H5N1 appear to have attenuated over time due to viral mixing, and the use of poultry vaccines may have masked symptoms of infection.
Indonesia's last reported human H5N1 infection was in 2017, but the virus is still endemic in the region. 
Several days ago, in Watching Indonesia Again For Avian Flu, we saw a flurry of media reports of poultry die offs in Tegal city, in central Java, that were assumed to be due to avian flu.  Since then, other communities (including Ceribon and Brebes) have reported large, sudden losses of poultry. 

Testing is reportedly underway, at least on some of the birds, as many were quickly burned and buried by locals. Results could take a week or longer to be made public.

 Several (translated) reports from Indonesian media follow:

Hundreds of Chickens Got Bird Flu
Smith's Sulastro

Radar Tegal - Issue October 19, 2019

Hundreds of chickens on the farm in the village of Rengaspendawa, District Prohibition of suspected bird flu. The hundreds of chickens died suddenly for no apparent reason.

Head of the Department of Animal Husbandry and Animal Health (DPKH) Brebes, Ismu Subroto said it was doing research related to the present invention. And the result was suspect bird flu, because there has been no confirmation of the diagnosis.

(Continue . . . )

Allegedly Got Bird Flu, Hundreds of Chickens in Brebes Sudden Death
BREBES - Hundreds of chickens on one farm in Brebes suddenly died. Events that occurred recently thought to be caused by bird flu disease that attacks the hundreds of chickens.
        (Continue . . .)

Government Investigate Bird Flu in South Tegal
Radar Banyumas Saturday, October 19, 2019
Tegal - After dozens of deaths and culling of chickens due to bird flu, a team from the Directorate General of Livestock and Animal Health (PKH) Center for Veterinary Wates, Yogyakarta went to the location in the Village findings Keturen District of South Tegal Tegal City on Thursday (17/10) afternoon. They want to take blood samples of poultry remaining in the local area.
        (Continue . . .)

Screen Shot From local TV Coverage

At this point, it isn't clear whether this is a resurfacing of Indonesia's existing H5N1, a new reassortment, or perhaps a different subtype entirely. Indonesia lies under the East Asian-Australian Flyway migratory bird flyway, and has yet to deal with H5N8 or H5N6, which has plagued other countries in the past few years.

Meanwhile, reports of pig die offs continue as well (see last week's Indonesia: Media Reports Of Unexplained Pig Deaths In Multiple Regions), with concerns that they may be due to either Classical Swine Fever (CSF) or African Swine Fever (ASF). A search in Bahasa for `dead pigs' (`Babi Mati') returns several new reports, including:

Pig Tails 1,000 Dead in Dairi, Stock Disinfectant Thinning
Every day, the number of dead pigs, increases. There is a possibility, threatening the population of 110,000 head of pigs in Dairi.

Dairi - The death of pigs in Dairi, North Sumatra, has been in the category of an outbreak.

Data compiled, according reports from the public, as of October 17, 2019, the number of 1,004 dead pigs tail. Material losses estimated at Rp 700 million.

Every day, the number of dead pigs, increases. There is a possibility, threatening the population of 110,000 head of pigs in Dairi.

This type of virus, has yet been found. 12 samples examined Institute of Veterinary Regional I Medan , three positive samples of hog cholera. 9 samples again, unconfirmed, but the suspect (allegedly) African Swine Fever (ASF).

(Continue . . . .)
While ASF isn't a human health threat, it is a serious threat to the agricultural economy and to local food security, and pigs deaths can also signal other, equally concerning infections. 
Surveillance, testing, and reporting out of Indonesia - particularly since the eviction of our NAMRU (Naval Medical Research Unit) 2 lab  a decade ago - has been spotty at best. 
Hopefully we'll get some solid information on these two (likely, unrelated) outbreaks sooner rather than later.

Friday, October 18, 2019

WHO EMRO MERS-CoV Summary - September, 2019


Although we've already seen 7 cases reported in the first 17 days of October, only 4 MERS infections were reported globally during the month of September, all hailing from Saudi Arabia.
While this reduced MERS activity is welcomed, over the past year new questions have been raised over the ability of current surveillance systems to identify mildly symptomatic, asymptomatic, or atypically presenting MERS infections in the community.

A few of those studies include:
J. Korean Med Sci: Atypical Presentation Of A MERS Case In A Returning Traveler From Kuwait

mBio: High Prevalence of MERS-CoV Infection in Camel Workers in Saudi Arabia

AJIC:Intermittent Positive Testing For MERS-CoV

JIDC: Atypical Presentation Of MERS-CoV In A Lebanese Patient
And just over a year ago - in Evaluation of a Visual Triage for the Screening of MERS-CoV Patients - we looked at what has been described as a serious flaw in Saudi Arabia's MERS surveillance program.

Once a month the WHO's EMRO (Eastern Mediterranean Regional Office) provides a summary of MERS activity in the Middle East - and around the world - based on what is officially reported by individual Ministries of Health to the World Health Organization.
Details of the September summary report follow:

MERS situation update, September 2019 
  • At the end of September 2019, a total of 2468 laboratory-confirmed cases of Middle East respiratory syndrome (MERS), including 851 associated deaths (case–fatality rate: 34.4%) were reported globally; the majority of these cases were reported from Saudi Arabia (2077 cases, including 773 related deaths with a case–fatality rate of 37.2%).
  • During the month of September, a total of 4 laboratory-confirmed cases of MERS were reported globally. All the 4 cases were reported from Saudi Arabia with 1 associated death. No cluster of cases was reported this month. All of the cases had their symptoms onset in September. The reported cases were between 39 and 74 years of age and all were male. No healthcare workers were affected this month.
  • The demographic and epidemiological characteristics of reported cases, when compared during the same corresponding period of 2014 to 2019, do not show any significant difference or change. The number of cases reported in this period was more than 2018, but significantly less than the 2014-2017 corresponding period.
  • The age group 50–59 years continues to be at the highest risk for acquiring infection of primary cases. The age group 30–39 years is most at risk for secondary cases. The number of deaths is higher in the age group 50–59 years for primary cases and 70–79 years for secondary cases.
Read the latest MERS update for September 2019

Subscribe to the Infectious Hazard Management monthly e-mail update for the latest data and analysis.

CDC Update On Acute Lung Injuries LInked To Vaping (Oct 17th)

Credit CDC


The CDC's investigation into unexplained acute pulmonary illnesses linked to using e-cigarettes (see CDC Clinical Action: Unexplained Vaping-Associated Pulmonary Illness) has entered its 3rd month and as more doctors become aware of the symptoms, the number of identified cases continues to rise.
Although the numbers thus far affected are relatively small compared to the number of people using e-cigs - until the cause can be identified (and hopefully eliminated) -  the entire industry remains under a cloud.
Last week the CDC released updated Interim Guidance in the MMWR for clinicians, and yesterday held a COCA Call to review the recommendations.

Excerpts from latest CDC update, posted yesterday, follow:

Outbreak of Lung Injury Associated with E-Cigarette Use, or Vaping

Updated October 17, 2019 at 3:00 PM ET

What We Know
  • As of October 15, 2019, 1,479* lung injury cases associated with the use of e-cigarette, or vaping, products have been reported to CDC from 49 states (all except Alaska), the District of Columbia, and 1 U.S. territory.
  • Thirty-three deaths have been confirmed in 24 states.
  • All patients have reported a history of using e-cigarette, or vaping, products.
  • We do know that THC is present in most of the samples tested by FDA to date, and most patients report a history of using THC-containing products.
  • The latest national and state findings suggest products containing THC, particularly those obtained off the street or from other informal sources (e.g. friends, family members, illicit dealers), are linked to most of the cases and play a major role in the outbreak.
  • As such, we recommend that you should not use e-cigarette, or vaping, products that contain THC.
  • Since the specific causes or causes of lung injury are not yet known, the only way to assure that you are not at risk while the investigation continues is to consider refraining from use of all e-cigarette, or vaping, products
  • The use of e-cigarettes, or vaping, products is unsafe for all ages, including youth and young adults. Nicotine is highly addictive and can harm adolescent brain development, which continues into the early to mid-20s.

What We Don't Know
  • At this time, FDA and CDC have not identified the cause or causes of the lung injuries in these cases, and the only commonality among all cases is that patients report the use of e-cigarette, or vaping, products.
  • No one compound or ingredient has emerged as the cause of these illnesses to date; and it may be that there is more than one cause of this outbreak. Many different substances and product sources are still under investigation. The specific chemical exposure(s) causing lung injuries associated with e-cigarette product use, or vaping, remains unknown at this time

What CDC Recommends

Thursday, October 17, 2019

NHC Watching A Late Season Tropical Disturbance


Although the models don't make it into much of a threat, late season storms can be unpredictable, and so interests along the northern and eastern Gulf of Mexico need to keep an eye on an area of suspicion in the Bay of Campeche which the National Hurricane Center is giving an 80% chance of further development.

Tropical Weather Outlook
NWS National Hurricane Center Miami FL
800 AM EDT Thu Oct 17 2019 For the North Atlantic...Caribbean Sea and the Gulf of Mexico:
1. Showers and thunderstorms associated with a broad area of low pressure located over the southwestern Gulf of Mexico continue to show signs of organization. Environmental conditions are expected to be conducive for additional development, and a tropical or subtropical storm is likely to form later today or tonight while the system moves generally northeastward over the western Gulf of Mexico.
The low is forecast to approach the northern or northeastern Gulf Coast on Friday or Saturday and regardless of development, the system is likely to produce gusty winds and rough surf over those areas. Locally heavy rainfall is also possible across portions of the southeast U.S. late this week and this weekend. Interests along the northern and northeastern Gulf coast should monitor the progress of this system. For more information about marine hazards while the low moves across the Gulf of Mexico, see products issued by the Tropical Analysis and Forecast Branch of the National Hurricane Center.
An Air Force Reserve reconnaissance aircraft is scheduled to investigate the system this afternoon, if necessary.
* Formation chance through 48 hours...high...80 percent.
* Formation chance through 5 days...high...80 percent.
A reminder that the Atlantic Hurricane Season extends to November 30th, and while we are past the peak of the season, serious storms are still possible.