Monday, November 18, 2019

Saudi MOH announces 198th MERS Case Of 2019


The Saudi MOH has announced the first new case of Epi Week #47, involving a 71 y.o. male with recent camel contact from Al Khormah, very near the city of Taif.

This is the 10th case reported during the month of November, and continues a recent uptick in cases that began in early October. 

African Swine Fever's (ASF) Other Impacts; Pharmaceuticals, Bushmeat, and Food Insecurity
Credit FAO


African Swine Fever (ASF) and Classical Swine Fever (CSF) continue to spread globally, and endanger anywhere from 25% to 50% of the world's pig supply.
Already, it has been estimated that half of China's pigs have been lost to ASF and much of their food supply has been contaminated (see Australia: Agriculture Minister - 49% Of September Seized Pork Tests Positive for ASF).
While China only reports (163 ASF outbreaks detected in 32 Provinces / Autonomous Regions / Municipalities / Special Administrative Region, about 1,192,000 pigs have been culled - cite Nov 14th FAO Update), outside experts put the real number 200 times higher.  
Although ASF and CSF pose no direct threat to human health, the loss of 200 million pigs has driven the price of pork sky high in China, and in some regions pork - even if you can afford it - is increasingly difficult to obtain. 
With 1.3 billion hungry mouths to feed, China is highly dependent upon its agricultural production. Between animal diseases like FMD, PED, PRRS, avian flu, and ASF, increasing droughts, heavy floods, and the arrival of the crop devastating Fall Armyworm (Spodoptera frugiperda) last spring (see China: Update: Fall Armyworm Now in 15 of China’s Provinces), China's food supply is under pressure.
As we've discussed previously, food insecurity - whether due to agricultural diseases, floods, droughts, pests, or other causes - can foment societal discord, up to and including revolution (see Iran: Bird Flu, Food Insecurity & Civil Unrest).
There are also concerns that a number of our critical pharmaceuticals are derived (at least, in part) from Chinese pigs - including Heparin - which has been in short supply for over a year (see Reuters report Congress seeks briefing on potential threat to U.S. heparin supply).
Heparin isn't the only pharmaceutical we get from pigs, but it is the most critical one.  And as ASF spreads out of China and across Asia, the world's pig supply will only decline further.
And we've already seen ASF turn up in Vietnam, North and South Korea, the Philippines, Laos, Cambodia, Myanmar, and Timor.   We are also watching reports of (as yet) unidentified pig die offs in Indonesia (see Indonesia: Media Reports Of Positive ASF Test Results In North Sumatra).

ASF is also spreading across large swaths of Russia, and continues to make inroads into Eastern and Central Europe (see UK DEFRA: Updated Outbreak Assessment (#02) African Swine fever in Europe.)
African Swine Fever is a juggernaut that appears unstoppable, at least until an effective vaccine can be developed.
Meanwhile hungry people are going to find ways to find meat protein, even it it means relying more on bushmeat.  While that can be devastating to the wild animal population (including endangered species), it can also serve as an easy conduit for zoonotic diseases to spillover into the human population.

Every year we see outbreaks of Monkeypox, Lassa Fever, and sometimes even Ebola in Africa, many of which are believed tied to the hunting, processing, and consumption of bushmeat.  This from the FAO Bushmeat Sourcebook.

What are the links between bushmeat and human diseases?

Hunting and bushmeat consumption entail some risks for emergence of wildlife-related diseases that can be transmitted from animals to humans, also commonly called ‘zoonoses’. It is estimated that approximately 60% of all human pathogens are zoonotic, with some 75% emerging from wildlife. Over one billion cases of human zoonotic disease are estimated to occur annually.

The risk of contracting a disease depends on several factors but may occur even in mosaic landscapes of farms and fragmented forests where human–wildlife interaction is generally indirect or incidental. The lack of personal protection or hygiene during killing, handling and butchering is thought to be the main route of infection. While the process of curing/cooking the meat generally reduces the risk, it also requires consideration.
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In 2002, the SARS Coronavirus swept across China, and emerged on the world stage, infecting thousands.  While the exact origins of the virus and spillover are still not known, it appears to have come from the `wild flavor' craze for exotic meats in Southern China early in the last decade.

From the WHO:
SARS (Severe Acute Respiratory Syndrome)
SARS coronavirus (SARS-CoV) – virus identified in 2003. SARS-CoV is thought to be an animal virus from an as-yet-uncertain animal reservoir, perhaps bats, that spread to other animals (civet cats) and first infected humans in the Guangdong province of southern China in 2002.
China has banned (repeatedly) the consumption of civet cats, and other `wild flavor' or endangered animals, since the SARS epidemic, but the practice continues (see Despite Crackdown, `Wild Flavor’ Trade Continues In China).

Although surveillance and reporting on spillover events is spotty at best, we see scattered reports of human anthrax infection, strep suis (see Tiết Canh - An Incredibly Bat Idea, and most recently plague (see China: Inner Mongolia Reports Another Plague Case) linked to animal contact nearly every year out of Asia. 

And wildlife surveillance programs have shown there are a number of dangerous pathogens carried by bats (and potentially other bushmeat species) in the region.
Emerg. Microbes & Infect.: Novel Coronaviruses In Least Horseshoe Bats In Southwestern China 
PNAS: SARS-like WIV1-CoV Poised For Human Emergence

Sci Rpts: Avian & Human Influenza Compatible Receptor Cells In Little Brown Bats

Study: Hotspots For Bat To Human Disease Transmission

In 2005, the CDC’s EID Journal carried a perspective article on the dangers of bushmeat hunting by Nathan D. Wolfe, Peter Daszak, A. Marm Kilpatrick, and Donald S. Burke.
Bushmeat Hunting, Deforestation, and Prediction of Zoonotic Disease
It’s a terrific article,and the events since then with Ebola and Monkeypox in Africa have only made it more relevant.

Whether the recent reports of plague in Mongolia (last May), and Inner Mongolia over the past week, have anything to do with the ASF induced pork shortage is unknown.
But at least three of theses cases have been linked to bushmeat. 
While bushmeat has always been part of the diet in some parts of Asia, it is likely as ASF spreads - and more people across Asia face increased food insecurity - the amount of bushmeat that will be hunted, processed and consumed will increase.
And that, unfortunately, increases the chances of seeing a new zoonotic spillover, either from an old scourge like anthrax or rabies, or perhaps something new, like an emerging Coronavirus. 
Human health and animal health are all intertwined, and even though ASF doesn't directly infect humans, its impact on our health and well being may prove to be far greater than we appreciate.

Sunday, November 17, 2019

China: Inner Mongolia Reports Another Plague Case

Credit Wikipedia


Earlier this week, in HK CHP Notification Of Two Plague Cases Being Treated In China, we looked at reports of two patients from Inner Mongolia being treated for pneumonic plague in Beijing. 
And for the past several days - despite aggressive censorship by the Chinese Government - there has been a lot of (unconfirmed) chatter on Weibo (a micro blogging site) - and in the dissident press - suggesting that there are more cases, and they are being covered up.
While rumors often prove unfounded, what we do have this morning is confirmation from Inner Mongolia's Ministry of Health that a 3rd (this time, bubonic) plague case has been identified, and that aggressive screening of patients is ongoing.

First, this (translated) press release from Inner Mongolia's MOH.

A patient in Xilin Gol League was diagnosed as a bubonic plague in Huade County, taking practical measures to increase prevention and control.
Release time: 2019-11-17 05:03:46 Manuscript: Li Chengcheng Editor: Huang Lihua Editor: Chai Yujia

On November 16, 2019, a person from the Bayin Tara Sumu quarry in Xilin Gol League, Inner Mongolia Autonomous Region, during the visit to the Huade County Hospital in Wulanchabu City, repeatedly had fever and was diagnosed as a confirmed case of bubonic plague by expert consultation. 

The patient, male, 55 years old, had been stripped of hare in the quarry on November 5, 2019. Currently, there is no epidemiological association between this case and the first two cases. At present, the patient has been isolated and treated in Huade County Hospital, Wulanchabu City, and relevant prevention and control measures have been implemented. 28 close contacts, have been in isolation medical observation, there is no abnormal performance such as fever. 

In addition, the medical observations of close contacts of the 2 cases diagnosed on November 12, 2019 showed no abnormalities such as fever.

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And from the same agency, a (translated) description of the steps they are taking to detect and contain the disease, which was published 3 days ago. 

Xilin Gol League is fully committed to the prevention and control of plague

Release date: 2019-11-14 10:19

Inner Mongolia Xilin Gol League Health and Health Committee, Beijing Chaoyang District Health and Health Committee on the evening of November 12 in the Beijing Chaoyang District Government website jointly announced the news: after the expert consultation, two patients in the Xilin Gol League were diagnosed as pneumonic plague cases. At present, the patients have been properly treated in the relevant medical institutions in Chaoyang District, Beijing, and relevant prevention and control measures have been implemented.

After the outbreak, the health and health departments at all levels of Xilin Gol League and the disease control and medical institutions quickly entered the actual state of combat and went all out to carry out relevant emergency work. On the 13th, the reporter learned from the plague emergency headquarters of Xilin Gol League that the local government has urgently launched the "Xilin Gol League plague control emergency plan", established a three-level emergency response mechanism, formulated a plague prevention and control work program, and further strengthened overall coordination, emergency dispatch and Comprehensive protection. Set up an emergency treatment expert consultation group, continue to carry out epidemiological investigations, track and manage close contacts, organize training for infectious disease prevention and treatment of medical personnel and popularization of epidemic infectious diseases.

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It is impossible to evaluate the veracity of the online rumors and dissident news reports claiming that China is dealing with a wider outbreak from this vantage point.

About all we can say is that China has a history of hiding disease outbreaks (SARS, African Swine Fever, etc.) when it suits them, and of late, we've heard very little about outbreaks of any kind from the mainland. 

Fortunately plague - while it remains a genuine public health concern, particularly in Asia and Africa - is far easier to contain, and cure, than it once was.
At least, as long as it remains susceptible to our armamentarium of antibiotics.  
But there are growing concerns that Y. pestis, like so many other bacteria, could acquire sufficient multi-drug resistance to loom large once more as a pandemic threat (see PLoS Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk).

So we watch reports, such as the ones coming out of China this week, with considerable interest.

Saturday, November 16, 2019

The WHO NPI Guidance : Environmental Measures

Credit WHO


A couple of weeks ago, in WHO Guidance: Non-pharmaceutical Public Health Measures for Mitigating the Risk and Impact of Epidemic and Pandemic Influenza, we took our first look at the World Health Organization's recently released 91-page NPI Guidance document.
Since then we've taken a closer look at the WHO's recommendations on Personal protective NPIs (hand hygiene, isolation, masks, etc.) and Social Distancing.
Today we'll look at the WHO recommendations for Environmental measures that could help reduce the spread, and hopefully the impact, of a pandemic (see Community Pandemic Mitigation's Primary Goal : Flattening The Curve).
These include surface and object cleaning, UV lights, ventilation, and adjusting indoor humidity levels.
The WHO bases their recommendations on the best available scientific evidence on their effectiveness - tempered by practical considerations and potential harms - but admits that in many cases the quality of scientific evidence is low, or even absent.

The major points are summarized in the chart below, after which we'll look at them individually.

Surface and Object Cleaning

Although most flu transmission is likely via a respiratory route, studies have found that infectious flu particles can remain viable for hours - or even days - on some surfaces (fomites).
When people touch a contaminated surface, they can not only infect themselves (generally by touching their mouth, nose, or eyes), they can carry the virus to other places and deposit them on new surfaces.
Five years ago, in ICAAC Video: How Quickly A Virus Can Spread In A Building, we looked at a study that showed that viruses from a single contaminated surface (door knob, tabletop, etc.) in an office environment can spread to contaminate an entire building in a matter of hours.

More recently, in 2018's Simulated Influenza A Transmission In An Office Environment - researchers found that `. . . long-range airborne, fomite and close contact routes contribute to 54.3%, 4.2% and 44.5% of influenza A infections, respectively.
They also noted that `Keyboards, headphones, desktops, mice and mobile phones are the five most-contaminated private surfaces around the infected student.'
Even though a minority of flu infections appear to be due to touching contaminated fomites, cleaning and disinfecting common surfaces ought to have some impact on the rate of transmission, and have little downside.

The WHO recommends surface and object cleaning for all epidemic and pandemic severity levels:

UV Lights

Although conventional UV lights can be quite effective in killing flu viruses, exposure can be both carcinogenic and cataractogenic, which severely limits how they can be used in public. 
A couple of years ago party goers at Hong Kong's Landmark experienced skin burns and eye damage when the wrong type of UVC lamps were used at a public event (see Partygoers left with burns and light sensitivity after Hypebeast event at The Landmark).
There are UV wavelengths (Far-UVC : 207–222 nm) that are much safer, yet still effective in killing viruses, but the equipment costs remain high (see Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases).

Given the costs, and the potential for the wrong type of UV lighting equipment to be used, the WHO has decided not to recommend UV lights as an NPI.


During the 1918 pandemic, people were advised to keep their windows open, and trolley cars routinely increased ventilation (and reduced the number of riders) in order to slow the spread of the flu.
Credit National Archives

While most of the evidence from 1918  is anecdotal, many believe those practices helped to significantly reduce transmission of the virus. The WHO cites a couple of modern studies (see below) in making a positive recommendation.
Increased ventilation
Summary of evidence
A simulation study predicted a reduction of transmission among kindergarten students by enhancing the air changes per hour (ACH) (92). Two simulation studies evaluated the effectiveness of increasing ventilation in reducing influenza transmission in community settings (93, 94). One of these two studies suggested a reduction of daily peak infections by increasing ACH under the baseline scenario (93), and the other predicted that the peak infection rate could be reduced by more than 60% by doubling or tripling the ventilation rate (94).

The rub here being that in most modern commercial buildings (built in the last 50 years), windows don't open, and air exchange is handled by the building's HVAC system. In most homes, open windows are an option, but only when temperatures aren't uncomfortably high or low.

Modifying Humidity

Over the past decade we've looked at a number of studies indicating that influenza viruses survive longer in the environment when temperature and humidity fall within certain ranges.
  • In 2008 researchers Jeffrey Shaman and Melvin Kohn established a correlation between the AH (Absolute Humidity) and the survival, and transmission of the influenza virus (see It's Not So Much The Heat, It's The Humidity).
  • In 2018's bioRxIv: Humidity As A Non-pharmaceutical Intervention For Influenza A, researchers reported finding:  An increase in average AH from 6.33 mb in control rooms to 9.89 mb in humidified rooms (RH ~42-45 %) was associated with a significant decrease in influenza A virus presence in fomite and air samples in humidified rooms compared to control rooms. 
While the research has been promising, poorly maintained humidifiers also have a downside, as they can be breeding places for bacteria, viruses, and mold.  
In 2011 we followed an outbreak of Idiopathic pulmonary fibrosis (IPF) that was ultimately traced to the sterilizing fluid used in home humidifiers, while humidifiers have also been linked to increased asthma in children and to rare legionella infection.
While better data may come out of the next pandemic, for now, the WHO is not recommending modifying humidity as an NPI during the next influenza pandemic. 

Taken individually, none of these recommended NPIs are likely to do very much. But when `layered' on top of one another, they can reduce the number of people infected at any given time.

While it probably won't make much of a difference in the number of illnesses or deaths caused by the virus, by spreading them out over a longer time period you can hopefully reduce the amount of collateral damage to society.
We'll finish out this series by looking at the WHO travel related NPIs in a future blog.

Japan MAFF Confirms 49th Farm Outbreak Of Classical Swine Fever (Yamanashi Prefecture)


Japan has been dealing with the return of Classical Swine Fever (CSF) - after an absence of 26 years - since September of 2018.  While similar in impact to ASF, CSF is caused by a different virus, and is considered a little easier to control.
Today Japan's MAFF reports on the first farm outbreak of CSF in Yamanashi Prefecture - which reported their first wild boar detection of the virus just over two weeks ago.
Farm outbreaks for the first 10 months were confined to Gifu and Aichi Prefectures, but since mid-summer we've seen a rapid expansion of the virus into the neighboring prefectures, with detections in both wild boar and in farmed animals.

Today's announcement from Japan's MAFF follows:

Confirmation of affected animals of CSF in Yamanashi Prefecture, about (49 case was in Japan)

Ryowa first year on November 16,
the Ministry of Agriculture, Forestry and Fisheries

Today, affected animals of CSF has been confirmed in wild boar positive confirmation point from there within 10km monitored and made to have Yamanashi Prefecture Nirasaki of the farm.

We are taken all possible measures for the quarantine measures for the disease.
Interview in the field, thank you for your cooperation as strictly refrain from such that there is a risk that cause the spread of the disease. 

1. Overview of the occurrence farm

Location: Yamanashi Prefecture Nirasaki
breeding situation: 871 head

2. Background 

(1) Yamanashi Prefecture, November 14 (Thursday), from the farm, received a report of a breeding pig has exhibited abnormal, we conducted a site inspection by animal health inspectors.
(2) Since the suspicion of CSF is caused by the inspection at the Livestock Hygiene Service Center, sent the material to Noken mechanism Animal Health Research Institute (Note), was subjected to a genetic analysis, today (November 16 (Saturday) ), it was found to be an animal subject of the CSF.
(Note) specialized research institutions on the only animal health in Japan
(Continue . . . )

While CSF doesn't pose a human health hazard, it - very much like African Swine Fever (ASF) - can be devastating to the pork industry.

Friday, November 15, 2019

India: Media Reports - Botulism Likely Cause Of Recent Bird Mortality In Rajasthan

Approx Location Of Sambhar Lake


Earlier this week we looked at reports of a large migratory bird die off at Sambhar Salt lake in the western state of Rajasthan, and while avian flu was considered unlikely by local officials, at the time no cause had been detected.
Today, local media are reporting that a team of researchers from the Rajasthan University of Veterinary & Animal Sciences have tentatively identified Botulism as the most likely cause of this unusual mortality event.  Additional tests for heavy metals and other toxins are still pending.
Clostridium botulinum is a naturally occurring anaerobic bacterium
commonly found in the soil. As the USGS explains, outbreaks in migratory waterfowl are not unusual. 
Botulism type C is concentrated in aquatic invertebrates that filter feed sediments or water. When birds eat the invertebrates, they get a concentrated package of toxin. A bird-to-bird cycle can also exist where maggots feeding on dead birds can concentrate the toxin and can then be eaten by and poison other birds.
A couple of links to English language reports on today's findings include:
Preliminary Report Says Thousands Of Birds Died Due To Botulism Near Jaipur

Rajasthan: Toxin responsible for death of birds around Sambhar Lake, says expert