Monday, May 20, 2019

Belgium Orders Enhanced Surveillance & Testing For LPAI H3


 Two weeks ago, in Belgium: Non-Reportable LPAI H3N1 Continues To Spread, we looked at more than 2 dozen outbreaks of a Low Path avian H3N1 virus - which is not considered a reportable disease by the OIE -  in and around West Flanders. 
Since H5 and H7 are the only LPAI viruses considered reportable by the OIE, this outbreak would have likely gone unnoticed were it not for its unusually high mortality rate (said to be as high as 60% in some flocks).
LPAI H3 infections are not uncommon in birds - particularly ducks - but occasionally turn up in poultry, although H3N2 and H3N8 appear to be more common than H3N1. 

Since LPAI H3 isn't covered by the OIE's Terrestrial Animal Code Article 10.4.1. - and local protocols for dealing with a low path non-H5 or H7 avian virus are ambiguous at best - farmers have been waiting for guidance (and financial assistance) from the Ministry of Agriculture.

Today Animal Health Care Flanders (Dierengezondheidszorg Vlaanderen)
has published the following (translated) statement via the Ministry of Agriculture. 
The Ministry of Agriculture is taking urgent measures to prevent the spread of low pathogenic H3 virus

May 20, 2019

To prevent the further spread of the low pathogenic avian influenza virus type H3, the Ministry of Agriculture is prescribing a number of urgent measures from today. These apply to all Belgian poultry herds. We list them for you.
Measures to prevent contamination

From now on, the criteria of increased vigilance (= submission of samples to exclude AI and ND) must be interpreted at the level of the stable and no longer at the level of the entire herd. The criteria are:

  • a decrease in normal feed and water consumption of more than 20%;
  • a mortality rate of more than 3% per week;
  • a decrease of the lay by more than 5% that lasts longer than two days;
  • clinical signs or lesions in post-mortem examinations suggesting avian influenza.
In commercial poultry farms, the vehicles must be cleaned with an authorized biocide upon entering and leaving the company (this link contains a list of permitted products: ).
From now on it is both prohibited to load poultry from different origins on the same vehicle and to unload poultry from the same vehicle at several companies.
Access to a poultry house or hatchery is prohibited for all persons who do not belong to the company. The responsible party takes all necessary measures to that end.
This prohibition does not apply to:
  • the personnel required for operational management;
  • the vet;
  • employees of the Food Agency, other governments, and the people who work on their behalf.
All these people - but also those who work at the farm daily - must use proprietary or disposable boots and clothing before they enter the poultry house or hatchery. Everyone takes every precaution to prevent the spread of diseases.
Measures for companies that are already infected

For farms infected with H3, the manure, slurry and litter from the infected stables must be disinfected with an authorized biocide (see link to list above) and then processed or treated according to Regulation (EC) No 1069/2009 ( animal by-products regulation).

At present, the presence of an H3 virus has been detected at 38 companies spread across West and East Flanders.

If you have any questions about this low pathogenic virus, please contact your company veterinarian or the DGZ Helpdesk on 078 05 05 23 or
While the number of new farms affected appears to be slowing, there is obviously considerable interest in what has made this particular LPAI H3 variant unusually virulent.

Hopefully we'll see a thorough genetic analysis published in the weeks ahead. 

China MOA Reports Two Outbreaks Of ASF & FAO Update


For the first time in nearly a month China's MOA has posted announcements of two new outbreaks of African Swine Fever; one detected at a slaughterhouse in Guiyang City, Guizhou Province and the other in Zoige County, Sichuan Province.
Reporting from China appears to be fragmented, and intermittent at best, with the MOA reporting just over 1 million pigs lost since September (see FAO Report).
Other estimates from outside observers and agencies (see African Swine Fever In China: Epizootic or An EpicZootic?) paint a far worse picture, with estimated losses pegged as anywhere from 100 million to 200 million pigs.

While the MOA reports may not reflect the full story of ASF in China, they are worth noting.  From May 18th, we get the following translated report:

A small slaughterhouse in Wudang District, Guiyang City, Guizhou Province, transferred to the pig rafts to detect the African swine fever
Date: 2019-05-18 15:06 Author: Source: Ministry of Agriculture and Rural Press Office 

The Information Office of the Ministry of Agriculture and Rural Affairs was released on May 18th. The foreign provinces of a slaughterhouse in Wudang District, Guiyang City, Guizhou Province, were transferred to the raw pork chops to detect the African swine fever.

At 13:00 on May 18, the Ministry of Agriculture and Rural Affairs received a report from the China Animal Disease Prevention and Control Center, which was diagnosed by the Guizhou Provincial Animal Disease Prevention and Control Center.
A slaughterhouse in Wudang District of Guiyang City detected the African swine fever epidemic. According to preliminary investigations, the batch of pigs was illegally transferred from the province by the owner. Up to now, the batch of 75 pigs has a total of 6 diseases and 6 deaths.

Immediately after the outbreak, the Ministry of Agriculture and Rural Affairs sent a steering group to the local area to carry out epidemic supervision and epidemiological investigation. The local government has initiated an emergency response mechanism as required to block the slaughterhouse, control all vehicles, pigs and pig products on the site, prohibit all pigs and their products from being released from the blockade zone, and prohibit pigs from being transported into the blockade. At present, the above measures have been implemented, and the local public security department has controlled two carriers.
And this, published today (May 20th).
Zoige County, Sichuan Province, diagnoses African swine fever
Date: 2019-05-20 18:11 Author: Source: Ministry of Agriculture and Rural Press Office

The Information Office of the Ministry of Agriculture and Rural Affairs was released on May 20, and the Zoige County of Aba Prefecture, Sichuan Province, detected the African swine fever epidemic.

At 14:00 on May 20, the Ministry of Agriculture and Rural Affairs received a report from the China Animal Disease Prevention and Control Center. It was diagnosed by the Sichuan Provincial Center for Animal Disease Control and Prevention, and the African swine fever epidemic occurred in the town of Zhagai, Aba Prefecture. Up to now, there have been 429 live pigs in the township epidemic area, with 111 diseases and 78 deaths.

Immediately after the outbreak, the Ministry of Agriculture and Rural Affairs sent a steering group to the local area. The local government has started the emergency response mechanism according to the requirements, and adopted measures such as blockade, culling, harmless treatment, disinfection, etc., to treat all the sick and culled pigs harmlessly. At the same time, all pigs and their products are prohibited from being transferred out of the blockade, and pigs are prohibited from being transported into the blockade. At present, the above measures have been implemented.

Meanwhile, the FAO has updated their ASF in Asia webpage, which includes the following summaries:

Situation update

Since the China Ministry of Agriculture and Rural Affairs (MARA) confirmed its first African swine fever (ASF) outbreak in Liaoning Province on 3 August 2018, 130 ASF outbreaks detected in 31 Provinces/Autonomous Region/Municipalities/Special Administrative Region. MARA reported on 23 April 2019 that 1,026,000 pigs have been culled in an effort to halt further spread [reference].

Hong Kong Special Administrative Region: ASF virus was detected in a single sample from Sheung Shui Slaughterhouse (SSSH). The pig was from a farm in Zhanjiang City, Guangdong Province. The sample submitted on 2 May tested positive for ASF on 10 May. Operations at SSSH have been suspended, around 6 000 pigs at the SSSH were destroyed, followed by cleansing and disinfection [reference1, reference2].

Since its first report on the 15 January 2019, 11 outbreaks in 6 provinces and in Ulaanbaatar have been reported, involving 105 farms/households. More than 3,115 pigs, more than 10 percent of the total pig population in Mongolia, have died/been destroyed due to the ASF outbreaks.

Viet Nam
Since the Ministry of Agriculture and Rural Development (MARD) confirmed its ASF outbreaks on 19 February 2019, a total of 30 provinces/cities reported outbreaks, and more than 1,300,000 pigs  pigs have been culled [reference].

Since the Ministry of Agriculture Forestry and Fisheries confirmed its first ASF outbreak in Som Kaninh village, Som Thom commune, O Ya Dav District, Ratanakiri Province on 2 April 2019, more than 2400 pigs have died or been culled.

Follow the link for the full update, which includes a list of FAO recommendations and the actions being take by the FAO in regards to this expanding epizootic.

CDC: Guidance for Human Infections with Swine Flu Viruses



As spring turns into summer we turn our flu attention away from seasonal flu (at least, in the Northern Hemisphere) to another influenza threat which has emerged in recent years; human infection with swine-variant flu viruses.
Over the past 15 years we've seen more than 460 confirmed human infections with these swine-origin viruses, mostly associated with pig exposure at county and state animal exhibits.
Swine Variant Human Cases : 2010-2018  - Credit CDC

While the number of cases vary greatly from year-to-year, with our county and state fair season beginning in June, it would not be unexpected to see outbreaks - in swine, and humans - in the coming months. 
Although most of the reported swine variant infections over the past decade have been mild-to-moderate in severity, some people have required hospitalization, and deaths - while rare - have occurred (see J. Virology: Analysis Of A Swine Variant H1N1 Virus Associated With A Fatal Outcome).
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
Last week the CDC released updated interim guidance for clinicians who may see suspected swine-variant influenza cases in the coming months.  In addition, a CDC Expert commentary has been published by Medscape (link).

Due to its length I've only posted the first two sections, follow the link to read it in its entirety.   I'll have a bit more when you return.
Guidance for Clinicians: Variant Virus Infections in People pdf icon[186 KB, 4 pages]
Influenza A viruses circulating in swine that have infected humans are referred to as “variant” viruses and denoted with a letter “v”. Human infections with H1N1v, H3N2v and H1N2v viruses have been detected in the United States.
Most commonly, human infections with variant viruses occur in people with exposure to infected swine (e.g., children near swine at a fair or workers in the swine industry). There have been documented cases of multiple people becoming sick after exposure to one or more infected swine and rare cases of limited spread of variant influenza viruses from person-to-person. The vast majority of human infections with variant influenza viruses do not result in person-to-person spread. However, each human infection with a swine influenza virus should be fully investigated to be sure that such viruses are not spreading in an efficient and ongoing way in humans and, if infected animals are identified, to limit further exposure of humans to these animals.
Clinical Presentation and Risk Groups
Clinical characteristics of human infections with variant viruses generally have been similar to signs and symptoms of uncomplicated seasonal influenza, including fever, cough, pharyngitis, rhinorrhea, myalgia, and headache. Vomiting and diarrhea also have been reported in some infections in children. Milder clinical illness is possible, including lack of fever. The duration of illness appears to be similar to uncomplicated seasonal influenza, approximately 3 to 5 days. While assumed to be similar to seasonal influenza virus infection, the duration of viral replication and possible infectiousness of variant virus infection has not been studied.

Exacerbation of underlying conditions (e.g., asthma) has occurred. The same people at increased risk for complications of seasonal influenza are likely at high risk for serious complications from variant virus infection, including children younger than 5 years, pregnant women, people 65 years and older, those who are immunosuppressed, and persons with chronic pulmonary, cardiac, metabolic, hematologic, renal, hepatic, neurological or neurodevelopmental conditions, as well as those with other co-morbidities, including extreme obesity.
        (Continue . . . )

We regularly cover swine and swine variant influenza in this blog, both in North America and around the world.  A few studies over the past year include:

Trop. Med & Inf. Dis.: Mammalian Pathogenicity and Transmissibility of H1 Swine Variant Influenza
BMC Vet.: Novel Reassortant H1N2 & H3N2 Swine Influenza A Viruses - Chile

J. Virology: Pathogenesis & Transmission of H3N2v Viruses Isolated in the United States, 2011-2016

JVI: Divergent Human Origin influenza Viruses Detected In Australian Swine Populations
The `Other' Novel Flu Threat We'll Be Watching This Summer
Emerg. Infect. & Microbes: Novel Triple-Reassortant influenza Viruses In Pigs, Guangxi, China

SPC Issues High Severe Warning For Parts Of Texas & Oklahoma


While the start of the Atlantic Hurricane season is still nearly two weeks away, we are in the heart of the spring tornado season, and NOAA's Storm Prediction Center (SPC) has issued a high severe warning for parts of northern Texas and western Oklahoma for later today.
Public Severe Weather Outlook (PWO)
Print Version
Experimental Multimedia Briefing MP4.
Please note this briefing may be out of date after 1414 UTC on 05/20/2019 and there will be no subsequent updates during the day. Please send comments or questions to or using the feedback page. 


Outbreak of tornadoes and severe thunderstorms expected over parts of the southern Plains this afternoon and tonight..
  • LOCATIONS... Northwest Texas Western and central Oklahoma
  • HAZARDS... Numerous tornadoes, several intense and long track Widespread damaging winds, some hurricane force Widespread large hail, some baseball size
  • SUMMARY... An outbreak of tornadoes, some potentially long-track and violent, is expected today into this evening over portions of northwest Texas into western and central Oklahoma. More-isolated but still potentially dangerous severe weather, including tornadoes, is possible in surrounding parts of Texas, Oklahoma, Kansas, and Arkansas. 
Preparedness actions... Review your severe weather safety procedures for the possibility of dangerous weather today. Stay tuned to NOAA Weather Radio,, or other media for watches and warnings. A tornado watch means that conditions are favorable for tornadoes to form during the next several hours. If a tornado warning is issued for your area, move to a place of safety, ideally in a basement or interior room on the lowest floor of a sturdy building. 
&& ..Edwards.. 05/20/2019

Suffice to say that if you live or work (or will travel through) any of the areas forecast to see severe weather today and tonight, you should be prepared to move to a safe location should conditions threaten.
Everyone in these forecast high risk areas should pay close attention to local weather reports or NOAA weather warnings, and ensure they have their emergency kits, and their disaster plans, up to date.
And those living in Missouri and Arkansas should be aware that the forecast is for their regions to be under the gun tomorrow. 

Sunday, May 19, 2019

Saudi MOH : 2 Primary MERS Cases


We are now just over two weeks into the Holy Month of Ramadan, which sees as many as a million religious pilgrims visiting Saudi Arabia, and their MOH has reported two new MERS cases.

The first, on the 17th - a 59 y.o. male with no known camel contact - closes out epi week #20 with 2 cases, and becomes the 4th primary case reported from Riyadh in the month of May.

Today's case (epi week #21) involves a 22 y.o. female from Al Kharj City, again a primary case with no known camel contact.

While contact with infected camels is a known conduit for reintroducing the MERS virus into the human population, for many primary cases (those outside of healthcare facilities and with no known contact with a MERS case), the source of their infection remains unknown.
Although the number of community MERS cases remains limited, they represent a serious gap in our understanding of how the virus is circulating among humans, and suggest that many (presumably mild) cases are being missed by surveillance.
Over the years, we've seen a number of analyses that have concluded that only a fraction of MERS cases are likely diagnosed, including:
While we haven't seen any indication of sustained or efficient transmission of the MERS virus in the Middle East, these unexplained community-acquired infections remain a serious concern, and bear watching. 

PNAS: Low Ambient Humidity Impairs Barrier Function & Innate Resistance Against Influenza Infection

Photo Credit PHIL (Public Health Image Library)


Although flu circulates at low levels year-round in the tropics, for most of the world influenza is primarily a seasonal threat, which appears to peak during times of of lower temperatures and humidity.

While the reasons are only partially understood, we've seen research 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).
The irony here is that hospitals are normally kept cool and dry in order to curb the growth of bacteria, but may be unintentionally providing an environment conducive to the spread of respiratory viruses like influenza, SARS & MERS.

Although largely anecdotal, there is growing evidence suggesting that raising the humidity inside homes, offices, and health care facilities might be a reasonably effective NPI (Non-pharmaceutical Intervention) during times of heightened flu activity (see PLoS One Humidity as a non-pharmaceutical intervention for influenza A).
This is not exactly a new idea, as the Chinese have boiled vinegar for centuries in their homes to `disinfect the air' during epidemics (including SARS).  While vinegar is unproven to add any beneficial effect, vinegar is 95% water, and boiling it undoubtedly raises the humidity inside their homes.
Unfortunately many Chinese cook indoors on coal stoves, and carbon monoxide poisoning using this method is not uncommon (see SCMP Two dead after boiling white vinegar). 
Most of the research on this topic has centered on the viability of the flu virus at lower humidity levels, but the impact of lower ambient humidity on the host's ability to fight off infection may also play a role. 
With the caveat that the following study was done using mice - which may or may not fairly represent a human response - researchers have found that lower ambient humidity can impair `. . . mucociliary clearance, innate antiviral defense, and tissue repair function'.
Low ambient humidity impairs barrier function and innate resistance against influenza infection
Eriko Kudo, Eric Song, Laura J. Yockey, Tasfia Rakib, Patrick W. Wong, Robert J. Homer, and Akiko Iwasaki
PNAS first published May 13, 2019

Contributed by Akiko Iwasaki, April 4, 2019 (sent for review February 19, 2019; reviewed by Gabriel Núñez and Peter Palese)


Influenza virus causes seasonal outbreaks in temperate regions, with an increase in disease and mortality in the winter months. Dry air combined with cold temperature is known to enable viral transmission. In this study, we asked whether humidity impacts the host response to influenza virus infections.

Exposure of mice to low humidity conditions rendered them more susceptible to influenza disease. Mice housed in dry air had impaired mucociliary clearance, innate antiviral defense, and tissue repair function. Moreover, mice exposed to dry air were more susceptible to disease mediated by inflammasome caspases.

Our study provides mechanistic insights for the seasonality of the influenza virus epidemics, whereby inhalation of dry air compromises the host’s ability to restrict influenza virus infection.


In the temperate regions, seasonal influenza virus outbreaks correlate closely with decreases in humidity. While low ambient humidity is known to enhance viral transmission, its impact on host response to influenza virus infection and disease outcome remains unclear.
Here, we showed that housing Mx1 congenic mice in low relative humidity makes mice more susceptible to severe disease following respiratory challenge with influenza A virus. We find that inhalation of dry air impairs mucociliary clearance, innate antiviral defense, and tissue repair. Moreover, disease exacerbated by low relative humidity was ameliorated in caspase-1/11–deficient Mx1 mice, independent of viral burden. Single-cell RNA sequencing revealed that induction of IFN-stimulated genes in response to viral infection was diminished in multiple cell types in the lung of mice housed in low humidity condition.

These results indicate that exposure to dry air impairs host defense against influenza infection, reduces tissue repair, and inflicts caspase-dependent disease pathology.
        (Continue . . . )

This is a lengthy, and highly detailed study and so you'll want to follow the link to read it in its entirety.  There are obviously a lot of unanswered questions, including the issue of influenza transmission in the tropics, or in the summer.

As with last year's Humidity as a non-pharmaceutical intervention for influenza A), the authors (in the discussion section) touch upon the potential  practical application of increasing ambient humidity.
Our study suggests that increasing ambient humidity may be a viable strategy to reduce disease symptoms and to promote more rapid recovery in influenza-infected individuals.
During the opening months of the next pandemic pharmaceutical interventions (vaccines & antivirals) may be unavailable, ineffective, or plagued by manufacturing delays, and so the immediate goal will be to slow the spread of the virus and to limit its impact through the use of NPIs (see Community Pandemic Mitigation's Primary Goal : Flattening The Curve).
While it is not entirely clear how valuable raising the humidity in your home or office would be during a pandemic - or even a bad flu season - it might be worth considering as an experimental adjunct to the other NPI's (hand washing, covering coughs, staying home when sick, avoiding crowds, etc.) that are likely to be promoted.

For more on environmental  factors that may affect virus viability, you may wish to revisit:
Sci. Ttl. Enviro.: Cold-Dry Days Favor H7N9 Transmission

EID Journal: Evidence-Based Options for Controlling Respiratory Virus Transmission
Formidable Flu Fomites

IDWeek: Persistence Of MERS-CoV On Hospital Environmental Surfaces
Study: Survival Of Aerosolized Coronavirus In The Ambient Air