Friday, July 28, 2017

CDC FluView: 11 H3N2v Swine Flu Cases Reported In Ohio
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Twice over the past couple of weeks we saw reports of county fairs in Ohio closing their pig barns when swine H3N2 was detected in exhibition pigs (see Second Ohio County Fair Closes Hog Barn Over Swine Flu).

When swine influenza viruses jump to humans, they are dubbed swine variant viruses. The CDC describes Swine Variant viruses in their Key Facts FAQ.

What is a variant influenza virus?
When an influenza virus that normally circulates in swine (but not people) is detected in a person, it is called a “variant influenza virus.” For example, if a swine origin influenza A H3N2 virus is detected in a person, that virus will be called an “H3N2 variant” virus or “H3N2v” virus.
Since the influenza subtypes that commonly circulate in swine (H1, H2 & H3) are also the same HA subtypes as have caused all of the human pandemics going back 130 years (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?), swine influenza viruses are watched carefully for signs of jumping to humans.
While only rarely reported, these infections probably happen far more often than we know. But since swine variant influenza infections look like seasonal flu, and testing for swine variant viruses is only sporadically done, we don't often hear about it.
The last swine variant infection in the US was reported from Texas last May. Today the CDC has announced 11 additional H3N2v (variant) infections, all from the state of Ohio and linked to county fair attendance in the past couple of weeks.  All were mild, no one was hospitalized, and all have recovered.

Novel Influenza A Virus:

Eleven human infections with novel influenza A viruses were detected in Ohio during week 29. All 11 persons were infected with influenza A (H3N2) variant (H3N2v) viruses and reported exposure to swine in a fair setting during the week preceding illness onset. Ten of the 11 patients were children less than 18 years of age and one patient was an adult aged 50-64 years. 

None were hospitalized and all have fully recovered from their illness. No human-to-human transmission has been identified. Swine influenza A (H3N2) viruses were identified from respiratory samples collected from pigs at the same fair. Public health and agriculture officials are investigating the extent of disease among humans and swine, but no increases in influenza-like illness in the community have been reported. These 11 infections bring the total number of H3N2v infections during 2017 to 12 and the cumulative total since 2011 to 376.

Early identification and investigation of human infections with novel influenza A viruses are critical to ensure timely risk assessment and so that appropriate public health measures can be taken. Additional information on influenza in swine, variant influenza infection in humans, and strategies to interact safely with swine can be found at

Last October, in MMWR: Investigation Into H3N2v Outbreak In Ohio & Michigan - Summer 2016,  we looked at the CDC's investigation into a cluster of 18 H3N2v cases across two states in August of 2016.  This was the biggest outbreak of swine variant infections we'd seen since 2012, when more than 300 cases were reported across 10 states. 
The `headline' in that report was that 16 of the 18 cases analyzed belonged to a new genotype not previously detected in humans.  Swine influenza viruses, like all flu viruses, are continually evolving.

As the state and county fair season continues over the summer and into fall, it would not be surprising to see additional, scattered reports of swine variant infection, as these venues tend to put a lot of people into close contact with pigs.

For more information on swine variant viruses, and how to protect yourself when in contact with farm animals, the CDC provides the following guides.

Arch. Of Virology: Novel Reassortant H5N6 Isolated From Cats - Eastern China



Until cats (both large and small) began dying in Asia from avian H5N1 back in 2004, it was generally believed that cats were relatively immune to influenza A infection. Gradually that perception has changed (see Catch As Cats Can) - particularly with regard to novel flu viruses (see Companion Animals And Novel H1N1). 
Last winter we saw a large, unprecedented outbreak of avian H7N2 among hundreds of cats in New York City animal shelters (see NYC Health Dept. Statement On Avian H7N2 In Cats) which eventually led to one human infection (link).
At almost the same time, South Korea announced the discovery of at least 3 cats infected with the H5N6 virus in Gyeonggi Province (see Korean CDC Statement On H5N6 In Cats).  MAFRA's Quarantine division immediately announced plans to test stray cats in and around multiple areas that have been hit by avian influenza. 
Increasingly cats (and dogs) are viewed as potential intermediate hosts for novel influenza viruses.
These companion animals - who often interface with wildlife - are in a unique position to serve as a conduit for zoonotic viruses to humans, even in urban settings.

Which brings us to the following study, whose details are sadly tucked behind a paywall. Luckily the abstract still provides us with a fair amount of information.
Genetic characterization of novel reassortant H5N6-subtype influenza viruses isolated from cats in eastern China

Xueliang Cao, Fan Yang,Haibo Wu, Lihua Xu
Brief Report  First Online: 21 July 2017

Cats are susceptible to influenza A viruses and therefore may act as transmission vectors within households, posing a potential public health concern. Two novel reassortant H5N6 influenza viruses were isolated from cats in Zhejiang Province, Eastern China, in 2016.
Both viruses were characterized by whole-genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis showed that these viruses received their genes from H5N6, H9N2, and H7N9 influenza viruses isolated from China. These H5N6 viruses were able to replicate in mice without prior adaptation. Our results show that continued circulation of these viruses could endanger humans.
We aren't provided with any details on this novel reassortant, other than its parental viruses (H5N6, H9N2, and H7N9).  It does, however, reaffirm that the promiscuous H5N6 virus continues to reassort with other viruses in China.

The discovery that these avian H5N6 viruses were able to replicate without adaptation in mice suggests that while these cats might have been infected through contact with infected birds, it could just as easily have come from contact with small mammals or rodents.

Over the years we've looked at the potential role of peridomestic animals (cats, dogs, rodents, small mammals, etc.) in spreading avian flu viruses, and affecting its evolution.

More evidence that things we used to think were rare with novel influenza viruses, may be more commonplace than we know.

Italy's IZSV Reports Three More HPAI H5 Outbreaks

2017 HPAI Outbreaks - Credit IZSV


Last week Italy's IZSV (Istituto Zooprofilattico Sperimentale delle Venezie) confirmed a pair of HPAI H5 outbreaks in Mantua Province, in northern Italy (see Italy Reports Two New Outbreaks Of H5N8), bringing their 2017 outbreak total to 19. 
Over the past couple of days three more outbreaks have been confirmed (2 as HPAI H5, 1 as HPAI H5N8).
Credit IZSV

It is very likely these HPAI H5 outbreaks will be be confirmed as H5N8 in the days to come.  A description of these latest outbreaks from the IZSV follows:
27/07/2017 – On 27 July, the National Reference Laboratory (NRL) for Avian Influenza and Newcastle Disease confirmed as positive for Avian Influenza A virus subtype H5 a fattening turkey farm in Verona province (Veneto region). At the moment of the epidemiological investigation, 12.200 turkeys (around 70 days-old) were present. The turkeys started to exhibit nervous symptoms last Sunday (23/07/2017), and the next day a slight increase in mortality was observed.

Still on 27 July, the Regional Laboratory of Lombardy and Emilia-Romagna confirmed as positive for Avian Influenza A virus subtype H5 a laying hens farm (about 120.000 birds) located in the province of Mantua (Lombardy region).

Further information on virus characterization and on the cases will be provided as soon as available.
Culling procedures for the positive fattening turkey farm in Verona (confirmed on the 25/07/2017) were concluded today, under the supervision of the Veterinary Services.
26/07/2017 – The virus detected in a fattening turkey farm in Verona province, confirmed yesterday (25/07/2017), has been characterised by the National Reference Laboratory as Highly Pathogenic Avian Influenza virus subtype H5N8.

25/07/2017 – On the evening of 24 July, an increase in mortality was reported in a fattening turkey farm in Verona province (Veneto region). On 25 July, the IZS delle Venezie confirmed the case as positive for Avian Influenza virus subtype H5. At the moment of the epidemiological investigation, 17.724 turkeys (112 days-old) were present. Starting on Sunday, a slight increase in mortality was observed in one of the five sheds at the farm. The farm is located in one of the most densely populated poultry areas in Italy.
Although this past winter's massive HPAI H5 epizootic has been over for most European countries for several months, during June and July we saw a small resurgence of outbreaks in poultry and wild birds cut a swath across Luxembourg, Belgium, and just barely into northern France (see Belgium Reports Another Outbreak of HPAI H5N8).
The UK, Finland, and the Netherlands all reported single outbreaks, while during the same time period, Italy has reported six new outbreaks.
This is a decided change over what was seen with the H5N8 virus during previous summers, when the virus all but disappeared  (see PNAS: The Enigma Of Disappearing HPAI H5 In North American Migratory Waterfowl).
The virus acquired significant changes (see EID Journal: Reassorted HPAI H5N8 Clade - Germany 2016) during the summer of 2016, and now appears to be more virulent in wild and migratory birds (see here), and has demonstrated an ability to infect a much wider range of birds (see here).
These changes in behavior are a reminder that influenza viruses change constantly, and have a remarkable ability to adapt to new hosts, and new environments, over time.  Simply put, what we think we know about any given flu virus today, might not hold true tomorrow.

Which is why we should expect surprises going forward.

Thursday, July 27, 2017

Saudi MOH Reports 2 MERS Cases Over 2 Days


After a two-week lull, Saudi Arabia reported a single primary MERS case from Riyadh yesterday listed in stable condition, and today is reporting a single primary (with camel contact) case from Buraidah, who is listed in critical condition.

After seeing 50+ cases in June, this slowdown is welcomed given the start of this year's Hajj (August 30th) is just a little over a month away.

COCA Call Today: Zika - Updated Clinical Guidance & Recommendations for Pregnant Women and Infants


Later today  the CDC will hold a COCA (Clinicians Outreach and Communication Activity) caall with their latest guidance and recommendations on Zika Virus infection in pregnant women and infants.
Primarily of interest to clinicians and healthcare providers, COCA (Clinician Outreach Communication Activity) calls are designed to ensure that practitioners have up-to-date information for their practices.
Follow the link below to review the different ways you can access this webinar.

Zika Virus: Updates to Clinical Guidance and Recommendations for Pregnant Women and Infants

Free Continuing Education 
Date:Thursday, July 27, 2017
Time: 2:00-3:00 pm (Eastern Time)
Please join the COCA Call webinar with digital audio, video and presentation formats from a PC, Mac, iPad, iPhone or Android device:

If you cannot join through digital audio, you may join by phone in listen-only mode: 1 646-558-8656 or 1 408-638-0968

Passcode: 974 205 265
International numbers are available:


CDC has updated its interim guidance for pregnant women with possible exposure to Zika virus to include separate recommendations for pregnant women with symptoms and pregnant women without symptoms. In addition, CDC recently released its latest findings from the Zika pregnancy and infant registries on pregnancy outcomes for pregnant women with Zika virus infection in the U.S. territories and has new updates for healthcare providers on pediatric ophthalmologic findings in infants with possible congenital Zika virus exposure. During this COCA Call, clinicians will learn about the recent updates to CDC’s interim guidance for pregnant women with possible exposure to Zika virus; hear about the latest findings on pregnancy outcomes in the U.S. territories, based on the Zika pregnancy and infant registries; and receive new information on pediatric ophthalmologic findings to assist in caring for patients based on currently available data.

Russia: Rosselkhoznadzor Finds More HPAI Contaminated Meat In Retail Stores


During April and May we followed a number of outbreaks of HPAI H5N8 in western Russia (see here, here, and here), with the largest reported at one of Russia's biggest turkey producing facilities in Rostov (see Link).
By mid-May Russia's Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) announced that HPAI Contaminated Poultry Had Been Shipped To At Least 9 Regions Of Russia.
During May and June we saw numerous reports of contaminated meat being found in the food chain (see Rosselkhoznador Investigation Into HPAI Contaminated Meat Distribution & Sale), along with allegations of illegalities on the part of Rostov's Regional Veterinary Laboratory which was charged with testing these products and overseeing the issuance of food safety certificates.

Although reports of bird flu outbreaks have diminished over the past two months, we continue to see scattered reports of the discovery of contaminated meat in the food chain.  Today, we get this out of Vladivosiok:

In Primorye, discovered and thwarted the realization of retail chains products with the genome of avian influenza

According to Rosselkhoznadzor (Moscow), at this year's poultry farms of the Rostov region LLC "Evrodon-South" observed mass death of turkey stock. In selected pathological material was discovered gene of influenza A virus of birds, and identified the H5 subtype. In this regard, all terupravleniya Rosselkhoznadzor and veterinary services of the Russian Federation was ordered to strengthen the veterinary control measures in respect of products from this manufacturer, as well as for enterprises and commercial organizations that have economic ties with it.

In this regard, the Office of Rosselkhoznadzor for the Primorsky Krai and the Sakhalin Oblast unscheduled inspections of a number of wholesale food stores, retail chains and stores the Primorsky Territory was organized in order to prevent trafficking and sale of dangerous poultry products.

In the course of supervisory activities the inspectors Rosselkhoznadzor in Vladivostok in one of the hypermarkets and large food warehouse was discovered products produced on the affected bird flu Rostov company. Immediately after the discovery of potentially unsafe poultry meat has been placed on isolated storage, precluding any unauthorized traffic.

Conducted FGBU "Maritime Interregional Veterinary Laboratory" Rosselkhoznadzor tests have shown that 2 tons of steaks of turkey, who were in the wholesale food warehouse, as well as 300 kg of products of turkey meat in assortment (splint, ase, steak, medallions, sets for fire , wings and steaks), found in urban hypermarket, contains the genetic material of the virus avian influenza A, subtype H5.

Subsequently conducted FGBU "Federal Center for Animal Health" Rosselkhoznadzor (ARRIAH) testing of selected production samples confirmed the presence in them of the influenza virus genome of birds.

However, without waiting for the results ARRIAH, all dangerous products were destroyed (burned) its owners at the complex for the destruction of bio-waste "Factor-Primorye" Vladivostok under the control of Rosselkhoznadzor inspectors.

As previously reported, in May of this year, inspectors Rosselkhoznadzor, in collaboration with the staff of the department of economic security and countering corruption Russian Ministry of Internal Affairs for the city of Vladivostok in the Soviet area was prevented by turnover and, accordingly, the implementation of the population of 3 tons of turkey genome with avian influenza, produced at the plant OOO "Evrodon" Rostov region. Dangerous products have been found on one of the wholesale food warehouses and subsequently destroyed (burned).

While HPAI H5N8 isn't as big of a health concern as H5N1 or H5N6 - both of which have a track record of infecting humans - this illustrates how easily avian flu can make its way into some country's food supply.
A little over a month ago, in Appl Environ Microbiol: Survival of HPAI H5N1 In Infected Poultry Tissues, we looked at the viability (via viral isolation) of H5N1 in experimentally infected chicken's feathers, muscle tissue, and liver stored at various temperatures ( +4°C or +20°C).
Refrigerated (+4°C) feathers retained viable virus for 8 months, tissue for 6 months, and in the liver for nearly 3 weeks. But even at the higher temperature (68F), the virus remained viable for a month in feathers, and just under 3 weeks in muscle tissue.

Beyond contaminated food concerns, this sort of prolonged viral persistence provides opportunities for dead birds in the wild to infect scavengers, and reinforces the need for people in contact with dead birds to take safety precautions.