Tuesday, January 16, 2018

Equine H3N8: Looking At A long-shot In The Pandemic Sweepstakes

Viruses 2018, 10(1), 31; doi:10.3390/v10010031


When it comes to influenza, conventional wisdom can often to blind us to an ever-changing fluscape.  Many things we thought we knew five, or ten years ago, we now find have either changed . . . or were never true to begin with.
Consider that just 15 years ago bats, cattle, and dogs and cats were not generally considered susceptible to influenza viruses.
Since then we've learned that:
I could go on, with reports on other improbable flu hosts, including camels, donkeys, seals and sea lions, minks, and skunks . . . .  but the point is, when it comes to influenza . . . there are more places to look than just in humans, birds, and pigs.

While long-shots in the influenza pandemic derby, canine and equine flu are of particular interest because the H3N8 and H3N2 subtypes they carry are similar to pandemic strains of the past (see chart below).

There is a lot of debate over these pre-1900 influenza pandemics, with conflicting views over whether the 1890-93 `Russian flu’ was due to the H2N2, H3N2, or H3N8 virus, but with most attributing the 1900 outbreak to H3N8 (see Transmissibility and geographic spread of the 1889 influenza pandemic). 

In the past couple of years we've looked repeatedly at the evolution, and potential threat, of canine influenza (see J. Virology: Zoonotic Risk, Pathogenesis, and Transmission of Canine H3N2 and J. Infect. Dis.: Molecular, Antigenic & Pathological Features of Canine H3N2 Influenza) - particularly since the Asian H3N2 canine flu has arrived in North America.

Equine H3N8 influenza - because it has remained relatively stable for 50 years (aside from jumping to dogs in 2004) - gets less attention, although we have ventured there occasionally (see J.Virol.: Experimental Infectivity Of H3N8 In Swine).
While we don't know the source of any of the older pandemics (or regional epidemics) going back several centuries, historical accounts have occasionally linked them to concurrent outbreaks in domesticated animals.

In 2010 the NIH tag team flu experts David Morens and Jeffrey K. Taubenberger penned a fascinating account of the 1872 equine epizootic - an epidemic in horses that spread from Canada to Mexico in a matter of months - and brought transportation to a standstill in this country (see A New Look At The Panzootic Of 1872)

This report provides a tantalizing review of anecdotal reports of a concurrent epizootic affecting poultry, and even causing human illness across the nation.
They wrote:

An explosive fatal epizootic in poultry, prairie chickens, turkeys, ducks, and geese occurred over much of the populated United States between November 15 and December 15, 1872. The epizootic progressed in temporal-geographic association with a well-reported panzootic of equine influenza, which had begun in or around Markham, Ontario, during the last few days of September 1872,1–4 at a time when human influenza had not been recently prevalent.

The equine epizootic spread rapidly into the United States along railroad lines, with separate simultaneous introductions into Michigan and upper New York State. It quickly spread over the entire United States to the Caribbean and Central America (Figure 1). Horses, mules, and menagerie/circus zebras were involved, with “spill over” infections into dogs and cats.4

Numerous individual human cases and localized outbreaks throughout the United States, often associated with exposures to ill horses, were reported. The human disease, generally mild and uncomplicated, was popularly referred to as the “epizooty”, or “zooty”.4
Whether this was an avian flu that jumped to horses, or an equine flu that spilled over into poultry - or two separate events - may never be known.  But Taubenberger and Morens wrote in their conclusion:
Another microbial agent could have caused the avian outbreak; however, its strong temporal and geographic association with the equine panzootic, and its clinical and epidemiologic features, are most consistent with highly pathogenic avian influenza. The avian epizootic could thus have been an early instance of highly pathogenic avian influenza.
All of which serves as prelude to a new study, published in Viruses, which looks at an oddball - isolated -  case of equine H3N8 in a horse from Montana.  The virus, surprisingly, carried both North American and Malaysian Equine H3N2 gene segments, and showed the ability to infect and replicate in a variety of non-equine cell lines.

A link, and a few excerpts, from a much longer (and fascinating) report:

Phylogenetic Analysis and Characterization of a Sporadic Isolate of Equine Influenza A H3N8 from an Unvaccinated Horse in 2015

Chithra C. Sreenivasan 1, Sunayana S. Jandhyala 1, Sisi Luo 1, Ben M. Hause 2, Milton Thomas 3, David E. B. Knudsen 3, Pamela Leslie-Steen 3, Travis Clement 3, Stephanie E. Reedy 4, Thomas M. Chambers 4, Jane Christopher-Hennings 3, Eric Nelson 3, Dan Wang 1,5, Radhey S. Kaushik 1,3 and Feng Li 1,3,5,*
Received: 26 December 2017 / Accepted: 9 January 2018 / Published: 11 January 2018

Equine influenza, caused by the H3N8 subtype, is a highly contagious respiratory disease affecting equid populations worldwide and has led to serious epidemics and transboundary pandemics. This study describes the phylogenetic characterization and replication kinetics of recently-isolated H3N8 virus from a nasal swab obtained from a sporadic case of natural infection in an unvaccinated horse from Montana, USA.

The nasal swab tested positive for equine influenza by Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR). Further, the whole genome sequencing of the virus confirmed that it was the H3N8 subtype and was designated as A/equine/Montana/9564-1/2015 (H3N8). A BLASTn search revealed that the polymerase basic protein 1 (PB1), polymerase acidic (PA), hemagglutinin (HA), nucleoprotein (NP), and matrix (M) segments of this H3N8 isolate shared the highest percentage identity to A/equine/Tennessee/29A/2014 (H3N8) and the polymerase basic protein 2 (PB2), neuraminidase (NA), and non-structural protein (NS) segments to A/equine/Malaysia/M201/2015 (H3N8).

Phylogenetic characterization of individual gene segments, using currently available H3N8 viral genomes, of both equine and canine origin, further established that A/equine/Montana/9564-1/2015 belonged to the Florida Clade 1 viruses.
Interestingly, replication kinetics of this H3N8 virus, using airway derived primary cells from multiple species, such as equine, swine, bovine, and human lung epithelial cells, demonstrated appreciable titers, when compared to Madin–Darby canine kidney epithelial cells. These findings indicate the broad host spectrum of this virus isolate and suggest the potential for cross-species transmissibility.

Overall, this study provided us insights about the evolutionary relationship and in vitro cross-species infectivity of A/equine /Montana/9564-1/2015 (H3N8) virus. A comprehensive genome-scale analysis of new isolates is essential to understand the molecular evolution and phylodynamics of EIV, which in turn would help in the strategic selection of vaccine strains, effective surveillance, and control.
Antigenic and genetic variations caused by evolutionary processes play a critical role in determining the dynamics of host range and tropism of influenza viruses. Further in vivo studies are needed to evaluate the cross-species transmissibility of EIV H3N8 and its ability to cause infections and respiratory diseases in other mammalian hosts, including humans.
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If you are betting on the source of the next influenza pandemic - human, avian, or swine hosts (or a combination) - are by far the most likely springboards.  At least based on the past 100 years of observation.

But influenza is notoriously unpredictable, and we have to be prepared for the fact that every once in awhile, a long shot may come in.

Monday, January 15, 2018

Saudi MEWA: Fri-Mon Reports 6 New Cases Of H5N8


A small number of new H5N8 cases continue to be reported by the Saudi Ministry of Environment, Water & Agriculture (MEWA), with the following reports posted since Friday.

Registration (3) new infections Panevlonz birds (H5N8)

25/04/1439  (Friday)

The ministry continues in cooperation with the relevant authorities efforts to contain the outbreak of high pathogenic avian influenza (H5N8), and during the twenty-four hours last make sure there is (3) injuries in both Quwaiya province in Riyadh and Buraidah in Qassim region, and the city of Medina in the backyard traditional breeding, except one injured in the bird market in the city of Medina.
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Recording injury (one) new bird flu (H5N8)

26/04/1439 (Saturday)

The ministry continues in cooperation with the relevant authorities efforts to contain the outbreak of high pathogenic avian influenza (H5N8), and during the twenty-four hours past and make sure there is injury (one) in the traditional monsters breeding birds Quwaiya province in Riyadh

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No new cases of avian influenza (H5N8) during the 24-hour last

27/04/1439  (Sunday)

The ministry continues to cooperate with the relevant authorities efforts to contain the outbreak of high pathogenic avian influenza (H5N8), where no new cases of the disease among birds did not appear during the four and twenty hours last

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Recording two goals new bird flu (H5N8)

28/04/1439 (Monday)

The ministry continues to cooperate with the relevant authorities efforts to contain the outbreak of high pathogenic avian influenza (H5N8), where the number of new infections confirmed in the laboratory of the disease among birds during the twenty-four hours last in the Kingdom (two cases) only in the city of Dammam and the province of Riyadh region Dhurma

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OIE Notification: H5N8 in Karnataka, India

Credit Wikipedia


For nearly two weeks there have been unconfirmed media reports of bird flu in Karnataka State, in southern India.  First described as H5N1, later reports (see FluTrackers' Thread India - Karnataka: chicken in Dasarahalli tested positive for bird flu H5N1 (media))
rolled back the identification to simply HPAI H5. 

Today the OIE has published a notification on this outbreak, which began on December 26th, and cites HPAI H5N8 as the culprit. 


DEFRA: Rapid Risk Assessment On H5N6 In Wild Birds In Dorset



Five days ago we saw the OIE Notification: 1st Occurrence Of H5N6 In The UK which listed 3 sick swans recovered in Dorset, in the south of England. Two days later in UK: DEFRA Announcement On H5N6 In 17 Wild Birds In Dorset, we saw the number and types of wild birds expanded with a warning that more could expected over the coming days.
The UK now joins The Netherlands, Germany, and Switzerland in reporting this recently arrived reassorted H5N6 (from last year's H5N8 epizootic virus).  H5N8, meanwhile, has recently been reported in Italy, Russia, Bulgaria, The Middle East and Africa.
Although H5N6 isn't spreading across Europe at anywhere near the speed that H5N8 did during last year's record bird flu season, during its first foray in to Europe - during the winter of 2014-15, when North America was in the throws of their own epizootic - H5N8 activity in Europe was similarly subdued.

We've a lengthy Rapid Risk Assessment today from the UK's DEFRA, which provides us with considerably more background on this reassorted virus than we've seen so far, along with an assessment of the risk to the UK's poultry interests.
Rapid Risk Assessment on the finding of H5N6 HPAI in wild birds in Dorset

January 2018

In December 2017, the Netherlands reported a new strain of H5N6 HPAI in a duck fattening farm in Flevoland; several cases in wild birds (mute swans, Cygnus olor) in the same region and cases in captive birds at a single site (mallard ducks, mute swans, greylag geese and guinea fowl) were reported in the following days.

In late December / early January two further cases in wild birds were reported, one in southern Germany and one in west Switzerland. In January 2018, three mute swans were found dead and tested positive for H5N6 HPAI in Dorset, on the South coast of England and initial analysis confirms this virus has the same characteristics as the Netherlands strain. 

The current numbers, as of 12th January, are 15 mute swans, 1 Canada goose and 1 pochard, all found dead and all testing positive. There have been no reports in domestic poultry, either commercial or small holding premises.


Hazard Identification

H5N6 HPAI viruses of the clades and d were detected first in China in 2014 and then continued to spread in poultry in China, Laos, Cambodia, South Korea, Vietnam and Japan and some viruses in clade have zoonotic potential and caused a small number of human cases (EFSA Panel, 2017).

According to a Promed report on 13 December 2017, “The OIE/FAO/EU International Reference Laboratory at APHA-Weybridge, UK, working with the Animal and Plant Quarantine Agency of the Republic of Korea, characterized a novel emerging highly pathogenic avian influenza A(HPAI) (H5N6) virus isolated from both wild birds and domestic poultry in the Republic of Korea.
Phylogenetic analyses of a representative of these viruses showed that it was different from previously circulating Korean H5N6 viruses in the 2016-2017 winter season and which had caused a very limited number of human cases. 

All genes of the novel HPAI virus except the neuraminidase were of the "European H5N8 HPAI lineage" that emerged last winter (16/17) and continues to be detected in some European countries. The neuraminidase N6 is most similar to the H5N6 reassortant virus isolated from chickens in Greece in early 2017, which had acquired a neuraminidase gene from the Eurasian low pathogenic avian influenza A virus lineage circulating in wild birds. These analyses demonstrate continued circulation of this H5 lineage in multiple geographic regions and likely wild-bird mediated spread.” See also Lee et al, 2017.

The current season (winter 2017/2018) has seen several outbreaks in poultry and cases in wild birds of H5N8 HPAI in Italy, Bulgaria and Germany (see Figure 1), but none in the northerly part of the EU; further outbreaks of H5N8 HPAI cannot be ruled out since the virus continues to circulate elsewhere including the Middle East and South Africa.

In December 2017, the Netherlands reported a single outbreak of avian influenza in fattening ducks in Flevoland region (OIE, 2017). Four week old ducks showed increased clinical signs and increased mortality. The birds tested positive at the National Reference Laboratory and the virus was confirmed as H5N6 HPAI; disease control measures were put in place, including a housing requirement for all commercial poultry. According to the Dutch laboratory, the sequence shows this was a reassortant between a low pathogenic HxN6 strain and the circulating Eurasian H5N8 HPAI strain (Wageningen, 2017). 

Further cases in wild mute swans were reported during December and January (OIE, 2017). At the end of December, Switzerland reported a case of H5N6 HPAI in a wild mute swan and on the 8th January, Germany reported a case of H5N6 HPAI in a wild duck (species not known; OIE, 2017). The H5N6 HPAI currently in Europe therefore appears to be an emerging strain.


Overall, the finding of wild birds infected with H5N6 HPAI virus at the site in Dorset does not substantially increase the risk of incursion to poultry on poultry farms in GB. There may be some unquantifiable increase in risk to poultry premises nearby, because of the contact with bridging species or other wild water birds; this is only a marginal increase and will be time limited by the level of infection circulating in the wild bird population. This will depend on the biosecurity practices at the premises.

There is no increase in risk of incursions of avian influenza to wild bird populations in the rest of the UK, above MEDIUM which is the current level. Wild waterfowl are unlikely to move far from the area at this time of year, according to the observed behaviour of the birds in previous seasons; this site is a high risk site during any season for avian influenza in Europe; previous incursions here did not lead to any spread to poultry farms. More wild waterfowl may test positive in the coming weeks not only from this site but elsewhere in the UK or continental Europe and this will continue to inform our risk level.

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PLoS One: Effectiveness of HPAI H5N1 Vaccination in Poultry - Indonesia


With H5N6, H5N8, H5N1 and an array of lesser HPAI H5 viruses continuing to expand globally we've seen desperate pleas from some hard hit farmers to allow the use of poultry AI vaccines (see South Africa: DAFF Statement On Vaccines For Avian Flu and USDA Issues 2nd Request for Proposals for HPAI Vaccine)
With the exception of China, Egypt, Indonesia, Vietnam, and Hong Kong, most countries eschew the use of bird flu vaccines, and opt instead for the OIE recommended course of culling and containment.
The reasons run the gamut from fears that poultry vaccines may only mask bird flu - not prevent it - to concerns over selling vaccinated  birds to foreign markets.  Once vaccinated, antibody tests would show positive titres, whether the birds were infected or not.

Reasons why, for more than a decade, the OIE has warned that vaccination of poultry cannot be considered a long-term solution to combating avian flu. And that “Any decision to use vaccination must include an exit strategy, i.e. conditions to be met to stop vaccination. – OIE on H7N9 Poultry Vaccines.

Countries that have gone the vaccine route over the past dozen years haven't found an easy way to that `exit strategy' - and while vaccine use may have them spared some economic pain - avian influenza has become increasingly entrenched in their poultry industries. 

The problem is that as avian viruses evolve, poultry vaccines become increasingly less effective; often only masking the symptoms of infection.
As an example, a 2012 study (see Egypt: A Paltry Poultry Vaccine), examined the effectiveness of six commercially available H5 poultry vaccines used in Egypt; only one (based on a locally acquired H5N1 seed virus) actually appeared to offer protection.
Poor vaccine matches can allow AI viruses to spread silently among flocks, to continue to reassort and evolve, and potentially lead to the emergence new subtypes of avian flu. A few earlier blogs on that include:
Subclinical Highly Pathogenic Avian Influenza Virus Infection among Vaccinated Chickens, China).

Study: Recombinant H5N2 Avian Influenza Virus Strains In Vaccinated Chickens

EID Journal: Subclinical HPAI In Vaccinated Poultry – China
We've a new study, published late last week in PLoS One, that looks at the effectiveness of HPAI H5 vaccination in Indonesia, a country once known as the world's hot spot for human H5N1 infection, but now (for reasons cloaked in mystery) has fallen off that list. 
Since Indonesia declared bird flu `endemic' in 2006, they haven't had to make regular OIE reports - and so like from Egypt - we get relatively little solid reporting on their bird flu struggles in recent years. 
Today's report, however, paints a less than impressive picture of poultry vaccination effectiveness in Indonesia over the past decade. The authors cite frequent low HI titres in poultry even after three rounds of vaccines, vaccination failures, and warn of silent infections and the generation of new H5N1 antigenic variants. 
While the authors recommend steps they believe would improve Indonesia's AI vaccine performance, the upshot is that effective poultry vaccination programs have been elusive in Indonesia even after a decade of use, and are far more complex to mount than most people believe.
I've only included some of the highlights from a much longer study, follow the link to read the paper in its entirety.
Field effectiveness of highly pathogenic avian influenza H5N1 vaccination in commercial layers in Indonesia 
Simson Tarigan ,Michael Haryadi Wibowo,Risa Indriani,Sumarningsih Sumarningsih, Sidna Artanto, Syafrison Idris,Peter A. Durr, Widya Asmara, Esmaeil Ebrahimie,Mark A. Stevenson,Jagoda Ignjatovic
Although vaccination of poultry for control of highly pathogenic avian influenza virus (HPAIV) H5N1 has been practiced during the last decade in several countries, its effectiveness under field conditions remains largely unquantified. Effective HPAI vaccination is however essential in preventing incursions, silent infections and generation of new H5N1 antigenic variants. 

The objective of this study was to asses the level and duration of vaccine induced immunity in commercial layers in Indonesia. Titres of H5N1 haemagglutination inhibition (HI) antibodies were followed in individual birds from sixteen flocks, age 18–68 week old (wo).
The study revealed that H5N1 vaccination had highly variable outcome, including vaccination failures, and was largely ineffective in providing long lasting protective immunity.
Flocks were vaccinated with seven different vaccines, administer at various times that could be grouped into three regimes: In regime A, flocks (n = 8) were vaccinated two or three times before 19 wo; in regime B (n = 2), two times before and once after 19 wo; and in regime C (n = 6) three to four times before and two to three times after 19 wo. HI titres in regime C birds were significantly higher during the entire observation period in comparison to titres of regime A or B birds, which also differed significantly from each other. 

The HI titres of individual birds in each flock differed significantly from birds in other flocks, indicating that the effectiveness of field vaccination was highly variable and farm related. Protective HI titres of >4log2, were present in the majority of flocks at 18 wo, declined thereafter at variable rate and only two regime C flocks had protective HI titres at 68 wo. 

Laboratory challenge with HPAIV H5N1 of birds from regime A and C flocks confirmed that protective immunity differed significantly between flocks vaccinated by these two regimes. The study revealed that effectiveness of the currently applied H5N1 vaccination could be improved and measures to achieve this are discussed.
HPAI vaccination, intensively applied in Sector 3 layers in Indonesia, had highly variable outcome, including vaccination failures and did not provide sufficiently long protective immunity in the majority of flocks. Indonesia adopted HPAI vaccination in 2004 with the aim of reducing the incidence of H5N1 infections in poultry, with the ultimate objective of achieving eradication of the virus.
Assessment of field effectiveness of the currently applied H5N1 vaccination was useful in demonstrating that vaccination, as practiced in Sector 3 poultry, could be improved. In particular, we have identified that the most frequently used vaccination regime, consisting of three vaccinations before 19 wo, does not provide sufficiently long lasting immunity and protection of layers with any of the commonly used HPAI vaccines.
Instead, four or five vaccinations, of which two are during the laying period at 26–28 and 40–48 wo, would ensure longer lasting protection and further reduce the risk from exogenously introduced H5N1 infections. Monitoring the level of immunity in vaccinated flocks would help to identify key factors that contribute to inadequate responses to vaccination, short duration of protective immunity and vaccination failures. The timing of re-vaccination could be adjusted according to the flock immunity, ensuring an effective response and longer lasting protective immunity.
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Saudi MOH Reports 1 New MERS Case & 3 Deaths


For the past couple of weeks we've been following what appears to be a modest uptick in (mostly) primary MERS cases across Saudi Arabia, along with an unusually high number of fatalities.  
Our last update came on Friday in Saudi MOH: 3 New Primary MERS Cases (Jan 11th), which brought their 2018 total to 12 MERS cases and 8 deaths.

Although the Saudi MOH maintains two (one in Arabic & one in English) daily MERS reports, sometimes - for reasons that aren't usually clear - postings are delayed by a day or two and sometimes entire days are skipped.

A snapshot taken this morning (see below) of the English language surveillance shows two daily reports (3rd & 13th) missing from the first two weeks of 2018.


While it hasn't been posted to the English language list, an entry for the 13th was posted on the Arabic site (see graphic at top of blog), showing 1 new case in Riyadh, along with 3 more fatalities.  Since these daily updates are posted in graphical form, regular translation software cannot be used.

Luckily a tweet (in Arabic) overnight from @UDHMED has helped me identify the 3 new fatal cases as the previously announced 72 y.o. male from Gurayat (Jan 11th), a 60 y.o. female from Buraidah (Jan 8th), and a 60 y.o. male from Riyadh (Jan 2nd).
Curiously, the 72 y.o. from Gurayat was listed in stable condition just two days before. This is the third initially-reported-as-stable-but-ultimately-expired case announced by the MOH in the past week.
Based on the available reports, during the first 14 days of January, KSA has seen 13 MERS cases (3 have been linked to recent camel exposure, 9 are primary (community acquired), and 1 was a secondary HCW exposure) along with 11 deaths and zero recoveries.
Several of these deaths were in patients infected and announced in late  December. Going back a full month (Jan14th-Dec 14th), however, we count 18 Cases and 12 Deaths (66.6%), which is substantially higher than the historical Saudi 40.5% average fatality rate since 2012.

While this is probably a temporary aberation, possibly due to an expected higher overall winter mortality rate, it is a trend we'll be watching. 

Also of interest, these 18 cases have all been reported in the last 20 days, and of those 13 are primary (community acquired) - with no listed risk exposure - while 4 had camel exposure.  Again a bit of a deviation from what we've seen historically.

Short term trends have a habit of evening out over time, and so we shouldn't make too much of all of this.  At least not yet.  
If we see a higher mortality rate continue in the months ahead, or a continued increase in the number of community acquired cases, then it may signify somethng of significance.  
For now, this is simply a short term deviation from the norm; worth noting and keeping an eye on.