Wednesday, June 20, 2018

Russia Reporting Avian Flu Outbreaks In Samara, Penza & Kursk Regions


While it isn't all that unusual to see avian flu activity in Russia during the spring and summer, the past five months have been unusually quiet, with nothing reported out of Russia since a large HPAI H5N2 outbreak was announced last December.
That is, until last week. 
In Rosselkhoznadzor & OIE: HPAI H5 Reported In Kursk Oblast, we learned of at least two outbreaks of an HPAI H5 virus (full subtype not yet identified) in Kursk Oblast.
The first in a small backyard flock in the village of N. Grayvoronka, and the second involved carcasses of poultry (chickens), found in the forest belt Ryshkovskogo.
While the Kursk Oblast office of Rosselkhoznadzor hasn't posted an update since June 14th, Russian media continues to report continued avian flu activity in the region, including this report from TASS.
In the Kursk region registered the third hearth of bird flu In the country

June 19, 18:12 UTC + 3

The governor of the region Alexander Mikhailov signed a decree on the introduction of quarantine in the district where the identified disease foci

Kursk, 19 June. / TASS /. Experts have registered the third focus of avian influenza in the territory of Kursk region. This was reported by TASS on Tuesday in the regional veterinary administration.

"At the moment we have [the flu outbreak of bird] in the Soviet area - two personal subsidiary farms in the same locality, in the Kursk region - a waste of bird carcasses, and the third case - the village Vasilevka This is also the Soviet area, but another location." , - said the source.

Experts have identified the first influenza virus hotbed of avian type A subtype H5 in the Kursk region last week in pathological material taken from dead chickens and ducks in a private farm in the village of Lower Grayvoronke Soviet area, the second - on the territory of the village council shelterbelts Ryshkovskogo Kursk region.

(Continue . . . )

Announced in just the last couple of hours - from the Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) of the Chelyabinsk region - are reports of fresh outbreaks of avian flu in both Samara and Penza, both of which lie several hundred miles to the west of Chelyabinsk.
Cases of bird flu in the Samara and Penza regions

Office of Rosselkhoznadzor for the Chelyabinsk region informs that on 16 and 17 June in the pathological material taken from the fallen poultry contained in private farms in Bolsheglushitsky district of the Samara region and Kolyshleysky District Penza region highlighted the genetic material of the virus avian influenza.

In Bolsheglushitsky district of the Samara region and Kolyshleysky District Penza Oblast cases poultry deaths recorded contained in private farms. Also Kolyshleysky District Penza Oblast cases deaths recorded turkey, contained in the Company 'PenzaMolInvest "at the site of rearing and fattening. Laboratory confirmed that the isolated genetic material of the virus avian influenza.

In areas all measures are taken to prevent the spread of avian influenza.

Recall that the avian influenza - a highly contagious, acute viral proceeding affecting agricultural, commensal and wild birds disease affecting the respiratory and gastrointestinal tracts. Avian influenza is able to take the form of epizootic diseases, causing massive population coverage and having widespread. In unfavorable aviary suspicious diseased and disease in poultry discarded kill bloodless manner and utilized. Apparently healthy livestock are killed for meat. In the case of visiting poultry farms (farms) bird flu, caused by the highly pathogenic virus, introduced stringent sanitary operation of the economy.

In the Chelyabinsk region avian influenza was detected in 2005. Then killed 480 birds, 500 more were killed in the village of Oktyabrsky Oktyabrsky district.

Curiously, as of this writing,  I can find no mention of these outbreaks on either the main Rosselkhoznadzor website, or on the Samara or Penza local web portals.

Since avian flu activity during the summer in Russia has previously been linked to seeing increased outbreaks in Europe later in the year (see FAO/EMPRES: H5N8 Clade Detected Over Summer In Russia), we pay attention to these types of events.
After several months of quiescence, over the past week we've seen a bit of a surge in avian flu reports in the Northern Hemisphere; specifically in Bulgaria, Northern Ireland, and now multiple locations in Russia

A subtle reminder that with the constant migration and mixing of potentially infected birds around the globe, that avian flu viruses have the ability to pop up when and where you least expect them. 

And that biosecurity against poultry diseases is now - out of necessity - a year-round endeavor.

June 19, 18:12 UTC + 3

The governor of the region Alexander Mikhailov signed a decree on the introduction of quarantine in the district where the identified disease foci

Kursk, 19 June. / TASS /. Experts have registered the third focus of avian influenza in the territory of Kursk region. This was reported by TASS on Tuesday in the regional veterinary administration.
"At the moment we have [the flu outbreak of bird] in the Soviet area - two personal subsidiary farms in the same locality, in the Kursk region - a waste of bird carcasses, and the third case - the village Vasilevka This is also the Soviet area, but another location." , - said the source.
Experts have identified the first influenza virus hotbed of avian type A subtype H5 in the Kursk region last week in pathological material taken from dead chickens and ducks in a private farm in the village of Lower Grayvoronke Soviet area, the second - on the territory of the village council shelterbelts Ryshkovskogo Kursk region. In connection with the incident, the governor of the region Alexander Mikhailov signed a decree on the introduction of quarantine areas in the territory, providing increased control of all poultry farms, operating in closed mode, as well as the number of poultry, which is contained in private farms.

Подробнее на ТАСС:

n the Kursk region registered the third hearth of bird flu

June 19, 18:12 UTC + 3

The governor of the region Alexander Mikhailov signed a decree on the introduction of quarantine in the district where the identified disease foci

Kursk, 19 June. / TASS /. Experts have registered the third focus of avian influenza in the territory of Kursk region. This was reported by TASS on Tuesday in the regional veterinary administration.
"At the moment we have [the flu outbreak of bird] in the Soviet area - two personal subsidiary farms in the same locality, in the Kursk region - a waste of bird carcasses, and the third case - the village Vasilevka This is also the Soviet area, but another location." , - said the source.
Experts have identified the first influenza virus hotbed of avian type A subtype H5 in the Kursk region last week in pathological material taken from dead chickens and ducks in a private farm in the village of Lower Grayvoronke Soviet area, the second - on the territory of the village council shelterbelts Ryshkovskogo Kursk region. In connection with the incident, the governor of the region Alexander Mikhailov signed a decree on the introduction of quarantine areas in the territory, providing increased control of all poultry farms, operating in closed mode, as well as the number of poultry, which is contained in private farms.

Подробнее на ТАСС:

DAERA: 2nd Wild Bird Confirmed With HPAI H5N6 At Lurgan Park in Northern Ireland

2018 H5N6 Reports - Northern Ireland


Last Friday, in DAERA: H5N6 Confirmed In Wild Bird In Northern Ireland, we learned of the recovery of a dead greylag goose from Lurgan Park in County Armagh, N.I. that has tested positive for HPAI H5N6.
This location holds some significant because earlier this month, Lurgan Park was also the site of a large agricultural show (see Crowds flock to Lurgan park as farming show celebrates 106th year), which included many animal exhibits, including poultry. 
All of which makes yesterday's announcement by DAERA of a second infected greylag goose found in that park worth noting. According to a report in Farming Life, DAERA representatives met with local poultry industry representatives after the first case was announced last week.

The OIE Report on the first bird, reported last week, gives a date of the start of the outbreak as June 14th, but it isn't entirely clear when the bird was recovered, or likely died.
While we've seen no sign of sick or infected poultry linked to this agricultural show, the Chief Veterinary Officer for Northern Ireland is urging all bird keepers to be vigilant, and to review their biosecurity.
This is only the third wild bird with HPAI H5N6 detected in Northern Ireland this year (see chart at top of blog), but it is a reminder that the virus continues to circulate in the wild, even well into summer.

Chief Vet stresses importance of biosecurity and vigilance against avian flu

Date published: 19 June 2018

The Department of Agriculture, Environment and Rural Affairs (DAERA) today confirmed that a second wild greylag goose, found in Lurgan Park, County Armagh, has tested positive for H5N6 Avian Influenza. The second goose, like the first, was reported to DAERA as part of its dead wild bird surveillance programme, and was submitted for testing at the Agri-Food and Biosciences Institute (AFBI), where initial testing has indicated avian influenza, sub-type H5N6.
The Chief Veterinary Officer for Northern Ireland, Dr Robert Huey, said: “This latest case in a wild bird further emphasises the requirement for all bird keepers to remain vigilant and to critically review their biosecurity measures, for example, feeding and watering birds under cover to help reduce the risk of their poultry coming in contact with wild birds. It is important that flock keepers report early any suspicions of disease.

“While it is not unexpected to find another case of avian flu in a wild bird in close proximity to the confirmed case of last week, and the risk to poultry remains low, it is important that flock keepers remain vigilant and it is essential that we take the necessary steps to protect our poultry industry, international trade and the wider economy.

“I continue to encourage strongly all bird keepers to register their flocks. This will ensure they receive the latest information from the Department and also allow them to be contacted in an avian disease outbreak enabling them to protect their flock at the earliest opportunity. I would also encourage bird keepers to subscribe to the Avian Influenza text service by simply texting: ‘BIRDS’ to 67300”.

Bird keepers visiting waterfowl sites such as lakes and ponds should also take measures to prevent disease spread to back yard flocks through contamination of footwear with wild bird faeces.

Advice from the Public Health Agency is that the risk to public health from the virus is very low, however, the general public is advised to take appropriate biosecurity precautions before touching or picking up birds that are dead, or appear to be sick or dying. Further advice can be found on the DAERA website.

The Food Standards Agency has confirmed that Avian Influenza does not pose a food safety risk for UK consumers. Thoroughly cooked poultry and poultry products, including eggs, are safe to eat.

Members of the public are encouraged to report dead waterfowl (swans, geese or ducks) or gulls, or five or more dead wild birds of other species in the same location, to the DAERA helpline on 0300 200 7840, Mon-Fri 9.00am to 5.00pm.

Tuesday, June 19, 2018

Neuroinfluenza: A Review Of Recently Published Studies


Although primarily a self-limiting infection of the respiratory tract, for a small subset of cases - most often among children - influenza can present with a variety of subtle, and sometimes profound, neurological symptoms.
Credit CDC 2018 COCA Call On Severe Influenza

The exact mechanisms behind these neurological manifestations are unknown, as seasonal flu viruses are generally regarded as being non-neurotropic. But some researchers have suggested that these neurological symptoms may be due to neuroinflammation induced by the host's immune response.
That said, we have seen evidence that some influenza viruses - particularly novel flu types - can be more neuroaffective than others.
In 2009, a PNAS study (link below) found that the H5N1 virus was highly neurotropic in lab mice, and in the words of the authors `could initiate CNS disorders of protein aggregation including Parkinson's and Alzheimer's diseases’.
Highly pathogenic H5N1 influenza virus can enter the central nervous system and induce neuroinflammation and neurodegeneration
In 2015, after the death of the first imported H5N1 case in Canada, we saw a study (see CJ ID & MM: Case Study Of A Neurotropic H5N1 Infection - Canada), where the authors wrote: `These reports suggest the H5N1 virus is becoming more neurologically virulent and adapting to mammals'.
In a Scientific Reports study on the genetics of the H5N1 clade virus - Highly Pathogenic Avian Influenza A(H5N1) Virus Struck Migratory Birds in China in 2015 – the authors warned of its neurotropic effects, and that it could pose a ` . . . significant threat to humans if these viruses develop the ability to bind human-type receptors more effectively.'
Far less certain are the long-term neurological impacts of severe (or repeated) influenza infections, although we've seen studies suggesting links to Parkinson's, Schizophrenia, and even Alzheimer's  (see Nature Comms: Revisiting The Influenza-Parkinson's Link). 
We last looked this topic in February, in JNeurosci: Another Study On The Neurocognitive Impact Of Influenza Infection, where we saw a study from the Technical University of Braunschweig, which found long-term neurocognitive impairment in mice following infection with specific types (H3N2 & H7N7) of influenza viruses - but not in others (H1N1).
Obviously, not-so-good news if you are a mouse, but how relevant these results are for humans remains an open question. 
Since February several new studies have been published on this topic, and so today a brief review, with links and excerpts.  I'll return with a bit more at the end. 
(Note: Although published in February,  the first study (below) was made available online in 2017).
Neuroinfluenza: evaluation of seasonal influenza associated severe neurological complications in children (a multicenter study)
Paksu, M.S., Aslan, K., Kendirli, T. et al. Childs Nerv Syst (2018) 34: 335.


Although influenza primarily affects the respiratory system, in some cases, it can cause severe neurological complications. Younger children are especially at risk. Pediatric literature is limited on the diagnosis, treatment, and prognosis of influenza-related neurological complications. The aim of the study was to evaluate children who suffered severe neurological manifestation as a result of seasonal influenza infection.


The medical records of 14 patients from six hospitals in different regions of the country were evaluated. All of the children had a severe neurological manifestations related to laboratory-confirmed influenza infection.


Median age of the patients was 59 months (6 months—15.5 years) and nine (64.3%) were male. Only 4 (28.6%) of the 14 patients had a comorbid disease. Two patients were admitted to hospital with influenza-related late complications, and the remainder had acute complication.
The most frequent complaints at admission were fever, altered mental status, vomiting, and seizure, respectively. Cerebrospinal fluid (CSF) analysis was performed in 11 cases, and pleocytosis was found in only two cases. Neuroradiological imaging was performed in 13 patients. The most frequent affected regions of nervous system were as follows: cerebellum, brainstem, thalamus, basal ganglions, periventricular white matter, and spinal cords. Nine (64.3%) patients suffered epileptic seizures. Two patients had focal seizure, and the rest had generalized seizures. Two patients developed status epilepticus. Most frequent diagnoses of patients were encephalopathy (n = 4), encephalitis (n = 3), and meningitis (n = 3), respectively.
The rate of recovery without sequelae from was found to be 50%. At discharge, three (21.4%) patients had mild symptoms, another three (21.4%) had severe neurological sequelae. One (7.1%) patient died. The clinical findings were more severe and outcome was worse in patients < 5 years old than patients > 5 years old and in patients with comorbid disease than previously healthy group.


Seasonal influenza infection may cause severe neurological complications, especially in children. Healthy children are also at risk such as patients with comorbid conditions. All children who are admitted with neurological findings, especially during the influenza season, should be evaluated for influenza-related neurological complications even if their respiratory complaints are mild or nonexistent.

Our next study comes from the journal Brain Development.

Influenza-associated neurological complications during 2014–2017 in Taiwan
Li-Wen Chen, Chao-Ku Teng, Yi-Shan Tsai, Jieh-Neng Wang, Yi-Fang Tu, Ching-Fen Shen,  Ching-Chuan Liu

Seasonal influenza-associated neurological complications had high mortality and morbidity rates in recent studies. We reported influenza-associated encephalitis/encephalopathy in children during 2014–2017 in Taiwan, focusing on neurological presentations, neuroimaging correlations, and critical care managements.


During January 1st 2014 to June 30th 2017, pediatric patients reported to the Taiwan Centers for Disease Control surveillance system for severe complicated influenza infections in the hospital were retrospectively reviewed. Children with influenza-associated encephalitis/encephalopathy were inspected for clinical presentations, laboratory data, neuroimaging studies, treatment modalities, and neurological outcomes.


Ten children with median age 5.9 years were enrolled for analysis. Influenza-associated encephalitis/encephalopathy appeared in the spring and summer, with a delayed peak comparing with the occurrence of pneumonia and septic shock.
The neurological symptoms developed rapidly within median 1 day after the first fever episode. All patients had consciousness disturbance. Seven patients (70%) had seizures at initial presentation, and six of them had status epilepticus. Anti-viral treatments were applied in all patients, with median door-to-drug time 0.9 h for oseltamivir and 6.0 h for peramivir. Multi-modality treatments also included steroid pulse therapy, immunoglobulin treatment, and target temperature management, with 85.2% of the major treatments administered within 12 h after admission.
Nine of the ten patients recovered without neurological sequelae. Only one patient had epilepsy requiring long-term anticonvulsants and concomitant cognitive decline.


In highly prevalent area, influenza-associated encephalitis/ encephalopathy should be considered irrespective of seasons. Our study suggested the effects of timely surveillance and multi-modality treatments in influenza-associated encephalitis/encephalopathy.

While influenza-related neurological complications are most often reported in children, adults are not necessarily immune, as reported in the following two studies. 
Acute necrotizing encephalopathy in an adult with influenza A infection
Nobuaki Ochi,1 Kento Takahashi,2 Hiromichi Yamane,1 and Nagio Takigawa1


Acute necrotizing encephalopathy following influenza infection is a rapidly progressing disease with high morbidity. Although the neurological disorder is sometimes reported in children, it is very rare in adults.
We herein describe an adult with acute necrotizing encephalopathy captured on a series of brain magnetic resonance images. A 55-year-old man had fever and impaired consciousness. He was diagnosed with influenza A (H1N1). Brain magnetic resonance imaging revealed symmetrical lesions in the cerebellum and basal nucleus, showing typical acute necrotizing encephalopathy. Physicians should know that influenza-associated acute necrotizing encephalopathy can occur even in middle-aged adults.
(Continue . . . )

And finally, this study from the Indian Journal of Critical Care Medicine.
Adult Influenza A (H1N1) Related Encephalitis: A Case Report
Devinder Midha, Arun Kumar, Pratibha Vasudev, Zafar Ahmad Iqbal, and Amit Kumar Mandal

The year 2009–2010 saw H1N1 influenza outbreaks occurring in almost all countries of the world, causing the WHO to declare it a pandemic of an alert level of 6. In India, H1N1 influenza outbreaks were again reported in late 2014 and early 2015. Since then, sporadic cases of H1N1 influenza have been reported.
H1N1 influenza usually presents itself with respiratory tract symptoms. In a minority of patients, abdominal symptoms may occur as well. Acute influenza-associated encephalopathy/encephalitis mostly occurs in the pediatric population, whereas in adults, it is a rare complication. The incidence of neurological complications appears to have increased after the 2009 H1N1 influenza A virus pandemic.
We would like to draw attention to an adult patient case who initially presented with respiratory symptoms but then deteriorated and developed encephalitis, which is rarely reported. As per literature reviewed by Victoria Bangualid and Judith Berger on PubMed, only 21 cases of neurological complications were found in adult influenza A patients, out of whom 8 had encephalopathy.
(Continue . . . )

Despite the mounting evidence, the neurological impacts of influenza are still largely unappreciated by the public, and even by a lot of doctors, and therefore cases likely go under reported.
It may also turn out that some, if not most, of the reported behavioral problems which have been previously (and tentatively) linked to the use of oseltamivir (aka Tamiflu) may have more do to with the neurocognitive effects of influenza infection than from taking the drug. 
But most of all, these studies - along with others, like NEJM: Acute Myocardial Infarction After Laboratory-Confirmed Influenza Infection and Eur. Resp.J.: Influenza & Pneumonia Infections Increase Risk Of Heart Attack and Stroke - are reminders that influenza is a far more complex, and far more dangerous, virus than most people give it credit for.

Something to seriously consider when you are deciding whether to bother getting that flu shot next fall.

Monday, June 18, 2018

HPAI H5Nx Clade Shedding In Cottontail Rabbits

Credit Wikipedia


Regular readers will recall that over the past several years we've been looking into the carriage of novel (and seasonal) flu by domestic and peridomestic animals, and how they might fit into the ecology and evolution of influenza viruses.

On the domestic front, dogs and cats take center stage, as both are susceptible to at least some novel flu strains.  A few (of many) blogs include:
mBio: Novel Reassortant Influenza A Viruses in Canines in Southern China
EID Journal: Avian H7N2 Virus in Human Exposed to Sick Cats

Study: Dogs As Potential `Mixing Vessels’ For Influenza
Korean CDC Statement On H5N6 In Cats

Influenza A(H6N1) In Dogs, Taiwan
On the peridomestic front, in recent years we've seen growing evidence that small mammals - like rabbits, skunks, mink, and even small rodents - can be infected by, and potentially spread, flu viruses.
While these types of animals may not pose as much as a direct threat of transmitting flu viruses to humans, they do provide a way for viruses in the wild to gain entry into farms, or to jump to dogs and cats.  
And carriage of novel flu viruses by any mammalian host provides the virus with an opportunity to develop host adaptations, potentially making it easier to jump to other mammals. 

A few past blogs include:
H9N2 Adaptation In Minks
Sci Rpts: Characterization of Avian H7N2 in Wild Birds and Pikas in Qinghai-Tibet Plateau Area
Taking HPAI To The Bank (Vole)
EID Journal: Guinea Pigs As Reservoirs For Influenza
One of the leaders in research into flu carriage and shedding by peridomestic animals is  Dr Jeffery Root - a Research Wildlife Biologist at the National Wildlife Research Center -  whose work we've been following for several years.
Which brings us to a new brief report (alas, mostly behind a pay wall) in the Archives of Virology, where Dr. Root et al. show that the HPAI H5 clade virus - which sparked last year's European record setting epizootic - can infect cottontail rabbits, and that they can then shed the virus for one or more days. 
This is of particular interest since most clade viruses - while causing huge losses in the poultry industry and among wild birds over the past four years - have shown a very limited ability to infect mammals. 
The exception (so far) being the HPAI H5N6 virus which has infected at least 17 people in China (see Human Clade A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets).

First the (very) brief abstract, then I'll return with a bit more.

Cottontail rabbits shed clade H5 highly pathogenic avian influenza A viruses
J. Jeffrey Root, Angela M. Bosco-Lauth, Nicole L. Marlenee, Richard A. Bowen
First Online: 13 June 2018


During 2014-2015, clade H5Nx highly pathogenic (HP) avian influenza A viruses (IAV) were first detected in North America and subsequently caused one of the largest agricultural emergencies in U.S. history.

Recent evidence has suggested that cottontail rabbits can shed multiple IAV subtypes. We experimentally infected cottontail rabbits with three HP H5Nx IAVs. All rabbits tested shed virus on at least one day by at least one route.

Cottontail rabbits appear to be an exception to the limited capacity for replication that has been previously reported for certain other mammalian species inoculated with clade HP H5Nx avian influenza A viruses.

While clade H5N8, H5N5 and (European Lineage) H5N6 viruses have not been shown to infect humans, we did see early reports out of South Korea in 2014 of dogs having been infected (see MAFRA: H5N8 Antibodies Detected In South Korean Dogs (Again)) and just over a year ago we looked at J. Vet. Sci.: Experimental Canine Infection With Avian H5N8.
So we know that mammalian infection with at least some genotypes of H5N8 is at least possible.  Today's report expands that host range a bit.
Over the past two years we've looked at a number of studies that have explored the potential for H5N8 or its spin offs to evolve into a human health threat. A few include:
J Vet Sci: Evolution, Global Spread, And Pathogenicity Of HPAI H5Nx Clade 
Study: Virulence Of HPAI H5N8 Enhanced By 2 Amino Acid Substitutions

Sci Rpts: H5N8 - Rapid Acquisition of Virulence Markers After Serial Passage In Mice 
Perhaps most telling of these came last September in J. Virulence : Altered Virulence Of (HPAI) H5N8 Reassortant Viruses In Mammalian Models, which found:
Taken together, our study demonstrates that a single gene substitution from other avian influenza viruses can alter the pathogenicity of recent H5N8 viruses, and therefore emphasizes the need for intensive monitoring of reassortment events among co-circulating avian and mammalian viruses.
Last October's J. Virulence Editorial: HPAI H5N8 - Should We Be Worried? reviewed and summarized the literature, and found enough reasons to be concerned over the future evolutionary path of H5N8, stating that:
The extensive distribution of HPAI H5N8, as well as the gene reassortment with other circulating avian viruses already observed for H5N8 suggests there is a potential risk for human cases of H5N8 infections.
While expanding H5's host range is always a concern, the ability of small mammals like rabbits, raccoons, and rodents to breach farm biosecurity measures, and infect poultry populations is also troubling.

And may require the the rethinking of some farm biosecurity measures in the future to prevent a repeat of 2016/17 epizootic.


WHO MERS-CoV Update - Saudi Arabia


With the Saudi MOH MERS-CoV information portal remaining shut down (33 days and counting - see More On The Silence Of The Saudis), today we've received a very welcome - and unusually long-delayed - update from the World Health Organization on MERS cases reported by Saudi Arabia since their last update in January. 
Of note: The format of this update's case line list differs from what we've seen with recent WHO MERS-CoV reports,  it is presented in static PDF Format (not as a spreadsheet), it only contains the most recent Saudi Cases, and it contains slightly fewer data columns than before.
Since this new format presents clusters separate from the rest of the cases, I must assume anything not listed as a cluster can be taken as not having had exposure to a MERS-CoV case. 
Which means of 54 non-cluster aka `primary' cases, 23 (42%) are reported to have known camel exposure while 31 (58%) are not, making their source of infection undetermined.   
Whether this is a new format that WHO is adopting, or is simply a one-off change due to the way data has been supplied these past few months from the Saudis remains to be seen.

Middle East respiratory syndrome coronavirus (MERS-CoV) – Saudi Arabia

Disease outbreak news
18 June 2018

Between 12 January through 31 May 2018, the National IHR Focal Point of The Kingdom of Saudi Arabia reported 75 laboratory confirmed cases of Middle East respiratory syndrome coronavirus (MERS_CoV), including twenty-three (23) deaths. 

Details of the cases
Among these 75 cases, 21 cases were part of four distinct clusters (2 health care and 2 household clusters). The details of these clusters are described below, followed by a table listing all 75 laboratory confirmed cases reported to WHO during this time period: 

Cluster 1: From 2 through 4 February, a private hospital in Hafer Albatin Region reported a cluster of three (3) health care workers in addition to the suspected index case (four [4] cases in total).

Cluster 2: From 25 February through 7 March, a hospital in Riyadh reported six (6) cases, including the suspected index. No health care workers were infected.
Cluster 3: From 8 through 24 March, a household cluster of 3 cases (index case and 2 secondary cases) was reported in Jeddah. No health care workers were infected. 

Cluster 4: From 23 through 31 May, a household cluster was reported from Najran region with eight cases including the suspected index case. This cluster is still under investigation at the time of writing. As of 31 May, no health care workers have been infected and the source of infection is believed to be camels at the initial patient’s home.

pdf, 488kb
As of 31 May, the total global number of laboratory-confirmed cases of MERS-CoV reported since 2012 is 2,220, including 1,844 cases that have been reported from the Kingdom of Saudi Arabia. Among these cases, 790 MERS-CoV associated deaths have occurred since September 2012.

The global number reflects the total number of laboratory-confirmed cases reported to WHO under IHR to date. The total number of deaths includes the deaths that WHO is aware of to date through follow-up with affected member states. 

WHO risk assessment

Infection with MERS-CoV can cause severe disease resulting in high mortality. Humans are infected with MERS-CoV from direct or indirect contact with dromedary camels. MERS-CoV has demonstrated the ability to transmit between humans. So far, the observed non-sustained human-to-human transmission has occurred mainly in health care settings.

The notification of additional cases does not change the overall risk assessment. WHO expects that additional cases of MERS-CoV infection will be reported from the Middle East, and that cases will continue to be exported to other countries by individuals who might acquire the infection after exposure to animals or animal products (for example, following contact with dromedaries) or human source (for example, in a health care setting). WHO continues to monitor the epidemiological situation and conducts risk assessment based on the latest available information.

WHO advice

Based on the current situation and available information, WHO encourages all Member States to continue their surveillance for acute respiratory infections and to carefully review any unusual patterns.

Infection prevention and control measures are critical to prevent the possible spread of MERS-CoV in health care facilities. It is not always possible to identify patients with MERS-CoV early because, like other respiratory infections, the early symptoms of MERS-CoV are non-specific. Therefore, health care workers should always apply standard precautions consistently with all patients, regardless of their diagnosis. Droplet precautions should be added to the standard precautions when providing care to patients with symptoms of acute respiratory infection; contact precautions and eye protection should be added when caring for probable or confirmed cases of MERS-CoV infection; airborne precautions should be applied when performing aerosol generating procedures.

Community and household awareness of MERS and MERS prevention measures in the home may reduce household transmission and prevent community clusters.

Until more is understood about MERS-CoV, people with diabetes, renal failure, chronic lung disease, and immunocompromised persons are considered to be at high risk of severe disease from MERS-CoV infection. Therefore, in addition to avoiding close contact with suspected or confirmed human cases of the disease, people with these conditions should avoid close contact with animals, particularly camels, when visiting farms, markets, or barn areas where the virus is known to be or potentially circulating. General hygiene measures, such as regular hand washing before and after touching animals and avoiding contact with sick animals, should be adhered to.

Food hygiene practices should be observed. People should avoid drinking raw camel milk or camel urine, or eating meat that has not been properly cooked.

WHO does not advise special screening at points of entry with regard to this event nor does it currently recommend the application of any travel or trade restrictions.

Sunday, June 17, 2018

EID Journal: Geographic Distribution of MERS-CoV among Dromedary Camels, Africa


Six years ago this week, Dr. Ali Mohamed Zaki - an Egyptian virologist working in Saudi Arabia - collected blood and sputum samples from a 60 year old Saudi male hospitalized with with pneumonia and acute renal failure and began testing to determine the pathogen involved (see Nature Middle East The story of the first MERS patient).
Although he was able to isolate and culture a virus, his laboratory lacked the facilities to sequence its genome. He decided to send a sample to Dr. Ron Fouchier, at the Erasmus Medical Centre in the Netherlands, who had the equipment to do a proper analysis.
Two months later, Dr. Zaki emailed ProMed Mail (see Sometimes They Come Back), announcing the discovery of a new `SARS-like' coronavirus. Dr. Zaki's eventual `reward’ was that he was fired by the Saudis for going public with his discovery, proving once again that no good deed goes unpunished.  

Roughly one year - and 91 confirmed cases MERS Cases later - dromedary camels were pegged as the likely zoonotic conduit of the virus to humans (see Lancet: Camels Found With Antibodies To MERS-CoV-Like Virus).
At first the Saudis were slow to accept the idea that camels - a beloved symbol of their country - could carry a deadly disease (see Saudi Health Minister denies relation between camels, Mers).
In the face of mounting evidence, however, (see EID Journal: MERS Coronaviruses in Dromedary Camels, Egypt & The Lancet: Identification Of MERS Virus In Camels), in May of 2014 the Saudi Ministry Of Agriculture Issued Warnings On Camels, urging breeders and owners to limit their contact with camels, and to use PPEs (masks, gloves, protective clothing) when in close contact with their animals. 

Once camels in KSA were implicated, researchers began testing camels in other regions of the Middle East and Africa. Looking for, and finding, evidence of carriage of the MERS coronavirus going back many years.
EID Journal: MERS Antibodies In Camels – Kenya 1992-2013
Kuwait Tests Camels - Finds 6% Positive For MERS-CoV

EID Journal: Three Decades Of MERS-CoV Antibodies In Camels
Last year, in MERS-CoV In Camels: The Gift That Keeps On Giving, we saw a study that demonstrated that camels can be reinfected by the MERS virus, despite having substantial antibody titers.  A finding that may significantly complicate vaccine creation.
One of the (many) mysteries surrounding MERS-CoV is that while camel infection appears common on the Arabian peninsula, Saudi Arabia accounts for roughly 90% of known human MERS infections in that part of the world.
Even further afield, in early 2017 we saw EID Journal: Serologic Evidence Of MERS-CoV Infection in Pakistani Camels, and in 2015 Eurosurveillance: MERS-CoV In Nigerian Camels, yet South Asia and Africa have never reported a human infection.
Today we can add another study, published in the EID Journal, that further expands the geographic range of MERS-CoV in African camels, and shows its prevalence to be very high.   
I've only posted some excerpts, so you'll want to follow the link to read it in its entirety.  I'll have a bit more when you return. 

Volume 20, Number 8—August 2014
Geographic Distribution of MERS Coronavirus among Dromedary Camels, Africa

Chantal B.E.M. Reusken1 , Lilia Messadi1, Ashenafi Feyisa1, Hussaini Ularamu1, Gert-Jan Godeke, Agom Danmarwa, Fufa Dawo, Mohamed Jemli, Simenew Melaku, David Shamaki, Yusuf Woma, Yiltawe Wungak, Endrias Zewdu Gebremedhin, Ilse Zutt, Berend-Jan Bosch, Bart L. Haagmans, and Marion P.G. Koopmans


We found serologic evidence for the circulation of Middle East respiratory syndrome coronavirus among dromedary camels in Nigeria, Tunisia, and Ethiopia. Circulation of the virus among dromedaries across broad areas of Africa may indicate that this disease is currently underdiagnosed in humans outside the Arabian Peninsula.

A novel betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), was identified as the cause of severe respiratory disease in humans during 2012 (1). In August 2013, dromedary camels (Camelus dromedarius) were implicated for the first time as a possible source for human infection on the basis of the presence of MERS-CoV neutralizing antibodies in dromedaries from Oman and the Canary Islands of Spain (2).

Since then, the presence of MERS-CoV antibodies in dromedaries has been reported in Jordan (3), Egypt (4,5), the United Arab Emirates (6,7), and Saudi Arabia (8,9). In October 2013, analysis of an outbreak associated with 1 barn in Qatar (10) found dromedaries and humans to be infected with nearly identical strains of MERS-CoV.

Further proof of widespread circulation of MERS-CoV among dromedaries was provided by studies from Egypt and Saudi Arabia (5,9). These findings have raised questions about the geographic distribution of MERS-CoV among camel populations elsewhere. Here, we report our assessment of the geographic distribution of MERS-CoV circulation among dromedaries in Africa by serologic investigation of convenience samples from these animals in Nigeria, Tunisia, and Ethiopia.
A question raised by these findings is whether human cases occur outside the Arabian Peninsula and if such cases are currently underdiagnosed in Africa. In addition, for the whole region, the possibility exists that MERS-CoV illness occurred before its discovery in 2012 and that such infection has been overlooked in the areas with evidence for virus circulation among animals during the past 10 years. Retrospective studies of cohorts of humans with respiratory illnesses of unknown etiology should address this notion.
Alternative explanations for the lack of cases in Africa could be the following: a different risk profile, for instance, related to demographics and local practices; or subtle genetic differences in the circulating virus strain.
Full-genome sequencing, virus isolation, and phenotypic characterization of viruses circulating outside the Arabian Peninsula will resolve this issue. Meanwhile, awareness of MERS-CoV infections should be raised among clinicians in Africa.
(Continue . . . )

While it may seem unlikely than any significant number of clinical MERS cases could go undetected in Africa, it isn't as far-fetched of an idea as it may sound.

Despite years of reporting outbreaks of H5N1 in Sub-Saharan African poultry, only one human infection with the virus has ever been confirmed there by the WHO (see 2007’s Nigeria Confirms Human Bird Flu Case).
There were three other suspected cases at the time  - including the mother of the confirmed case in Lagos – but testing was `inconclusive’.
According to local media reports at the time (see The Nigerian Paradox), the only reason we have the one confirmed case is because the husband/father of the two related victims paid for a private autopsy and lab testing when his daughter died two weeks after his wife. 

The reality is, in Nigeria (pop. 175 million) - the average life expectancy is about 53 years - and roughly 6,000 people die each and every day.  Many are never  afforded medical care, and testing for exotic diseases like H5N1 or MERS-CoV is rarely - if ever - done.
According to the CDC, the top 10 causes of death in Nigeria are:
Deaths from lower respiratory infections in Nigeria, which can cover a lot of territory – including novel influenza or MERS-CoV – are second only to malaria.
The story is much the same in many other African nations where MERS has been detected in camels, with lower respiratory infections claiming 4% of lives in Egypt, 10% in Ethiopia, 5.4% in Tunisia, and while good data is hard to come by, at least 10% in Sudan.
Even in Saudi Arabia, where decent medical care is available, and the threat of MERS is well recognized, we've seen estimates that many - perhaps even most - MERS cases go undetected.
In 2016, in EID Journal: MERS-CoV Antibodies in Humans, Africa, 2013–2014, we looked at the results of a seroprevalence study conducted in Kenya, which produced remarkably similar results to what Drosten & Memish et al found in KSA;  
1.52% vs. 1.43% positivity by rELISA and 0.15% vs. 0.18% positivity by PRNT for Kenya vs. Saudi Arabia, respectively.
Whether the MERS virus carried by African dromedaries pose the same human health risks as those on the Arabian peninsula remains an open question - but given the limits of surveillance and testing in the region - we’d be remiss in excluding that possibility simply because we haven't seen any confirmed cases.