Friday, June 30, 2017

HK CHP Notified Of 6 H7N9 Cases On The Mainland

H7N9 Epidemic Waves- Credit FAO - July 28th













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After reporting 10 cases last week, today China's NHFPC has notified Hong Kong of 6 additional H7N9 infections, four of which were reported on Wednesday (see Yunnan Province Reports 4 Recent H7N9 Case).  Since the 1st of June, China has announced 41 cases, already making this the most active H7N9 summer by far. 
Since it emerged in the spring of 2013, H7N9 has always taken a pronounced summer break, usually beginning in May and running through September.
Last year a dozen `out of season' summer cases fueled a lot of speculation that the virus might be becoming more `heat tolerant', a concern that will no doubt be raised again given the level of activity in June.

While the media's main focus on this year's H7N9 epidemic has been on the record number of cases (and deaths) from H7N9 since October, the bigger story is the growing genetic diversity and geographic spread of both LPAI and HPAI H7N9 viruses (see CIDRAP Report Genetic analysis of H7N9 finds adaptations, clade patterns).
Simply put, nature's laboratory has been working working overtime in China, and doesn't appear likely to take the summer off.
Hong Kong's notification statement on these latest 6 cases follows:

The Centre for Health Protection (CHP) of the Department of Health is today (June 30) monitoring a notification from the National Health and Family Planning Commission that six additional human cases of avian influenza A(H7N9) were recorded from June 23 to 29, and strongly urged the public to maintain strict personal, food and environmental hygiene both locally and during travel.

The three male and three female patients, aged from 4 to 72, had onset from June 11 to 23. Four of them are from Yunnan and one each from Guizhou and Shanxi. Among them, five were known to have exposure to poultry or poultry markets.

Travellers to the Mainland or other affected areas must avoid visiting wet markets, live poultry markets or farms. They should be alert to the presence of backyard poultry when visiting relatives and friends. They should also avoid purchasing live or freshly slaughtered poultry, and avoid touching poultry/birds or their droppings. They should strictly observe personal and hand hygiene when visiting any place with live poultry.

Travellers returning from affected areas should consult a doctor promptly if symptoms develop, and inform the doctor of their travel history for prompt diagnosis and treatment of potential diseases. It is essential to tell the doctor if they have seen any live poultry during travel, which may imply possible exposure to contaminated environments. This will enable the doctor to assess the possibility of avian influenza and arrange necessary investigations and appropriate treatment in a timely manner.

While local surveillance, prevention and control measures are in place, the CHP will remain vigilant and work closely with the World Health Organization and relevant health authorities to monitor the latest developments.

The CHP's Port Health Office conducts health surveillance measures at all boundary control points. Thermal imaging systems are in place for body temperature checks on inbound travellers. Suspected cases will be immediately referred to public hospitals for follow-up.

The display of posters and broadcasting of health messages in departure and arrival halls as health education for travellers is under way. The travel industry and other stakeholders are regularly updated on the latest information.

(Continue . . . )

Thursday, June 29, 2017

EID Journal: Influenza D in Animal Species in Guangdong Province












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One of the more intriguing influenza discoveries of the past few years has been the discovery of a previously unknown type of flu - Influenza D - infecting swine, cattle, and possibly even humans as well.
We first learned of this new flu early in 2013 when researchers reported finding a novel influenza virus in swine from Oklahoma - initially classified as a novel Influenza C virus - but which would later be designated as Influenza D
Their research – published PLoS Pathogens – was called Isolation of a Novel Swine Influenza Virus from Oklahoma in 2011 Which Is Distantly Related to Human Influenza C Viruses, and it immediately caused a stir in the flu research community.

The authors wrote:

Based on its genetic organizational similarities to influenza C viruses this virus has been provisionally designated C/Oklahoma/1334/2011 (C/OK).
Phylogenetic analysis of the predicted viral proteins found that the divergence between C/OK and human influenza C viruses was similar to that observed between influenza A and B viruses. No cross reactivity was observed between C/OK and human influenza C viruses using hemagglutination inhibition (HI) assays.
Additionally, the authors found that this new (provisional) influenza C virus could infect, and transmit, in both ferrets and pigs. The following year, in mBio: Characterizing A Novel Influenza C Virus In Bovines & Swine, cattle were added to the list, and appeared to be the virus's primary reservoir.  

Since then, researchers have found evidence of a much wider spread of this virus (now provisionally called Influenza D)  than just in the American Midwest. (see EID journal’s Influenza D Virus in Cattle, France, 2011–2014 and EID Journal: Influenza D In Cattle & Swine – Italy).

And while it isn't known if Influenza D can cause symptomatic illness in humans, last summer in Serological Evidence Of Influenza D Among Persons With & Without Cattle Exposure, researchers reported finding a high prevalence of antibodies against Influenza D among people with cattle exposure.  They wrote:

IDV poses a zoonotic risk to cattle-exposed workers, based on detection of high seroprevalence (94–97%). Whereas it is still unknown whether IDV causes disease in humans, our studies indicate that the virus may be an emerging pathogen among cattle-workers.

All of which serves as prelude to a new study, just published in the EID Journal, which finds Influenza D circulating widely in Guangdong Province, China, among goats, pigs, cattle, and buffalo. 
They also report finding evidence of ongoing evolution of influenza D viruses in their hosts.
I've only included some excerpts from a much longer, detailed, reports.  Follow the link to read it in its entirety.

Volume 23, Number 8—August 2017

Dispatch
Influenza D Virus in Animal Species in Guangdong Province, Southern China

Shao-Lun Zhai1Comments to Author , He Zhang1, Sheng-Nan Chen1, Xia Zhou, Tao Lin, Runxia Liu, Dian-Hong Lv, Xiao-Hui Wen, Wen-Kang Wei1, Dan Wang, and Feng Li 

Abstract

Molecular tests revealed influenza D viruses of D/OK lineage widely circulating in farmed animal species in Guangdong Province, southern China. In particular, we found high levels of influenza D virus infection in goats and pigs. We also detected viral RNA in serum specimens and feces of animals with certain severe diseases.

Four types of influenza viruses (A–D) have been confirmed (https://www.cdc.gov/flu/about/viruses/types.htm). The recently discovered influenza D virus is thought to cause respiratory diseases primarily in cattle and to a lesser extent in pigs (1–4). Moreover, serologic evidence for influenza D virus infection in small ruminants and humans has been established (5, 6). Since the initial influenza D virus isolation in the United States in 2011 (1), the virus has been reported in China, Mexico, France, Italy, and Japan (7–11).
Genetic analysis of the hemagglutinin-esterase-fusion gene demonstrated that these viruses had 2 distinct lineages, represented by D/OK and D/660 (12). Recently, a novel influenza D virus that emerged in Japan has been proposed as the third lineage (11). D/OK lineage–related viruses were previously identified in native Luxi yellow cattle in Shandong Province, northern China (7). Despite good progress in identifying domestic cattle as the primary reservoir of influenza D virus, we know little about prevalence in other animals. We conducted a study to clarify the origin and transmission dynamics of influenza D virus in goats, buffalo, and pigs as well as farmed cattle.

(SNIP)
Conclusions

When first discovered, influenza D virus was reported in diseased pigs in the United States (1). Later, it was identified in cattle and swine herds in several other countries, with or without clinical manifestation (7–11). Moreover, antibodies to influenza D virus were detected in goats, sheep, and humans (5–6). Under experimental conditions, influenza D virus replicated and transmitted among ferrets and guinea pigs (13). 


We confirmed that influenza D virus is widely present in cattle species (dairy cattle, yellow cattle, and buffalo). We also found influenza D virus at a high prevalence (> 30%) in pigs and goats (Table), which is in contrast to the low prevalence found in previous investigations (1,5,10). The high prevalence may be caused by poor biosecurity measures and high-density feeding mode practices in China’s animal industry as well as possible cross-species transmission (13). Taken together, our findings expand the host range of influenza D virus and further emphasize the health concern this virus poses to multiple animal species.

(SNIP)

In summary, our study investigating the infection status of influenza D virus in different farmed animal species in Guangdong Province provides novel insights into the epidemiology and evolution of IDV. In particular, we document the molecular evidence for influenza D virus infection in goats and buffalo.
 (Continue . . . )

South Africa Rejects Vaccination to Control Bird Flu














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The arrival of HPAI H5N8 to South Africa last week has set off alarm bells among local poultry producers, and while only two South African farms have been confirmed infected, there are already calls to introduce a poultry avian flu vaccine.
While attractive to farmers who fear losing their flocks - and a mainstay of China's poultry industry - poultry vaccines bring with them some serious drawbacks (see MPR: Poultry AI Vaccines Are Not A `Cure-all’).
First, while vaccines can often protect poultry against illness - with increasingly diverse and rapidly evolving avian flu viruses - they cannot always prevent infection.  The end result being that subclinical infections can go undetected, and AI viruses continue to circulate.
That can not only allow viruses to spread stealthily, it can also put human health at risk (see Zhong Nanshan's 2009 comments in Chinese expert issues new bird flu warning).
And secondly, the use of poorly matched or improperly administered vaccines can actually drive the evolution of `vaccine escape' viruses (see cites below), which may account for some of the past decade's growing diversity of avian influenza in China.
The HPAI Poultry Vaccine Dilemma
Study: Recombinant H5N2 Avian Influenza Virus Strains In Vaccinated Chickens
         EID Journal: Subclinical HPAI In Vaccinated Poultry – China

Lastly, vaccinated poultry may not be readily accepted by foreign markets, since it hinders testing for the virus.  All good reasons why South Africa's DAFF has decided for now against using AI vaccines to control H5N8 in South Africa.
The following excerpts come from today's Media Briefing by Minister Senzni Zokwana.
 
AVIAN INFLUENZA OUTBREAK IN SOUTH AFRICA
29 JUNE 2017

(Excerpt)
The Department, in its alert notification, called for all chicken keepers to observe basic biosecurity measures in order to prevent contact with wild birds. This can be achieved in commercial farms by improving biosecurity and in free range farms by simply removing feed and water from where it attracts wild birds.
Despite the warnings, the disease still managed to get into our flocks. Two cases, one in a broiler breeder farm in Villiers and another in an egg laying farm in Standerton, were reported since 22nd of June. Both these farms are in the Mpumalanga province. There seems to have been confusion with the location of one farm which is near Villiers, as its closest town. I confirm that this farm is on the Mpumalanga side of the provincial boundary. No cases have been reported so far in the Free State, or in any other province.
Our team of veterinarians has swiftly responded to this threat. We have placed the affected farms under quarantine and the affected birds have been euthanised and the eggs destroyed. Approximately two hundred and sixty thousand (260 000) birds have been culled.
Section 19 of the Animal Diseases Act, gives the Director Animal Health the legal mandate to compensate for any animals or birds killed by the state pursuant to any disease control measure. The Director of Animal Health will consider each case on its own merit.

There have been several calls to permit vaccination against the disease; I have been advised by my team of experts that this will not be in the best interest of both the country and the producers. Vaccination of birds will create an endemic situation, affect surveillance efforts and affect our export certification because all our trade partners only want products from a country that is free of avian influenza where vaccination is not practised.
In order to contain the disease, our team called for the ban on the sale of live chickens to manage the further spread. This triggered a nation-wide concern since a number of livelihoods had been affected. However this measure was imposed in the interest of the country and the poultry producers at large, and I can assure you that it was not taken lightly.
My team has since met with the Poultry Producers and have devised a solution that will provide the desired disease management outcomes and improve traceability, while ensuring that micro businesses continue with their operations.
The buyers or sellers of more than 5 live chickens for any purpose other than direct slaughter at a registered abattoir will be subjected to the following conditions:
  1. The sellers of live chickens, including commercial farmers, as well as the traders who buy and resell these chickens must register with the Poultry Disease Management Agency (PDMA). The Director Animal Health, of the DAFF has authorised the PDMA to register and keep records of all parties selling and buying live chickens. The PDMA is an independent organization and all information about the trade of live chickens will be kept strictly confidential.
  2. Only registered sellers and buyers are allowed to trade and it is the responsibility of both the seller and the buyer to ensure that their counterpart is registered.
  3. Farmers may only sell live chickens certified as healthy by a veterinarian or Animal Health Technician.
  4. Traders may only sell healthy chickens and must keep records as prescribed.
  5. Sellers and buyers registering with the PDMA would have to sign an undertaking to adhere to the required control measures.
These conditions apply to sellers of live broiler chickens, live spent layer hens, live spent breeder birds, point of lay pullets and any chickens that may fall into these categories. The conditions also apply to any buyers and traders who buy more than 5 live chickens that fall into the above categories.
All stakeholders are implored to comply with the registration and other requirements that are designed to allow the trade of live chickens to continue without compromising animal health. Depending on the level of compliance that is achieved with these conditions, the Director Animal Health will review future requirements for blanket bans.
         (Continue . . . .)

This is the first serious intrusion of HPAI H5 into the southern hemisphere, and while the number of farms affected remains small, the long-term impact remains a big unknown. 


Hong Kong's Late Season Flu Surge Continues To Increase











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Hong Kong's flu season - declared over in mid-April - sprung back to life in early May and over the past 7 weeks has produced more flu-related severe illness and death than either of the last two seasonal outbreaks (fall 2016 & spring 2017).  
While Hong Kong often sees a second yearly flu season, it usually arrives in late July or August - not in early May - and it is usually milder than the spring season (see chart above).
During the first wave of 2017, which ran from February through April, Hong Kong reported  74 severe cases (including 42 deaths). So far in this second wave (starting May 5th), Hong Kong has reported 143 severe cases (including 102 deaths).
While the timing is unusual, and the severity elevated, this second wave pales in comparison to 2016's spring (primary) flu season, which saw nearly 440 severe cases, and more than 200 deaths (cite Flu Express wk 21 2016).
This late season surge is reportedly a mixture of seasonal H3N2, H1N1, and influenza B.  Thus far we've seen nothing to suggest anything unusual about these viruses - beyond the timing and high number of severe cases - and none have shown resistance to antivirals.

While we are always concerned over the emergence of a pandemic strain, seasonal flu kills hundreds of thousands of people every year, and from time to time can ramp up its virulence to near-pandemic intensity (see When Influenza Goes Rogue).
So any deviation from the norm is worthy of our attention. 
First some excerpts from today's Flu Express, then I'll be back with a bit more.

VOLUME 14, NUMBER 25 (PUBLISHED ON Jun 29, 2017)

FLU EXPRESS

 
Flu Express is a weekly report produced by the Respiratory Disease Office of the Centre for Health Protection. It monitors and summarizes the latest local and global influenza activities.
Local Situation of Influenza Activity (as of Jun 28, 2017)

Reporting period: Jun 18 – 24, 2017 (Week 25)

  • The latest surveillance data showed that the local influenza activity continued to increase.
  • The Centre for Health Protection (CHP) has collaborated with the Hospital Authority (HA) and private hospitals to reactivate the enhanced surveillance for severe seasonal influenza cases (i.e. influenza-associated admissions to intensive care unit or deaths) among patients aged 18 or above since May 5, 2017. As of Jun 28, 133 severe cases (including 100 deaths) were recorded. Separately, ten cases of severe paediatric influenza-associated complication/death (including two deaths) (aged below 18 years) were recorded in the same period.
  • Apart from adopting personal, hand and environmental hygiene practices against respiratory illnesses, those members of the public who have not received influenza vaccine are urged to get vaccinated as soon as possible for personal protection.
  • Influenza can cause serious illnesses in high-risk individuals and even healthy persons. Given that seasonal influenza vaccines are safe and effective, all persons aged 6 months or above except those with known contraindications are recommended to receive influenza vaccine for personal protection.
 (SNIP)

Surveillance of severe influenza cases

(Note: The data reported are provisional figures and subject to further revision)


Since the activation of the enhanced surveillance for severe influenza infection on May 5, 2017, a total of 143 severe cases (including 102 deaths) were recorded cumulatively (as of Jun 28) (Figure 9). These included:

  • 133 cases (including 100 deaths) among adult patients aged 18 years or above. Among them, 104 patients had infection with influenza A(H3N2), 16 patients with influenza A(H1N1)pdm09, seven patients with influenza B and six patients with influenza A pending subtype. Forty-two (31.6%) were known to have received the influenza vaccine for the 2016/17 season. Among the 100 fatal cases, 39 (39.0%) were known to have received the influenza vaccine. In the winter season in early 2017, 66 adult severe cases (including 41 deaths) were filed.
  • Ten cases (including two deaths) of severe paediatric influenza-associated complication/ death. Nine (90.0%) cases did not receive the influenza vaccine for the 2016/17 season. To date in 2017, 18 paediatric cases (including three deaths) were filed.
Enhanced surveillance for severe seasonal influenza (Aged 18 years or above)
  • In week 25, 21 cases of influenza associated ICU admission/death were recorded, in which 16 of them were fatal. In the first 4 days of week 26 (Jun 25 to 28), 18 cases of influenza associated ICU admission/death were recorded, in which 13 of them were fatal.
Surveillance of severe paediatric influenza-associated complication/death (Aged below 18 years)
  • In week 25 and the first 4 days of week 26 (Jun 25 to 28), there were no cases of severe paediatric influenza-associated complication/ death.
 (Continue . . . )

Elsewhere around the world, we aren't hearing a lot about seasonal influenza, with most countries reporting to be at or near their inter-seasonal norms. The WHO's most recent seasonal influenza report (#292) states:
In the temperate zone of the southern hemisphere, influenza activity continued to increase and was above seasonal threshold levels in South America but remained low in general in Oceania. Influenza activity in the temperate zone of the northern hemisphere continued to decrease. Worldwide, influenza A(H3N2) and B viruses co-circulated.
One notable exception is Taiwan, which continues to report surge in influenza over the past few weeks (see graph below), although reportedly not as severe as Hong Kong's.



Overnight Australian media is reporting a spike in flu cases in New South Wales (see Flu season in New South Wales tracked to be worst on record) although the level of flu reported across the rest of Australia appears near average for this time of year.

While it isn't necessarily a harbinger of what the Northern Hemisphere can expect next fall, we'll continue to keep a close eye on the Southern Hemisphere's flu season as it progresses over the next few months.

Wednesday, June 28, 2017

Yunnan Province Reports 4 Recent H7N9 Cases

















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Until February of this year, Yunnan Province had never reported a human H7N9 infection (see Yunnan: 2nd Imported H7N9 Case (Mother of Last Week's Case). While those cases were reported as imported, today the Yunnan Provincial Health & Family Planning Commission is reporting 4 recent, apparently locally acquired, cases.
   
Wenshan City confirmed four cases of H7N9 cases

[Index: 01510047-20170628-7196] Date: 2017-06-28

Yunnan Health and Family Planning Commission June 28 briefing: Health and Family Planning Commission in Yunnan Province, to strengthen influenza surveillance and unexplained pneumonia, influenza cases detected from the H7N9 virus nucleic acid positive specimens were sent to the national CDC review, consistent test results. 


Provincial expert group based on clinical manifestations, laboratory testing, epidemiological investigation, according to people infected with H7N9 avian influenza diagnostic criteria for diagnosis of H7N9 cases. After the outbreak, Health and Family Planning Commission and the Yunnan Wenshan government attaches great importance to the timely mobilization of experts to treat the patient provinces and states to carry out epidemic disposal.
Currently, a patient has fully recovered lift the quarantine, isolation and treatment of the remaining three patients in hospital, condition stable. In close contact with the four patients who did not appear abnormal, it found no case of human transmission. Wenshan City on June 25 has been closed city live animal markets.

There is no indication on how any of these 4 cases were infected, or if any of them have epidemiological links between them.
Wenshan City is only 100 km from the Vietnamese border town of Lao Cai, which is sure to capture the attention of the Vietnamese health authorities  who have been on constant vigil  over the potential arrival of H7N9 all winter (see H7N9 Inches Closer To Vietnam's Northern Border).

An outbreak this far south, and this deep into the summer, is yet another sign that H7N9 continues to move in unexpected ways (see EID Journal: 2 Expedited HPAI H7N9 Studies).

WHO MERS-CoV Update - June 28th















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The Saudi daily MERS reports continue to be a bit fragmented and confused (see listing above), with days skipped, and link descriptions not always matching the entries, but today we've an update from the World Health Organization that provides an update on the three hospital clusters we've been watching since June 1st.

Middle East respiratory syndrome coronavirus (MERS-CoV) – Saudi Arabia
Disease outbreak news
28 June 2017

Between 16 and 23 June 2017, the national IHR Focal Point of Saudi Arabia reported seven additional cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection, including two deaths, and four deaths among previously reported cases.

Details of the cases

Detailed information concerning the cases reported can be found in a separate document (see link below). 


MERS-CoV cases reported between 16 and 23 June 2017.
xlsx, 40kb

Three of the seven newly reported cases are associated with clusters 1 and 3 as reported in the Disease Outbreak News published on 13 June 2017 and 19 June 2017


Cluster 1

An additional two cases have been reported in this cluster in Riyadh City, Riyadh Region. In total, 34 laboratory-confirmed cases reported to WHO are associated with this cluster. 


Cluster 2

No newly reported cases are associated with cluster 2 as reported in the Disease Outbreak News published on 13 June 2017.

 
Cluster 3
An additional case has been reported in this cluster in Riyadh City, Riyadh Region. Thus far, this cluster involves nine laboratory-confirmed patients.

Globally, 2036 laboratory-confirmed cases of infection with MERS-CoV including at least 710 related deaths have been reported to WHO. 


Public health response

The Ministry of Health is evaluating each case and their contacts and is still implementing the measures to limit further human-to-human transmission and bring these outbreaks to a control as described in the DON published on 19 June 2017


WHO risk assessment


MERS-CoV causes severe human infections resulting in high mortality and 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.
         (Continue . . . )

While we continue to get a fair amount of detail on these individual cases (see xlxs list), what will be of even greater interest will be an analysis of the chains of infections in these three clusters, and how this nosocomial outbreak got so far out of control.
 

EID Journal: A New Bat-HKU2–like Coronavirus in Swine, China, 2017



















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Until SARS emerged on the world stage in 2003 (see SARS and Remembrance), coronaviruses were believed only capable of producing mild `cold-like’ illnesses in humans.  Six coronaviruses capable of infecting humans have now been identified, but only two of them (MERS-CoV & SARS-CoV) are routinely linked to severe illnesses.
The remaining four are Alpha coronaviruses 229E and NL63, and Beta coronaviruses OC43 & HKU1.
These four `milder’ coronaviruses are probably responsible for 15%-30% of the `common colds’ around the world, and only rarely migrate to the lower respiratory tract (cite).

But as we've come to learn over the past decade, there are many other coronaviruses that infect other species - including horses, cattle, and swine - but they are particularly common among bats. Both SARS and MERS are believed to have originated in bats and jumped to intermediate hosts (civets, camels, etc.) before infecting humans. 
Despite all the good they do for the environment, bats are increasingly viewed as host species for dozens (perhaps hundreds) of viruses with zoonotic potential. 
There are those we already know about or strongly suspect -  like SARS, MERS, Rabies, Nipah, Hendra, Ebola, Marburg, etc. - and those we are just starting to discover, such as last year's announced WIV1 virus (see PNAS: SARS-like WIV1-CoV Poised For Human Emergence).

Just last week, researchers from EcoHealth Alliance published a letter in Nature (Host and viral traits predict zoonotic spillover from mammals) providing he first comprehensive analysis of viruses known to infect mammals. From their website summary:
The study shows that bats carry a significantly higher proportion of viruses able to infect people than any other group of mammals; and it identifies the species and geographic regions on the planet with the highest number of yet-to-be discovered, or ‘missing’, viruses likely to infect people. This work provides a new way to predict where and how we should work to identify and pre-empt the next potential viral pandemic before it emerges.
Although an old disease, Porcine epidemic diarrhea (PED) - which is caused by a coronavirus (PEDV) - erupted with a vengeance in China in 2010, and subsequently arrived in North America in 2013. It causes diarrheal disease, and often death, in young piglets.

A few of our looks at this emerging disease include: 

We’ve seen no evidence of human infection due to these swine coronaviruses, so they are not currently considered zoonotic diseases.  Which is not to say that one or both couldn’t someday pose a threat. Coronaviruses – like all RNA viruses – tend to evolve and mutate at a fairly rapid rate (see discussion of new zoonotic coronaviruses).
As pigs are physiologically fairly close to humans (if that bothers you, think how the pig feels), we watch porcine adapted viruses with particular interest.
All of which brings us to a new study, published yesterday in the CDC's EID Journal, that describes the recent discovery of a new HKU2-like coronavirus in Chinese pigs showing symptoms of PED, which had tested negative for the usual suspects.
HKU2 is one of a number of coronaviruses discovered in the wild (in this case, in Horseshoe bats) by Hong Kong researchers in the years immediately following the SARS epidemic.
One of the things that caught researcher's attention was that genome sequencing suggested a common evolutionary origin in the spike protein of bat-CoV HKU2 and the SARS virus. Today's report finds a similar bat-CoV HKU2-like virus has jumped to pigs in Guangdong Province China, which they've dubbed porcine enteric alphacoronavirus [PEAV]).

Research Letter
A New Bat-HKU2–like Coronavirus in Swine, China, 2017

Lang Gong1, Jie Li1, Qingfeng Zhou, Zhichao Xu, Li Chen, Yun Zhang, Chunyi Xue, Zhifen WenComments to Author , and Yongchang CaoComments to Author

Abstract

We identified from suckling piglets with diarrhea in China a new bat-HKU2–like porcine coronavirus (porcine enteric alphacoronavirus). The GDS04 strain of this coronavirus shares high aa identities (>90%) with the reported bat-HKU2 strains in Coronaviridae-wide conserved domains, suggesting that the GDS04 strain belongs to the same species as HKU2.
Several pathogens are thought to be responsible for porcine diarrhea, including porcine epidemic diarrhea virus (PEDV) (1), transmissible gastroenteritis virus (2), porcine deltacoronavirus (3), porcine group A rotavirus (4), and emerging viruses like porcine kobuvirus (5). To add to the list, we have identified from suckling piglets with diarrhea in China a new bat-HKU2–like porcine coronavirus (porcine enteric alphacoronavirus [PEAV]).
Since December 2010, large-scale outbreaks of diarrhea in suckling piglets have been reported across China (1), and vaccination against PEDV has been relatively effective for diarrhea prevention. However, in February 2017, outbreaks of severe diarrhea occurred in swine herds vaccinated against PEDV in Guangdong, China.
All ill pigs showed severe watery diarrhea, and their clinical onset occurred a few days later than those infected with PEDV. In initial tests with reverse transcription PCR using specific primers for PEDV, transmissible gastroenteritis virus, porcine group A rotavirus, or porcine deltacoronavirus, none of these viruses could be detected in all clinical samples. Furthermore, the recovered sows showed no seroneutralizing antibodies against PEDV.
         (SNIP)
 In summary, we report preliminary data on our detection of a new coronavirus-like virus, PEAV. PEAV is thought to be responsible for the most recent diarrhea endemic in pig herds in southern China. Virus isolation and serologic testing are underway. The outbreak of the newly discovered virus arose among swine with severe diarrhea in swine breeding farms in southern China, suggesting the regional outbreaks of diarrhea could contribute to the emergence of new pandemic viruses. Extensive surveillance for GDS04 PEAV is required to define its epidemiology and evolution.
Mr. Gong is a PhD student in life sciences school at Sun Yat-sen University. His primary research interests include the molecular epidemiology of novel coronaviruses and influenza vaccine.

At this time, we've no indication of a zoonotic threat posed by this emerging swine-adapted coronavirus, but the experiences of SARS and MERS have taught us to be wary whenever a novel coronavirus jumps species. .

Tuesday, June 27, 2017

MERS-CoV In Camels: The Gift That Keeps On Giving


















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This summer will mark the 5 year anniversary of the discovery of the MERS Coronavirus, and we are just shy of 4 years since camels were pegged as the likely zoonotic conduit of the virus to humans (see Lancet: Camels Found With Antibodies To MERS-CoV-Like Virus).
After nearly 6 months of denial that their beloved camel could carry such a deadly disease, Saudi officials announced in the spring 2014 that work would begin on a vaccine (see Health announces the imminent arrival of a global company specialized to discuss manufacturing a vaccine against Corona).

But, as I wrote in April of 2014's Obstacles To A MERS Vaccine, after more than a decade of trying, we still had no safe and effective SARS vaccine, and the development of a MERS vaccine was likely several years away – assuming one could be created at all.

After discussing the SARS vaccine failures, I wrote:
A vaccine for non-humans – most notably camels – could possibly be created and tested quicker than a human vaccine, but early research suggests that camels are susceptible to re-infection despite having high antibody titers (see EID Journal: MERS Coronavirus In A Saudi Dromedary Herd) which raises questions over how well a vaccine would work in dromedaries
I wasn't alone in questioning a timely MERS vaccine, of course. The fast-track to a vaccine narrative was coming mainly from the Saudi government, who were battling a major nosocomial outbreak in Jeddah at the time (400+ cases), and desperately needed something positive to report. 
Since then, we've seen additional evidence that humans may not develop long-lasting antibodies to MERS either. 
In In April of 2016, in EID Journal: Antibody Response & Disease Severity In HCW MERS Survivors, we looked at a study that tested 9 Health care workers who were infected during the 2014 Jeddah outbreak (2 severe pneumonia, 3 milder pneumonia, 1 URTI, and 3 asymptomatic), that found only those with severe pneumonia still carried detectable levels of antibodies 18 months later.

This waning antibody response in all but the most severely affected patients raised a number of interesting, and potentially serious, questions.
  1. Are those who only experienced mild or moderate illness at risk of re-infection?
  2. Would convalescent plasma donated by those without severe illness be less or ineffective?
  3. Does this skew (under count) the community seroprevalence studies we've seen coming out of Saudi Arabia and Kenya?
  4. How will all of this play into the development of a MERS-CoV vaccine (for camels or humans)?
We revisited this topic again last May, in EID Journal: MERS-CoV Antibody Response After 1 Year, where researchers followed and tested 11 survivors of South Korea's 2015 MERS outbreak at 6 and 12 months, and like earlier studies, found that those with mild illness saw significant reduction in antibody titers over a year's time.
Today we've a new study published in Emerging Microbes & Infections with an impressive pedigree (Webby, Poon, Peiris, et al) that tracks two camel herds between September 2014 and May 2015, and pretty much removes any doubts that camels can be reinfected by the MERS virus, despite having substantial antibody titers.

A finding that significantly complicates vaccine creation. I've posted some excerpts from the open access study below, follow the link to read it in its entirety:

Longitudinal study of Middle East Respiratory Syndrome coronavirus infection in dromedary camel herds in Saudi Arabia, 2014–2015

Open

Maged Gomaa Hemida1,2,*, Abdulmohsen Alnaeem3,*, Daniel KW Chu4,*, Ranawaka APM Perera4,*, Samuel MS Chan4, Faisal Almathen5, Emily Yau4, Brian CY Ng4, Richard J Webby6, Leo LM Poon4 and Malik Peiris4

ABSTRACT


Two herds of dromedary camels were longitudinally sampled with nasal and rectal swabs and serum, between September 2014 and May 2015, and the samples were tested for Middle East Respiratory Syndrome (MERS) coronavirus RNA and antibodies. Evidence of MERS-CoV infection was confirmed in one herd on the basis of detection of virus RNA in nasal swabs from three camels and significant increases in the antibody titers from three others. The three viruses were genetically identical, thus indicating introduction of a single virus into this herd.
There was evidence of reinfection of camels that were previously seropositive, thus suggesting that prior infection does not provide complete immunity from reinfection, a finding that is relevant to camel vaccination strategies as a means to prevent zoonotic transmission.

INTRODUCTION

Middle East Respiratory Syndrome coronavirus (MERS-CoV) was initially identified in Saudi Arabia in 2012.1 As of 5 December 2016, there were over 1800 laboratory-confirmed cases.2 Camels are known to be the natural host for MERS-CoV and the source of zoonotic infection.3, 4, 5 Zoonotic transmission events may be mild and unrecognized but may lead to transmission between humans, thus leading to MERS outbreaks in health care facilities.6, 7 The SARS epidemic of 2003 was heralded by repeated small zoonotic outbreaks in 2002 that were self-limited until a strain of SARS CoV that was well adapted to humans emerged and led to a global epidemic that affected approximately 8000 patients in 25 countries across five continents.8 Given this demonstration of the capacity for novel coronaviruses to emerge from animals to cause major outbreaks in humans, the threat from MERS-CoV remains a cause for global health concern.

Vaccination of dromedary camels has been proposed as a means to reduce the threat of zoonotic MERS.9 It is therefore important to establish the epidemiology of MERS-CoV transmission within camels, and especially whether prior infection protects against subsequent reinfection. We therefore carried out a longitudinal study of two camel herds in the Kingdom of Saudi Arabia to elucidate MERS-CoV infection and transmission.


(SNIP)


The present study provides conclusive evidence that reinfection of previously seropositive camels can occur. This observation has important implications for the feasibility of using vaccination of camels as a means to control MERS-CoV transmission within camel herds with the aim of reducing zoonotic transmission.
Reinfection in previously seropositive animals may occur because MERS-CoV infection in camels is a mucosal infection and the serum antibody might not be an accurate predictor of the effective mucosal antiviral immunities that can provide sterilizing immunity. None of the studies to date, including our own, have tested for evidence of mucosal IgA immunity in the oral or nasopharyngeal cavity, and this deficiency remains a crucial gap in the understanding of protection from reinfection.

The lack of protection against natural reinfection in the field thus raises questions about the potential duration of protection conferred by MERS-CoV infection or vaccines.
         (Continue . . . . )


None of this means that researchers won't eventually develop a MERS vaccine for camels, only that there are substantial challenges to doing so.
What we won't know - with any certainty - is how long any vaccine candidate  would be protective until long-term follow up studies are completed on vaccinated animals. 
A process that will add significant time to the development/testing cycle of any vaccine trial.


Belgium Reports Their 12th H5N8 Outbreak Of June















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While Belgium went relatively unscathed during this past winter's HPAI H5 epizootic, it is making up for it now, with a dozen outbreaks reported this month.

This (translated) press release from Belgium's AFSCA (Federal Agency For Food Safety).

Avian influenza: situation.
New contaminated poultry Wangenies (Fleurus) (06/27/2017)

    The highly pathogenic H5N8 avian flu has once again been found in a particular livestock Wangenies (Fleurus). The AFSCA again ask anyone who has recently purchased a poultry market to be vigilant and call a veterinarian if their birds are sick or die suddenly.

The Agriculture Minister Willy Borsus states: " The fight against bird flu measures are systematically adapted according to the updated epidemiological data and must be proportionate to the risks I am aware of the difficulties this creates for all breeders. . present in restricted areas, however I encourage bird breeders. - particuliers- professionals and to continue to comply with firmness all measures necessary for the protection of animal health in our country "

a temporary buffer zone a radius of 3 km was delineated around this new case Wangenies. In this zone, poultry movements, other captive birds and hatching eggs are prohibited. All captive birds and poultry should be fed and watered inside. Holders of birds and poultry in this area should send their mayor, within 48 hours, an inventory which incorporates, by species, the number of animals present. This area must be at least 3 weeks.

In the rest of the country, no new measures are imposed. As decided in the last few weeks, the sale of birds and poultry on public procurement, as well as other gatherings (exhibitions, competitions, sales ...) poultry are banned. The AFSCA also reminds each holder to be vigilant and to immediately call a veterinarian if his birds show symptoms of disease.

An abnormal mortality in wild birds can still be notified via the toll-free number 0800/99777 .
We can reassure consumers: meat and poultry eggs are quite healthy and can be consumed safely.

The package of measures is available on the website of the FASFC:
- www.afsca.be/santeanimale/grippeaviaire/
- For fans: www.favv.be/santeanimale/grippeaviaire/detenteursamateurs.asp


Breaking the pattern that HPAI H5 usually goes to ground - at least in temperate zones - during the summer months, Belgium joins Finland, Luxembourg, and the UK in reporting HPAI H5N8 during the past month in Europe, and it's turned up (for the first time) in South Africa, the  DRC, and Zimbabwe in the Southern Hemisphere.



HK CHP Avian Flu Report Week 25 & CIDRAP's BioRxiv Summary

H7N9 Epidemic Waves - June 14th - Credit FAO












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In years past, by early May - or early June at the lastest - China's winter epidemic of H7N9 had run its course, and at most, we might see a dozen widely scattered cases over the summer (June through September). 
But this 5th epidemic wave - apparently driven by multiple genetic changes in the H7N9 virus - has been anything but ordinary.  In week 25, Hong Kong reports what would be a summer's worth of H7N9 cases (n=10) in any other year.
The virus's evolutionary changes are far from fully understood - and continue down several evolutionary pathways. But last night CIDRAP News published a summary by Lisa Schnirring of a new study in BioRxiv that describes several recent genetic changes in the virus.

A couple of excerpts, but follow the link to read it in its entirety.

Genetic analysis of H7N9 finds adaptations, clade patterns

Lisa Schnirring | News Editor | CIDRAP News
Jun 26, 2017

In the latest genetic analysis of H7N9 avian influenza samples from China, researchers said viruses circulating in the current fifth wave fall into two geographically separate clades of Yangtze River Delta lineages that have undergone substantial adaptation

(SNIP)
Researchers have known that H7N9 forms two lineages, the Pearl River Delta (PRD) and the Yangtze River Delta (YRD). Most human cases in the current wave are from the YRD lineage, which aren't as reactive to existing candidate vaccine viruses. The YRD viruses have formed two subsets, YRD-1 and YRD-2.

Within the YRD-2 subset, the team observed two clades, one (YRD-2a) circulating in central and eastern China and the other (YRD-2b) mainly found in eastern Guangdong province, its likely origin. They said the YRD-2b clade also includes the recently identified highly pathogenic H7N9 viruses.

(SNIP)


Call for close monitoring for spread

Analysis shows a higher rate of adaptation for YRD-2b, which the researchers said is concerning, given the emergence of highly pathogenic H7N9 within the clade. The investigators added that the highly pathogenic avian flu in domestic poultry can pose a serious risk, similar to what happened when H5N1 spilled back into wild birds, triggering the longest global outbreak to date.

(Continue . . . )


As we've seen in other studies this spring (see here, here, and here), the pace of H7N9's evolution and adaptation appears to be picking up. The recent spread - particularly of the newly emerged HPAI version (see OIE Confirms HPAI H7N9 In Heilongjiang Province), has raised new concerns that H7N9 may not remain just China's problem for much longer.

After dipping to just 5 new cases reported from the mainland two weeks ago, in week 25 China's NHFPC reported 10 cases, which Hong Kong's CHP summarizes below.

Avian Influenza Report
Avian Influenza Report is a weekly report produced by the Respiratory Disease Office, Centre for Health Protection of the Department of Health. This report highlights global avian influenza activity in humans and birds.

VOLUME 13, NUMBER 25
Reporting period: June 18, 2017 – June 24, 2017 (Week 25)
(Published on June 27, 2017)


Summary

  1. Since the previous issue of Avian Influenza Report (AIR), there were 10 new human cases of avian influenza A(H7N9) reported by the National Health and Family Planning Commission (NHFPC) from Beijing (2 cases), Sichuan (2 cases), Anhui (1 case), Guizhou (1 case), Hebei (1 case), Inner Mongolia (1 case), Jiangsu (1 case) and Tianjin (1 case). Since March 2013 (as of June 24, 2017), there were a total of 1548 human cases of avian influenza A(H7N9) reported globally. Since October 2016 (as of June 24, 2017), 742 cases have been recorded in Mainland China.
  2. Since the previous issue of AIR, there were no new human cases of avian influenza A(H5N6). Since 2014 (as of June 24, 2017), 16 human cases of avian influenza A(H5N6) were reported globally and all occurred in Mainland China. The latest case was reported on December 1, 2016.
  3. Since the previous issue of AIR, there were no new human cases of avian influenza A(H5N1). From 2011 to 2016, 10 to 145 confirmed human cases of avian influenza A(H5N1) were reported to the World Health Organization (WHO) annually (according to onset date). In 2017, there have been so far three cases in Egypt.*
http://www.chp.gov.hk/files/pdf/2017_avian_influenza_report_vol13_wk25.pdf
 http://www.chp.gov.hk/files/pdf/2017_avian_influenza_report_vol13_wk25.pdf
 (Continue . . . )


As usual, we see the skewing towards older males, and mild cases are almost never reported. Between Mainland, Hong Kong, Macao and Taiwan - 750 cases have been reported since October - although it isn't known how many mild or asymptomatic cases go undetected.
For now, clusters are few, and human-to-human transmission has only rarely been reported. The virus, for all of its evolutionary strides, still hasn't adapted well enough to human physiology to spread effeciently.

How long that will hold true remains the $64 question.

Monday, June 26, 2017

Saudi MOH Resumes MERS Updates: 4 Cases Added












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After 5 days without posting, the Saudi MOH began adding daily MERS updates to their website this afternoon, although some of the data is still missing.

As the graphic below shows, there is no entry for June 24th, and the link descriptions only cite two new cases. By cross checking with the Arabic page, we actually find new cases reported on the 22nd, 23rd, 24th, and 25th. 




Over the six days (June 21st-June 26th) the MOH reports 4 new cases, 11 Recoveries, and 4 deaths.  A considerable drop over what was being reported just a week or so ago. 


While reporting from the MOH has been a bit erratic over the past week, and we may have to wait for a WHO update to really sort things out, it is a relief to see that the Saudis are continuing to post their daily reports.

Bird Flu Murmurs From Thailand














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In the middle of the last decade, when H5N1 was still pretty much a Southeast Asian problem, Thailand was one of the hardest hit countries. In 2004, they reported 17 human infections and 12 deaths, coming in second to Vietnam.

They also lost more than a hundred rare tigers that year, as reported by the WHO:
In October 2004, captive tigers fed on fresh chicken carcasses began dying in large numbers at a zoo in Thailand. Altogether 147 tigers out of 441 died of infection or were euthanized. Subsequent investigation determined that at least some tiger-to-tiger transmission of the virus occurred.
By the end of 2006 - the last year Thailand reported a human infection - they had done a remarkable job controling the virus, although scattered outbreaks in poultry would be reported over the next few years.
Thailand filed their last OIE report on Avian flu in 2009.

But given their location and immediate neighbors - and the recent surge of H7N9 in China, the spread of H5N8 in Asia, Europe, and Africa, and the recent escape of H5N6 from China - it is safe to say Thailand remains on high alert for any signs of the virus.

While it may be nothing more than a timely reminder, the Thai language press overnight has been echoing a vague report referencing `sick poultry in the north', and urging increase surveillance and reporting (note: the website url mentioned in the article isn't responding right now).
(Translated)
The Department of Prevention and Control of Avian Influenza After the outbreak of the province.
Credit: manager.co.th

Mr. Sopon Mektanat, Permanent Secretary, Ministry of Public Health said that the Ministry of Public Health. Has joined with related agencies. Avian influenza surveillance is intensive and continuous. Although Thailand has not reported human infection with avian influenza in humans since 2006 to date. But there are still risks due to climate change and the movement of animals along the border. 


From the surveillance, it was found that the poultry were sick in the lower North. The Provincial Health Office ordered the Department of Disease Control together with the Department of Livestock. Send the team to investigate the swiftly moving disease into action. By integrating all agencies and all levels in the area. To maintain safety and promote self-defense awareness of the people.

The Department of Disease Control ordered 12 Disease Control Offices nationwide. And the Institute for Disease Control and Prevention. Accelerate surveillance and preparedness for avian influenza. Together with the Provincial Public Health Office Provincial Livestock Office And related agencies Practice emergency preparedness plan.
Situation of bird flu outbreak Especially high risk areas such as border areas. Dense poultry area And a lot of reptiles. People can keep track of information and advice on bird flu prevention at the Bureau of Emerging Infectious Diseases, Department of Disease Control. Http://beid.ddc.moph.go.th For more information, contact the Department of Disease Control Hotline on 1422.

Admittedly, not a lot of details here.  The `outbreak' - whatever it is - is being investigated.  Hopefully more details will be released soon.

Updating the CDC's IRAT (Influenza Risk Assessment Tool) Rankings

Credit NIAID












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Last September, before H7N9 reinvented itself (twice) in China, we looked at the CDC's ranking (see CDC: IRAT Evaluation Of Novel Avian & Swine Flu Risks) of 11 novel flu subtypes/strains that circulate in non-human hosts and are believed to possess some degree of pandemic potential.

The CDC is quick to point out the Influenza Risk Assessment Tool (IRAT) is not meant to be predictive.  As stated in their FAQ:
Can the IRAT predict a future pandemic?
No. The IRAT is an evaluative tool, not a predictive tool. Flu is unpredictable, as are future pandemics.
But the IRAT can help planners decide which viruses pose the greatest risks, so they can prioritize their efforts and investments. And ten months ago, out of the 11 viruses on the list:
Not all novel flu viruses are created equally.  Some show signs of being more likely to jump to humans than others, while some have shown more virulence in humans than others.   
A mild flu, even if it spreads easily, isn't that much of a threat to public health. But a severe flu that spreads easily, is another matter entirely. 
The CDC uses two sets of criteria to evaluate novel viruses.  One to estimate a virus's potential for sustained human-to-human transmission, and another to guage it's potential for significant impact on public health. 

Fast forward to June 2017, and the CDC has added two new viruses to their IRAT list (a second H7N9 [A/Hong Kong/125/2017] variant, and the recently arrived Canine H3N2) and has further refined their rankings.   
Where there were 11 last September, there are now 13. It is worth nothing that of the 13 novel viruses on this list, 10 have been added in the past 6 years. 
Below you'll find the latest rankings, with the new H7N9 virus nudging out the old version in both Emergence and Impact scores, putting both (A & B) far ahead of the pack.

https://www.cdc.gov/flu/pandemic-resources/monitoring/irat-virus-summaries.htm


Summaries on the two new entries, follow:
H3N2: [A/canine/Illinois/12191/2015]
The H3N2 canine influenza virus is an avian flu virus that adapted to infect dogs. This virus is different from human seasonal H3N2 viruses. Canine influenza A H3N2 virus was first detected in dogs in South Korea in 2007 and has since been reported in China and Thailand. It was first detected in dogs in the United States in April 2015. H3N2 canine influenza has reportedly infected some cats as well as dogs. There have been no reports of human cases.
Summary:  The average summary risk score for the virus to achieve sustained human-to-human transmission was low risk (less than 4). The average summary risk score for the virus to significantly impact public health if it were to achieve sustained human-to-human transmission was in the low risk range (less than 4).
Some past blogs on the Canine H3N2 virus include:
A Canine H3N2 Virus With PA Gene From Avian H9N2 - Korea

Canine H3N2 Reassortant With pH1N1 Matrix Gene

Virology J: Human-like H3N2 Influenza Viruses In Dogs - Guangxi, China

The bigger concern comes from the recently emerged Yangtze River Delta lineage of H7N9 (we don't have enough data yet on the risks posed by the recently emerged HPAI version).

H7N9: [A/Hong Kong/125/2017]
Low pathogenic avian influenza (LPAI) H7N9 viruses were first reported from China in March 2013. These viruses were first scored using the IRAT in March 2013 and again in April 2013, and then annually in 2014, 2015, and 2016 with no change in overall risk scores. Between October 2016 and May 2017 evidence of two divergent lineages of these viruses was detected – the Pearl River Delta lineage and the Yangtze River Delta lineage. The IRAT was used to assess LPAI H7N9 [A/Hong Kong/125/2017], a representative of the Yangtze River Delta viruses.

Summary:  A risk assessment of H7N9 [A/Hong Kong/125/2017] was conducted in May 2017. The overall IRAT risk assessment score for this virus falls into the moderate-high risk category and is similar to the scores for the previous H7N9 viruses. The summary average risk score for the virus to achieve sustained human-to-human transmission is in the moderate risk category (less than 7). The summary average risk score for the virus to significantly impact public health if it were to achieve sustained human-to-human transmission was in the moderate-high risk category (less than 8).

While IRAT can't tell us which virus will spark the next pandemic, or when that might happen, there are three major takeaways from these reports.
  1. There are a lot of novel flu threats out there with at least some pandemic potential. IRAT currently evalluates 13, but that is by no means an exhaustive list.
  2. New viruses appear to be emerging at an accelerated rate over the past decade.
  3. Viral evolution requires that these viruses be re-evaluated from time to time, as nothing is static in the flu world. A virus that ranks relatively low today might be viewed as a serious contender a year or two from now.
All very good reasons why pandemic preparedess is getting renewed attention by the CDC, the WHO, and other government and NGO agencies around the world.  You'll find some recent blogs on that below:
HHS Pandemic Influenza Plan - 2017 Update
OpenWHO: Preparedness Training For Epidemics, Pandemics & Health Emergencies

World Bank: World Ill-Prepared For A Pandemic

Are We Prepared to Help Low-Resource Populations Mitigate a Severe Pandemic?
Community Pandemic Mitigation's Primary Goal : Flattening The Curve