Wednesday, June 28, 2017

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


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


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.
 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. .