Pandemic watching getting closer to source of primary vectors – next we will nail that it is human interventions that create the imbalances which give rise to viral outbreaks that are nature’s way of re-balancing the system

How Bat Viruses Jump Species

#13,246

Until SARS emerged from China roughly 15 years ago (see SARS and Remembrance), only four coronaviruses (Alpha coronaviruses 229E and NL63, and Beta coronaviruses OC43 & HKU1) were known to infect humans. 

These viruses generally produced mild upper respiratory illnesses in humans, are probably responsible for 15%-30% of the `common colds’ around the world, and only rarely migrate to the lower respiratory tract (cite).

In 2003 SARS-CoV emerged, followed in 2012 by the MERS-CoV virus, both causing severe, often fatal respiratory illness in humans.  Both are zoonotic viruses spread via intermediary hosts, and are believed to be of bat-origin.  

There are many other coronaviruses that infect other non-human  species – including horses, cattle, and swine – but they are particularly common among bats.

In 2017 researchers from EcoHealth Alliance published a letter in Nature (Host and viral traits predict zoonotic spillover from mammals) providing the 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.

Last summer, in EID Journal: A New Bat-HKU2–like Coronavirus in Swine, China, 2017, we looked at the recent discovery of a new HKU2-like coronavirus in Chinese pigs showing symptoms of PED (Porcine Epidemic Diarrhea), which they tentatively dubbed porcine enteric alphacoronavirus (PEAV). 

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.

Fast forward to yesterday, and we get a letter (alas, behind a pay wall) in Nature that further describes this (or a very similar) virus isolated from pigs in Guangdong Province, and also finds a close match in nearly 10% of local bats they tested.

To help fill in the gaps we also have accompanying press releases from the NIH, and EcoHealth Alliance.

Letter

Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin

Peng Zhou, Hang Fan,[…] Jing-Yun Ma

Nature (2018)
doi:10.1038/s41586-018-0010-9
Download Citation

Published online:04 April 2018

Abstract

Cross-species transmission of viruses from wildlife animal reservoirs poses a marked threat to human and animal health1. Bats have been recognized as one of the most important reservoirs for emerging viruses and the transmission of a coronavirus that originated in bats to humans via intermediate hosts was responsible for the high-impact emerging zoonosis, severe acute respiratory syndrome (SARS)2,3,4,5,6,7,8,9,10.

Here we provide virological, epidemiological, evolutionary and experimental evidence that a novel HKU2-related bat coronavirus, swine acute diarrhoea syndrome coronavirus (SADS-CoV), is the aetiological agent that was responsible for a large-scale outbreak of fatal disease in pigs in China that has caused the death of 24,693 piglets across four farms.

Notably, the outbreak began in Guangdong province in the vicinity of the origin of the SARS pandemic. Furthermore, we identified SADS-related CoVs with 96–98% sequence identity in 9.8% (58 out of 591) of anal swabs collected from bats in Guangdong province during 2013–2016, predominantly in horseshoe bats (Rhinolophus spp.) that are known reservoirs of SARS-related CoVs.

We found that there were striking similarities between the SADS and SARS outbreaks in geographical, temporal, ecological and aetiological settings. This study highlights the importance of identifying coronavirus diversity and distribution in bats to mitigate future outbreaks that could threaten livestock, public health and economic growth.

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From the NIH we get:

New coronavirus emerges from bats in China, devastates young swine Identified in same region, from same bats, as SARS coronavirus.

What

A newly identified coronavirus that killed nearly 25,000 piglets in 2016-17 in China emerged from horseshoe bats near the origin of the severe acute respiratory syndrome coronavirus (SARS-CoV), which emerged in 2002 in the same bat species. The new virus is named swine acute diarrhea syndrome coronavirus (SADS-CoV).

It does not appear to infect people, unlike SARS-CoV which infected more than 8,000 people and killed 774. No SARS-CoV cases have been identified since 2004.

The study investigators identified SADS-CoV on four pig farms in China’s Guangdong Province. The work was a collaboration among scientists from EcoHealth Alliance, Duke-NUS Medical School, Wuhan Institute of Virology and other organizations, and was funded by the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health. The research is published in the journal Nature.

The researchers say the finding is an important reminder that identifying new viruses in animals and quickly determining their potential to infect people is a key way to reduce global health threats.

SADS-CoV began killing piglets on a farm near Foshan in Guangdong Province in late October 2016. Investigators initially suspected porcine epidemic diarrhea virus (PEDV) as the cause. PEDV is a type of coronavirus common to swine that had been identified at the Foshan farm. Detection of PEDV ceased by mid-January 2017, yet piglets continued to die, suggesting a different cause. Scientists say separating sick sows and piglets from the rest of the herd helped stop the outbreak of SADS-CoV by May 2017.

Investigators confirmed the connection of SADS-CoV to bats by identifying the new virus in the small intestine of piglets from the outbreak. They then determined that the genetic sequence of SADS-CoV is similar to that of a bat coronavirus discovered in 2007 and looked for evidence of SADS-CoV in bat specimens collected from 2013 to 2016 in Guangdong Province. The new virus appeared in 71 of 596 specimens (11.9 percent).

The researchers also tested 35 farm workers who had close contact with sick pigs, none of whom tested positive for SADS-CoV.

Currently six coronaviruses are known to cause disease in people, but so far only two of them — SARS-CoV and Middle East Respiratory Syndrome coronavirus — have caused large outbreaks of fatal illness in people.

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And from EcoHealth Alliance:

EcoHealth Alliance Announces Discovery of New Bat-Origin Virus Impacting Pig Farms in Southern China

NEW YORK – April 4, 2018 – EcoHealth Alliance, a nonprofit organization working at the intersection of animal, environmental, and human health on a global scale, announced that–in collaboration with local partners–it has discovered a novel coronavirus in China called Swine Acute Diarrhea Syndrome (SADS-CoV). The virus has, so far, has caused the deaths of 24,693 piglets between 2016 and 2017 on several farms in the southern Chinese province of Guangdong, where the human pandemic SARS emerged in 2002.

Published today by the journal Nature, the virus’ discovery solves the mystery of mass pig die-offs on four farms in Guangdong Province. Particularly harmful to newborn piglets, SADS-CoV causes severe and acute diarrhea, acute vomiting, and eventually death due to rapid weight loss. It has a fatality rate as high as 90 percent for piglets five days or younger, but that drops in older pigs.

(Continue . . . )

The very good news here is – for now, anyway – there is no indication that this recently discovered virus can infect humans.

While the addition of yet another porcine diarrhea coronavirus (see SECD: Another Emerging Coronavirus Threat) may seem mostly a concern for pig farmers and the pork industry, coronaviruses – having a large RNA genome – tend to evolve over time (see slide below).

Already well adapted to pigs – who share a high degree of physiology with  humans (if that bothers you, think how the pig feels) – it is not much of a stretch to see one of these viruses someday becoming a zoonotic threat. 

In recent years we’ve seen a series of reports on bat viruses that pose potential zoonotic threats – making this an excellent time to be a Chiropterist.  

Some recent blogs include:

Emerg. Microbes & Infect.: Novel Coronaviruses In Least Horseshoe Bats In Southwestern China

PNAS: SARS-like WIV1-CoV Poised For Human Emergence

Sci Rpts: Avian & Human Influenza Compatible Receptor Cells In Little Brown Bats

Study: Hotspots For Bat To Human Disease Transmission