Deadly new Coronavirus traced to Egyptian tomb bat

[Gert van der Hoek]

aug 21, 2013

Deadly new MERS virus traced to Egyptian tomb bat


inaturalist.org - Taphozous perforatus - Egyptian tomb bat

A deadly new virus that has killed 47 people has been traced to an Egyptian Tomb Bat, researchers reported on Wednesday.

The virus causes Middle East respiratory syndrome, MERS for short, and it’s sickened 96 people with links to the Middle East – most of them in Saudi Arabia. It’s a coronavirus, a distant relative of the SARS virus that caused a global outbreak of severe acute respiratory syndrome in 2003.

Experts had long suspected bats, and a team led by Dr. Ian Lipkin of Columbia University started testing animals in Saudi Arabia soon after the virus killed its first known victims last year. Now they’ve found it, in a species of bat called Taphozous perforates. The infected bat was found just a few miles from the first victim’s home, they report in the journal Emerging Infectious Diseases.

“There have been several reports of finding MERS-like viruses in animals,” Lipkin says. “None were a genetic match. In this case we have a virus in an animal that is identical in sequence to the virus found in the first human case. Importantly, it’s coming from the vicinity of that first case.”

Lipkin says only one bat was found to carry the virus, out of hundreds tested. But now scientists can monitor bats and keep an eye out for potential outbreaks of the virus. West Nile virus first appeared in the United States in 1999, and once researchers discovered which birds and mosquitoes carried the virus, they started monitoring them to predict when the virus would start being a threat to people.

More: NBC news

Egyptian Tomb Bat area

wikimedia

[Ronan Kelly]

Re: Deadly new Coronavirus traced to Egyptian tomb bat

Volume 19, Number 11?November 2013
Dispatch
Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia


Ziad A. Memish, Nischay Mishra, Kevin J. Olival, Shamsudeen F. Fagbo, Vishal Kapoor, Jonathan H. Epstein, Rafat AlHakeem, Mushabab Al Asmari, Ariful Islam, Amit Kapoor, Thomas Briese, Peter Daszak, Abdullah A. Al Rabeeah, and W. Ian LipkinComments to Author
Author affiliations: Ministry of Health, Riyadh, Saudi Arabia (Z.A. Memish, S.F. Fagbo, R. AlHakeem, A.A. Al Rabeeah); Columbia University, New York, New York, USA (N. Mishra, V. Kapoor, A. Kapoor, T. Briese, W.I. Lipkin); EcoHealth Alliance, New York (K.J. Olival, J.H. Epstein, P. Daszak); Ministry of Health, Bisha, Saudi Arabia (M. Al Asmari); EcoHealth Alliance, Dhaka, Bangladesh (A. Islam)

Abstract
The source of human infection with Middle East respiratory syndrome coronavirus remains unknown. Molecular investigation indicated that bats in Saudi Arabia are infected with several alphacoronaviruses and betacoronaviruses. Virus from 1 bat showed 100% nucleotide identity to virus from the human index case-patient. Bats might play a role in human infection.
...
Conclusions
A wide range of CoV species are circulating among bats in Saudi Arabia. Although the prevalence of CoVs was high (≈28% of fecal samples), MERS CoV was found in only 1 bat. A 3.5% MERS CoV infection rate (n = 29; 95% CI 0?20%) in T. perforatus bats is low compared with that for severe acute respiratory syndrome?like CoV in rhinolophid bats in China (10%?12.5%) but consistent with CoV prevalence among bats in Mexico (4). Furthermore, the sensitivity for viral nucleic acid detection in samples collected in October 2012 was probably reduced because of failure in cold chain transport. Whereas 219 (32%) of 675 of fecal pellets collected in April revealed a CoV sequence by PCR, only 8 (5%) of 148 of rectal swab samples or fecal pellets collected in October were positive by the same assays. We were unable to recover additional sequences beyond the 190-nt RdRp fragment represented in Figure 2 but are confident in the fidelity of the finding. First, although RdRp is a conserved portion of the CoV genome, there is no precedent for 100% identity of a bat sequence with a human MERS CoV sequence. Second, when this work began we did not have cultured MERS CoV, human MERS samples, or MERS CoV cDNA in the laboratory at Columbia University where samples were removed directly from the tubes in which they were collected in the field for nucleic acid extraction, PCR, and sequence analysis. Third, the only MERS-positive signal was obtained in PCR analysis of the T. perforatus bat captured in Bisha near the home and workplace of the MERS index case-patient used to generate the human β-CoV 2c EMC/2012 sequence.
Bats are reservoirs of several viruses that can cause human disease, including rabies, Hendra, Nipah, Marburg, severe acute respiratory syndrome CoV, and probably Ebola viruses (11?14). Cross-species transmission from bats to humans can be direct, through contact with infected bats or their excreta, or facilitated by intermediate hosts (15). Bat CoVs are typically host specific; however, MERS-related CoVs have reportedly been found in many bat families, including Vespertillionidae, Molosidae, Nyteridae, and now Emballonuridae (sheath-tailed bats) in Africa, the Americas, Asia, and Europe. We sampled only a small sample of bats in Saudi Arabia. Nonetheless, given the rarity of MERS CoV sequences detected by our survey and the broad distribution of MERS cases throughout the Middle East, we speculate that there are probably other hosts. Future work should investigate additional bat and other wildlife species and domestic animals for CoV infection and potential linkage to human disease.
Dr Memish is deputy minister for public health, director of the WHO Collaborating Center for Mass Gathering Medicine in the Ministry of Health, and professor in the College of Medicine of Alfaisal University in Riyadh. His research interests include emerging infectious diseases, infection control, and preventive medicine.

http://wwwnc.cdc.gov/eid/article/19/11/13-1172_article.htm

[Giuseppe]

Re: Deadly new Coronavirus traced to Egyptian tomb bat

Having an egyptian 'tomb's bat' does not add much to our understand of current events in Middle East regarding the spread of novel coronavirus.

Citing this anecdotal - literary - old 'tomb's raiders' scourge is likely only a marketing move to sell more articles and books.

To business advisors for this great idea - useless in public health protection. GM

[sharon sanders]

Re: Deadly new Coronavirus traced to Egyptian tomb bat

MERS-CoV genetic sequences found in Taphozous perforatus bat


Profs Ziad Memish and Ian Lipkin, and a team of collaborators have published, in Emerging Infectious Diseases, their discovery of viral sequences in the faecal pellet of an Egyptian tomb bat.


It was only found in 1 of 29 Taphozous perforatus (Egyptian tomb bat, see some more detail on these in my next post) animals. These and 67 other bats captured in mist nets for this study, were observed nesting in abandoned ruins.

Samples from Bisha, Unaizah and Riyadh (Kingdom of Saudi Arabia) were snap-frozen on site, collected during October 2012 and April 2013. The October shipment was opened and thawed by US customs. Samples included wing biopsy, blood, throat swab, rectal swab and faecal pellets were collected for testing. Apart from RNA virus testing bats were speciated by DNA analysis (cytochrome B gene). The T. perforatus bat identity could not be confirmed genetically because there was no reference sequence on GenBank - but it was similar to another member of the genus.

Helicase, RNA-dependent RNA polymerase (RdRp) and nucleocapsid or envelope regions were targeted for amplification and sequencing. 227/1003 samples (22.6%) were positive for an alpha or beta-CoV.


The finds, represented by a phylogenetic tree using on a 181nt RNA fragment of sequence from the RNA-dependent RNA polymerase gene (100% identical to a sequence from the index case in Bisha, betaCoV 2c EMC/2012 over this region), secures bats as the/a primary animal source. So long as there was no contamination at customs or that the sample actually came from a food source. Not too likely that.

Obviously more work will need to be done to find more instances, complete the genome or at least sequence larger genetic fragments to make everyone happy and isolate infectious virus - but this finding is a significant step in confirming a starting point for understanding how humans get infected by the MERS-CoV.

Perhaps we can re-visit the transmission chain issue with a view to how bats might infect a (probable) secondary host - say the camel for now - I'd suggest that palm trees might have a role in this as well as a possible role in direct human infections if sap/dates/drinks were consumed by the most at risk groups; elderly men with underlying conditions. Perhaps this consumption even has a role in them developing a chronic kidney-related disease? I previously wrote a little about this 19th June and on risk in a post 28th July.





Posted by Ian M Mackay, PhD

[sharon sanders]

Re: Deadly new Coronavirus traced to Egyptian tomb bat

EID Journal: Detection Of MERS-CoV In Saudi Arabian Bat




Credit Wikipedia


# 7588

A story that I?m sure we are going to be hearing a good deal more about in the coming days is a dispatch that appears in today?s EID Journal announcing than an international team ? including Saudi researchers led by Deputy Health Minister Ziad A. Memish, Dr. Ian Lipkin?s team at Columbia University, and researchers from EcoHealth Alliance - have found a virus from a bat in Saudi Arabia that they call `A 100% genetic match? to the MERS Coronavirus.

Additional animal testing is ongoing, and we are likely to see more results announced in the coming days and weeks ? but this represents the first detection of the MERS coronavirus in an animal host.

In this study a live virus was not isolated, but rather a genetic match was determined using PCR amplification of a portion of the virus. Still, the researchers appear very confident they have a match.

First a link to the study, followed by a press releasefrom Columbia University, and then on to Helen Branswell?s report for the Canadian Press.

Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia

Ziad A. Memish, Nischay Mishra, Kevin J. Olival, Shamsudeen F. Fagbo, Vishal Kapoor, Jonathan H. Epstein, Rafat AlHakeem, Mushabab Al Asmari, Ariful Islam, Amit Kapoor, Thomas Briese, Peter Daszak, Abdullah A. Al Rabeeah, and W. Ian Lipkin

Abstract

The source of human infection with Middle East respiratory syndrome coronavirus remains unknown. Molecular investigation indicated that bats in Saudi Arabia are infected with several alphacoronaviruses and betacoronaviruses. Virus from 1 bat showed 100% nucleotide identity to virus from the human index case-patient. Bats might play a role in human infection.
(Continue . . .)

This from the newsroom at Columbia University.

MERS Virus Discovered in Bat Near Site of Outbreak in Saudi Arabia

Posted 8/21/2013 10:04:37 AM
<hr> First Study of MERS Animal Host in Saudi Arabia; Led by Columbia University, EcoHealth Alliance, and the Ministry of Health of the Kingdom of Saudi Arabia.

Image courtesy of Jonathan H. Epstein/EcoHealth Alliance
NEW YORK (August 21, 2013) A 100% genetic match for Middle East Respiratory Syndrome (MERS) has been discovered in an insect-eating bat in close proximity to the first known case of the disease in Saudi Arabia. The discovery points to the likely animal origin for the disease, although researchers say that an intermediary animal is likely also involved.

Led by team of investigators from the Center for Infection and Immunity (CII) at Columbia University?s Mailman School of Public Health, EcoHealth Alliance, and the Ministry of Health of the Kingdom of Saudi Arabia, the study is the first to search for an animal reservoir for MERS in Saudi Arabia, and the first to identify such a reservoir by finding a genetic match in an animal. Results appear online in Emerging Infectious Diseases, a journal of the U.S. Centers for Disease Control and Prevention.
(Continue . . .)

And last, but far from least, this report from Helen Branswell.

MERS virus isolated from bat; other animal may be involved in spread

Helen Branswell / The Canadian Press
August 21, 2013
Scientists from Saudi Arabia and the United States have found the MERS coronavirus in a bat in Saudi Arabia.

The scientists are reporting the finding in a paper published online today.

While bats have been suspected to be the reservoir of the new virus, this is the first time a match for the human virus has been found in an animal.
(Continue . . .)

I expect Helen will have an expanded version of this story later today or tomorrow, so check back.

Posted by Michael Coston at <a class="timestamp-link" href="http://afludiary.blogspot.com/2013/08/eid-journal-detection-of-mers-cov-in.html" rel="bookmark" title="permanent link"><abbr class="published" title="2013-08-21T13:35:00-04:00">1:35 PM</abbr>

[sharon sanders]

Re: Deadly new Coronavirus traced to Egyptian tomb bat

Monday, 26 August 2013

Prof Lipkin: There is no more sequence coming from that bat sample


Many thanks to Prof Ian Lipkin's indulgence of my eMail questions.
Also, check out the TWiV webcast by Prof Lipkin.

So, I guess to carry on from last night's post....I stand surprised.

Not even next-generation sequencing could pull any more sequence from the MERS-CoV-positive T.perforatus bat samples that thawed after the dry shipper (not a box+dry ice as I previously guessed, but a vacuum sealed vessel previously brought to -150?C then all free liquid nitrogen removed for transport; shipped by FedEx) was opened and the cold chain interrupted after arriving from the Kingdom of Saudi Arabia (KSA).

According to Prof Lipkin, in an email exchange we had last night, the group also tried a couple of runs of next-gen sequencing.


..we tried two separate ion torrent runs with no joy.

So why was only 1 October 2012 sample positive for the MERS-CoV strain? Prof Lipkin concludes that..

..the concentration of template was already extremely low in the sample at the time of field collection and lower still at the time of arrival in our Center. I would not be surprised if two aliquots of the same sample yielded different results in different labs. However, we will never have an opportunity to know because there is no more sample to test.

At the time of receiving the October samples (no MERS-CoV was found in the April samples), no viral gene/gene fragment/genome cloning had been done in Prof Lipkin's lab. A common potential source of PCR contamination ruled out.

How does your group know that this 182 basepair nucleotide sequence was not a contaminant from somewhere else?

The one sample came up positive repeatedly with the same assay. No other sample did so. We have recovered no other fragments that correlate with a MERS-like CoV in samples collected in the October 2012 or in the subsequent April 2013 field collections.

Antibodies were not sought in the massive 10μl of bat blood obtained per bat (the bats were released after sampling). But do these findings exclude the possibility that other bats, like those from genus Pipistrellus and Neoromicia (both from the family Vespertilionidae), or genus Nycteris, family Nycteridae, may be a host for MERS-CoV? At a World Health Organisation meeting in Cairo, Prof Lipkin told the the audience that..

...our findings don't exclude the presence of virus in a Vesper bat and that we were doing everything anyone suggested to test alternative explanations, including reagent contamination. We went back to the original materials using every specific and consensus primer set we and others had designed until all of the original material was exhausted. The results were the same. I sat on these data for months hoping to find another positive bat in subsequent field expeditions where we could report more sequence.

The decision to report it now was multifactorial. First and foremost, we tested every possible alternative explanation for the sample coming up positive other than that this fragment is bona fide-we can't find an alternative explanation. Second, there are no other reports from animals in KSA-I discussed phylogenetic analyses with several people in light of what was found elsewhere in Africa in Vesper bats. This fragment, although short and located in the RdRp is informative....Third, the scientists who did the work in the US and the Ministry of Health of KSA wanted to see it reported. There is a point where one has to get the work out in the public domain.

What's next in the search for animals hosting this virus and in trying to confirm what the group has just reported? There will also be a new European collaborative report (UK and KSA) coming out very soon that has new human MERS-CoV sequences suggesting multiple human introductions (animal to human?) with much more sequence variation in the MERS-CoV genome than we have seen thus far. This will further support the conclusion that the T.perforatus CoV is one and the same virus as that which infects humans.

...field expeditions should begin in the next few months and we will look again. The amount of time and resource invested already is far more than intended. I've never put in so much to recover so little.

Thank you to Prof Lipkin. This gives a some valuable insight into his careful efforts to deduce what animals may host a MERS-CoV strain,m as the first step in tracking how humans in the KSA are getting infected. It also highlights that finding even a basic piece of information requires many steps, lots of people, much effort and some luck. But if virus hunting was easy, everyone would do it right?

Some slight editing for brevity, and to account for mobile phone thumbs, was undertaken by VDU.


Posted by Ian M Mackay

[Emily]

Re: Deadly new Coronavirus traced to Egyptian tomb bat

http://www.thelancet.com/journals/la...lsca3=E24A35F#

The Lancet, Volume 383, Issue 9931, Page 1793, 24 May 2014
doi:10.1016/S0140-6736(14)60866-7
David Holmes

...

...Another zoonotic infection, Nipah virus, has been shown to stem from the consumption of date palm sap contaminated by infected fruit bats, but Christian Dorsten, a virologist at the University of Bonn, Germany, who is working with local researchers in Saudi Arabia, says talk of a similar link between bats and MERS is far-fetched. ?There are several aspects in recent hypotheses around MERS and bats that make no biological sense at all. For example, it is not true that Taphozous feeds on dates from which the virus could be acquired. Taphozous is insectivorous?, he says...