Tuesday, November 20, 2012

mBio: New Coronavirus Linked To Bats



Japanese pipistrelles – Credit Wikipedia

# 6727



Later today the open access journal mBio will publish a genetic analysis of the new coronavirus – recently detected in three Middle Eastern men - and will show that it is most closely related to two bat viruses (BtCoV-HKU4 and BtCoV-HKU5) previously isolated in Asia.


Regular readers will recall that we’ve seen this link suggested before.


Last September, in Coronavirus `Closely Related’ To HK Bat Strains, I wrote that researchers from the University of Hong Kong had compared the genetic structure of the newly discovered coronavirus with other coronaviruses, and found it to be a 90% match to the HKU4 and HKU5 strains collected in the middle of the last decade in Hong Kong.


With the emergence of Nipah and Hendra in the 1990s, and the discovery of the 2003 SARS coronavirus in Asian bat populations - and deep suspicions they may also be the reservoir host for Ebola and Marburg -  bats are increasingly looked upon as major players in the world of emerging infectious diseases.


A few recent blogs on this include:


Queensland: A Hendra Watch & A New Vaccine
Virology Journal: Ebola Virus In Chinese Bats

A New Flu Comes Up To Bat


The mbio article will be published online later today at http://mBio.asm.org.  For now we have a press release, with comments from the author Ron Fouchier, courtesy of the American Society for Microbiology.



Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans

  • Sander van Boheemen, Miranda de Graaf, Chris Lauber, Theo M. Bestebroer, V. Stalin Raj, Ali Moh Zaki, Albert D. M. E. Osterhaus, Bart L. Haagmans, Alexander E. Gorbalenya, Eric J. Snijder and Ron A. M. Fouchier




    Here we learn that a comparison of the viruses carried by the first two patients showed only 99 single nucleotide differences – making them more than 99.5% identical. A comparison with the third patient’s virus has not yet been completed.


    And while not an exact match to coronaviruses isolated in Asian bats, this new coronavirus is considered a close cousin.   


    Some excerpts from the press release follow.


    New coronavirus related to viruses from bats

    Public release date: 20-Nov-2012

    The virus that is causing alarm among global public health authorities after it killed a man in Jeddah, Saudi Arabia earlier this year and is now linked to two other cases of disease is a novel type of coronavirus most closely related to viruses found in bats, according to a genetic analysis to be published in mBio®, the online open-access journal of the American Society for Microbiology, on November 20. Researchers studied the genome of the HCoV-EMC/2012 virus in detail to learn about its relatedness to other viruses and about possible sources. The results of the sequencing and analysis could be used to develop diagnostic methods and possibly in creating therapies and vaccines if they are eventually needed for this emerging disease.

    "The virus is most closely related to viruses in bats found in Asia, and there are no human viruses closely related to it," says Ron Fouchier of the Erasmus Medical Center in the Netherlands, who headed up the  study. "Therefore, we speculate that it comes from an animal source."



    The HCoV-EMC/2012 virus is under increasing scrutiny today as two other patients suffering from infections with similar viruses have been identified. Since the patient in Saudi Arabia died in June, an individual from Qatar has been diagnosed with a very similar condition and is currently being cared for at a hospital in London. The full genomic sequence of the virus from that patient was made available on November 13, and Fouchier says it is a very close match with the HCoV-EMC/2012 virus sequence he analyzed in the mBio® paper, showing only 99 single nucleotide differences (in an unpublished analysis).


    "That makes it clear they are the same species. Ninety-nine nucleotides on the full genome amounts to only 0.3 – 0.4% difference," says Fouchier. "That, of course raises new questions."




    Phylogenetic analyses place the virus within the Betacoronavirus genus, where its closest fully sequenced relatives are viruses called BtCoV-HKU4 and BtCoV-HKU5, both of which were originally isolated in Asia from Lesser bamboo bats (Tylonycteris pachypus) and Japanese house bats (Pipistrellus abramus), respectively.


    HCoV-EMC/2012 bears only 77% sequence similarity with the BtCoV-HKU5 virus, however, making it distinct enough to be called a novel species of virus, says Fouchier. A partial sequence from a virus that was isolated from a species of bat in the Netherlands appears to be a closer match with HCoV-EMC/2012, but without a full genome sequence the exact degree of relatedness is impossible to tell.


    Based on the similarities the HCoV-EMC/2012 virus shares with viruses from bats, and taking into account a separate serological study carried out in Saudi Arabia that showed 2,400 hospital visitors had no antibodies to the virus, Fouchier feels confident saying the virus is new to humans. That source may well be bats, he says, since Pipistrellus bats are present in Saudi Arabia and neighboring countries.


    The relatedness between the HCoV-EMC/2012 virus and the virus that infected the patient in the unnamed London hospital is interesting, says Fouchier, since they are similar enough to be the same species but different enough that they are probably not directly linked. "It is unlikely they would be infected from the same source. We really need to understand whether these viruses are coming from a single source or multiple sources" before more cases come to light, he says.

    (Continue . . . )



    While this virus is similar to those previously detected in bats, there may be other intermediate animals hosts involved. We’ve seen with the Nipah virus that pigs can be vectors even though bats are the primary reservoir.


    With only three known cases over a period of several months, this emerging infectious disease isn’t exactly busting down the door to get at humans.  Still, anytime a new, highly pathogenic virus jumps species, we take notice.


    For now, this novel coronavirus appears to pose more of a epidemiological enigma than a genuine threat to public health. But we know that viruses can change over time, as can their threat level.


    Making it vital that we learn as much about this virus and its ecology now, while we have the luxury of time in which to to study it.