Novel coronavirus – Eastern Mediterranean: bat reservoir

NOVEL CORONAVIRUS – EASTERN MEDITERRANEAN: BAT RESERVOIR
New coronavirus-like virus found in bats
—————————————-
Viruses closely related to the new coronavirus that emerged last year
[2012] in the Middle East have been discovered in specimens from a
number of species of bats found widely throughout Europe and beyond, a
new study shows.

The work suggests bats common to Europe, Russia, parts of Asia and
Africa, and the Middle East may carry viruses that are very closely
related to the new coronavirus, called EMC 2012 [the virus has also
been referred to as nCoV — novel coronavirus].

The study will be published in the March [2013] issue of the journal
Emerging Infectious Diseases.

The findings, while interesting, don’t help to narrow down how a dozen
or more people in 3 countries have been sickened by the new virus, or
whether more have been infected but have escaped notice because their
symptoms were mild.

The researchers said bats from the Arabian Peninsula should be tested
to see if they carry similar viruses. But senior author Dr Christian
Drosten cautioned that because of the wide geographic distribution of
these bats, it cannot be concluded that the bat virus that evolved
into the new coronavirus did so in the Middle East.

“It could have come up in any other region where those bats are
prevalent,” said Drosten, a coronavirus expert and director of the
Institute of Virology at the University of Bonn Medical Centre in
Germany.

While it is believed the new virus came from bats, it’s not known
whether it moved directly from bats to people — through exposure to
bat guano or urine, for instance — or whether some other animal or
animals such as some form of livestock became infected and passed the
virus on.

The SARS coronavirus, a cousin of EMC 2012, evolved from a bat virus
that made its way into wild animals — civet cats and raccoon dogs —
that are eaten as delicacies in China. “We don’t know (yet) what the
raccoon dog is for this virus, but there may be one,” Drosten said.

He and colleagues had done previous research on bats in Ghana and in 4
countries in Europe — the Netherlands, Romania, Germany, and Ukraine.
As a result of that earlier work, they had stored fecal samples from
nearly 5000 bats. After EMC 2012 emerged, they tested the samples
looking for coronaviruses.

They found previously unknown viruses related to the new coronavirus
in nearly 25 per cent of _Nycteris_ bats, and 15 per cent of
_Pipistrellus_ bats. The viruses from the latter were most closely
related to EMC 2012. In one case, the genetic codes differed by less
than 2 per cent.

Three of 4 _Pipistrellus_ bat species tested positive for the similar
coronaviruses, Drosten said. “The whole Old World region is full of
different _Pipistrellus_ species. And I wouldn’t be surprised if all
of them contain related viruses.”

So if these bats commonly carry viruses similar to the new coronavirus
and carry them throughout many parts of the world, why have infections
only been seen in Saudi Arabia, Qatar, and Jordan? And why now?

Do the cases — 9 confirmed plus a similar number of probable cases —
represent multiple introductions of virus from bats to people, like
sparks from a fire? Or did the virus jump once and spread, mostly
unseen, from person to person?

At present, those questions have no answers. But there are ways to
find clues, particularly to the question of whether the virus made
multiple jumps from its bat reservoir.

Generating genetic sequences from all the viruses that have infected
humans — where virus has been isolated or virus fragments are
available — would give scientists information to compare.

Each type of virus evolves at a particular rate. The speed is referred
to as its molecular clock. Comparing genetic sequences from the 1st
known cases to later cases should show if the human viruses have
evolved from one another.

The 1st spotted case was a man from Jeddah, Saudi Arabia who died in
June [2012]. But in November [2012], a Cairo-based US naval research
laboratory confirmed that 2 people who died in Jordan in April 2012
had been infected with the new virus.

“We will never have a definite answer unless we find the source. But
we will have very, very clear hints if we sequence more viruses,”
Drosten said. “The further apart in time, and in geography, those
virus sequences are, the more we will learn.”

[Byline: Helen Branswell]

—
Communicated by:
ProMED-mail from HealthMap alerts
<promed@promedmail.org>

[According to Shalmon’s field guide to the land mammals of Israel, the
following 6 _Pipistrellus_ bats have been identified in Israel: _P.
ariel_, _P. kuhlii_, _P. pipistrellus_, _P. rueppellii_ and _P.
savii_.

In Jordan, the following 6 _Pipistrellus_ bats have been recorded: _P.
ariel_, _P. kuhlii_, _P. nathusii_, _P. pipistrellus_, _P. pygmaeus_,
and _P. rueppellii_ – Mod.AS]

[The article referred to, Annan A, Baldwin HJ, Corman VM, Klose SM,
Owusu M, Nkrumah EE et al: Human betacoronavirus 2c EMC/2012-related
viruses in bats, Ghana and Europe. Emerg Infect Dis [Internet]. 2013
Mar [accessed 21 Jan 2013], can be found at
<http://wwwnc.cdc.gov/eid/article/19/3/12-1503_article.htm>.

Abstract
——–
“We screened fecal specimens of 4758 bats from Ghana and 272 bats from
4 European countries for betacoronaviruses. Viruses related to the
novel human betacoronavirus EMC/2012 were detected in 46 (24.9
percent) of 185 _Nycteris_ bats and 40 (14.7 percent) of 272
_Pipistrellus_ bats. Their genetic relatedness indicated EMC/2012
originated from bats.”

The authors mention that “Within the Arabian Peninsula, the
International Union for Conservation of Nature (<http://www.iucn.org>)
lists 50 bat species, including _P. arabicus_, _P. ariel_, _P.
kuhlii_, _P. pipistrellus_, _P. rueppellii_, and _P. savii_ bats.”

The identification of betacoronaviruses related to the nCoV associated
with severe acute respiratory infections affecting individuals in
Saudi Arabia, Jordan, and Qatar last year (2012) in several bat
species in Ghana and Europe that include bat species found in the
Eastern Mediterranean region is not surprising and further supports a
hypothesis that the human infections were a result of species jump
from bat to humans. What is not known as yet, is whether this species’
jump was directly from human contact with infected bat secretions or
if there is/was an intermediate host such as livestock in the region
that may have been infected through contact with bat secretions, and
humans were then infected through contact with the infected animals in
the region as mentioned in the above newswire. Results of studies on
the animal populations in the region are eagerly awaited. – Mod.MPP]

[A relevant reference on the role of bats as a reservoir for emerging
viruses is Calisher CH, Childs JE, Field HE, et al: Bats: important
reservoir hosts of emerging viruses. Clin Microbiol Rev. 2006 Jul;
19(3): 531-45 (full article available at
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539106/>, references
available at source URL).

“Bats evolved early and have changed relatively little in comparison
with mammals of other taxa (69). Although the fossil record of bat
evolution is incomplete, a recent analysis of 17 nuclear genes dated
the origin of chiropterans to the Eocene period (52 to 50 million
years ago), coincident with a significant rise in global temperature.
3 major microchiropteran lineages were traced to Laurasia and a 4th to
Gondwana. The correspondingly ancient origins deduced for certain
zoonotic viruses maintained in bats, such as the henipaviruses and
lyssaviruses, suggest a long history of cospeciation. Viruses that
evolved with bats may have used for replication cellular receptors and
biochemical pathways, which are conserved in mammals that evolved
later and which underwent radiation in later geological periods. If
so, these conserved cellular receptors and pathways could enhance the
capacity for transmission of bat-associated viruses to other mammals.

“In 2002, a previously unrecognized coronavirus (family
_Coronaviridae_) was found to cause a new, severe acute respiratory
syndrome in humans [92, 125). This virus, named SARS-CoV, is a distant
relative of the group 2 coronaviruses that infect rodents, cattle,
dogs, pigs, and humans and has been assigned to group 2b (58). It is
distinct from 2 other coronaviruses recently identified in bats in
southern China (84, 119).

“Epidemiologic studies showed that the earliest cases of SARS were
associated with the wildlife meat industry. A survey of wildlife in a
Shenzhen market recovered SARS-CoV-like viruses from masked palm
civets (_Paguma larvata_) and raccoon dogs (_Nyctereutes
procyonoides_) and detected antibodies to the SARS-CoV-like virus in a
hog badger (_Arctonyx collaris_)(63). Interestingly, the epidemiology
of the outbreak in animals in the wildlife meat market resembled that
of shipping fever, a viral syndrome that occurs when animals from
different farms are comingled under crowded, stressful conditions.
Under such circumstances, immune responses to persistent virus
infections are reduced, virus shedding is increased, and susceptible
animals become infected and shed virus. In the marketplace where
SARS-CoVs were detected, viral RNA from some animals that were
seronegative was detected by reverse transcription-PCR, suggesting
acute infection, while other animals had antibodies to SARS-CoV but
continued to shed virus, suggesting persistent infections (63).
Although no pathology was associated with SARS-CoV in animals in this
market, civets inoculated with human isolates of SARS-CoV had severe
lung pathology (156). By sequencing many viral genomes from SARS
patients, wild and farmed civets, and other animals, a dendrogram was
generated that showed that the 1st human SARS coronaviruses were
closely related to a contemporary virus from masked palm civets and
that point mutations were selected and accumulated later, as the virus
passed from human to human (139).

“Extensive surveys of viruses in domestic animals, poultry, and
wildlife were done by reverse transcription-PCR to identify the
natural reservoir of SARS-CoV. Palm civets were found to be an
incidental host rather than the principal host for SARS-CoV. Recently,
several groups simultaneously identified bats from different locations
in southern China as being infected with SARS-CoV-like viruses or
having antibody to these newly recognized coronaviruses, including
members of several species of Chinese horseshoe bats (suborder
_Microchiroptera_, family _Rhinolophidae_, genus _Rhinolophus_)
(Tables 1 and 2) (42, 84, 86). The prevalence of antibody to bat
SARS-CoV in some species of Chinese horseshoe bats was as high as 84
percent. Pathology has not yet been associated with SARS-CoV infection
of bats.

“The genomes of SARS-CoV isolates recovered from civets and humans
during the 2002-to-2003 outbreak of SARS lay phylogenetically within
the broad group of SARS-CoV-like viruses of bats (86). These data show
that the virus responsible for the 2002-to-2003 outbreak most likely
originated from this group of bat-associated viruses. Antibody against
SARS-CoV-like viruses of bats was also detected in Leschenault’s
rousette (_Rousettus leschenaultia_), a cave-dwelling megachiropteran,
suggesting that fruit bats also may support infection with
SARS-CoV-like viruses. Thus, the natural history of SARS-CoV appears
to involve a previously unrecognized SARS-CoV-like virus of bats being
transmitted in meat markets to amplifying hosts, including masked palm
civets, raccoon dogs, and a hog badger, and then spilling over to
infect humans in close contact with these intermediate hosts or their
tissues. Subsequent human-to-human transmission of the virus was
associated with adaptive mutations in the viral genome (139).” –
Mod.CP]