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Habitatnews 2003-07: Tuesday, 8th April 2003
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Nature-related news for the busy Singaporean.
Information and archives at: http://habitatnews.nus.edu.sg
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Contents
In mining the net for information, good search skills and citing sources are
crucial. Ironically, the best way to learn is by conducting traditional
literature search in a library! A decent command of English helps. E.g in
picking out differences between “a cause of disease” and “the cause of
disease”.
So when you find a reliable place for information, you celebrate. Some of us
had relied on the New Scientist, but reporting SARS seems to have tested
their mettle. Strange for a publication that had witnessed the mad cow
disease and all its political ramifications unfold in Britain.
In the ensuing search for reliable information, New York Times has done
remarkably well. Just a simple registration and you have access to some
pretty good articles!
"Killer pneumonia virus linked to birds", by Debora MacKenzie,
Emma Young and Damian Carrington (Thu 3 April 03)
http://www.newscientist.com/news/news.jsp?id=ns99993587 (amongst others) reported that "Researchers have identified a
coronavirus as the cause of SARS, but have yet to publish full details."
While the new coronavirus is strongly associated with SARS, it has not
yet been clinically confirmed as the cause. Instead, it is a leading hypothesis.
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From: CDC Telebriefing Transcript: CDC Update on Severe Acute
Respiratory Syndrome (SARS), April 4, 2003.
http://www.cdc.gov/od/oc/media/transcripts/t030404.htm
“Evidence for this previously unrecognized Coronavirus has been found now in
at least 10 laboratories, including the laboratories here at CDC. The
preponderance of the evidence continues to mount and continues to favor an
etiologic role or this previously unrecognized Coronavirus in the cause of
SARS.” [Dr Hughes]
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Scientists in the WHO network are still investigating the possibility that a
paramyxovirus, a culprit earlier identified by some agencies, is a cause of
SARS. The possibility of more than one virus acting in concert has not been
ruled out either. Other bacterial and viral agents that have appeared have
not yet been completely dismissed.
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From: “Step by Step, Scientists Track Mystery Ailment.”
By Lawrence K. Altman, M.D.
New York Times, 1 Apr 2003
http://www.nytimes.com/2003/04/01/health/01DOCS.html?pagewanted=1-------------------------------------------------------------------
“[WHO] has long had networks of laboratories for influenza and other
diseases, but such networks have rarely been pressed into emergency service.
In less than two weeks, with an alacrity and a degree of cooperation seldom
seen in science, the laboratories identified two previously unknown viruses
as the leading suspected agents. (They belong to the coronavirus and
paramyxoviridae families.)
Far from being the last link in the discovery process, identification of a
new virus in a laboratory is only the first of many steps needed to prove
that a suspect virus actually causes a disease. It is likely to take weeks
more to determine which virus, singly or in combination, actually causes
SARS. In that time, the leading suspects may be displaced by other
candidates.
For now, the leading suspect is a coronavirus, though proof is far from
certain.”
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Pinning a name on a new disease helps us better deal with it, but the first
names thrown up in haste can persist in the media. The Sarawak outbreak of
1997 was (and often still is) tagged to the coxsackie virus despite
subsequent reports refuting this.
Mistakes in nomenclatural terminology can have significant consequences. The
Nipah virus outbreak in Malaysia of 1998 struggled against a predisposition
by health officials towards Japanese Encephalitis (JE), despite
demonstration of significant differences in disease behaviour that had some
farmers themselves questioning JE as the cause (Malaysia has some 48 years
experience with JE).
The cost of misnomers?
Habitatnews No. 99-29 featured “Lessons from the Nipah virus outbreak.”
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From: "Killer unmasked," by Meng Yew Choong.
The Star, Malaysia (24th May 1999)
http://groups.yahoo.com/group/habitatnews/message/45-------------------------------------------------------------------
"Believing the vector to be the Culex mosquito, many workers dutifully
wore protective clothing, applied insect repellent, fogged their farms and
made sure they left the farm before 6pm. But they failed to do one thing
which could have been the best protection: refrain from touching the pigs."
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“Hendra Virus Disease and Nipah Virus Encephalitis”
CDC Special Pathogens Branch
http://www.cdc.gov/ncidod/dvrd/spb/mnpages/dispages/nipah.htm
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Was this the simple reason for the Chinese health officials’ silence. Just
the usual flu in Southern China? In the end it took Dr Carlo Urbani, an
expert clinician diagnostician to sound the alert. Tragically, but not
unexpectedly, the disease took him as well.
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Disease's Pioneer Is Mourned as a Victim
By Donald G. McNeil Jr.
http://www.nytimes.com/2003/04/08/science/sciencespecial/08PROF.html
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In the meantime, a symptomatic name like SARS satisfies the need for a
handle while the WHO network of scientists race to identify the cause.
Who does the Search?
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From: “Step by Step, Scientists Track Mystery Ailment.”
By Lawrence K. Altman, M.D.
New York Times, 1 Apr 2003
http://www.nytimes.com/2003/04/01/health/01DOCS.html?pagewanted=1-------------------------------------------------------------------
W.H.O. is restricting research to its network.
Although scientists at the network are swamped with work, W.H.O. does not want to enlarge it for now. "We have not expanded the network," Dr. Salter
said, "because we are looking at a very dangerous virus and we don't want to
encourage laboratories elsewhere to start working with it if they do not
have the appropriate containment facility."
All laboratories in the network operate at the second-highest hazard level,
known as P-3, reserved for all but the most deadly pathogens.
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In new disease outbreaks, the media is providing 'first hand news' by
interviewing clinicians racing against time. It is important to be
particularly careful with their language and to help propagate an exact
understanding of the challenges facing scientists. There are no quick
answers.
And I hope lots of young Singaporeans students with Life Sciences exposure
are helping parents make sense of this all!
“Now, it's your turn.” By Ivan Fernandez. The New Paper, ?8 April 2003
http://newpaper.asia1.com.sg/top/story/0,4136,21908,00.html?
Well aware of the danger of jumping the gun
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“To Contain Ailment, a Test Heads the Wish List”
By Lawrence K. Altman, M.D.
New York Times, 8 Apr 2003
http://www.nytimes.com/2003/04/08/science/sciencespecial/08DOCS.html-------------------------------------------------------------------
“A main problem is that the cause of SARS is not known. The leading suspect
is a previously unknown member of the coronavirus family. But scientists are
studying additional viruses for their possible role, and health officials
have cautioned against drawing premature conclusions that any of them causes
SARS.
...In the absence of a diagnostic test, the network is working on the
assumption that the coronavirus causes SARS. It is a gamble the researchers
are unhappy to be taking.”
"We are running a risk, and we are sticking our neck out, but we have a
culprit and we have no better hypothesis on the table," Dr. Stöhr said.
The C.D.C. has developed two promising but rudimentary tests. But the tests
need substantial refinement before they can be used widely, in part because
they cannot detect infection from the new coronavirus in its earliest
stages. Also, the tests must be validated by tests on thousands of
additional specimens from SARS patients and healthy people, the C.D.C. has
said.
Still, late last week C.D.C. began releasing to state health departments
findings from experimental tests conducted among suspect cases in this
country. The tests measure the amount of antibodies that these individuals'
immune systems formed to fight the new coronavirus. But the C.D.C. cautioned
against interpreting that the findings proved the virus caused SARS and that
these individuals had it.
One reason for the caution is that the C.D.C. was embarrassed in 1999 when
its scientists initially misidentified the cause of the first cases of West
Nile fever detected in this hemisphere, in New York City. The C.D.C. first
said the outbreak was from the virus that causes St. Louis encephalitis.
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Malaysia’s television station, RTM, more than a year after the Nipah Virus
incident, apparently made the mistake of referring to this incident as “the
St Louis JE outbreak”. They were soundly scolded by an Aliran press release,
so at least there is a watchdog process there, ensuring that the lessons
learnt from the Nipah outbreak are not easily forgotten. It makes for
satisfactory reading!
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‘"JE" Pandemic?’, by Chan Chee Khoon,
Aliran Press Release, 15 September 1999
http://www.malaysia.net/aliran/ms990916a.html
“The confusion spawned by the "Nipah/JE" disinformation is remarkably
persistent, and RTM has fallen victim to its own propaganda. Not content
with sticking the JE (Japanese encephalitis) label indiscriminately on viral
encephalitis of diverse etiology in Malaysia (inflammation of the brain
caused by different viruses), TV1 made the astonishing reference on Sept 12,
1999 (Sunday, 11pm news bulletin) to "the St Louis JE outbreak" currently
assailing New York City. St Louis JE epidemic? St Louis encephalitis caused
by the JE virus? Japanese encephalitis caused by the St Louis virus? This
idiocy is going pandemic.
Let’s be clear on terminology before we embarrass ourselves further with
claims that it took us only 5 days to isolate the "Nipah JE" virus, and a
further 2 weeks to establish its identity distinct from the "Hendra JE"
virus. Japanese encephalitis is caused by a mosquito-borne flavivirus (JE
virus). Nipah disease is another encephalitic illness caused by close,
physical contact with live pigs infected with the recently discovered,
newly-named Nipah virus (a paramyxovirus). St Louis encephalitis is caused
by yet another distinct flavivirus (SLE virus).
Mistakes in viral nomenclature are not merely academic, or a cause for
embarrassment. The resulting misdiagnoses, as we have seen, are tragically
lethal and the authorities seem reluctant to clear up the confusion left by
their bungled handling of the Nipah tragedy.
Could it be that if we look east for too long, all things begin to appear
Japanese?”
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More about the chief suspect.
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"Fear Reigns as Dangerous Mystery Illness Spreads."
by Denise Grady New York Times, 7 Apr 2003
http://www.nytimes.com/2003/04/07/science/sciencespecial/07SARS.html?pagewanted=1Additional reporting by Elisabeth Rosenthal, Keith Bradsher,
Lawrence K. Altman, Clifford Krauss, Donald G. McNeil Jr.
and Amy Harmon.
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[...only one section featured, complete article at webpage...]
A Suspect From the Ranks of Minor Illnesses
No one is certain what causes SARS, but a microbe known as a coronavirus is
the chief suspect, most likely a new strain that originated in Guangdong
province.
Coronaviruses take their name from their appearance under the electron
microscope: a circular, crownlike shape with protruding spikes. Until now,
these viruses were thought to produce only minor illnesses in people, like
colds, diarrhea and other intestinal disorders. In cats, dogs, chickens,
pigs and cattle, coronaviruses cause severe and often fatal illness.
All coronaviruses have an extraordinary ability to capture stray bits of
genetic material from related viruses and weave them into their own genomes,
a feat biologists call recombination. Such natural recombination favors the
creation of new viruses, and in theory could turn a benign microbe into a
biological time bomb.
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"Deadly virus effortlessly hops species" By Helen Pearson
Nature Science Update, 2 Apr 2003
http://www.nature.com/nsu/030331/030331-4.html ----------------------------------------------------------------------------------------------
"In a simple overnight experiment, researchers transformed a coronavirus
that is lethal to cats into one that infects mouse cells by replacing a
single gene."
"Coronaviruses are unusual in their ability to reshuffle genes easily in
this way, explains Michael Lai of the University of Southern California in
Los Angeles, who works on them. The study shows that the viruses "can easily
switch their host range by switching genes", he says.
The SARS virus might also have arisen when an existing animal or human
coronavirus mutated into a more deadly form, says Lai. Which of these
explanations is true will become clear when the full genetic sequence of the
virus is pieced together, possibly this week."
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For a virus already inclined to transform into new identities, there could
be no better environment than southern China. The region is known to be one
of the world's great incubators of new viruses, particularly influenza.
Though coronaviruses are not related to influenza, scientists said that
coronaviruses could easily take advantage of the same conditions that make
the region the birthplace of new flu strains.
Southern China is populated by millions of farmers living on small plots of
land in close quarters with pigs, ducks, chickens and other livestock -
ideal for passing microbes back and forth between species and for viruses to
swap genetic material.
Gene swapping is not the only way a new coronavirus could emerge. Another
possibility is that an earlier version of the virus, one that did not cause
severe illness in people, underwent a genetic mutation making it more
virulent. It is also possible that an animal virus "jumped" to humans. Such
jumps are known to occur, sometimes with severe consequences.
Coronaviruses became the chief suspect in SARS when scientists used a device
called a gene chip, or microarray, to scan tissue samples from disease
victims. The chip is a glass slide containing bits of genetic material from
about 1,000 viruses. If the tissue sample contains genetic material from any
of them, it will stick to the corresponding bit on the slide.
When tissue samples from SARS victims were scanned, the slides indicated
matches with coronaviruses not only from humans, but also ones that normally
infect turkeys and cows - suggesting a strain that has never been seen
before.
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WHO Update 23 - Status of the main SARS outbreaks in
different countries, 7 April 2003
http://www.who.int/csr/sarsarchive/2003_04_07/en/ -------------------------------------------------------------------
Status of diagnostic tests
The development of a diagnostic test, which is being pursued around the
clock by the WHO collaborating network of 11 laboratories, has proved more
problematic than hoped. Three diagnostic tests are now available and all have limitations as tools for bringing the SARS outbreak quickly under
control.
The ELISA detects antibodies reliably but only from about day 20 after the
onset of clinical symptoms. It therefore cannot be used to detect cases at
an early stage before they have a chance to spread the infection to others.
The second test, an immunofluorescence assay (IFA), detects antibodies
reliably as of day 10 of infection, but is a demanding and comparatively
slow test that requires the growth of virus in cell culture.
The presently available PCR molecular test for detection of SARS virus
genetic material is useful in the early stages of infection but produces
many false-negatives, meaning that many persons who actually carry the virus
may not be detected – creating a dangerous sense of false security for a
virus that is known to spread easily in close person-to-person contact.
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