This page is now less rich, as a consequence of the existence of
a great many quite visible sources that need not
be duplicated. Many sites provide interesting news about the
seasonal flu (type A H3N2 in particular), avian flu (H5N1)
and swine influenza A (H1N1). Crawford
Kilian's blog,
which has now spread to all sorts of other diseases and monitors
the Web carefully, is highly recommended. The Center for Infectious
Disease Research Policy (CIDRAP),
University of Minnesota, and the site of the World Health Organization
(WHO) are major sources
of information. In contrast with the situation 10 years ago,
when not much information was available there is now a wealth
of data sources. We only provided updated complementary information
here. For H7N9 flu, see
the Hong Kong Health Authorities alerts
 |
19 may 2013. The
new SARS-Like coronavirus is suspected to have infected patients now in intensive
care in New York. The coronavirus
recently emerged in the Middle East has infected 41 persons worldwide and
caused 20 deaths. According
to the Wall Street Journal, nurses working at a St. Luke's hospital in
New York have claimed that there are several cases of the new SARS-like virus
in the hospital's ICU, which have gone misdiagnosed and that are in fact
the new deadly virus. |
|
8 may 2013. The
new coronavirus is detected in France in a person coming back from Middle
East. In the mean time questions are
raised about the real number of cases in Saudi Arabia. It seems that clusters
of infection are hospital contaminations, as happened during the SARS outbreak
in 2003. The new virus causes rapid kidney failure in addition to respiratory
impairment.
|
|
6 may 2013. 129
cases and 31 fatalities caused by H7N9 flu in China.
|
|
5 may 2013. Multiple
questions about viral infections: reassortment of genes in the influenza
virus, and a new coronavirus. While
the H7N9 flu epidemic appears to be slowing down (128 cases, 27 fatalities),
viral infections of this type remain of considerable concern. Genome analysis
of the H7N9 virus shows that it probably comes from a reassortment of four
different viruses, H9N2, H7N3, H4N9, H11N9 avian influenza, viruses we discussed
repeatedly since the beginning of these notes. This indicates a series of
events that have progressively developed time. It is therefore very likely
that the genesis of dangerous viruses can take many paths. The idea of conducting
experiments in the laboratory to understand this highly variable process,
far from being justified, seems very dangerous, since it will only increase
the natural propensity of the virus to generate novel and dangerous forms.
In this regard, the experiences that have just been published in the journal Science,
describing a reassortment between the H5N1 virus and the current pandemic
virus H1N1 that can spread between mammals, seems particularly unwelcome.
The quest for fame, and the desire to learn at any cost, coupled with the
ubris that makes us believe that this is possible, is a natural tendency,
unfortunately. But not
every truth is good to say! Finally, the coronavirus
present in the Middle East has made new victims (27 cases, 16 deaths):
we still do not know its origin or the source of the contamination, which
is also very worrying. However the corresponding infections can be more
easily controlled than flu because, unlike the latter, it appears that
only feverish patients are contagious, which allows the establishment of
an effective quarantine. |
|
20 april 2013. The
toll of the H7N9 outbreak increases linearly. 101
cases, 20 fatalities, with a bias for elderly men (but the statistics is
not significant). And the origin of the disease still remains mysterious,
with some hints of a possible person to person transmission. The earthquake
in Sichuan might trigger population movements that might spread the disease.
It may be important to remember that in many cases of H7 flu, contamination
was via the eyes. |
|
17 april 2013. The
source of H7N9 contamination is still unknown. 83
cases, 17 fatalities, suggesting a small increase in the rate of infection.
With warmer days, it seems likely that the disease will disappear, but it
may reappear in autumn at new places, having been moved away from the present
centers by migrating birds (which are apparently only mildly affected). A
significant proportion of the infected patients did not have identified contacts
with birds, which makes the origin of the disease quite puzzling. The economic
consequences for the poultry market are considerable. |
|
14 april 2013. H7N9,
new cases Updated
map. 60 cases, 13 fatalities,
Henan is now affected. |
|
13 april 2013. The
first case of avian flu H7N9 has been identified in Beijing. The
7 years old daughter of a poultry trading professional has been hospitalized
in Beijing with flu symptoms, identified as due to the virus H7N9. This brings
to 44 the number of identified cases, with 11 deaths. As the increase in
the number of cases remains linear we will no longer report them. The mainstream
media and reference sites listed at the beginning of this page are sufficient
to provide relevant information. The last case in Shahghai is the husband
of and earlier case. Health authorities are investigating whetehre this might
be a H2H transmission. At 9pm (HK time) the
summary of cases provided by the Hong Kong health authorities is 49 persons
infected, 11 fatalities. |
|
11 april 2013. The
outbreak continues its steady fairly linear course. It
is now possible to have a picture of the situation of identified foci of
infection (click
on the map  to
go to Google Maps). A
major problem with the present outbreak is overreaction, in particular with
wrong information progagated via Twitter. In particular the number of serious
cases is probably not reflecting the true number of cases, which might be
more if the disease is mild in most persons. The Xinhua
agency reports 38 cases with 10 fatalities.
The Key Laboratory of Pathogenic Microbiology has ascribed
the H7N9 avian influenza to a genetic reassortment of wild birds from east
Asia and chickens from east China. The researchers found that no genes in H7N9 were traceable
to pigs, thus excluding pigs as intermediate hosts for the deadly new strain
of bird flu, despite the fact that apparently the first two identified cases had
only had contact with pigs.
|
|
10 april 2013. Emerging
Microbes and Infections publishes the history of the H7N9 outbreak. With
its strong base at Fudan University the journal EMI publishes
a first detailed account of the H7N9 outbreak. The total number of cases
in China is 33, with 9 fatalities.
|
|
9 april 2013. Linear
increase in the number of avian flu H7N9 cases. The
number of contaminated persons is now reaching 28, with 8 fatalities. A conspirationist
rumor is spreading in China, attributing this outbreak to an American bioterrorism
action! This reminds us of the situation during SARS, when I had to fight
against this idea within my own laboratory in Hong Kong.
|
|
7 april 2013. Many
types of the flu virus exist in the world. We
reported the fatal infection of groups of seals by a yet unknow disease last
year. The cause of the disease is a flu virus, of the H3N8 type
(which infects dogs). The H7N7 virus is present in poultry everywhere, but
for the moment it causes relatively mild infections in humans. Recently,
an H4N8 virus was found
in a pig farm in Guangdong, H11N3
virus in ducks in Jiangsu Province, and a H4N2 strain
in ducks in Shanghai. There are many other types, and within the
same type there are many variants. The most common triad leading to
human infection is the sequence duck -> pig
-> man.
There are now 21
cases in China, with 6 deaths. Luckily, it seems that the
N9 neuraminidase type (the enzyme that plays an essential role in release
and spread of progeny viral particles, following the intracellular viral
replication cycle) is sensitive
to the inhibitor peramivir (shown in
2006).
|
|
6 april 2013. Mind
contamination of your eyes. The live
poultry market of Nanjing are closed in the wake of further contaminated
birds. More should be learnt about H7 flu viruses. They have long been known
to contaminate the personnel of aviaries, in particular causing
conjunctivitis.
It is therefore important to remember not to touch one's eyes in a contaminating
situation. |
|
5 april 2013. Shanghai
live
poultry markets are closed due to H7H9 bird flu.
The
number of persons infected has increased and
a pigeon has been found to be carrying the virus, despite the fact that
it appeared apparently healthy. Animals suspected to carry the virus are
slaughtered. Butchers, breeders and sellers of poultry, and those in the
meat processing industry are particularly monitored.
Hong Kong has raised its alert level. We are at the WHO phase 0 level 2
of the WHO: Phases of pandemic response (Human infection confirmed in two
or more cases) but no human to human (P2P) transmission.
Background flu is a disease of Anatidae (ducks, geese and the like); the
reason why it used to spread to humans is a route centred on the standard
living custom of Chinese farmers who keep together ducks and pigs for their
living (the Chinese ideogram for "family" is a pig under a roof).
It goes from ducks, to pigs, to humans. Usually the disease is fairly innocuous
to ducks. From time to time the virus spreads to other birds, with more severe
symptoms (as it is less adapted there). This is the case of the recent H5N1
chicken flu, which probably started from a complex reassortment from several
bird strains in 1997. New forms of the virus always tend to explore new hosts.
The H7N7 virus is widely spread in poultry, world wide, and it is expected
that the new H7N9 came from reassortment of that virus with another virus
containing the N9 marker, after co-infection. New viruses are either killed
rapidly by the various levels of the immune system - and nothing is visible
- or they cause havoc, often being extremely dangerous. In such cases, because
they are less adapted, they do not propagate easily in the community of the
new hosts. This appears to be the situation of the present avian flu outbreak,
with no P2P transmission yet.
The danger will come when virus mutants will
begin to adapt to their new human hosts. While they will be less (but still)
lethal, they will begin to propagate from humans to humans. This is the situation
monitored by all health authorities in the world. A consequence of these
observations is that the viruses which might become the most dangerous are
either those which will take a route from Anatidae to a mammal and then to
humans, or viruses infecting another type of birds and attenuated directly
in humans (this may be the route followed at the moment by the virus). It
is important to be aware that the virus which will create the epidemic will
be present in the environment well before the epidemic starts. It is therefore
of the utmost importance to monitor the molecular changes (analyse the virus
genome) in a systematic way. The situation in China is not well understood,
and under investigation.
This virus strain has only rarely been identified
previously, in particular in a mallard in Spain in 2010. |
|
3 april 2013. China
is stepping up monitoring of H7H9 bird flu. Several new
patients have been discovered infected by the H7N9 virus. There is
as yet no indication of person to person contamination. However the origin
of the new strain of the virus is unknown. Until recently this strain of
the flu virus had only been found to cause mild infections in humans. However
the H7N9 virus could
replicate in the upper and lower respiratory track of ferrets, a good model for the study of the human disease. |
|
31 march 2013. The
situation of 2002-2003 is repeating itself with novel lethal
flu virus and
coronavirus. While the Middle East
coronavirus keeps making victims a new avian
flu virus, of the H7N9 type
(similar to the widely spread N7H7 avian virus) killed
two persons in Shanghai. |
|
5 march 2013. Genetics
of behaviour: SNPs that predict social success? A
variant polymorphism in the serotonin receptor genes appears to be strongly
correlated with social success in young males. It is likely that this type
of observation will become more and more common as we get more human genome
sequenced. The traditional reluctance that meets genetic studies will have
to cope with these results and come about a socially acceptable answer to
inevitable genetic variations. |
|
13 february 2013. A
SARS-like
coronavirus still lingers in the Middle East. A
man who returned recently from the Middle East and Pakistan is under intensive
care in a Manchester hospital where he has been confirmed to be infected
by a coronavirus of a type similar to that which infected
several persons recently. |
|
21 december 2012. An
outbreak of avian influenza in ducks in Indonesia raises concern. Hundreds
of thousands of ducks died in Indonesia as a result of an infection with
the H5N1 virus, a class (clade 2.3) known to have infected a man in the Chinese
province of Guangdong in 2011. It is important to know whether the
corresponding mutations are among those that have recently been identified
as particularly dangerous. |
|
14 december 2012. May
SARS
come back? A
virus causing lethal pneumonia has appeared
recently in the Middle East. We know that it may infect mammals close to Primates,
as did his cousin that was at the origin of SARS (Severe
Acute Respiratory Syndrome) back in 2003. |
|
4 december 2012. Invasive
weeds have a considerable ability to adapt to novel environments. In
a context when misleading studies tend to focus on GMOs invasive species
cause havock everywhere. This wrong focus is diverting our efforts from the
truly dangerous species, natural organisms that tend to invade alien environments.
The Asian short-day flowering annual grass Microstegium vimineum (Nepalese
browntop) rapidly
evolves novel phenotypes that allow it to survive in environments very
different from its original place of development, allowing the selection
of novel adaptive mutations that will make it difficult to eradicate. |
|
24 november 2012. The high pathogenicity of last years's outbreak of E.
coli O104:H4 infection explained. A serious epidemic of a lethal infection by a strain of Escherichia
coli affected Germany and other European countries in 2011. Virulence factors were found in the genome, but the particularly high pathogenicity was not explained readily. Scientists in the USA now discovered that a particular bacteriophage (virus) imbedded in the genome of the bacteria carried with it a gene coding for multiple
tagging (by methylation) of the genome with concomitant alteration of the
overall expression of virulence genes. |
|
3 november 2012. A
new tick-borne disease has emerged in Switzerland. Ticks
transmit many bacterial and viral diseases, such as the agent of Lyme disease
(borreliosis) or the Crimea-Congo virus. A new pathogen, discovered only
in 1999 and still without a recognized official name (Candidatus
Neoehrlichia mikurensis) causes relapsing fever. Patients have been
discovered in the region of Zürich, where about 10% of the local tick are
infected by the pathogen. Nothing is known yet about the efficiency of contagion,
but the disease needs to be carefully monitored. |
|
30 september 2012. A
new coronavirus with SARS-like symptoms and a new haemorrhagic fever. A
new bat coronavirus has caused concerned at the WHO after patients were found
in the Middle East with SARS-like symptoms. Fortunately the
disease did not spread easily ,
but it shows that coronaviruses remain a matter of concern. As in the preceding
cases (including an early outbreak in pigs in the
'80s), the virus seems
to be able to change its tropism from the gut to the lung. A novel
rhabdovirus (family of the rabies virus), has now been identified as
the cause of a local outbreak of haemorrhagic fever in the Democratic Republic
of Congo in 2009. Nothing is known about its reservoir and contamination
route, making it a possible candidate for a novel emerging disease. |
|
8 august 2012. Last
year's lethal disease that affected seals in North America is a flu variant
that may infect humans. A particularly
lethal disease, caused by an unknown virus affected
seals last year. Analysis of DNA in seal corpses has now revealed
the presence of an influenza
type A virus, previously known to infect waterfowls in the region. This virus is a variant of the H3N8 strain, apparently highly
lethal for mammals. The situation should therefore be monitored seriously
as it may be expected that the virus could propagate much more easily from
a mammal to humans than from birds to humans. |
|
4 august 2012. The
western arctic passage to Asia is open to navigation. This year will establish a new record low for the ice cover at the North Pole in july. |
|
2 august 2012. The
danger of making an imperfect vaccine against a highly versatile pathogen. The
holy grail of vaccination is to find a vaccine against the malaria parasite
or the AIDS virus. This has been a very challenging task (and some do not
believe that it will ever succeed) because both pathogens evolve so rapidly
that they circumvent the host defences triggered by the vaccine. The
situation is even worse, as discovered by a team of american scientist
working on a model of malaria in mice. Indeed the vaccine
may trigger the selection of variants of the parasite more virulent than
the original parasite ... |
|
1 august 2012. Barn
swallows nestlings take care of their kins. Scientists
in MIlano, Italy, showed that
the barn swallows youngs while in their nest, when sufficientlly fed
by their parents, reduced their competitiveness to the advantage of their
nestmates when their were deprived of food. Moderation of selfishness
can be adaptive in the presence of a needier kin, because the
indirect fitness benefits of promoting its condition can outweigh the costs
of forgoing being fed, and because it limits the cost of competitive begging
for food. |
|
27 july 2012. At
least three
populations of the out-of Africa humans make the present human build-up with
no sign of positive selection. Recent
genome analyses show that two major human populations are resulting from
admixture with archaic hominins. Some 1%–3% of the genome of all Eurasians
and native Amerindians is of Neanderthal origin, and Melanesians from Papua
New Guinea and Australia have another 3.5% of their genome of Denisovan origin.
While this renews the debate on the existence of human
races, there does not seem to have been any strong adaptation to novel
environments, while admixture
with related hominins was the rule rather than the exception. Indeed,
some sub-saharan african populations may have signs of admixture with still
other hominins, differing from Neanderthal or Denisovans. The most remarkable
observation at this point is that human polymorphism can essentially be
explain by space-related admixture, and not by any significant positive
selection event. |
|
29 june 2012. Circadian production of melatonin is better understood. A team
led by Peter McCormick of the University of Barcelona reports that adrenergic
receptors form complexes with D4 dopamine receptors to block melatonin production during the day.These findings elucidate the previously unknown role of D4 receptors in the pineal gland, and provide evidence for a novel molecular mechanism for controlling melatonin production in mammals. |
|
26 april 2012. Hong Kong has suspended the import of poultry products from Liaoning province of the Chinese Mainland for three weeks. A confirmed case of avian influenza H5N1 in Dalian, Liaoning has been diagnosed. The Center for Food Safety of the Hong Kong Special Administrative Region has implemented a
specific response to ban import from regions affected by human cases of
the H5N1 virus. |
|
25 april 2012. A
lethal skin disease, previously detected in 2011, is killing children in
Vietnam. A previously unknown disease,
first observed last year, has
affected 161 young people and killed 19 children in a poor Vietnam district.
The cause of the disease, which appears to be contagious by contact, is
unknown. As in the case of foot and mouth disease it affects hands and
feet, causing rashes and blisters. In another domain, it remains important
to monitor the development of H9N2 avian flu: a Korean
study shows how
the virus develops in poultry farms. |
|
9 april 2012. The mysterious disease that kills seals in Alaska is now affecting polar bears. Polar bears living south of Beaufort Sea in Alaska are losing their fur and have skin lesions. This is similar to the disease that killed many seals last year. The cause of the disease has not yet been identified. A similar disease appeared in 1998-1999. |
|
12 march 2012. An
outbreak of E. coli infection back in 2006 might be related to that
of 2011 in Germany. A
virulent strain of Escherichia coli affected Norway in 2006.
This strain, dubbed O103:H25, appears to be related to the O104:H4 that created
an epidemy in Germany last year. Both the 2006 and the 2011 strains carry
a similar toxinogenic bacteriphage (virus) and have similar genome organisation.
This opens again the question of the origin of the strains that caused the
disease. |
|
27 february 2012. An
emerging virus disease affects cattle in Europe. The
virus of Schmallenberg was discovered last november. It infects domestic
ruminants. The contamination route is not yet entirely understood, but it
is suspected that the virus is transmitted by insect vectors. It is a bunya
virus. This family comprises a great many negative-sense,
single-stranded RNA viruses that infect animals, insects, and plants.
For the time being nothing is known about wild animals. The virus does not
appear to cause human diseases. Up to a quarter of new born lambs, when their
mother is affected have malformations. |
|
29 january 2012. Several
fatalities caused by the Nipah virus in Bangladesh; diagnostic confirmed
as an infection by Escherichia coli
O104:H4 in French tourists back from Turkey last autumn. In another domain,
volcanic activity might be waking up south of the island of Santorini (Greece). The Nipah
virus
is endemic in Bangladesh, where it lingers in fruit-eating bats. Five
persons just died from the infectionthat causes fatal encephalitis.
Contagion is usually indirect, often caused by poorly cleaned fresh dates.
The O104:H4 E.
coli strain that caused an epidemic
of diarrhoea in French tourists back from Turkey is related, but distinct
from the strain that caused the German outbreak last spring. In Greece,
likely volcanic activity south of Santorini (Thira) spurs
a debate about its immediate developments. |
|
22 january 2012. The government informs the population about a case of avian flu in Guizhou province.
A 39 years old man has been infected by the H5N1 virus on january 6th. This case must be carefully monitored as the
patient did not appear to have had contact with poultry. However it must be remembered that similar situations were observed several times during the past decade. |
|
19 january 2012. Vietnam
and Cambodia report the death of patients infected by the avian flu virus.
While these
countries had not been affected by human cases for several months (two
years for Vietnam) two deaths are unfortunately reported. In Hong Kong the H5N1 virus
has been identified in a little egret. |
|
6 january 2012. Credit card payment was used to identify the source of contamination for the Escherichia
coli O104:H4 outbreak in Germany.
Risk factors for the large E.
coli outbreak that started in Germany last year have been identified
using credit card payments in cafeterias. This type of information has been recently used and led to important epidemiological data, pointing to the source of contamination (in that particular case, fenugreek sprouts). It is likely to become an important data source in the future. |
|
3 january 2012. The
brand new complex for government offices is contaminated by Legionella in Hong Kong.
Contamination of water by amoeba containing Legionella species is fairly frequent. It may lead to serious pulmonary infections if the legionella density is more than one colony forming unit per mililiter. The level found after a government official has been hospitalized with the disease raised 14 times that level. Investigation continues. In the mean time several black
headed seagulls were found to have died from the H5N1 flu virus. |
|
1 january 2012. The
SAR Hong Kong health authorities maintained the avian flu alert to the "serious" level.
Hong Kong SAR suspends poultry import from around the residence of the patient
who died from avian flu (H5N1). |
