2012-2013: Several large human groups come from ancestral hybridizations with Homo neanderthalensis and Homo denisova
Many discoveries are changing our views of
the world. Europeans, Asians and Oceanians come from hybridization
with ancestral forms of the Homo genus. An epidemic caused by an E.
coli O104:H4 is quickly controlled. A deadly epidemic caused
by a coronavirus, MERS, finds its intermediate reservoir in camels.
H7N9 avian flu seems to be spreading.
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|22 december 2013. Four new cases of H7N9 flu in Guangdong and an outbreak of avian flu H5N2 in poultry in northern China. Chinese health authorities seal off and disinfect a farm in Hebei province after an outbreak caused by the H5N2 flu virus killed thousands of hens.|
|18 december 2013. Another letal flu virus in China. A 73 years old patient coming from Jiangxi province has died from a H10N8 avian flu infection. The virus has been identified in Guangdong markets in 2012 and workers of slaughter houses in Australia had been found positive for the H10 marker in 2010. In parallel another H7N9 case has been reported on sunday.|
|6 december 2013. A second case of H7N9 flu in Hong Kong. A 80 years old patient coming from Shenzhen has been shown to carry the avian flu H7N9 virus.|
|3 december 2013. The H7N9 avian flu virus reaches Hong Kong, where the "serious" alert response level has been activated. A patient coming back from Shenzhen has brought the H7N9 virus to Hong Kong, where the Health Authorities have decided to quarantine 17 persons who have been in contact with the patient. 200 more persons are monitored for flu signs as well.|
|12 november 2013. The MERS coronavirus is for the first time discovered in a camel. As we remarked for a mysterious outbreak in camels in Pakistan as suggesting a possible origin for the MERS coronavirus. An origin in camels is now probable.|
|1 novembrer 2013. Visceral leishmaniosis (kala-azar) is becoming drug-resistant in India. Kala-azar is a severe parasitosis, transmitted by phlebotome midges, which left untreated kills infected persons within a year. It is cured using drugs based on antimony. Unfortunately, because ground water is heavily contaminated by arsenic in India, the parasites have become resistant to antimony, as there is a considerable cross-resistance built up against arsenic and antimony in the parasites.|
|25 october 2013. A second case of H7N9 flu is identified in Zhejiang province. In another domain an outbreak of coronavirus gut infection is reported in pig farms in the USA.|
|15 october 2013. A man from Zhejiang province is hospitalized with severe H7N9 influenza.This is the second case reported in Zhejiang since late April. The patient is in critical condition.|
|20 september 2013. Confusion around the genome sequence of the MERS-CoV.While a first sequence was published by the Erasmus Medical Centre in Rotterdam, the Sanger Centre in Hinxton just published a second one. The two sequences differ by 98 nucleotides, suggesting that they belong to two substantially different viruses. Yet they are supposed to come from the same patient! This increases the feeling of mismanagement of the epidemic, while we still do not know where the virus came from.|
|8 september 2013. While several new infections and deaths are reported due to MERS-CoV in the Middle East the source of contagion is still unknown. The WHO issued an alert about the outbreak of MERS but would not recommend travel restrictions. At the same time Asia is preparing for a resurgence of H7N9 flu in the fall or next winter.|
|9 august 2013. Camels might be at the origin of MERS-CoV infections. On the 18th of november, 2010 we noticed a severe flu like outbreak in camels in Pakistan: could this be the origin of the MERS-CoV?|
|25 july 2013. An outbreak caused by a coronavirus is causing mass pig killing in the USA. A new coronavirus, the porcine epidemic diarrhoea virus (PEDV) is causing letal diarrhoea and vomiting in pigs in 14 US states. This is highly reminiscent of a disease that caused havoc in the '80s, with a shift from gut to lung, in a way that predated the SARS episode. A new coronavirus found in the feces of a South African bat is more closely related to MERS-CoV than any other known virus. In parallel a new influenza H7N9 case has been discovered in the Hubei province in China.|
|13 july 2013. An Emirati man is infected by the MERS-CoV. With the beginning of pilgrimage in Mecca, health authorities in Saudi Arabia strongly suggest pilgrims to wear masks. Turkey denies to have registered cases of the infection. One may relate the present situation with a die off of camels in Pakistan, with symptoms similar to those of flu, back in november 2010 and caused by an unknown pathogen.|
|12 july 2013. Considerable shrimp die off in Thailand. Breeding shrimps has been common for many years, with concomitant increase in a variety of diseases, in particular caused by Microsopiridia parasites. Thailand is now affected by a huge epidemic of a letal Vibrio parahaemolyticus, a seafood-borne pathogenic bacterium that is a major cause of gastroenteritis worldwide.|
|27 june 2013. The outbreak is not finished: 77 cases of MERS-CoV infection and the death toll has reached 40. Beside rumors such as what happened three weeks ago in Italy, reality is sobering, with a continuous spread of the disease. Curiously, the imbalance between the excess of male cases and that of female cases may be explained by the fact that women wear burquas in Saudi Arabia...|
|4 june 2013. Ten cases of asymptomatic infection by MERS-CoV in Italy? If true, the identification of asymptomatic infection of contacts of the patients in Italy are both reassuring and very worrying, as this means that the virus would propagate unseen, causing sporadic letal cases.|
|2 june 2013. Three new cases of MERS-CoV infection in Italy. The first French patient infected by MERS-CoV passed away, and the Italian Health Ministry reported their first cases of MERS-CoV in a citizen who recently traveled to Jordan and stayed there for 40 days and in two persons connected to him. The incubation time of the disease seems to be longer than suspected, probably up to 12 days, so that hidden cases might have been travelling far from the original place where they got infected. The source of contamination remains unknown.|
|25 may 2013. New cases of Middle East Respiratory Syndrome (MERS) suspected. The coronavirus recently emerged in the Middle East (MERS-CoV) has infected at least 44 persons worldwide, 33 in Saudi Arabia. The personnel of the Central Hospital in Buraidah, Saudi Arabia, appears to be reluctant to come back to work.|
|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) letal, 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 letal 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 letal 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 letal 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 letal disease that affected seals in North America is a flu variant that may infect humans. A particularly letal 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 letal 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 letal 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 infection that 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).|