Glossaire de bactériologie
http://coproweb.free.fr/gbearemi/dico/glossindex.htm

Dictionnaire de bactériologie vétérinaire
http://www.bacterio.cict.fr/bacdico/garde.html

Dictionnaire de biologie générale (en anglais)
http://www.ucmp.berkeley.edu/glossary/gloss4cell.html

Dr David Heymann, Executive Director of Communicable Diseases, OMS

Dr Zhang Wenkang, Ministre Chinois de la santé

World Health Organization :
Dr Pascale Gilbert-Miguet, Chief Medical Officer, Joint Medical Service (JMS)
Dr Farida Djelloul, Medical Officer, JMS
Dr Guenael Rodier, Director, Communicable disease surveillance and response (CSR)
Dr Mark Salter, Medical Officer, CSR
Dr Sandy Cocksedge, Scientist, CSR Dr Isabelle Nuttall, Medical Officer, CSR
Ms Peggy Creese, Technical Officer, CSR
Mr Dick Thompson, Communications Officer

Yoshihiro Kawaoka
Title: Professor
Department: Pathobiological Sciences
School/College: School of Veterinary Medicine
Address: 3174 Veterinary Medicine
2015 Linden Drive West Madison, WI 53706
Phone: (608) 265-4925
Email: kawaokay@svm.vetmed.wisc.edu
Research Areas: Virology
Profile : http://www.cmb.wisc.edu/profiles/KawaokaYoshihiro.html

WILLIAM A. HASELTINE, who has a doctorate in biophysics from Harvard University, is the chairman of the board of directors and chief executive officer of Human Genome Sciences; he is also editor in chief of a new publication, the Journal of Regenerative Medicine, and serves on the editorial boards of several other scientific journals. He was a professor at the Dana-Farber Cancer Institute, an affiliate of Harvard Medical School, and at the Harvard School of Public Health from 1988 to 1995. His laboratory was the first to assemble the sequence of the AIDS virus genome. Since 1981 he has helped found more than 20 biotechnology companies.

Chinese scientists have traced the severe acute respiratory syndrome (SARS) virus back to a similar virus found in the civet cat and the raccoon dog, both animals found in the wild in China and elsewhere. Scientists have detected four isolates of a SARS-like coronavirus through a PT-PCR (reverse-transcription polymerase chain reaction) diagnostic test — which allows detection of the distinctive genetic information for SARS — from six Himalayan palm civets and a raccoon they took as samples from a market in Shenzhen in South China’s Guangdong Province on May 8. Guan Yi, a doctor at the University of Hong Kong’s Department of Microbiology, said: « We have charted a complete genetic map of the SARS-like coronavirus detected in the Himalayan palm civet, which shares 99.8 percent of the genetic code of the human SARS coronavirus. » According to the joint research by the University of Hong Kong and Shenzhen Centre for Disease Control and Prevention, there are only a minimal 80 differences in the 29,780 or so nuleotide and amino-acid substitutions between the coronavirus in humans and that in Himalayan palm civets, which are catlike mammals. Yuen Kwok-yung, head of microbiology at the university, said animals kept for food should be raised, slaughtered and sold with careful monitoring to prevent more outbreaks of SARS in people. However, officials with the National Headquarters for SARS Prevention and Control said earlier on Friday that they had not heard of the research results and declined to comment. The WHO announced in the Swiss city of Geneva that it had removed its travel warning for Hong Kong and Guangdong Province beginning on Friday this week, according to the Chinese Ministry of Health. The WHO said it took the decision because the SARS situation in these areas had improved significantly. On Thursday, the WHO proposed establishing a worldwide system for disease surveillance and response to fight SARS, including building epidemiology and public health laboratory facilities in China and the surrounding regions. The study by the University of Hong Kong linking civet cats to the coronavirus that causes SARS was described on Friday as a « significant breakthrough » by the World Health Organization. « If these findings are true, then this is a significant breakthrough, » Peter Cordingley, spokesman for the Manila-based WHO Western Pacific regional office, was quoted as saying in the Philippine Star online edition.

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Experts from the World Health Organization (WHO) welcomed the finding announced by Hong Kong scientists of possible cause of SARS virus from civet cats as « important, » according to news reaching here from the organization Saturday. WHO said the new finding would help direct future research into the virus. Scientists have been researching on the possible links between wild animals and the killer virus since the disease broke out. Francois Meslin, a WHO expert on diseases acquired from animals, told reporters the findings are « clearly quite exciting. » However, he also noted it is still too early to draw final conclusions on those findings. Meslin said it still cannot rule out the possibility the animals acquired the virus from humans, or that the virus jumped to humans from another animal altogether. Hours after WHO lifted the travel advisory against Hong Kong on Friday, scientists from the University of Hong Kong announced they had successfully isolated a type of coronavirus that causes SARS and it came from civet cats. Professor Yuen Kwok Yung, head of microbiology at the University of Hong Kong, said they believe the SARS virus jumped straight from civet cats to people. However, He also acknowledged they could not rule out the possibility other animals were involved in the transmission chain. Yuen’s team made the research in collaboration with the Center for Disease Control and Prevention of Shenzhen. They tested a large number of animals in south China’s Guangdong province, including civet cats, wild rabbits and barking deer, and found coronavirus in four masked palm civets. Civets, belonging to a large group of mostly nocturnal mammals, are not a true cat though they look like cats. The masked palm civets are one type of civets cats which have a white and black striped face. Yuen said it was important that the civet cats and other game food animals should be raised, slaughtered and sold under careful monitoring to prevent more outbreaks of SARS in people. « If you cannot control further jumping of such viruses from animals to humans, the same epidemic can occur again, » he said. Yuen’s team had previously said SARS came from animals but they had not been sure which kind. His team is the earliest in the world to identify that SARS virus is a type of coronavirus.

Meeting on SARS virus detection and survival in food and water, Madrid, 8-9 May 2003 22 May 2003 Investigations of the global outbreak of SARS have shown that the major mode of transmission of the SARS virus is through close person contact, in particular exposure to droplets of respiratory secretions from an infected person. However, in a cluster of SARS cases in an apartment block in Hong Kong, sewage is believed to have played a role through droplets containing coronavirus from the sewage system. The World Health Organization sees the need for research to better define the modes of transmission of the SARS virus through sewage, faeces, food and water. The potential for infection by ingestion, in addition to the close person contact route, must also be considered. At a meeting in Madrid, May 8th – 9th 2003, WHO, in collaboration with FAO and OIE, brought together a group of concerned scientific experts who are ready to pursue this research agenda. The purpose was to gain a better understanding of how the SARS coronavirus survives in the environment, with particular reference to food, water, faeces and sewage. As a result, the group will work together in a research network, as part of the international effort to coordinate our collective understanding of the science of SARS and prevent it from becoming endemic. The proposed agenda for research covers standardized methods for isolation and quantification of the virus in the environment. Recommendations were also made for relevant studies on the resistance, persistence and inactivation of the virus under conditions commonly found in food and water processing as well as sanitation and sewage treatments. Investigation related to faecal-oral transmission would be precautionary in nature since there is no evidence or epidemiological indication that the virus can be transmitted through this route. Nevertheless the research network is looking into potential future scenarios and the research needs that would follow. The report of the first network meeting will soon be available on the WHO web site. As stated on 11 April 2003, WHO does not at present conclude that any goods, products or animals arriving from SARS-affected areas pose a risk to public health. WHO is actively pursuing further efforts to investigate and develop advice related to the prevention of SARS transmission. WHO is aware of and supports national efforts to ensure that good hygienic practices for food production is adhered to in SARS affected as well as in other areas. As with any infectious disease, an important general precautionary approach is to reinforce procedures relating to food worker hygiene, including active assessment for diseases.

Looking like a scene in a movie, all hopes have been focused upon ferreting out the first SARS infected in a dramatic way and then trace the origin of SARS virus. Although Severe Acute Respiratory Syndrome (SARS) first floated up in Foshan, it didn’t spread out there. Huang Xingchu, the first reported SARS case, has naturally become an important clue to this mysterious disease. However, he lost the sight from the horizon. Heyuan Center for Disease Control & Prevention Hopes to Find Huang Xingchu « We have been looking for him too, while we don’t know his whereabouts after he was discharged from hospital. » Said Mr. Fu Aifeng, deputy head with Heyuan Center for Disease Control and Prevention, denying that Huang Xingchu is now under the center’s protection. According to Huang’s own statement, he worked at a game restaurant.

Some experts from WHO therefore held that SARS virus was closely related to wildlife. Such a view almost became the verdict in the early stage when SARS broke out in Guangdong Province and judged by the fact that chefs made up the majority of SARS patients in Heyuan. However, among the SARS patients later reported in Guangdong their occupations had nothing to do with the wildlife. Mr. Fu Aifeng also acknowledged, « We thought so. But now it seems that the view is short of sufficient evidence. » Heyuan Center for Disease Control and Prevention hopes to find Huang Xingchu. « We are keeping in touch with Huang’s family so as to get to know his whereabouts. From the perspective of epidemiology or whatsoever, it is very important to find him. He’d better have further consultation with doctors. » « Besides, we have to be responsible for Shenzhen. For instance, which restaurant has Huang Xingchu ever worked in? Is there anyone else who’s contracted SARS but did not exhibit the symptoms? » « We have nowhere to find him now. We neglected the importance, but when we realized it, he disappeared. »

« Mysterious Disease » Brought about Pressure to Patients In regard to Huang Xingchu’s disappearance, Mr. Fu Aifeng gave a relatively convincible account: due to this mysterious disease, Huang’s whole family was isolated in the countryside. As a matter of fact, no one would like to let others know. « Since contracting SARS, the patient has to bear huge social pressure. This calls for understanding of the society. » « We will make an investigation of the patients in respect of epidemiology. » And so, « everybody is looking for Huang Xingchu. » By April 30 when Heyuan’s last SARS patient was cured and discharged from hospital, Heyuan had a total of 19 SARS cases, including 9 medical workers while no death. On May 2, Heyuan’s last suspected case was ruled out. « Up to now there hasn’t been any SARS patient for a week in Heyuan, » said Mr. Fu Aifeng with gratification. Although nearly half a year has passed since the first report of the SARS case, the world has so far witnessed no progress concerning the origin of the SARS virus. Even if Huang Xingchu were found, no problem would be solved in any practical sense, because nobody has been infected except the medical workers. How on Earth Are People Infected with SARS Virus? In an interview, a staff member of Guandong Center for Disease Control and Prevention said, « All agencies for disease control and prevention have been working deep into the night. All others except those engaged in disease control and prevention have been out for investigation, but no advancement has yet been made. » « We still have no idea about what kind of virus it is, how it infects people and where it comes from. » « Experts from WHO are also here together with us. Maybe we will find the answer soon, maybe not forever. » There are too many doubts as to the outspread of SARS in China. Academician Zhong Nanshan pointed out especially on TV that 96 percent of the SARS patients in the Chinese mainland didn’t come into contact with SARS infection. In other words, unlike other countries and regions such as Hong-Kong and Singapore where there are infectious chains, the majority of Chinese SARS patients caught the virus in an unaccountable way. There were no intimate contacts between patients. Moreover, patients are concentrated in Guangdong and Beijing.

It is not imposable that diseases emerge in cities, considering cities have dense population and henceforth virus spreads fast there. The spread of SARS depends on whether it is ventilated. Before we get a clear understanding of the disease, it is still too early to jump to the conclusion about the SARS in China.

By PD Online Staff Zhu Lizhen

FAO Organisation des Nations Unies pour l’Alimentation et l’Agriculture

Interview de Peter Roeder, spécialiste de la santé animale à la FAO

La propagation du Syndrome respiratoire aigu sévère (SRAS) a soulevé une inquiétude planétaire. Certains médias ont émis l’hypothèse selon laquelle l’élevage intensif pourrait être un foyer du virus. Peter Roeder, de la Division de la production et de la santé animales de la FAO, commente le lien possible entre l’agriculture, l’élevage et la pandémie de Sras.

Y-a-t-il des preuves que le virus du SRAS provienne des animaux?

Il n’y a aujourd’hui aucune preuve permettant d’imputer l’origine du virus aux animaux d’élevage (boeufs, cochons, volaille, etc) et cela semble improbable, même si l’origine du virus est toujours un mystère. En admettant que le SRAS soit causé par le nouveau coronavirus qui a été associé à la maladie, la prise d’empreinte génétique de ce virus montre qu’il ne ressemble à aucun coronavirus animal ou humain connu.

Y-a-t-il un lien quelconque entre le SRAS et la « grippe du poulet » qui sévit actuellement en Europe et aux USA?

Non, ces deux maladies sont causées par deux virus complètement différents. Peut-on accuser l’élevage intensif et la concentration d’animaux d’être des foyers du virus? Instinctivement, on pourrait penser que c’est le cas, mais comme il n’y a aucune preuve que le virus provienne des animaux d’élevage, ces facteurs ne peuvent pas être tenus pour responsables dans cette affaire. L’importante densité de population dans la Chine méridionale aurait pu tout aussi bien être un facteur important dans la genèse de cette maladie, quelle que soit son origine.

Une production animale plus «durable» pourrait-elle réduire les risques de telles maladies?

Certainement, mais ce n’est pas de cela dont il s’agit dans cette affaire. Ceci dit, il est de plus en plus démontré que les systèmes de production animale intensifs et industrialisés sont vulnérables aux épizooties. Cela jette le doute sur la viabilité de ces systèmes. La promiscuité des humains avec plusieurs espèces d’animaux élevés de manière intensive peut fournir un substrat pour une transmission entre les espèces, l’évolution et l’amplification de plusieurs agents pathogènes.

Des scientifiques au Canada et en Australie projettent d’importer le virus du SRAS pour l’inoculer à des animaux. La FAO soutient ces expériences. Qu’en attendez-vous ?

Ce travail expérimental est nécessaire afin d’accorder les études de terrain pour examiner l’improbable circulation du virus dans les populations animales. Le travail a déjà commencé au Centre national canadien des maladies animales exotiques et nous espérons qu’il sera complété par d’autres études menées en Australie. Nous nous attendons à ce que ce travail nous en dise plus sur la capacité du virus d’infecter les animaux, la nature de tout signe de la maladie et la probabilité que les animaux transmettent le virus. Le virus peut-il être transmis par les produits animaux et le commerce? Nous ne disposons d’aucune preuve que le virus du SRAS infecte les animaux d’élevage et, par conséquent, sa présence dans les produits animaux et les produits alimentaires n’est que spéculation. Même s’il était présent, le virus serait probablement complètement détruit lors de la cuisson et la transformation. Les coronavirus, auxquels l’agent infectieux du SRAS appartient probablement, ont tendance à être très fragiles hors du corps animal et auraient une durée de vie très courte – quelques heures – en tant que résidus du conditionnement des aliments. Il n’y aucune raison de penser que le commerce des animaux ait été la voie de propagation de la maladie dans les zones affectées et autour du monde. Tout montre que le virus est un pathogène humain transmis principalement à partir de gouttelettes émises par les voies respiratoires des personnes malades. Les restrictions commerciales pourraient-elles aider à enrayer la propagation du virus? Le commerce ne semble pas jouer un rôle, des restrictions en ce sens ne seraient donc pas pertinentes.

Est-ce que le virus pourrait être véhiculé par les produits alimentaires transportés par les voyageurs?

Ici encore, la réponse semble être clairement « non ».

Quel est le rôle de la FAO dans la lutte contre le SRAS?

Il importe avant tout à la FAO qu’une caractérisation complète et parfaite de l’agent du SRAS et de son évolution soit réalisée. L’implication des animaux d’élevage et du commerce doit être exclue. En partenariat avec l’OMS, la FAO suit tout particulièrement le contexte d’exploitation et de manipulation des aliments. De manière générale, l’évolution des agents pathogènes dans les systèmes agricoles intensifs dans les zones très peuplées est, pour elle, un souci permanent. Comprendre l’évolution des pathogènes en relation avec les systèmes de production et la chaîne alimentaire est un composant essentiel du travail de la FAO en santé vétérinaire.

Le problème actuel du coronavirus : avoir le SRAS sans le coronavirus ? avoir le coronavirus sans le SRAS.

Des tests canadiens de dépistage du coronavirus ont été positifs chez des personnes sans le SRAS. Le Laboratoire National de Microbiologie Canadien à Winnipeg a constaté la présence du coronavirus chez 14% des 550 personnes qui étaient sous observation pour le SRAS mais dont l’état n’a jamais correspondu aux critères de définition des cas de pneumonie atypique.

Le Dr Frank Plummer, directeur scientifique du laboratoire ajoute que certains avaient été exposés à un cas de pneumonie atypique ou avaient voyagé dans des régions infectées mais d’autres pas.

Il fait partie des personnes qui doutent que le coronavirus est responsable du SRAS contrairement à l’OMS ou au CDC d’Atlanta.

De plus le Laboratoire ne trouve la trace du virus que dans environ 40% des Canadiens diagnostiqués comme des cas probables et dans 30% des cas suspects.

Il comprend encore moins le groupe des 14% indiqué plus haut.

Le Dr Stephen Ostroff du CDC admet que les résultats de tests effectués par son organisme s’avèrent également troublants : sur 20 cas probables et 40 cas suspects de SRAS, le coronavirus n’ést présent que dans six des cas probables et aucun des cas suspects… (affaire à suivre)

The following biosafety guidelines have been prepared by WHO for handling clinical specimens associated with SARS. SARS specimens should be handled according to appropriate biosafety practices in order to avoid laboratory-related infections and spread of disease to close contacts. As the primary route of infection is thought to be via droplets, extreme caution must be exercised to eliminate the unguarded production of aerosols. Detailed information about containment facilities and biosafety practices recommended in this document may be found in the WHO Laboratory Biosafety Manual, 2nd revised edition, available from the WHO web site . According to the latest findings, the etiologic agent responsible for the syndrome is a previously unknown coronavirus, currently called SARS coronavirus, or SARS-CoV . Accordingly, all laboratory work practices should be appropriate for work with viral agents, with particular emphasis on potential spread by droplets, air, and/or contaminated surfaces and objects. No procedure should be undertaken in which there is any doubt about the ability to adequately contain the specimen and prevent the uncontrolled release of the virus. WHO biosafety guidelines for handling SARS clinical specimens and materials derived from laboratory investigations of SARS: The following activities may be performed in biosafety level 2 (BSL-2) facilities with appropriate BSL-2 work practices: Routine diagnostic testing of serum and blood samples Manipulations involving known inactivated (lysed, fixed or otherwise treated) virus particles and/or incomplete, non-infectious portions of the viral genome Routine examination of mycotic and bacterial cultures. Final packaging of specimens for transport to diagnostic laboratories for additional testing. Specimens should already be in a sealed, decontaminated primary container The following precautions are strongly recommended by WHO for work in BSL-2 laboratories with potential SARS specimens: Any procedure that may generate aerosols should be performed in a biological safety cabinet. Laboratory workers should wear protective equipment, including disposable gloves, solid-front or wrap-around gowns with cuffed sleeves, eye protection and a surgical mask, or full-face shield, according to the risk of aerosols and exposure when performing specific manipulations. When working at a biological safety cabinet, a full face shield is not necessary. Centrifugation of human specimens should be performed using sealed centrifuge rotors or sample cups. These rotors or cups should be unloaded in a biological safety cabinet. Procedures performed outside of a biological safety cabinet should be performed in a manner that minimizes the risk of exposure to an inadvertent release of the etiologic agent. Work surfaces and equipment should be decontaminated after specimens are processed. Standard decontamination agents that are effective against lipid-enveloped viruses should be sufficient. Biological waste should be treated as outlined in the WHO Laboratory Biosafety Manual, 2nd revised edition which renders viral particles inactive. In cases where laboratory facilities are marginal, consideration should be given to referral of specimens to a suitably equipped reference laboratory for primary diagnostic tests. The following activities require BSL-3 facilities and BSL-3 work practices. Viral cell culture of the etiologic agent. Manipulations involving growth or concentration of the etiologic agent. When a procedure or process cannot be conducted within a biological safety cabinet, then appropriate combinations of personal protective equipment (e.g., respirators, face shields) and physical containment devices (e.g., centrifuge safety cups or sealed rotors) must be used. The following activities require Animal BSL-3 facilities and Animal BSL-3 work practices: Inoculation of animals for potential recovery of the agent from SARS samples. Any protocol involving animal inoculation for confirmation and/or characterization of putative SARS agents. Transport of human specimens: Transport of specimens within national borders should comply with current national regulations. International air transport of human specimens from suspect or confirmed SARS cases must follow the current (2003) edition of the International Air Transport Association (IATA) Dangerous Goods Regulations.

- Dangerous goods index

- Consignment of diagnostic

specimens 2003 Current IATA regulations (2003) allow specimens known or suspected of containing the SARS agent to be transported as UN 3373 “Diagnostic Specimens” when they are transported for diagnostic or investigational purposes. Specimens transported for any other purposes must be transported as UN 2814, and marked as: “Infectious substance, affecting humans (Severe Acute Respiratory Syndrome virus)”. Cultures prepared for the deliberate generation of pathogens may not be transported as diagnostic specimens, but as UN 2814, Infectious Substance, affecting humans (Severe Acute Respiratory Syndrome virus). All specimens to be transported (UN 3373 or UN 2814) must be packaged in triple packaging consisting of three packaging layers: UN 3373, Diagnostic Specimens, shall be packed in good quality packagings, which shall be strong enough to withstand the shocks and loads normally encountered during transport.

Packagings shall be constructed and closed so as to prevent any loss of contents that might be caused under normal conditions of transport, by vibration or by changes in temperature, humidity or pressure. Primary receptacles shall be packed in secondary packagings in such a way that, under normal conditions of transport, they cannot break, be punctured or leak their contents into the secondary packaging. Secondary packagings shall be placed in a final outer package with suitable cushioning material. Any leakage of the contents shall not substantially impair the protective properties of the cushioning material or of the outer packaging.

For Liquids

The primary receptacle(s) shall be leakproof and shall not contain more than 500 mI. There shall be absorbent material placed between the primary receptacle and the secondary packaging; if several fragile primary receptacles are placed in a single secondary packaging, they shall be either individually wrapped or separated so as to prevent contact between them. The absorbent material shall be in sufficient quantity to absorb the entire contents of the primary receptacles and there shall be a secondary packaging which shall be leakproof. The primary receptacle or the secondary packaging shall be capable of withstanding without leakage an internal pressure producing a pressure differential of not less than 95 kPa (0.95 bar). The outer packaging shall not contain more than 4 litres.

For Solids

The primary receptacle(s) shall be siftproof and shall not contain more than 500 g. If several fragile primary receptacles are placed in a single secondary packaging, they shall be either individually wrapped or separated so as to prevent contact between them and there shall be a secondary packaging which shall be leakproof. The outer packaging shall not contain more than 4 kg.

For air transport, the smallest overall external dimension of a completed package must be at least 10 mm. Packaging must conform to certain performance standards. For further information about definitions, packaging requirements, markings and labels, accompanying documentation, and refrigerants, please refer to the competent authority, current IATA shipping guidelines, commercial packaging suppliers, or available courier companies.

*Numbers in the brackets refer to cases among medical staff.