Saturday, September 29, 2012

Finding a new virus: Spit, sequencing and serendipity

September 28, 2012


The story of how Zambon's team got to this stage is one of smart scientific detective work, timely checking of emails and a bit of serendipity. But it starts right back at the basics, with a call from a worried doctor and some spit.
"Fresh secretions - basically sputum, or spit - were obtained" from the patient, Zambon explains, after an initial call from doctors treating the Qatari man caused scientists in her lab to be concerned he might have a rare infection.
"If you're a virologist in a laboratory like ours and handing clinical material, whether it be human on animal, you always have to be alive to the possibility that once in a while you might turn up something unusual," she said.
Maybe because of that, it happened that two key HPA scientists had both spotted a post on an internet-based reporting system called ProMED-mail - the Program for Monitoring Emerging Diseases.

Full Article:

WHO: Influenza update

September 28, 2012 - Update number 169


• Seasonal influenza transmission has not been picked up yet in the northern temperate zone. Most countries in this zone have started or are yet to begin seasonal reporting.
• In the tropical areas most countries are reporting low or decreasing trends of influenza detections. The exceptions are Nicaragua in the Americas and India and Thailand in Asia.
• Influenza activity decreased in most of the temperate countries of the southern hemisphere. Australia, Chile, New Zealand, Paraguay and South Africa continue to report declines in influenza indicators. On the other hand, Argentina has reported some late influenza activity.
• WHO has recommended the influenza vaccine composition for use in the 2013 southern hemisphere influenza season following technical consultations in September 2012.

Friday, September 28, 2012

WHO: Influenza Virus Activity in the World, as of 25 Sept. 2012

hat-tip A Times Memory Blog:

[Source: World Health Organization, full page: (LINK). Edited.]
Influenza virus activity in the world, 28 September 2012
Source: Laboratory confirmed data from the Global Influenza Surveillance and Response System (GISRS).

Based on FluNet reporting (as of 25 September 2012, 11:00 UTC), during weeks 36 to 37 (2 to 15 September 2012), National Influenza Centres (NICs) and other national influenza laboratories from 75 countries, areas or territories reported data.
The WHO GISRS laboratories tested more than 17 228 specimens.
1 501 were positive for influenza viruses, of which 968 (64.5%) were typed as influenza A and 533 (35.5%) as influenza B.
Of the subtyped seasonal influenza A viruses, 161 (20.5%) were influenza A(H1N1)pdm09 and 624 (79.5%) were influenza A(H3N2).
Of the characterized B viruses, 6 (50%) belong to the B-Yamagata lineage and 6 (50%) to the B-Victoria lineage.
In addition, 7 detections of A(H3N2)v viruses were reported from the United States of America.

During weeks 36 and 37, influenza activity in general remained low in the southern hemisphere. Globally, influenza A(H3N2) viruses remained the predominant subtype followed by influenza B and A(H1N1)pdm09 viruses.
Influenza virus detections decreased in Australia and New Zealand with A(H3N2) and influenza B viruses co-circulating.
In Africa, influenza B activity remained high in South Africa, while in eastern and western Africa, sporadic activity of A(H1N1)pdm09, A(H3N2) and B viruses was reported.
In Asia, increased activity of influenza A(H1N1)pdm09 and B viruses was reported in Nepal. Local outbreaks of influenza A(H1N1)pdm09 and B continued in India and local outbreaks of A(H3N2) continued in Japan.
Influenza activity in Central and South America remained low. At low levels, influenza A(H3N2) and B viruses co-circulated in Central America. In Argentina, the number of influenza A(H1N1)pdm09 viruses detected increased slightly. Sporadic detections of influenza were reported from elsewhere in the region.
Influenza activity remained low in Europe and North America.
To date, 305 laboratory confirmed cases of infection with (H3N2)v viruses have been detected in the United States of America with 1 death and 16 hospitalizations reported.
Following the WHO Consultation on the Composition of Influenza Virus Vaccines for the Southern Hemisphere 2013, from 17 to 19 September 2012, it was recommended that the influenza vaccines for the southern hemisphere 2013 season contain the following viruses:
For the trivalent vaccine:
  • an A/California/7/2009 (H1N1)pdm09-like virus;
  • an A/Victoria/361/2011 (H3N2)-like virus;
  • a B/Wisconsin/1/2010-like virus;
This is the same composition as that recommended by WHO for the vaccine for the northern hemisphere 2012-2013 season.
For the quadrivalent vaccine containing two B viruses, it is recommended to include the above three viruses and a B/Brisbane/60/2008-like virus.

Most swine flu hospitalizations, only death from virus spread by fair animals were in Ohio

[The report they are speaking of in this article has been posted on the right side-bar under H3N2v]

DAYTON, OHIO: A new report from the Centers for Disease Control and Prevention shows that more than two-thirds of the people in the U.S. hospitalized after contracting a flu virus spread by swine at county fairs were from Ohio.

The report released Thursday showed that 11 of 16 people hospitalized in the U.S. for H3N2v this summer were Ohioans. That’s 69 percent.


Vaccine Strains for the 2012–13 Influenza Season

[This is the composition of the Flu Vaccine for this year]

U.S. influenza vaccines for 2012–13 will contain A/California/7/2009 (H1N1)-like, A/Victoria/361/2011 (H3N2)-like, and B/Wisconsin/1/2010-like (Yamagata lineage) antigens.

The influenza A(H3N2) and B antigens differ from the respective 2010–11 and 2011–12 seasonal vaccine antigens (3).

The influenza A(H1N1) vaccine virus strain is derived from an influenza A(H1N1)pdm09 (2009[H1N1]) virus and was included in the 2009(H1N1) monovalent pandemic vaccine as well as the 2010–11 and 2011–12 seasonal vaccines.

Also, this [A copy of the minutes of the meeting to approve the above vaccines:

Food and Drug Administration
Center for Biologics Evaluation and Review
February 28-29, 2012

These summary minutes for the February 28-29, 2012 Meeting of the Vaccines and Related Biological Products Advisory Committee were approved on March 13, 2012.
I certify that I participated in the February 28-29, 2012 Meeting of the Vaccines and Related Biological Products Advisory Committee and that these minutes accurately reflect what transpired.

From the pdf file:

Full document is located here:

Costa Rica: 49 Children Admitted, 29 Required Mechanical Ventilation

 September 28, 2012

The rise in reported cases, in the month of September from diarrhea or respiratory infections in the National Children’s Hospital, rose the situation to the category of epidemic.

This was stated yesterday by the hospital director, Rodolfo Hernandez, and he urged to the parents to implement all preventive measures such as hand washing or use sneeze protocol.

In the hospital there were 49 children, of which 29 required mechanical ventilation. Last year at this time, only 15 children needed this device.

Meanwhile, emergency service have been saturated. “From 450 emergencies attended per day, 67% are for one of the two conditions,” said Hernandez.

Generally, the area of this hospital emergency care on 320 patients per day.
For his part, Fernando Morales, director of the National Hospital of Geriatrics and Gerontology, noted that daily received 15 patients with respiratory problems and ten with diarrhea.
However, Morales said that there is no increase in cases compared to 2011, but he said that this is a time of year which recorded more patients with pneumonia.


HPA: Infection Control Advice for Suspected & Confirmed Coronavirus Cases

[This pdf file will be located on the right side-bar under the category "Coronavirus".  Editing is mine.]
Version 1.2 September 26 2012

This document outlines infection control and other general advice for personnel who may be involved in receiving and caring for patients, primarily within healthcare settings, who may be infected with a novel coronavirus. It should be used in conjunction with local policies.
In the absence of effective drugs or a vaccine, control of this disease relies on the appropriate management of cases, (including isolation of suspected and confirmed cases) and their close contacts. In preparation, healthcare facilities who may receive and care for any cases should: Review their local policies and ensure that operational procedures are described and staff are familiar with them, for example where personal protective equipment is stored and how it should be used Ensure staff are aware of how to access surveillance forms from the HPA and any local record sheets etc Ensure that adequate supplies/equipment are available, including:
o supplies of FFP3 respirators
o Gloves - disposable and latex free alternatives, eg nitrile
o Gowns/Aprons - disposable fluid resistant full sleeve gowns and single-use plastic aprons
o Eye protection eg. tight fitting goggles or face shield - disposable, or if non disposable, with a wipeable surface, not with elastic straps
o Leak-proof, clinical waste disposal bags,
o Hand hygiene supplies.
o General-purpose detergent and disinfectant solutions Ensure that staff are aware of where a case will be isolated and the need for a negative pressure room Ensure that there is guidance available on actions to be taken if a case presents

Coronaviruses are mainly transmitted by large respiratory droplets and direct or indirect contact with infected secretions. They can also be detected in faeces and urine and under certain circumstances airborne transmission can occur from aerosolised respiratory secretions and faecal material. As coronaviruses are enveloped a very wide range of disinfectants would be effective. Personal protective equipment and good infection control can be extremely useful but never completely eliminate risk as they are user dependent.
Record keeping
A record of all staff that have contact with a suspected/confirmed patient should be kept
Patients who meet the current HPA case definition and present at the Emergency Department should be placed in a single room whilst awaiting assessment. Staff should wear protective clothing as detailed below. Rooms to be appropriately decontaminated before being used again (see below: Cleaning)


Eurosurveillance Novel Coronavirus Volume 17, Issue 39, 27 September 2012

Eurosurveillance, Volume 17, Issue 39, 27 September 2012
Rapid communications
Novel coronavirus associated with severe respiratory disease: Case definition and public health measures
  1. European Centre for Disease Prevention and Control, Stockholm, Sweden
  2. The members of the team are listed at the end of the article
  3. Health Protection Agency, London, United Kingdom

Citation style for this article: Danielsson N, on behalf of the ECDC Internal Response Team, Catchpole M. Novel coronavirus associated with severe respiratory disease: Case definition and public health measures . Euro Surveill. 2012;17(39):pii=20282. Available online:
Date of submission: 27 September 2012

Two cases of rapidly progressive acute respiratory infection in adults associated with a novel coronavirus have generated an international public health response. The two infections were acquired three months apart, probably in Saudi Arabia and Qatar. An interim case definition has been elaborated and was published on the World Health Organization website on 25 September 2012.

Case 1

On 13 June 2012 a patient in their sixties presented with deteriorating pneumonia in Jeddah, Saudi Arabia and a seven day history of respiratory symptoms. The patient developed acute renal failure and died on 24 June 2012. A novel beta-coronavirus was isolated in Saudi Arabia* and sequenced at the Erasmus Medical Centre (EMC) in Rotterdam, the Netherlands [1].

Case 2

On 11 September 2012 a patient in their forties with severe respiratory symptoms was evacuated from Qatar to a United Kingdom hospital and was admitted to intensive care there on 12 September.  The patient remains in hospital and has been on life support with pulmonary and renal failure. Extensive diagnostic tests for a causative agent were negative but on 21 September a pan-coronavirus RT-PCR test performed on lower respiratory samples was positive for a conserved sequence of the coronavirus polymerase gene [2]. Comparison with the nucleotide sequence at the EMC indicated a close match with the novel virus isolated from Case 1.  Contacts of Case 2, many of them healthcare workers, are being actively identified, monitored and investigated for coronavirus infection. Some of them have reported mild respiratory symptoms but none have tested positive for the novel virus or developed severe disease to date [3].


Coronaviruses are globally distributed and are found in humans, other mammals and birds.  They are enveloped RNA viruses classified in alpha, beta and gamma genera. Up to one third of mild upper respiratory tract infections in adults are caused by human coronaviruses. The zoonotic severe acute respiratory syndrome (SARS) beta-coronavirus (SARS-CoV) caused the SARS outbreak in 2003 when over 900 people died. [4] Human coronaviruses are transmitted through direct contact with secretions and via aerosol droplets. Infected patients also excrete virus in faeces and urine and under certain circumstances, airborne transmission can occur from aerosolised respiratory secretions and faecal material [5].

The detection of a novel coronavirus associated with severe respiratory disease and renal failure requires urgent assessment and careful management. The United Kingdom Health Protection Agency (HPA) alerted European Union (EU) Member States and other countries via the Early Warning and Response System (EWRS) and International Health Regulations (IHR) mechanisms. Control measures

The HPA has recommended stringent control measures and developed an early case definition [6]. The European Centre for Disease Prevention and Control (ECDC) has developed a risk assessment in response to the cases [2]. A surveillance strategy has been agreed between ECDC and WHO with the first priority being to determine whether there are additional severe cases. The initial virology results and the separation in time of the only two confirmed cases suggest an infection that quite probably is of zoonotic origin and different in behaviour from SARS [5]. It is essential to rule out there being additional severe undiagnosed cases, especially since the transfer of severely ill patients in air ambulances meant that cases may be missed by conventional surveillance that is based on clinical notification by the original diagnosing physician, particularly primary care physicians. Hence the interim case definition has been developed with the aim of providing a high level of sensitivity for identifying cases ill enough to require hospital care or having pneumonia while avoiding cases with only mild symptoms [7]. 

Case definition

The case definition applies the established link that both cases stayed in the Arabian Peninsula but makes it conditional of hospitalisation or pneumonia, which means that cases with a link to an affected area but only mild symptoms do not require investigation.  The affected area is currently defined as Saudi Arabia and Qatar but can be expanded as needed.  Human coronaviruses have a short incubation period of 3 to 4 days. The longest incubation period observed during the SARS outbreak was 12 days. However, this was an outlier and a pragmatic incubation period of up to 10 days has been adopted for the case definition.  The case definition should be used by clinicians for deciding which patients require investigation for possible novel coronavirus infection and which patients should be reported to national authorities. An interim case definition was published on the WHO website on 25 September [8]. It is expected to be amended once more epidemiological and diagnostic information becomes available and clinicians and public health managers should stay updated with the latest version on the website.

EU Member States have been requested to report patients meeting the case definition to ECDC through the EWRS and countries should continue to report probable or confirmed cases through the IHR contacts at WHO regional offices as mandated by the IHR. There is currently no rapid diagnostic test that easily confirms infection with this novel virus. Virus detection and serological testing is being developed by the HPA, the EMC and the University of Bonn, Germany and this was facilitated through close collaboration including the provision of preliminary sequences and a virus isolate between those institutions [9].
Infection control advice

The HPA has developed specific infection control advice for suspected or confirmed novel coronavirus cases. The guidelines take a strict precautionary approach, whereby patients are isolated in negative-pressure single rooms or, if this is not possible then a single room with en-suite facilities. Full personal protective equipment (PPE), including gowns, gloves and FFP3 masks are worn by staff and others having direct contact with the patient [6].

This situation is still evolving and there are many unknowns to consider in hypothesis generation and control measures. There is strong evidence that a novel virus caused the severe disease in the two patients. Based on this assumption it can be concluded that the virus poses an as yet poorly defined level of threat to people’s health. There may have been other cases in the past that were missed and serological testing of stored sera and other specimens from such cases will be important. Serological testing will also determine whether the two cases represent the most severe end of a spectrum of clinical presentations which also includes mild and asymptomatic infections or if they are isolated events. To date, the long period between occurrence of the two cases and the lack of secondary cases among contacts suggest the disease is poorly communicable in humans. Our assessment, based on the limited information currently available, is that the risk of wide spread transmission resulting in severe disease is low. However, the emergence of a novel coronavirus requires a thorough assessment which is currently being coordinated at international level. 

The ECDC internal response team
Katrin Leitmeyer, Pete Kinross, Herve Zeller, Niklas Danielsson, Pasi Penttinen, Rene Snacken, Anna-Pelagia Magiorakos, Amanda Ozin, Romit Jain, Eve Robinson, Lara Payne Hellstrom, Angus Nicoll, Josep Jansa and Denis Coulombier.

* Authors' correction: The country in which the virus was isolated was added on 28 September 2012 at the request of the authors.

  1. ProMED-mail. Novel coronavirus - Saudi Arabia: human isolate Archive Number: 20120920.1302733 20 September 2012 21:51:30 CEST. Available from:
  2. European Centre for Disease Prvention and Control (ECDC). Rapid Risk Assessment . Severe respiratory disease associated with a novel coronavirus. Stockholm: ECDC; 2012. [Accessed 26 Sep 2012]. Available from:
  3. Health Protection Agency (HPA). HPA Press release. Acute respiratory illness associated with a new virus identified in the UK. London:HPA; 2012. [Accessed 25 Sept 2012]. Available from:
  4. World Health Organization (WHO). WHO final summary SARS, 15 August 2003:Summary table of SARS cases by country, 1 November 2002 - 7 August 2003. Geneva: WHO; 2003. Available from:
  5. World Health Organization (WHO). Consensus document on the epidemiology of severe acute respiratory syndrome (SARS) 2003. Geneva: WHO; 2003. Available from:
  6. Health Protection Agency (HPA). Infection control advice: Suspected or Confirmed Novel Coronavirus Cases. London:HPA; 2012. [Accessed  25 Sep 2012].
  7. World Health Organization (WHO). WHO Case-finding interim case definition.  Geneva: WHO; 2012. [Accessed 26 Sep 2012]. Available from:
  8. World Health Organization (WHO). Case definition for case finding severe respiratory disease associated with novel coronavirus. Geneva: WHO; 2012. Available from:
  9. Health Protection Agency (HPA). Partial genetic sequence information for scientists about the Novel Coronavirus 2012. London: HPA; 2012. [Accessed  25 Sep 2012].  Available from: 

Central Illinois elementary school closed after half its students call in sick

ASHMORE — A stomach ailment, not food poisoning, might have been the cause of the illness that kept about half of Ashmore Elementary School’s students out of school Wednesday, a Coles County health official said.
Investigators “seriously doubt” that food was the cause of the illness that sickened enough of the school’s students and staff for district officials to order the school closed Wednesday, county health department director Dan Stretch said.
Stretch said there doesn’t appear to be any “common food” that those who became ill and those who did not both ate. Based on interviews, the department found about as many of the ill students ate the school lunch as did not, he said.
Fifty-five of the school’s 100 students were absent again Thursday, Charleston School District Superintendent Jim Littleford said. About 40 of them were still ill or still had some symptoms, while parents kept the rest home as a precaution, he said.
The illness also affected five of the school’s 14 staff members, but all but one of them, a custodian, were back at school Thursday, Littleford said.
Stretch said the health department is trying to collect stool samples from some of the infected people so they can be sent to the Illinois Department of Public Health for testing. He didn’t know when tests might be complete.

Egypt: Health Minister launches campaign together against influenza

Collaboration with 11 medical society specialized launched Egyptian Minister of Health Dr. Mohammad Mustafa national campaign new under the slogan "Together against flu" in order to increase community awareness of the importance of prevention of seasonal influenza, particularly as we on the cusp of winter, which increases the infection rates. For his part, Dr. Omar Kandil, First Undersecretary of the Ministry of Health and Population and Preventive Medicine that the Ministry of Health attaches great importance to the prevention of risks seasonal influenza, and the ministry is of many years to monitor the flu of all kinds at the level of governorates of Egypt and to monitor cases and to monitor any mutation in the influenza virus to ensure rapid treatment. as confirmed Dr. Omar that the mortality rate of influenza in Egypt less than global averages were discovered about 6 cases of avian influenza were mortality rate is about 36% while the longer the world average of 59%. explained Dr. Omar that the prevention of seasonal influenza simple through hygiene washing lady regularly and you in case of the emergence of a private cold symptoms for heart patients, sugar and respiratory patients who are the most vulnerable groups of the injury must go to the doctor to avoid the risk of complications.

Thursday, September 27, 2012

Report: Two-thirds of those hospitalized by new flu strain were from Ohio

[There is additional information on H3N2v located on the right side-bar]

By Peggy O'Farrell
Staff Writer
More than two-thirds of the people who contracted a new flu virus spread by swine at county fairs around the nation were from Ohio, federal health data show.

A report released Thursday by the Centers for Disease Control and Prevention showed that 11 of 16 people hospitalized for H3N2v this summer were from Ohio. Ohio reported also the only death associated with the outbreak, a 61-year-old Madison County woman who died Aug. 26.

But so far, the available data on H3N2v flu and the people sickened by it do not explain why Ohio had so many hospitalizations, said Dr. Celia Quinn, author of the report and a CDC Epidemic Intelligence Service officer. Quinn is assigned to work with the Ohio Department of Health through 2014.

As new flu strains emerge, public health experts monitor how easily they spread and how sick they make people. In the case of H3N2v, they are watching it to see it develops the ability to spread easily from person-to-person, instead of only from pigs to people. The concern is that new flu viruses could spur a pandemic, or worldwide flu epidemic, with the potential to sicken millions. The last pandemic was the H1N1 pandemic in 2009-2010. The H3N2v flu strain contains a gene from that strain.


New Flu Shot Guards Against Newest Strains

Philippines: DOH readies 'SARS rooms' to deal with new SARS-type cases

September 26, 2012
The Department of Health is preparing the "SARS Rooms" in government hospitals to treat patients infected by a new coronavirus similar to one that causes Severe Acute Respiratory Syndrome.

DOH National Epidemiology Center head Enrique Tayag said this Thursday even as he said they have not received any report of Filipinos being infected by the new virus.

"Na-maintain natin ang SARS Room sa DOH hospitals. Naglagay tayo ng mga room na ito nang tinamaan tayo noon ng SARS,"Tayag said in an interview on dzBB radio, when asked about initial measures should there be cases of the new infection in the Philippines.

He also said Philippine authorities remain on alert after the World Health Organization issued an alert on the matter.

In 2003, the Philippines was affected by the SARS scare that began in neighboring China.

SARS is a severe respiratory illness that is caused by a coronavirus (species Severe acute respiratory syndrome virus of the genus Coronavirus), is transmitted especially by contact with infectious material (as respiratory droplets or body fluids), and is characterized by fever, headache, body aches, a dry cough, hypoxia, and usually pneumonia.

A Reuters report said SARS appeared in China in 2002 and infected more than 8,000 people around the world, killing around 800 of them before being brought under control.

Also in the Thursday morning dzBB interview Tayag said airports have already started routine screening of incoming passengers.

"Kung may darating sa ating bansa na makitang anumang sakit bibigyan natin ng option na magpatingin sa DOH hospitals," he said.

Among the symptoms of the new infection are difficulty in breathing and kidney failure, which is the unique characteristic of the recent cases.

Because of this, Tayag advised Filipinos experiencing coughs and [general body] weakness to seek treatment at a hospital.

On the other hand, he reminded doctors and medical personnel at hospitals to practice hygiene by washing their hands.

"Sa hospital dapat maagap sa paghugas ng kamay. Maraming sinisipon at inuubo, mag-practice na tayo ng hygiene," he said.

Tayag also admitted there is little information about the disease at this time since there have only been three recorded cases of the newest infection so far.

"Hindi pa malinaw kasi tatlong kaso ang nare-report (We still don't have a very clear picture because there have so far been only three reported cases)," he said.

CIDRAP: Full genome sequence of novel coronavirus expected shortly

Sep 27, 2012 (CIDRAP News) – British health officials said today that a Rotterdam lab that first characterized the novel coronavirus linked recently to two severe illnesses hopes to publish the whole genome in the next 24 to 48 hours, and the UK's Health Protection Agency (HPA) launched guidance to help clinicians investigate and manage possible cases. 

The HPA said in an update that the full genome sequence will be published by Ron Fouchier, PhD, based at Erasmus University in the Netherlands. The sequence will be based on cultured virus that has been at the lab since early July. 

Yesterday the agency gave the same time frame for release of the full sequence and did not change the estimate in today's update. 

The HPA had earlier released the partial sequence for the virus's polymerase gene, obtained from an infected patient undergoing treatment in London, which enabled scientists to compare it with others and determine that the new virus is related to bat coronaviruses. The HPA said it doesn't yet have a viral isolate, but clinical material from the patient is being cultured to make isolates. 

Also, the HPA shared new details about molecular diagnostics for identifying the new virus. It said pan-coronavirus primers described by an international group of researchers in 2003 and in a 2008 report from Belgian researchers should both be useful. However, the clinical material the HPA has does not react with specific assays it has for OC23, 229E, NL64, or SARS. It said it welcomed offers of reagents and information from scientists who specialize in the area.
In other developments, the HPA published some clinical tools to help clinicians manage suspected and confirmed cases along with close contacts. The tools include an algorithm for investigating and managing possible cases; it describes the testing process, protective actions to take if an infection is confirmed, and the next steps to take for sample collection and data reporting. 
Another algorithm walks clinicians through investigating close contacts of patients with confirmed novel coronavirus infections. For contacts who don't have clinical symptoms during the initial visit, the HPA recommends that baseline clotted blood samples be taken as soon as possible, ideally no later than 7 days after exposure. The algorithm recommends that follow-up samples be taken at least 14 days after baseline or 28 days after exposure if a sample couldn't be taken when the case-patient was asymptomatic. It says a contact form should be completed 10 days after the initial data is collected. 

The HPA also issued a nine-page infection control resource for handling confirmed and suspected cases. It noted that coronaviruses are mainly transmitted by large respiratory droplets and direct or indirect contact with secretions. The agency also said the viruses can be detected in feces and urine and in some instances can be transmitted by aerosolized respiratory droplets and feces. It detailed steps to take in addition to standard precautions, such as what type of respirator and personal protective equipment (PPE) to use. 

In developments elsewhere, Hong Kong's Centre for Health Protection (CHP) said today that the process to make novel coronavirus infection a notifiable disease is under way. It said a legislative amendment will be recorded tomorrow, taking effect immediately. Health practitioners will be required to notify the CHP's director of health if they suspect the disease, and labs will be required to report virus leaks that may pose a public health risk. 

No new infections involving the novel coronavirus have been detected beyond the Qatari man hospitalized with a severe respiratory illness and renal failure in a London intensive care unit and a 60-year-old Saudi Arabian man who was infected with a virtually identical virus who died in June. 

The identification of a new coronavirus has raised global health worries, because a then-novel one in 2003 caused the SARS epidemic that sickened 8,422 people, killing 916 of them. Health officials have said the new virus is clearly different than the one that caused SARS, and some have said that an animal source can't be excluded. 

HPA: Algorithm for Investigation & Mgmt of Possible SAR Illness assoc. w/Novel Coronavirus

[These 2 pdf files will be located on the right side-bar for reference in the future]



Factbox: New virus can cause fever, cough, breathing problems

LONDON | Thu Sep 27, 2012 5:00pm IST

(Reuters) - The World Health Organisation (WHO) has issued a global alert about the emergence of a new virus that was previously unknown in humans and can cause a potentially fatal acute respiratory infection.

Here is an at-a-glance guide to the virus:
* The virus belongs to a family called coronaviruses and has so far been confirmed in only two cases globally. Both occurred between July and September 2012.

* The first case was in a 60-year-old man in Saudi Arabia and proved fatal. The second is in a 49-year-old Qatari man who recently visited Saudi Arabia. He had the infection diagnosed after travelling to London in early September.

* The WHO has not yet given the virus a name, but scientists at Britain's Health Protection Agency (HPA) refer to it as "London1_novel CoV 2012".


MOH Indonesia: Indonesian pilgrims and No Need to Worry Can Still Make Travel to Saudi Arabia

 September 27, 2012

WHO is currently collecting information from the focal point of England, Kingdom of Saudi Arabia (KAS) and Qatar to determine the level / new coronavirus possible impact on public health of confirmed cases. Specifically, more information is required on how exposure / transmission, work and travel history to determine possible sources of infection or virus container.
It originated from the information given IHR focal point of United Kingdom on 22 September 2012, the WHO about one case of acute respiratory syndrome with history of renal failure with a trip to Saudi Arabia and Qatar.
WHO has conducted a rapid assessment of risk, and there are currently no reports of acute respiratory syndrome with renal failure from other WHO member states. WHO requested that all National IHR Focal Point reported an abnormal increase in the number of patients admitted to the ICU with kidney failure and respiratory problems that can not be known cause. WHO case definition will be presented in the coming days.
The case is not yet a serious impact on public health. In the UK, all the contacts and healthcare workers who provide care, not sick or showing symptoms. In the Kingdom of Saudi Arabia and Qatar, there are no reports about the influx of patients to the ICU at the hospital.
Currently, there are no high risk that encourage the adoption of international travel or trade restrictions. KAS has increased surveillance in connection with the pilgrimage season and increased travel. WHO and health authorities of Saudi Arabia has yet to declare anything serious with respect to the new virus. Therefore there is no prohibition to visit the Middle East. That means, Indonesian pilgrims no problem and still can carry out a trip to Saudi Arabia.
So far no Indonesian pilgrims and also no pilgrims from any country affected by this new coronavirus infection. The data also showed the world no new confirmed cases of the novel coronavirus that while this is called "London1_novel CoV 2012.". The virus is different from the coronavirus that causes SARS a few years ago.


Saudi Arabia assures no outbreak of SARS during Hajj

2012-09-26 20:43:15

RIYADH, Sept. 26 (Xinhua) -- Saudi Arabia assured Wednesday that the coming Hajj season will be safe from the outbreak of a virus from the family of deadly Severe Acute Respiratory Syndrome (SARS).
Spokesperson of the Saudi health ministry, Khaled Al-Mirghalani, told Arab News that there have been two recent cases of flu and this is normal.
The undersecretary for preventive medicine at the ministry, Ziyad Memish, said the virus "has been in the kingdom for three months," insisting that the situation is "stable and no new cases have been recorded."
Memish said the kingdom is not planning to impose new preventive measures on pilgrims.
Editor: Tang Danlu 

CDC: Spread of Influenza Virus A (H5N1) Clade to Bulgaria in Common Buzzards

October 2012
Atanaska Marinova-Petkova, Georgi Georgiev, Patrick Seiler, Daniel Darnell, John Franks, Scott Krauss, Richard J. Webby, and Robert G. WebsterComments to Author 
Author affiliations: Regional Diagnostic Laboratory on Avian Influenza and Newcastle Disease in Birds, Varna, Bulgaria (A. Marinova-Petkova); National Diagnostic and Research Veterinary Medical Institute, Sofia, Bulgaria (A. Marinova-Petkova, G. Georgiev); and St. Jude Children’s Research Hospital, Memphis, TN, USA (P. Seiler, D. Darnell, J. Franks, S. Krauss. R.J. Webby, R.G. Webster)


On March 15, 2010, a highly pathogenic avian influenza virus was isolated from the carcass of a common buzzard (Buteo buteo) in Bulgaria. Phylogenetic analyses of the virus showed a close genetic relationship with influenza virus A (H5N1) clade viruses isolated from wild birds in the Tyva Republic and Mongolia during 2009–2010. Designated A/common buzzard/Bulgaria/38WB/2010, this strain was highly pathogenic in chickens but had low pathogenicity in mice and ferrets and no molecular markers of increased pathogenicity in mammals. The establishment of clade highly pathogenic avian influenza viruses of the H5N1 subtype in wild birds in Europe would increase the likelihood of health threats to humans and poultry in the region.


On March 15, 2010, the carcass of a common buzzard (Buteo buteo) containing HPAIV (H5N1) was found at St. Konstantin and Helena Black Sea Resort in Bulgaria and submitted to the Regional Diagnostic Laboratory on Avian Influenza (Varna, Bulgaria). The virus was characterized as clade

The 50% mouse lethal dose of A/common buzzard/Bulgaria/38WB/2010 was 30 EID50 (EID50 of the virus was 109/mL). All 3 donor ferrets were shedding virus by day 5 postinfection; however, only 1 was still shedding virus by day 7 postinfection (Figure). Virus titers were not detected in the nasal washes of contact ferrets, indicating that A/common buzzard/Bulgaria/38WB/2010 is not transmissible by direct contact or respiratory droplets. All ferrets used in this study were healthy during the experiment and showed no clinical signs of disease; they were alert, playful, and eating and drinking normally.

Compared with that of A/goose/Guangdong/1/96, the amino acid sequence of A/common buzzard/Bulgaria/38WB/2010s neuraminidase had a 20-residue deletion in the stalk region (residues 49–68), which was thought to be required for influenza viruses to adapt from wild aquatic birds to domestic chickens (24). This deletion causes a loss of the N terminal NQS glycosylation site (positions 50–52). Residues E119, H275, or N295 (N1 numbering) were not mutated, which suggests sensitivity to oseltamivir and zanamivir (25,26).

The M gene–encoded ORF of matrix (M) 1 protein consists of 252 aa, and that of M2 consists of 97 aa. Residues 26L, 27V, 30A, 31S, and 34G of M2’s transmembrane region indicate that A/common buzzard/Bulgaria/38WB/2010 is an amantadine-sensitive strain (29).

To assess possible reassortment in the A/common buzzard/Bulgaria/38WB/2010 genome, we performed phylogenetic analysis of the remaining genes using the same group of viruses that had been used to make the HA tree. In the N1, PB1, PB2, PA, NS, and NP phylogenetic trees, A/common buzzard/Bulgaria/38WB/2010 clustered with the other subtype H5N1 viruses from clade (data not shown). In the M gene tree, the Bulgarian subtype H5N1 virus clustered with the clade 2.3.4 subtypes from Guangxi, Hunan, Fujian, Shantou, and Hong Kong that were isolated in 2005, 2006, and 2008; all other subtype H5N1 viruses from clade clustered in a separate group (Technical Appendix Figure Adobe PDF file [PDF - 838 KB - 3 pages]). The evolutionary distance between the 2 groups of isolates in the M tree is long, indicating that the M gene of A/common buzzard/Bulgaria/38WB/2010 originates from a non–clade 2.3.2 ancestor.


The day after we received the HPAIV (H5N1)–containing common buzzard carcass, officials in Romania notified the OIE of an outbreak of an HPAIV (H5N1) in Letea Village (Danube Delta); 47 backyard chickens were found dead. These reports are considered to be the introduction of HPAIV (H5N1) clade into Europe. Furthermore, the European Reference Laboratory on Avian Influenza and Newcastle Disease (Weybridge, UK) found that the HA gene sequence of the Bulgarian isolate is 99.9% similar to that of the Romanian isolates from Letea Village (34), confirming that both viruses are derived from a common source, which is most likely wild birds.

Map of Buzzard/Bulgaria/38WB/2010 & OIE Report of Letea Village Backyard Chickens 

Our results show that chickens are highly susceptible to influenza virus A/common buzzard/Bulgaria/38WB/2010 (H5N1) and that the virus is highly pathogenic in them. Mammals appear not to be susceptible. Although buzzards can serve as intermediate hosts of HPAIV (H5N1) between migratory birds and poultry, the lack of gross pathologic findings in the buzzard carcass we examined indicates that the bird died shortly after infection. Thus, in this case, the buzzard could not have served as a reservoir of infection to spread the virus over a long distance. Additionally, the lack of poultry farms within 10 km of the area where the buzzard carcass was found may partially explain why no outbreak occurred. As part of a regular avian influenza surveillance plan, we tested 1,709 cloacal and fecal samples from mule ducks that were collected monthly during January 1, 2010–April 30, 2010, from 64 farms in 5 regions of Bulgaria (Plovdiv, Pazardjik, Stara Zagora, Haskovo, and Dobrich). No notifiable avian influenza viruses were isolated from any sample.

The potential of clade HPAIV (H5N1) to cause an outbreak is heightened because vaccines currently in use do not efficiently protect poultry flocks from a strain of this clade that was recently identified in Vietnam (40). Now that clade has spread to Europe, implementing active surveillance plans in all high-risk areas and monitoring the wild birds in the region will play key roles in early detection of incidences of HPAIV (H5N1) infection and in prevention of outbreaks. The expansion of the geographic distribution of HPAIV (H5N1) in wild birds and poultry and the virus’s repeated interspecies transmission to humans make this virus a substantial pandemic threat.

Full Document:

Wednesday, September 26, 2012

Blog Reorganization

I did a bit of a reorganization of sorts here tonight.  The right side-bar has been cleaned up, and will now represent the variety of influenza activity.  I am hoping this will help my readers in their attempts to keep up with all the news.  I'll provide up-to-date information on the right side-bar for your convenience.  Thank you all for viewing.


Ontario H1N1 Variant Influenza First Human Case

First pig-to-human transmission of H1N1 is confirmed
September 26, 2012
Ontario has identified its first case of a human contracting the H1N1 virus from a pig.

The province's chief medical officer confirmed the case to the Toronto Star, but declined to say where the person lives.

The adult male is reportedly in critical but stable condition in an Ontario hospital. H1N1 is a variant influenza virus.

Spread of variant swine flu unlikely: officials

CTV Toronto
Health officials say they are monitoring a new kind of swine flu that landed an Ontario man in hospital, but the chances of the virus spreading are slim.

The province confirmed that an Ontario man contracted a strain of the H1N1 virus on Tuesday.
The man, who contracted the flu after having frequent and direct contact with pigs, is being treated in a southwestern Ontario hospital.

The strain affecting him is called variant H1N1, or H1N1v, meaning it's a strain of H1N1 swine flu that's made a leap into humans. The term variant is added to flu virus names when viruses that normally circulate among animals cause infections in humans.
Dr. Arlene King, Ontario's chief medical officer of health, said the case which was discovered by the province's health surveillance system is likely an isolated one.
"We know that there have been extensive contact investigations done and we have no infections even within close contacts," she said.

In an earlier statement King said the chances of variant virus spreading are slim.

"I would like to reassure Ontarians that this variant influenza virus rarely spreads from animals to humans. Subsequent human-to-human transmission is also rare," King said.

"I would also like to stress that this is not a food safety issue; the consumption of properly cooked pork continues to be safe. Proper cooking of meats, including pork, kills all bacteria and viruses."

Health Minister Deb Matthews stressed that hand washing and thorough cooking of pork would help protect people.

"It's very important that people wash their hands," she said. "This is not something you can get from eating pork, so cook your pork and enjoy it."

Officials say the fact that the strain was identified so quickly is proof that the province's surveillance system is working.

"Labs have become more sophisticated since H1N1 to pick out these very new types of virus," said infectious disease expert Dr. Neil Rau.

Since the strain was identified health officials have been hunting for other cases, but have so far not found any.

Officials say the strain is a distant cousin of the one that caused an H1N1 pandemic in 2009, but not the same one that passed from pigs to humans in the U.S. this past summer.

Some 300 people in the U.S. have been infected by that strain, which is an H3N2-variant. That strain has not been found in Canada.

A man in Missouri was also infected with a H1N1v virus this summer. It's not known if the Ontario and Missouri viruses are closely related.

King added that hand washing is the best way to prevent infections. She also said Ontarians should be sure to get their flu shot, to protect them from humans strains of flu.

With files from CTV Toronto's Natalie Johnson and The Canadian Press

H1N1 variant influenza virus - Investigating an illness

September 25, 2012
The Public Health Agency of Canada is assisting the Ontario Ministry of Health and Long-Term Care in investigating a Canadian case infected with an H1N1 variant influenza A virus. This virus is genetically similar to a virus that is found in swine.

The public health risk is considered low, as there has been no evidence so far to support that this virus would be able to spread from person to person. It is not the same virus that caused the pandemic in 2009.

The Agency's National Microbiology Laboratory positively identified the virus by testing samples from the affected person.

The Agency is also assisting by notifying international partners through an established standard process under the International Health Regulations.

More information about the investigation into this case of illness is available through the Ontario Ministry of Health and Long-Term CareExternal link.

Ukraine: State Sanitary Service Predicts Influenza And ARVI Incidence Rate To Grow In November

 September 26, 2012

The State Sanitary and Epidemiological Service predicts that the influenza and acute respiratory viral infections incidence rate will grow in November, agency chairman, Anatolii Ponomarenko, has told a news briefing.

"There are preliminary forecasts on the incidence rate scaling up in November. An early wave is not planned in October, which we had judging from the monitoring experience," he said.
Ponomarenko remarks, at the moment the situation in the country regarding the influenza and ARVI incidence rate is stable, manageable and controllable.

In his turn, deputy minister of healthcare Oleksandr Tolstanov characterised preparedness of medical institutions for the epidemiological season.

"The system of medical institutions and the system of sanitary and epidemiological stations, their laboratories is absolutely ready for the possibility of both definition of virus type and of rendering appropriate level of aid patients need," he said.

Besides, as to Tolstanov, they arranged a reserve of beds for patients, more than 30,000 for today, for probable breakout of incidence.

Apart from this, in his words, they compiled and approved a list of medications that must be available at medical treatment facilities.

Tolstanov underlines, more than 12 million packs of medicines are now in the retail chains, required for provision of medical aid in cases of acute respiratory viral infections, including more than 2.7 million packs of vaccines.

As Ukrainian News earlier reported, the Healthcare Ministry predicted incidence rate of acute respiratory viral infections in the 2011/12 epidemiological season of more than 8 million people.

The Healthcare Ministry expects influenza incidence rate to grow from November in the 2011/12 epidemiological season.
The 2010/11 epidemiological season brought 20 lethal cases of influenza and ARVI (there was no epidemy), while the 2009/2010 season 1,126 (there was an epidemy).

Ukraine Readies Itself For New Strain of Influenza

Ukraine expects new strain of influenza

Circulation of a new strain of influenza Victoria is expected in Ukraine in the coming autumn-winter period, deputy health minister Oleksandr Tolstanov told a briefing after the Cabinet meeting, ForUm correspondent reports.
Tolstanov noted that health facilities are ready for the coming epidemiological season.
"Provision of beds amounts to more than 30 thousand. Pharmacies have already received more than 12 million packages of drugs against acute respiratory infections including 2.7 packages of vaccines," the deputy minister said.
According to him, the vaccines in pharmacies will cost 50-75 UAH.

Partial genetic sequence information for scientists about the Novel Coronavirus 2012

Phylogenetic tree constructed with partial sequences from the polymerase gene (nsp12) of representative coronaviruses from different groups is displayed in the attached Figure. The sequence obtained at HPA has been tentatively named as London1_novel CoV 2012 (boxed in red). The HPA sequence data is based on direct detection from clinical material from the London case. HPA do not yet have a virus isolate. There will shortly be a GENBANK accession number for the sequence. The attached phylogenetic tree is considered preliminary, as is virus nomenclature, and liable to change as more information or a virus isolate becomes available.

You may download the fasta file (as a zip file) from the link below:

Last reviewed: 25 September 2012

CIDRAP: UK agency picks name for new coronavirus isolate

Sep 25, 2012 (CIDRAP News) – As the investigation of two severe illnesses associated with a novel coronavirus continued today, the United Kingdom's Health Protection Agency (HPA) released a preliminary phylogenetic tree for the virus and tentatively named it "London1_novel CoV 2012."
As reported previously, the virus has been identified in a 49-year-old Qatari man who is in a critical care unit in a London hospital and in a 60-year-old Saudi Arabian man who died in July in his home country. Both cases involve pneumonia and kidney failure, and the Qatari man had traveled to Saudi Arabia before he got sick.
In 2003, a then-novel coronavirus caused the SARS (severe acute respiratory syndrome) outbreak, which killed 774 people worldwide. Other coronaviruses are linked to the common cold.
The phylogenetic tree, constructed from partial sequences from the polymerase gene of various coronaviruses, shows that the new one is closely related to bat coronaviruses. The HPA also released the partial sequence for the virus's polymerase gene.
In other developments, the European Centre for Disease Prevention and Control (ECDC) said today the available information suggests that the current risk associated with the new virus is low.
Noting that there has been no sign of human-to-human transmission, the agency said, "The newly identified coronavirus is not genetically similar to the SARS coronavirus and does not signal the start of a new SARS outbreak."
Also today, the World Health Organization (WHO) commented via Twitter that the kidney failure reported in both patients infected with the new virus is a "unique feature" of the infection.
In addition, late today the WHO released an update and an interim case definition to help countries be on guard against the new virus. On the basis of the cases so far, the definition includes criteria for "a patient under investigation," a probable case, and a confirmed case, using clinical, epidemiologic, and laboratory variables. The update said no new cases were identified today.
And in Hong Kong, the region's Hospital Authority said that a previously reported cluster of coronavirus-related respiratory illnesses in Castle Peak Hospital was caused by a known coronavirus. The cases occurred in a "female long-stay ward" and are due to human coronavirus NL63, a strain that usually causes mild respiratory illness such as the common cold, the agency said in a statement.
See also:
Sep 25 HPA statement showing phylogenetic tree

Indonesia: Chicken Husbandry Department Samarinda Find Ketawa Positive Bird Flu

September 23, 2012

Department of Fisheries and Livestock of Samarinda weekend again find poultry (chicken) were positive for the bird flu virus.

The findings were originally known from the reports of the Animal Husbandry Department had reported that chickens died suddenly. After the officer down checking spaciousness, and perform rapid test (rapid test), was one of seven chickens owned by a resident of Jl Bungtomo Sei Keledang Samarinda was positively infected with bird flu.

"Last week in the Sei Keledang Jl Bungtomo Samarinda Seberang, we find a positive laughter chicken bird flu, according to results of rapid tests that we do," said Jumianti, Head of Animal Health and Livestock Fisheries Samarinda to the Tribune, Sunday (23 / 9/2012).

According Jumianti, chicken coop bird flu that we have isolated, while 7 chickens had been culled. 

"Poultry cages were empty and we had our isolation. During one month of the cage can not be used and needs to be cleaned by spraying disinfectant on a regular basis," said Jumianti.

Said to him, the Animal Husbandry Department officials have done spraying disinfectant on chicken coop belonging to the bird flu and in a chicken coop belonging to others around them.

Asked about the cause of the bird flu virus in chickens are laughing? He said it was likely that brought laughter chicken owners outside Samarinda.

"We have not had time yesterday to ask the owner, he bought a chicken laugh from, but probably from outside Kaltim" he said.

He appealed to the citizens to immediately report to the Department of Animal Husbandry through local RT or RW if found chickens that died suddenly, so that the Animal Husbandry Department immediately check whether the chickens are infected with bird flu or not. 

"Animal Husbandry Department officer will act quickly if there are reports of people," he said.

Added Jumianti, the case of chickens that died suddenly suspected of contracting bird flu in Dublin this year is somewhat reduced compared to previous years. 

Up to September this year, the number of chickens that died suddenly reported only about 50 birds.From the report, which was positively infected with bird flu is only a part, as well as chickens owned by residents in Sei laughed Keledang, it stated piositif bird flu.

Indonesia: Samarinda - Dangerous Disease Control Simulation

September 25, 2012

tribunkaltim / nevrianto hp tribunkaltim / nevrianto hp

tribunkaltim / nevrianto hp
tribunkaltim / nevrianto hp

SAMARINDA, - Port Health Team led both ship's (ABK) are infectious diseases AI out of the ship Queen Soya special evacuation to the tent as Public Health Emergency Response Simulation Of International Concern (PHEIC) in the port of Samarinda, Tuesday (25/9). Health teams are also taking action infusion. Simulation is witnessed PHEIC sub head of the Directorate General of Health Quarantine (Karkes) Directorate General of Environmental Control (DG and PL) Ministry of Health, Dr. Zahimir Setiawan, Vice Mayor Ishmael Nusyirwan Samarinda Samarinda Bay Head Adpel M Hasani, Representative kppp.

Indonesia: Simulation - Samarinda 2 Crew Aboard ABK Queen Soya Suspected #H5N1 #Birdflu

Two crew KM Quen Soya "Suspect" Bird Flu September 25, 2012 Two Queen Soya crew who had been due to depart from the Port of Samarinda towards Pare-pare flui suspected infected birds were found on Tuesday (25/9). That day the ship will depart and have begun to increase passenger and freight activities. But 3 hours prior to departure suddenly get a report from the agency posts that get a report from the Master Vessel that two crew boats are sick. Following the post got the information from agents, officers Port Health Office (KKP), which is in the post immediately contacted the captain to seek infomasi about the symptoms of the two people who are sick crew. Because the disease is similar to ABK pandemic disease, then the Dublin Port Office stating KM ship Queen Soya temporarily not allowed to get out of the Samarinda, and must remain in place to wait for the examination and investigation of the officer CTF. Suddenly the atmosphere is inviting noise from passenger which will set out on the edge of the dock. They asked the ticket is refundable if the ship did not depart. Chief Administrator Office of the harbor (Ka Adpel) as a responsible authority in the port of Samarinda immediately ordered the Rapid Response Team command post for immediate action. Ports in the region immediately tighten vigilance. Tim Verification ensures that two crew was suspected. After that, the officer Immigration, Customs and Quarantine farm further examination on board the ship, using the Personal Protective Equipment (PPE) exhaustive. The medical team declared that suspects need to be reconciled in hospitals AWS. The medical team in the tent to report to the command post to contact AWS for the preparation of a referral hospital. Meanwhile, due to ship in quarantine it can not do the activities of people and goods up and down a passenger who had entered the ship became restless and afraid of contracting an infectious disease influenza type new, they demanded to be lowered from the ship, the ship demo, passenger anxiety began to subside after the CTF team and security team of Unity Port Security Administrator (KP3) and the Marine and Coastal Unity Babysitting (KPLP) gives verbal comprehension. With the fret board community particularly the Passenger Vessel will rise, and ojeg Street vendors who have worked in the port area, because they are forced to enter the restless harbor area. The situation can be controlled after the team provide a thorough understanding of the circumstances that happen to people. scenes Simulations That's part of public health emergency response is troubling the world (PHIEC) in the port of Samarinda.

WHO: Case Definition for Case Finding Severe Respiratory Disease associated with NOVEL CORONAVIRUS

Interim case definition as of 25 September 2012

Patient under investigation:

Clinical definition:
A person with acute respiratory syndrome which may include fever (≥ 38°C , 100.4°F) and cough
• requiring hospitalization
• with suspicion of lower airway involvement (clinical or radiological evidence of consolidation)
not explained by any other infection or any other aetiology.

Epidemiological criteria:
Close contact* within the last 10 days before onset of illness
• with a probable or confirmed case of novel coronavirus infection while the case-contact was ill
• travel to or residence in an area** where infection with novel coronavirus has recently been reported or where transmission could have occurred.

Probable Novel Coronavirus Case:

A person fitting the clinical definition AND epidemiological criteria above but no laboratory confirmation.

Confirmed Novel Coronavirus Case:

A person with laboratory confirmation of infection with the novel coronavirus.

* Close contact is defined as:

• Anyone who provided care for a confirmed or probable case including HCW and family members in a health care setting or in the community.
• Anyone who stayed at the same place (e.g. lived with, visited) as a probable or confirmed case while they have been symptomatic.
• Anyone with significant casual exposure with the patient such as sitting nearby in a classroom, sharing a taxi, sitting close by on an airplane.

** Area where infection with novel coronavirus where transmission could have occurred:

Kingdom of Saudi Arabia, Qatar (as of 25 September 2012)

WHO: Novel coronavirus infection - update


As of 25 September 2012, no additional cases of acute respiratory syndrome with renal failure due to infection with a novel coronavirus have been reported to WHO. WHO is continuing investigations into two recently confirmed infections identified as a novel coronavirus. Today WHO issued an interim case definition to help countries strengthen health protection measures against the new virus. 

The case definition, based on the cases so far, includes criteria for identifying a ‘patient under investigation’, a ‘probable case’ and a ‘confirmed case’. These criteria are based on clinical, epidemiological and laboratory indicators. 

Following the confirmation of the novel coronavirus, WHO - under the International Health Regulations - immediately alerted all its Member States about the virus and has been leading the coordination and providing guidance to health authorities and technical health agencies. WHO is also identifying a network of laboratories that can provide expertise on coronaviruses for countries. 

On 22 September 2012, the United Kingdom (UK) informed WHO of a case of acute respiratory syndrome with travel history to the Kingdom of Saudi Arabia (KSA) and Qatar.

The case is a previously healthy, 49 year-old male Qatari national that presented with symptoms on 3 September 2012 with travel history to KSA several days prior to onset of illness. On 7 September he was admitted to an intensive care unit in Doha, Qatar. On 11 September, he was transferred to the UK by air ambulance from Qatar. The Health Protection Agency of the UK (HPA) conducted laboratory testing and subsequently confirmed the presence of the novel coronavirus. 

The HPA compared the sequencing of the virus isolate from the 49 year-old Qatari national with that of a virus sequenced previously by the Erasmus University Medical Centre, Netherlands. This latter isolate was obtained from lung tissue of a fatal case earlier this year in a 60 year-old Saudi national. This comparison indicated 99.5% identity, with one nucleotide mismatch over the regions compared. 

Though it is a very different virus to SARS, given the severity of the two confirmed cases so far, WHO is engaged in further characterizing the novel coronavirus. As such, international efforts are being stepped up across all WHO six regions to ensure an appropriate and effective response with a WHO specialist team in daily contact with more than a dozen international and regional technical partners.

In addition WHO is working closely with KSA, as in previous years, to support the country’s health measures for all visitors participating in the Haji pilgrimage to Mecca next month.

Monday, September 24, 2012

Ron Fouchier on the New Coronavirus: We Need to Fulfill Koch's Postulates

Bird Flu Outbreaks Reported Around China

September 24, 2012
Outbreaks of H5N1 avian influenza, better known as bird flu, have occurred across China this year.

Information on bird flu’s spread in China was made public in January in a Hong Kong health report to the World Health Organization (WHO), saying that China was one of the 15 affected countries in the world with 18 provinces and cities experiencing H5N1 avian influenza outbreaks. Now, the Guangdong Province Department of Agriculture has also admitted that there is an outbreak.

A 2-year-old boy from Hong Kong contracted bird flu in early June as confirmed by the Department of Health in Hong Kong. A duck sample from Jiangnan Market in the Haizhu District of Guangzhou, Guangdong Province, where the boy had visited in mid-May, was tested positive for the H5N1 virus. Samples from another market in the same district also tested positive, according to the Center for Disease Control and Prevention in Guangdong Province.


BBC: How threatening is the new coronavirus?


As it has only been recently described, and this is only the second laboratory confirmed case, there is limited information on how much of a threat it may pose to humans.

At this point it is not clear whether these cases are typical of infection with this virus or whether it could be circulating more widely and only very rarely causing a severe illness.

Doctors do not yet know what the best treatment is, but people with severe symptoms will need intensive medical care to help them breath. There is no vaccine for it.
As with any newly identified virus that may be associated with severe illness, it is better to err on the side of caution. All infection control precautions to prevent the spread of this virus are therefore being taken in the case of the London patient with the confirmed diagnosis. This includes isolation of the patient, barrier nursing and making sure that all staff wear the appropriate protective equipment.

Experts do not yet know where the virus originated from. It may have been the result of a new mutation of an existing virus. Or it may be an infection that has been circulating in animals and has now made the jump to humans.