Recombinomics: Human Betacoronavirus 2c EMC/12 - Human SARS CoV Match

September 28, 2012  

The Ron Fouchier Viroscience lab at the Erasmus Medical Centef has released the complete sequence (30118 BP) of an isolate, Human betacoronavirus 2c EMC/2012, from the recent fatal case (60M) from Saudi Arabia (at Genbank).  The lab is to be congratulated for its rapid release of this important sequence.

Earlier the Health Protection agency had released a 208 BP fragment from a case from Qatar (47M requiring an ECO machine for breathing), which was 99.5% identical to the above sequence, confirming the emergence of a novel human cornavirus from group 2c, which was most closely related to bat coronavirus sequences from isolates from Guangdong Province.  The full sequence was also most closely related to these group 2c bat isolates, which is incorporated in the name assigned to the isolate by the Fouchier lab.

The group 2c coronaviruses are distinct for the human SARS  CoV, which maps to group 2b.  However, coronavirus rapidly evolve via homologous recombination and portions of genes show regions of identity of high homology with coronavirus segments from other species or phylogenetic groups.

An example of this type of homology is seen for positions 14628-14656 which match to the polymerase gene in pp1a, where 28 of the 29 positions match human SARS CoV (see list here).

Correction:  The above match is with human HKU-1, which is from group 2a.  Example with human SARS Cov (group 2b) here (24/25 matches at positions 15475-15499).

The rapid evolution via recombination with sequence present in human SARS CoV raise concerns of human adaptation and species jumping of a novel coronavirus which produces severe and fatal disease in humans.

http://www.recombinomics.com/News/09281201/Beta_CoV_SARS.html

A Few Older Articles on the H3N2v

[These are older articles, that I am discovering today. All boding is mine]

Study: Children, middle-aged most vulnerable to variant H3N2

CIDRAP:  Robert Roos  News Editor

Aug 10, 2012 (CIDRAP News) – A serologic study from Canada suggests that children and middle-aged adults have little or no immunity to the swine-origin variant H3N2 influenza virus (H3N2v), but about half of adolescents and young adults have some degree of immunity as measured by antibody levels.

The researchers also found that seasonal flu vaccines used in the past two seasons did not improve participants' ability to mount an immune response to H3N2v. Their report was published this week in the Journal of Infectious Diseases.

Given the results, "A specific vaccine would be needed in the event A(H3N2)v establishes epidemic spread," says the study, which was led by Danuta M. Sowronski, MD, of the British Columbia Centre for Disease Control as first author.

-snip-

The CDC has prepared a candidate vaccine for the novel virus, and clinical trials are expected this fall.

A CDC expert, Jacqueline Katz, PhD, said the Canadian findings generally agree with previous smaller studies conducted by her agency and a group in Norway. But she said the study is much larger and offers greater insight into the age-related differences in seroprotection against H3N2v. Katz is chief of the immunology and pathogenesis branch of the CDC's Influenza Division.

"Overall, the three studies agree that there is negligible cross-reactive antibody to the H3N2v virus detected in younger children," Katz said. The work also confirms previous findings that seasonal trivalent flu vaccine containing an H3N2 strain does not trigger much of a cross-reactive response to the novel virus, she added.

"What's novel about Skowronski's study is it's the largest to date and had the ability to look more closely at different age groups," she said. "They have quite an interesting finding that middle-aged adults, ages 40 to 69, show a substantial reduction in the level of cross-reactive antibody compared with younger adults."

The Norwegian study had a similar finding, but in a tighter age-group of adults, she said, adding that further research is warranted to try to find an explanation for the phenomenon.

Katz concurred with the Canadian team's suggestion that different childhood exposures may be a reason for the age-related differences in seroprotection.

"It may be that that particular group [middle-aged adults] had a different exposure, that they saw an earlier H3N2 virus for the first time, and didn't have the same robustness of response to the viruses from the 1990s that are closest to the H3N2v strain," she said. "We're interested in looking into that a little more."

"When you do genetic and antigenic analysis, you can see that viruses from the early 1990s are genetically most closely related to the hemagglutinin of the H3N2 variant viruses," Katz said. "So it does make sense that individuals who were of an age to be exposed to those in the early 1990s and made a robust response may have the highest cross-reactive antibody response to the variant strain."

Skowronski D, Janjua NZ, De Serres G, et al. Cross-reactive and vaccine-induced antibody to emerging swine influenza A(H3N2)v. J Infect Dis 2012 (Early online publication) [Full text] [Abstract]

http://www.cidrap.umn.edu/cidrap/content/influenza/general/news/aug1012serology.html  
  


CDC:  (I'll put this over on the right side-bar for future reference):

Influenza A (H3N2) Variant Virus Outbreaks

Since July 2012, there have been outbreaks of H3N2 variant viruses with the matrix (M) gene from the 2009 H1N1 pandemic virus in multiple U.S. states. Investigations into H3N2v cases indicate that the main risk factor for infection is prolonged exposure to pigs, mostly in fair settings. Found in U.S. pigs in 2010 and humans in July 2011, this virus appears to spread more easily from pigs to people than other variant viruses. Though limited person-to-person spread with this virus has occurred, no sustained community spread of H3N2v has been detected at this time. Associated illness so far has been mostly mild with symptoms similar to seasonal flu and most cases have occurred in children who have little immunity against this virus. Like seasonal flu, however, serious illness, resulting in hospitalization and death is possible. People at high risk of serious complications from H3N2v include children younger than 5, people with certain chronic conditions like asthma, diabetes, heart disease, weakened immune systems, pregnant women and people 65 years and older. These people are urged to avoid pigs and pig arenas at fairs this season. The Centers for Disease Control and Prevention (CDC) is working with states to respond to these outbreaks and continues to monitor the situation closely.

Continued with links to many resources. 
http://www.cdc.gov/flu/swineflu/h3n2v-outbreak.htm

A Research Project on the H3N2 strain that's part of this years Seasonal Flu Shot

These are snippets regarding the H3N2 strain that is incorporated in this years Seasonal Vaccine (flu shot).  It is not to be confused with the H3N2v, which you can read up on, from documents located on the right side-bar.  All editing below is mine.

FDA U.S. Food & Drug Administration News Release:

FDA approves vaccines for the 2012-2013 influenza season

The U.S. Food and Drug Administration announced today that it has approved the 2012-2013 influenza (flu) vaccine formulation for all six manufacturers licensed to produce and distribute the vaccines in the United States.

Each year experts from the FDA, the World Health Organization, the Centers for Disease Control and Prevention (CDC), and other public health experts study influenza virus samples and global disease patterns to identify virus strains likely to cause the most illness during the upcoming flu season.

Based on that information and the recommendations of the FDA’s Vaccines and Related Biological Products Advisory Committee, the strains selected for inclusion in the 2012-2013 flu vaccines are:

• A/California/7/2009 (H1N1)-like virus
• A/Victoria/361/2011 (H3N2)-like virus
• B/Wisconsin/1/2010-like virus.

The manufacturers licensed to produce the nation’s 2012-2013 flu vaccines and the brand names of the vaccines for the upcoming flu season are:

• Afluria, manufactured by CSL Limited;
• Fluarix, manufactured by GlaxoSmithKline Biologicals;
• FluLaval, manufactured by ID Biomedical Corporation;
• FluMist, manufactured by MedImmune Vaccines Inc.;
• Fluvirin, manufactured by Novartis Vaccines and Diagnostics Limited; and
• Fluzone, Fluzone High-Dose and Fluzone Intradermal, manufactured by Sanofi Pasteur.

http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm315365.htm

The H3N2 information starts on Slide 18 of 65

Influenza A(H3N2) virus activity, September 2011 - January 2012 (posted 17 February 2012)

page 37:

http://tinyurl.com/9qjg62n

And lastly, this piece from the Clinical Virology Symposim, April 2012:

DETECTION OF ANTIGENIC DRIFT AMONG RECENT INFLUENZA A H3N2 VIRUSES THROUGH VIROLOGIC SURVEILLANCE 

Wendy Sessions, Angie Foust, Lizheng Guo, Rebecca Garten, John Barnes, Kyung Park, Elisabeth Blanchard, Teresa Wallis, Henrietta Hall, Thomas Rowe, Jan Mabry, Alexander Klimov, and Xiyan Xu 

Virus Surveillance and Diagnosis Branch, Influenza Division, Centers for Disease Control and Prevention 

 

Influenza A H3N2 viruses first appeared in humans in 1968 and since then have co-circulated along with influenza A H1N1 (seasonal or pdm09) and influenza B.  The H3N2 subtype has been associated with significant morbidity and mortality compared to the other human influenza viruses.  During the 2011-2012 influenza season, influenza A H3N2 has been the dominant subtype circulating in the United States although, as of February, activity has remained low.  This differs from the previous season, when H3N2 was the predominant virus however influenza B and H1N1pdm09 also circulated widely. 

 

     The Influenza Division at CDC antigenically characterized nearly 450 H3N2 viruses collected between Sept 2011 thru Feb 2012 by the hemagglutination inhibition (HI) assay using post infection ferret antisera raised against the current vaccine strain, A/Perth/16/2009, and a panel of reference viruses.  Of the H3N2 viruses tested, the proportion of viruses that demonstrated a > 8 fold reduction in HI titer to A/Perth/16/2009 virus has increased from < 2% to 17% in recent months.  Most viruses tested were well inhibited by antisera raised to recent H3N2 viruses including A/Victoria/361/2011.  A small subset of H3N2 viruses were further characterized in the plaque-reduction neutralization assay and results confirmed findings of the HI assay. These data indicate that an increasing proportion of recent viruses are antigenically distinct from current vaccine strain A/Perth/16/2009.  In addition to antigenic characterization, a subset of viruses were genetically characterized by sequencing of the hemagglutinin (HA) and neuraminidase (NA) genes.  Phylogenetic analysis indicates that the H3N2 viruses can be divided by shared amino acid changes into 7 genetic groups.  The most recent viruses fall into group 3 and 6, with group 3 being the dominant and expanding group.  A/Victoria/361/2011 is a representative virus from genetic group 3.

     Similar findings were observed by other WHO Influenza Collaborating Centers located at Tokyo, Melbourne, Beijing, and London.  Thus, during the recent WHO influenza vaccine selection meeting, the H3N2 component of the vaccine for the northern hemisphere 2012-2013 influenza season has been updated; A/Victoria/361/2011 H3N2-like virus has been recommended to replace the current vaccine strain.  

     Virologic surveillance remains critical for detection of antigenic drift among the evolving influenza viruses and to ensure the vaccine strains match circulating viruses as close as possible to provide optimum protection.

http://pascv.ivdnews.net/public/show_abstract/1223

 

Philippine Health Secretary Statement on potential Infectious Disease Threats

September 28, 2012

Excerpt:
MANILA, Philippines - The Department of Health (DOH) is preparing for the pilgrimage of Muslims to Mecca next month after the World Health Organization (WHO) monitored cases of a deadly new coronavirus linked to Saudi Arabia.

“Many (Filipinos) attend the Hajj. They would eventually come home to various destinations in our country. So (how to deal with them) is a challenge for us,”said Assistant Health Secretary Eric Tayag.
-snip-

Tayag could not give an assurance that the Philippines is prepared in case the new virus enters the country.

“This is new, there is really no data on this and there are only three cases reported. The WHO is closely monitoring this. And because it is new, the WHO found it wise to alert countries,”he added.

Tayag, however, assured the public that the contingency measures implemented by the country during the SARS epidemic are still in place.

“We were able to maintain the SARS (isolation) room in our hospitals and we have asked the RITM (Research Institute for Tropical Medicine of the DOH) to prepare its laboratory. We already have our surveillance system so the moment the WHO tells us, we will activate that,”he said.
But as a precautionary measure, Tayag advised the public to observe proper hygiene through regular handwashing and covering mouth and nose when coughing or sneezing since coronavirus could be transmitted through respiratory droplets.
“If you are three feet away from a person and this person coughs, you will not get the virus. That is the distance where the virus can be transferred to others,”he added.
The WHO is also reviewing the implementation of International Health Regulations (IHR) in the Western Pacific amid the threats posed by a new virus.
-snip-

Health Secretary Enrique Ona assured the people that the DOH is ready to respond to the new virus.
In a statement, Ona said the Philippines is “more prepared today in responding to potential infectious disease threats such as severe respiratory illness caused by a novel coronavirus being reported today from the Middle East.”
“Our experience in the previous global public health emergencies such as the SARS Coronavirus in 2002-2003, the Pandemic Influenza H1N1 in 2009-2010, has given us the necessary capacity to respond to similar threats,” he added.

The National Epidemiology Center will be in charge of public health surveillance in collaboration with the RITM and the Bureau of Quarantine.

OFWs warned

The Philippine Overseas Employment Agency (POEA) warned departing overseas Filipino workers (OFWs) at the Ninoy Aquino International Airport (NAIA) to observe proper hygiene to avoid contracting the coronavirus when they go abroad.
Health and labor authorities have issued an advisory to OFWs who are planning to leave for Middle East, especially Saudi Arabia and Qatar, after WHO issued a Global Alert and Response (GAR) bulletin after the new virus was identified in United Kingdom last Saturday.

WHO: Novel coronavirus infection - update - revised interim case definition

[This will be located on the right side-bar under Coronavirus, for future reference]

29 September 2012 - WHO has continued to monitor the situation. No additional confirmed cases have been reported and there is no evidence so far of person to person transmission of the novel coronavirus. 

In order to ensure an appropriate and effective identification and investigation of patients who may be infected with the virus, without overburdening health care systems with unnecessary testing, a revised interim case definition has been issued by WHO (see related links to right of this page). It should be noted that this case definition was developed based on data from two confirmed cases and as such some degree of clinical judgment is required where individual cases are concerned.

WHO has been cooperating closely with the laboratories which were responsible for the confirmation of the presence of the novel coronavirus in the two confirmed cases. These laboratories have been working on the development of diagnostic reagents and protocols which can be provided to laboratories that are not in a position to develop their own, and these are now available. WHO is now seeking to broaden the number of laboratories that will be able to assist Member States with the detection or confirmation of this novel virus.
WHO has received offers of support from a number of major public health institutions around the world to assist with testing, should the need arise. The complete nucleic acid sequence of the virus has been uploaded to Genbank and the testing protocol, utilizing real-time PCR, has been published.

WHO does not advise special screening at points of entry with regard to this event nor does it recommend that any travel or trade restrictions are applied.
WHO continues to inform its Member States through the designated National Focal Points under the International Health Regulations (2005).

http://www.who.int/csr/don/2012_09_29/en/index.html 

WHO: Novel coronavirus infection - update 9/28

As of 28 September 2012, no additional confirmed cases due to infection with the novel coronavirus have been reported to WHO.
 
WHO is working closely with the national authorities of the involved countries (Qatar, Saudi Arabia, United Kingdom) and international partners in order to better understand the public health risk from the novel coronavirus. 

From the information available thus far, it appears that the novel coronavirus cannot be easily transmitted from person-to-person.

Given the severity of the two laboratory confirmed cases, WHO is continuing to monitor the situation in order to provide the appropriate response, expertise and support to its Member States.

Rapid progress has been made in the characterization of the novel coronavirus, and in the development of sensitive and specific diagnostic assays. WHO is collaborating with partner laboratories to make these available as quickly as possible. It is anticipated that the first batch of reagents, together with information and testing algorithms, will be available for urgent testing within the coming days. 

Tests for novel coronavirus infection of patients under investigation - based on the case definition issued by WHO – are currently available by some partner laboratories. National Health Authorities can contact these laboratories through WHO.

WHO continues to inform its Member States through the designated National Focal Points under the International Health Regulations (2005). 

No travel or trade restrictions have been recommended by WHO for Saudi Arabia or Qatar with respect to the novel coronavirus infections.

http://www.who.int/csr/don/2012_09_28/en/index.html 

Finding a new virus: Spit, sequencing and serendipity

September 28, 2012

Excerpt:

SPIT AND SERENDIPITY
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:  http://wkzo.com/news/articles/2012/sep/28/finding-a-new-virus-spit-sequencing-and-serendipity/

WHO: Influenza update

September 28, 2012 - Update number 169

Summary

• 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.

• -Full version Epidemiological influenza surveillance update
  pdf, 697kb

• - Virological influenza surveillance update

• - Peer-reviewed literature
  Vaccination of Health Care Workers to Protect Patients at Increased Risk for Acute Respiratory Disease

• Recommended composition of influenza virus vaccines for use in the 2013 southern hemisphere influenza season
  pdf, 175kb

http://www.who.int/influenza/surveillance_monitoring/updates/latest_update_GIP_surveillance/en/

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

hat-tip A Times Memory Blog: http://hygimia69.blogspot.com/2012/09/influenza-virus-activity-in-world-28.html

[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.

Summary
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]

September 28, 2012
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.

Continued:  http://www.ohio.com/news/break-news/most-swine-flu-hospitalizations-only-death-from-virus-spread-by-fair-animals-were-in-ohio-1.337896

 

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.

http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6132a3.htm

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
SUMMARY MINUTES
VACCINES AND RELATED BIOLOGICAL PRODUCTS ADVISORY COMMITTEE
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:  http://www.fda.gov/downloads/advisorycommittees/committeesmeetingmaterials/bloodvaccinesandotherbiologics/vaccinesandrelatedbiologicalproductsadvisorycommittee/ucm296193.pdf

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.
-snip-
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.

Continued:  http://www.costaricanewssite.com/8001/outbreak-of-diarrhea-and-respiratory-infections-for-costa-rican-children/

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

Introduction
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
Isolation
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)

Continued:  http://www.hpa.org.uk/webc/HPAwebFile/HPAweb_C/1317136232722

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

N Danielsson ()¹, on behalf of the ECDC Internal Response Team², M Catchpole³

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: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20282
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].

Background

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].
Conclusions

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. 

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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.

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

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References

1. ProMED-mail. Novel coronavirus - Saudi Arabia: human isolate Archive Number: 20120920.1302733 20 September 2012 21:51:30 CEST. Available from: http://www.promedmail.org/direct.php?id=20120920.1302733
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: http://ecdc.europa.eu/en/publications/Publications/RRA-Novel-coronavirus-final20120924.pdf
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: http://www.hpa.org.uk/NewsCentre/NationalPressReleases/2012PressReleases/120923acuterespiratoryillnessidentified/
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: http://www.who.int/csr/sars/country/country2003_08_15.pdf
5. World Health Organization (WHO). Consensus document on the epidemiology of severe acute respiratory syndrome (SARS) 2003. Geneva: WHO; 2003. Available from: http://www.who.int/csr/resources/publications/CDS_CSR_ARO_2004_2.pdf
6. Health Protection Agency (HPA). Infection control advice: Suspected or Confirmed Novel Coronavirus Cases. London:HPA; 2012. [Accessed  25 Sep 2012]. http://www.hpa.org.uk/webc/HPAwebFile/HPAweb_C/1317136232722
7. World Health Organization (WHO). WHO Case-finding interim case definition.  Geneva: WHO; 2012. [Accessed 26 Sep 2012]. Available from: http://www.who.int/csr/disease/coronavirus_infections/en/index.html
8. World Health Organization (WHO). Case definition for case finding severe respiratory disease associated with novel coronavirus. Geneva: WHO; 2012. Available from: http://www.who.int/csr/disease/coronavirus_infections/en/index.html
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: http://www.hpa.org.uk/Topics/InfectiousDiseases/InfectionsAZ/RespiratoryViruses/NovelCoronavirus/respPartialgeneticsequenceofnovelcoronavirus/

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20282 

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.
-snip-
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.

http://herald-review.com/news/local/illness-at-ashmore-elementary-believed-to-be-stomach-ailment-not/article_cb3a61de-0931-11e2-9658-0019bb2963f4.html

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.
 

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.

-snip-
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.

Continued:  http://www.daytondailynews.com/news/news/report-two-thirds-of-those-hospitalized-by-new-flu/nSNdg/

New Flu Shot Guards Against Newest Strains

By LAURAN NEERGAARD AP Medical Writer

WASHINGTON September 27, 2012 (AP)

 

Time to get your flu vaccine — and a surprising new report shows babies and toddlers seem to be getting protected better than the rest of us.
Last year's flu shot won't shield you this year: Two new strains of influenza have begun circling the globe, and the updated vaccine appears to work well against them, government officials said Thursday.
Just because last year was the mildest flu season on record doesn't mean the virus might not bounce back to its usual ferocity this winter.
-snip-
Flu specialists can't say how bad this winter's flu season might be. Influenza strains constantly evolve, and some cause more illness than others.
But strains from the H3N2 family tend to be harsher than some other flu types, and a new H3N2 strain is included in this year's vaccine because it is circulating in parts of the world.
Because of that strain, "I am pretty confident that this year will be a more traditional flu season" than last year, CDC's Jernigan told The Associated Press. "People won't have had any real exposure to that."
Only one ingredient in this year's flu vaccine was retained from last year's, protection against the H1N1 strain that caused the 2009 swine flu pandemic and has been the main kind of influenza circulating since. Also new in this year's shot is protection against a different Type B strain.

Full article:  http://abcnews.go.com/Health/wireStory/years-flu-vaccine-guards-strains-17338927#.UGTZIRgXqkI

 

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

Lisa Schnirring  Staff Writer

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. 

http://www.cidrap.umn.edu/cidrap/content/other/sars/news/sep2712corona.html