Wednesday, June 19, 2013

Branswell:The NEJM Saudi MERS-CoV Cluster Report

Coronavirus

Photo Credit NIAID

 


# 7411

 

Today the New England Journal of Medicine published an extensive analysis of the (possibly ongoing) outbreak of MERS-CoV at four hospitals in Eastern Saudi Arabia, between April 1st and May 23rd.

 

The authors – which included Canadian SARS expert Dr. Allison McGeer - tracked the likely transmission routes, incubation times, and serial intervals (time between onset of symptoms individuals in a chain of infections) of 23 confirmed coronavirus infections.


As Helen Branswell tells us in her article tonight, MERS-CoV appears to transmit in a hospital environment very much in the same as did SARS ten years ago. 

 

First stop, Helen’s in-depth report, which includes comments by Dr. McGreer, and Dr. Michael Osterholm of CIDRAP, followed a link to the full  NEJM report.

 

Saudi MERS outbreak showed SARS-like features, including possible superspreader

Helen Branswell, The Canadian Press Jun 19, 2013 05:00:17 PM

TORONTO – A long-awaited report on a large and possibly still ongoing outbreak of MERS coronavirus in Saudi Arabia reveals the virus spreads easily within hospitals, at one point passing in a person-to-person chain that encompassed at least five generations of spread.

 

The study, co-written by Toronto SARS expert Dr. Allison McGeer, also hints there may have been a superspreader in this outbreak, with one person infecting at least seven others.

 

The study lays out what is known about an outbreak of MERS that erupted this spring in four hospitals in the Eastern Province of Saudi Arabia, in an area whose name translated into English can be spelled Al-Ahsa or Al-Hasa (the study uses the second version). It was reported online on Wednesday by the New England Journal of Medicine.

(Continue . . .)

 


The full NEJM article is available online, and you’ll no doubt want to read it in its entirety, but a few key points (bolding & underlining mine) lifted the discussion include:

 

  • Most of the case patients were men, and the median age was 56 years
  • The most common symptoms were fever (87%) and cough (89%), while 35% presented with gastrointestinal symptoms (vomiting or diarrhea)
  • Laboratory testing for MERS-CoV remains a challenge. Validated serologic assays are not yet available, and this may have limited the identification of cases.
  • Because some patients presented with gastrointestinal symptoms, and transmission appeared to occur between rooms on the ward, the current WHO recommendations for surveillance and control should be regarded as the minimum standards;
  • The Case Fatality Ratio was 65%

 

 

Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus

Abdullah Assiri, M.D., Allison McGeer, M.D., Trish M. Perl, M.D., Connie S. Price, M.D., Abdullah A. Al Rabeeah, M.D., Derek A.T. Cummings, Ph.D., Zaki N. Alabdullatif, M.D., Maher Assad, M.D., Abdulmohsen Almulhim, M.D., Hatem Makhdoom, Ph.D., Hossam Madani, Ph.D., Rafat Alhakeem, M.D., Jaffar A. Al-Tawfiq, M.D., Matthew Cotten, Ph.D., Simon J. Watson, Ph.D., Paul Kellam, Ph.D., Alimuddin I. Zumla, M.D., and Ziad A. Memish, M.D. for the KSA MERS-CoV Investigation Team

June 19, 2013DOI: 10.1056/NEJMoa1306742

WHO: H5N1’s Pandemic Phase Status

The current WHO phase of pandemic alert for avian influenza A(H5N1) is: ALERT

 

# 7410


A little over a week ago the World Health Organization released their (interim) updated guidance on influenza (and other) pandemics (see WHO Unveils New Pandemic Guidance).

 

Among the changes was the announcement of a new, 4 tier, pandemic phase alert system; 

  • Interpandemic Phase
  • Alert Phase
  • Pandemic Phase
  • Transition Phase

 

We are currently in the Alert Phase for H5N1, H7N9, and the MERS coronavirus, which places the world’s health agencies in a mixed preparedness and response mode.

 

Yesterday the WHO released the following updated Pandemic Phase assessment for the H5N1 virus, the first since this new system was announced.

 

 

Current WHO global phase of pandemic alert: Avian Influenza A(H5N1)

Current phase of global alert according to criteria described in the WHO Pandemic Influenza Risk Management Interim Guidance

The pandemic influenza phases reflect WHO’s risk assessment of the global situation regarding each influenza virus with pandemic potential that is infecting humans. These assessments are made initially when such viruses are identified and are updated based on evolving virological, epidemiological and clinical data. The phases provide a high-level, global view of the evolving picture.

 

As pandemic viruses emerge, countries and regions face different risks at different times. For that reason, countries are strongly advised to develop their own national risk assessments based on local circumstances, taking into consideration the information provided by the global assessments produced by WHO. Risk management decisions by countries are therefore expected to be informed by global risk assessments, but based on local risk assessments.

 

The current WHO phase of pandemic alert for avian influenza A(H5N1) is: ALERT


Alert phase: This is the phase when influenza caused by a new subtype1 has been identified in humans. Increased vigilance and careful risk assessment, at local, national and global levels, are characteristic of this phase. If the risk assessments indicate that the new virus is not developing into a pandemic strain, a de-escalation of activities towards those in the interpandemic phase may occur.

 

Please consult the interim guidance document for complete information on pandemic phases:

More information on avian influenza H5N1 in humans can be found at the:


1 The IHR (2005) Annex 2 includes “human influenza caused by a new subtype” among the four specified diseases for which a case is necessarily considered “unusual or unexpected and may have serious public health impact, and thus shall be notified” in all circumstances to WHO.

 

While news of H5N1 has been eclipsed in recent months by the emerging H7N9 avian flu virus in China and MERS-CoV on the Arabian peninsula, H5N1 remains endemic and a threat in a number of countries, including Egypt, Indonesia, Vietnam and China.


As the WHO indicated at the end of March (2 days before we learned of H7N9) in WER: Update On Human Cases Of Influenza At Human-Animal Interface, the risks posed by the H5N1 virus, along with other emerging influenza viruses, remain very real. 

 

In the discussion portion of that report, the authors write:

 

Influenza viruses are unpredictable. Their constant evolving nature raises concerns that these viruses could adapt or reassort with other influenza viruses, thereby gaining potential to become more transmissible to or more pathogenic in humans.

 

Continued monitoring of the occurrence of human infections with non-seasonal influenza viruses and ongoing characterization of the viruses to assess their pandemic risk are therefore critically important for public health.

 

Close collaboration with animal health partners allows information regarding viruses circulating in animal populations and human populations worldwide to be shared to improve assessment of global influenza risks to health.

 

WHO continues to stress the importance of global
monitoring of influenza viruses and recommends all
Member States to strengthen routine influenza surveillance. All human infections with non-seasonal influenza viruses should be reported to WHO under the International Health Regulations (2005).

Arkansas: Scott County Chicken Positive for H7N7 Avian Flu

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# 7409

 

 

According to the Poultry Federation, Arkansas is the only state that ranks in the top 10 for Broiler Chicken, Turkey, and Egg production. The state is second only to Georgia in producing broiler chickens, and third in the nation in the raising of turkeys.

 

Combined, the value of poultry operations in Arkansas (in 2009) exceeded $3 billion dollars.  Neighboring Oklahoma (Scott county is on the border) produces more than 1/2 billion dollars in poultry each year.

 

All of which makes the discovery yesterday of H7N7 avian flu on a farm in Scott County, a serious economic concern.

 

First, the announcement from Arkansas.gov, then I’ll return with a bit more about this particular strain of avian flu.

 

Scott County Chicken Tests Positive for Avian Flu

 

LITTLE ROCK - The Arkansas Livestock and Poultry Commission received confirmation Tuesday evening that a chicken in a Scott County, Arkansas, chicken house has tested positive for H7N7 Low Pathogenic Avian Influenza.

 

Thirty Livestock and Poultry personnel have quarantined all poultry within a 6.2-mile radius of the growing operation where the infected bird was located. They are coordinating their response and additional testing with the U.S. Department of Agriculture. Only the USDA can officially confirm avian flu cases.

 

Chickens tend to contract avian flu via infected waterfowl or water contaminated by waterfowl. Livestock and Poultry officials believe the recent flooding in Scott County contributed to this transmission.

 

Leaders at the Arkansas Department of Health say the positive test poses no public-health threat.
Avian flu cannot be transmitted to people through the consumption of properly prepared poultry.

 

Reassurances that H7N7 `poses no public health threat’ are perhaps a bit overstated, although the threat to the public is likely extremely low. We have seen sporadic human infection from various H7 strains of avian influenza – including H7N7 – in the past. 

 

The most famous (and most recent) being the H7N9 virus in China, but other – far more common -  H7 strains have been known to infect humans as well.

 

 

The largest known cluster of H7N7 human infection (89 confirmed, 1 fatality) was reported in the Netherlands a decade ago. Details are available in this report from the December 2005 issue of the Eurosurveillance Journal.

 

Human-to-human transmission of avian influenza A/H7N7, The Netherlands, 2003

M Du Ry van Beest Holle, A Meijer, M Koopmans3 CM de Jager, EEHM van de Kamp, B Wilbrink, MAE. Conyn-van Spaendonck, A Bosman

An outbreak of highly pathogenic avian influenza A virus subtype H7N7 began in poultry farms in the Netherlands in 2003. Virus infection was detected by RT-PCR in 86 poultry workers and three household contacts of PCR-positive poultry workers, mainly associated with conjunctivitis.

 

While nearly all of these cases were mild, the impact on the poultry industry was major. More than 30 million birds residing on more than 1,000 farms were culled to control the outbreak.

 

Before the middle of the last decade, there were no uniform requirements to report or  track LPAI (Low Pathogenic Avian Influenza) infections.  That changed in 2006 when the OIE made reporting of LPAI H5 & H7 viruses mandatory.

 

In 2008 we saw a study in  PNAS that suggested the H7 virus might just be inching towards adapting to humans. For more details on that study, you may wish to revisit H7's Coming Out Party and H7 Study Available Online At PNAS.

Last summer in Mexico we saw two mild human cases of H7N3 (see MMWR: Mild H7N3 Infections In Two Poultry Workers - Jalisco, Mexico).

 

But for now, these LPAI viruses are primarily a threat to the poultry industry, and to a far lesser extent, people working in direct contact with infected fowl.

 

Thus far, this Arkansas outbreak is reportedly limited to one poultry farm.  We’ll have to wait to see if testing reveals that this virus has managed to spread beyond this one location.

ECDC: Updated MERS-CoV Rapid Risk Assessment

 

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# 7408

 

The ECDC, which last updated their MERS-CoV Risk Assessment in mid-May, has published an impressive update today that adds:

 

  • Updated epidemiological situation including cases in new EU country
  • Guidance on aircraft contact tracing
  • Incubation period extended to 14 days
  • Guidance to travelers to the Middle East.

 

In this update the authors express – on more than one occasion – their concerns over the lack of data being provided on cases from inside Saudi Arabia (e.g. reservoir host, risk groups, incubation period, mode of transmission, etc.) despite `the requirements formulated in Article 6.2 of the 2005 International Health Regulations.’

 

Citing the difficulties in making an accurate risk assessment when `insufficient data’ is being provided, the authors warn:

Consequently, it is not possible to estimate the disease risk with any degree of accuracy. As a result, ECDC has to consider a number of underlying scenarios that are compatible with the information available.

At this stage, it is not possible to exclude a future SARS-like scenario, especially in the light of the hospital-related outbreaks in Jordan and Al-Ahsa, Saudi Arabia.

 

This undercurrent of frustration over the lack of epidemiological data surfaces again in the final statement in their conclusions section, which reads:

 

  • These conclusions should be viewed in the light of the many uncertainties surrounding the investigation of cases in the Middle East. It is unusual to have such a degree of uncertainty at this stage in an outbreak.

 

As we’ve come to expect from the ECDC, this risk assessment does a great job summarizing what we know (and don’t know) about this emerging threat, provides some new graphics, and is well worth reading in its entirety.

 

The news release, along with links to the revised document follow:

 

 

Middle East respiratory syndrome coronavirus: updated guidance in ECDC Rapid Risk Assessment

19 Jun 2013

Middle East respiratory syndrome coronavirus: updated guidance in ECDC Rapid Risk Assessment

ECDC

The latest update of ECDC Rapid Risk Assessment on Middle East respiratory syndrome coronavirus(MERS-CoV) addresses:

  • Epidemiological situation since publication of the previous Rapid Risk Assessment on 17 May
  • Guidance on contact tracing, including aircraft contact tracing
  • Extension of the incubation period to 14 days, in line with WHO decision
  • Guidance to EU travellers to the Middle East.

 

As of 17 June 2013, 64 cases of MERS-CoV have been reported worldwide, including 38 deaths. All cases remain associated with transmission in the Arabian Peninsula and Jordan. This includes indirect association following secondary person-to-person transmission in the UK, Italy, Tunisia and France.

 

The reports of new infections in Saudi Arabia over the past few weeks indicate that there is an ongoing source of infection and low risk of transmission to humans in the Middle East. The source of infection and the routes of transmission have not yet been determined.

 

EU citizens travelling to the Middle East need to be aware of the presence of MERS-CoV in this area and of the small risk of infection. EU Member States may consider active information efforts for travellers to risk areas. Travellers who develop symptoms during travel or up to 14 days after their return are encouraged to seek medical attention, sharing their history of travel.

 

For any confirmed cases of MERS-CoV, close contacts must be monitored for symptoms for 14 days after the last exposure. Countries should trace contacts of confirmed MERS-CoV cases on aircraft.

 

The five person-to-person transmissions that have been documented in Europe, two of which are nosocomial, indicate that the risk of onward transmissions in Europe is significant, in particular in healthcare settings.

More:

Tuesday, June 18, 2013

CDC MERS-CoV COCA Call: Transcript Plus Video/Audio Files Available

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# 7407

 

Last week the CDC held a Clinician Outreach Communication Activity (COCA) call on the emerging MERS Coronavirus.  Today, for those who were unable to attend last Thursday, the transcript, audio and webinar video of this hour long presentation are now available for download.

 

 

Middle East Respiratory Syndrome Coronavirus (MERS-CoV): Information and Guidance for Clinicians

Date: Thursday, June 13, 2013

Presenter(s):

Susan Gerber, MD

Medical Epidemiologist
Division of Viral Diseases
National Center for Immunization and Respiratory Disease
Centers for Disease Control and Prevention

Alexander Kallen, MD, MPH
Medical Officer
Division of Healthcare Quality Promotion
National Center for Emerging and Zoonotic Infectious Diseases
Centers for Disease Control and Prevention

Overview:

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a newly identified virus that can cause severe acute respiratory illness and death. MERS cases have been linked to the Middle East, and there is documented spread of the virus internationally. So far, no cases of MERS have been reported in the United States. However, clinicians need to remain vigilant.

 

Epidemiologic investigations have demonstrated that this unique virus spreads from person to person during close contact, such as within families and healthcare facilities. Clinicians have a critical role in recognizing and managing suspect cases of MERS. During this COCA call, a CDC subject matter expert will discuss the clinical signs, epidemiology and infection control recommendations for MERS-CoV.

all Materials:

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CDC Medscape Commentary

Be on the Alert for This Novel Coronavirus

 

Additional Resources:

MERS
Planning

MERS-CoV: Early Serological Results

Coronavirus

Photo Credit NIAID

 

 

 

# 7406

 

 

During my brief absence yesterday Helen Branswell of the Canadian Press broke the big story of the day, the long awaited results from retrospective testing of suspect cases from Jordan MERS-CoV cluster in April of 2012.

 

If there’s anyone who hasn’t already read her article, I would invite you to do so now.  When you return, I’ll have more:

 

Earliest known MERS outbreak, in Jordan, infected at least 10 people

Helen Branswell The Canadian Press  June 17, 2013

 

 

The serological testing methods employed in testing these Jordanian cases are still in the early stages of development, and have not been fully validated. So, the actual number of contacts in this cluster who may have been infected could eventually go higher.

 

The CDC appears confident that the positive results they’ve returned are truly positive, but negative results are less certain.

 

At least one of the newly identified seropositive cases reports not having been ill during the outbreak while another reported only mild symptoms. These two cases raise new questions over asymptomatic or subclinical infection with the virus.  

 

A topic that Dr. Ian Mackay addresses in his Virology Down Under column overnight.

 

MERS-CoV in the Asymptomatic?

ProMED noted an article by Helen Branswell (here), that reports on serology results we'd previously mentioned were coming from a collaboration between the Jordanian MOH and the US CDC.

 

124 people were tested from the April 2012 outbreak of pneumonia in Zarqa, Jordan - and 8 people were antibody-positive, identifying an immune response to infection by the MERS-CoV.

 

This brings the MER-CoV total up to 72 with 38 deaths and drops the CFR from 59% to 52%; as happens when you raise the denominator.

 

<SNIP>

So, (yet again-seems like only yesterday I was talking about this) there are signs that this respiratory virus, like other before it, may present in a spectrum of clinical situations ranging from severe (where the virus is an opportunistic pathogen among predominantly older males with "underlying medical conditions") through to asymptomatic.

 

It should come as no surprise to readers of this blog, what my next comment will be. We need to test prospectively and not reactively. Not just using serological assays but also by PCR. Otherwise we keep stumbling around in the dark.

 

Perhaps we could even go so far as to start assuming that each virus can travel both stealthily and "loudly", instead of assuming they can't. Just sayin'

(Continue . . . )

 

 

If Ian’s blog isn’t already part of your daily internet infectious disease tour, I would encourage you to add it to your itinerary.

 

Whenever a new virus begins to circulate in humans we tend to only see the `sickest of the sick’ show up at hospitals. This initially skews our perception of just how deadly an outbreak might be.

 

Over time, as better diagnostics are developed and more samples are tested, we usually discover a broader spectrum of clinical illness, which brings down the mortality rates.

 

Mild or asymptomatic infections are a hallmark of nearly every infectious disease, although their incidence varies widely. How a disease presents in an individual depends greatly on the competence of their immune system, previous exposures, age, and other comorbidities.

 

Last year, in The Very Common Cold, we looked at a study of college students that found asymptomatic Rhinovirus infections led symptomatic infections by a whopping factor of 4 to 1.

 

Those with asymptomatic infections showed lower viral loads than those displaying cold symptoms - suggesting that they may be less efficient spreaders of the virus – but we don’t have enough data to know how much of a viral load it takes to spread the virus.

 

In 2011, in EID Journal: Pre-Symptomatic Influenza Transmission, we saw evidence of presymptomatic spread of the H1N1 virus in three clusters in Japan, which also suggests that asymptomatic carriers ought to be able to spread the virus as well.

 

And last year, in  PLoS One: Influenza Viral Shedding & Asymptomatic Infections, we saw a small study that found 21% of adult secondary influenza cases were asymptomatic or subclinical, yet they shed roughly the same quantity of virus as those showing clinical signs of illness.

 

Of course, MERS-CoV isn’t influenza or a Rhinovirus, which makes comparisons difficult. We do, however, have a serology study from the 2003 SARS (coronavirus) epidemic that found a small, but significant percentage of asymptomatic cases as well.

 

Volume 11, Number 7—July 2005
Dispatch

Asymptomatic SARS Coronavirus Infection among Healthcare Workers, Singapore

Annelies Wilder-Smith , Monica D. Teleman, Bee H. Heng, Arul Earnest, Ai E. Ling‡, and Yee S. Leo

Author affiliations: *Tan Tock Seng Hospital, Singapore; †National Healthcare Group, Singapore; ‡Singapore General Hospital, Singapore

 

We conducted a study among healthcare workers (HCWs) exposed to patients with severe acute respiratory syndrome (SARS) before infection control measures were instituted. Of all exposed HCWs, 7.5% had asymptomatic SARS-positive cases. Asymptomatic SARS was associated with lower SARS antibody titers and higher use of masks when compared to pneumonic SARS.

 

<SNIP>

 

Patients with a positive SARS serologic result, fever, respiratory symptoms, and radiologic changes consistent with pneumonia were defined as having pneumonic SARS. SARS-CoV–positive patients with fever and respiratory symptoms without radiologic changes were defined as having subclinical (nonpneumonic) SARS. SARS-CoV–positive patients without fever or respiratory symptoms were defined as having asymptomatic SARS-CoV infection.

 

<SNIP>

 

Of these 80 hospital staff, 45 (56%) were positive by SARS serology. Of the 45 SARS-CoV–positive study participants, 37 (82%) were classified as having pneumonic SARS, 2 (4%) as having subclinical SARS, and 6 (13%) as having asymptomatic SARS-CoV infection (Table 1). Four staff members had fever and cough but negative SARS serologic test results; none of them was diagnosed as having suspected SARS by the hospital's SARS outbreak team. The overall incidence of asymptomatic SARS-CoV infection was 6 (7.5%) of 80.

 


In this study, the incidence of severe disease among those seropositive for the virus was 82%. Only 4% displayed milder symptoms, while surprisingly, 13% were asymptomatic

 

Admittedly, MERS-Cov isn’t SARS either. But it's the closest analogue we have right now.

 

 

It will take validation of the serology tests and more extensive seroprevalence testing before we can get a good idea of how well MERS-CoV spreads among humans, it’s average severity, and the spectrum of disease it produces.

 

But at least the tools needed to do that are beginning to become available.