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**alert** · September 21, 2012, 10:04 AM

Re: Jeddah, Saudi Arabia: Pneumonia patient tests positive for novel animal coronavirus

Hat-tip Mike Coston.

http://afludiary.blogspot.com/

Covering Pandemic and Seasonal Flu, H5N1 `Bird Flu, Emerging Infectious Diseases, public health, community & Individual preparedness, and anything else that piques my admittedly eclectic interests

Sometimes They Come Back

Credit Wikipedia

# 6568

This November will be the 10 year anniversary of the SARS (Severe Acute Respiratory Syndrome) outbreak that began in Guangdong Province, China. An epidemic that would – over the ensuing six months – move well beyond the borders of China, infecting more than 8,000 people, and killing nearly 800.

Source World Health Organization

The SARS epidemic was eventually contained due to the combined efforts of public health agencies around the globe, helped along no doubt by the fact that – unlike with influenza – patients didn’t appear to be contagious until after symptoms appeared.

By the summer of 2003, the crisis was over – but the investigation into how it came about was still underway.

SARS appears to have emerged due the penchant of some prosperous Chinese to dine on exotic animals. These animals were slaughtered, and served, in `Wild Flavor' restaurants, particularly in Guangdong Province.

There you could partake in all sorts of exotic dishes – including dog, cat, civet, muskrat, ferret, monkey, along with a variety of snakes, reptiles, and birds.

What are commonly referred to as `bushmeat’.

For a horrific description of the conditions in these restaurants, I would direct you to an essay by Karl Taro Greenfeld called Wild Flavor which appeared in the Paris Review in 2005.

Greenfeld, you may recall, is also the author of The China Syndrome: The True Story of the 21st Century's First Great Epidemic. Perhaps the most authoritative (and absolutely riveting) account of the SARS outbreak of 2003, and how it was directly linked to the practice of consuming bushmeat in China.

It was finally determined that a previously unknown coronavirus, which was detected in civet cats served in these establishments, was the cause of the SARS outbreak (see A Civets Lesson).

Since that time, bats have also been shown to carry this Coronavirus (among others) as well. The jury is out on whether the virus was transmitted directly to man from bats, or perhaps from bats to civits to humans.

Since 2003 the Chinese government has outlawed the use of civits as a food source, although reportedly it can still be purchased in some eating establishments and live markets.

There have been no new reports of SARS anywhere in the world since 2003, but the threat has certainly not gone away. The virus, presumably, resides in an animal reservoir somewhere, and could potentially re-emerge.

And there is always the possibility that there are other, equally pathogenic coronaviruses, yet to be discovered.

Which is why, a report that appeared yesterday in ProMed Mail has perked up the ears of many infectious disease watchers the world.

It isn’t SARS, but it is a report on a human infection with another, previously unknown coronavirus.

Published Date: 2012-09-20 15:51:26
Subject: PRO/EDR> Novel coronavirus - Saudi Arabia: human isolate
Archive Number: 20120920.1302733
NOVEL CORONAVIRUS - SAUDI ARABIA: HUMAN ISOLATE
***********************************************
A ProMED-mail post
http://www.promedmail.org
ProMED-mail is a program of the
International Society for Infectious Diseases
http://www.isid.org
Date: Sat 15 Sep 2012

From: Ali Mohamed Zaki [edited]

A new human coronavirus was isolated from a patient with pneumonia by Dr Ali Mohamed Zaki at the Virology Laboratory of Dr Soliman Fakeeh Hospital Jeddah Saudi Arabia.

The virus was isolated from sputum of a male patient aged 60 years old presenting with pneumonia associated with acute renal failure. The virus grows readily on Vero cells and LLC-MK2 cells producing CPE in the form of rounding and syncetia formation.
[The clinical isolate] was initially tested for influenza virus A, influenza virus B, parainfluenza virus, enterovirus and adenovirus, with negative results. Testing with a pancoronavirus RT-PCR yielded a band at a molecular weight appropriate for a coronavirus. The virus RNA was tested also in Dr. Ron Fouchier's laboratory in the Netherlands and was confirmed to be a new member of the beta group of corononaviruses, closely related to bat coronaviruses. Further analysis is being carried out in the Netherlands.

There is a lot we don’t know about this case, including results of any epidemiological investigation, and the patient’s outcome.

Hopefully more details will be forthcoming.

Coronaviruses - of which there are many - are pretty much ubiquitous, as roughly 30% of all `common colds’ are due to either the OC43 or 229E human coronaviruses.

Various coronaviruses are also known to infect bats, cattle, pigs, horses, turkeys, cats, dogs, rats, and mice.

But it has only been the SARS-Coronavirus – isolated in 2003 – that has been linked to severe respiratory disease in humans.

At least, until now.

We’ve no reports (thus far) of secondary transmission with this novel coronavirus, so with luck this will prove to be a dead-end infection.

But this reminds us that nature’s laboratory continues to cook up new, and potentially dangerous, human pathogens.

And that influenza, while always atop our list of viruses to watch, isn’t the only possible pandemic threat we need to be wary of.

For more on the SARS virus, you may wish to visit the CDC’s website:

Severe Acute Respiratory Syndrome (SARS)

Posted by Michael Coston at <a class="timestamp-link" href="http://afludiary.blogspot.com/2012/09/sometimes-they-come-back.html" rel="bookmark" title="permanent link"><abbr class="published" title="2012-09-21T09:01:00-04:00">9:01 AM</abbr>

**alert** · September 21, 2012, 11:17 AM

Re: Jeddah, Saudi Arabia: Pneumonia patient tests positive for novel animal coronavirus

I will admit there is something missing in this story. The facts as we know them do not add up. Thousands of people around the world contact severe respiratory illnesses each year, many of them even dying, and if the illness isn't due to influenza or certain other common agents, the etiology is just never determined. No matter how severe this man's illness was (we don't know the outcome), severity alone would not garner this degree of testing. Something else must have drawn attention to this patient that his doctors decided to send samples abroad for this degree of testing.

Might the man have had some kind of unusual animal occupational exposure? Perhaps, if he was a butcher or something like that, they might have wanted to ensure that his illness was not caused by something that could end up in the food chain (such as anthrax or plague). Could have have had enough of a travel history that H5N1 was suspected? The choice of Fouchier's laboratory in the Netherlands (and not, say, the CDC in Atlanta) is also slightly odd.

Personally, I'm wondering the the reason for heightened testing might have been transmission of an ARDS-type illness to contacts, perhaps even HCW. We have no information as to whether anyone else is/was ill. I would imagine a cluster of severe respiratory illness might get such international testing, even if a single case would not. We had a cluster of severe ARI, including at least one fatality in an HCW, from neighboring Jordan earlier this year:

Jordan - Cluster of approximately 13 people with acute pneumonia type illness, 2 fatalities - April 20 - May 2012 - Novel coronavirus confirmed - FluTrackers News and Information

http://www.flutrackers.com/forum/showthread.php?t=185880

in which samples were sent internationally, but as far as we know, no diagnosis was reached.

**alert** · September 21, 2012, 07:44 PM

Re: Jeddah, Saudi Arabia: Pneumonia patient tests positive for novel animal coronavirus

Hat-tip Shiloh.

NEWS SCAN: Cheese Listeria outbreak update, hospital Listeria cases, Sierra Leone cholera ebbs, novel coronavirus

http://www.cidrap.umn.edu/cidrap/content/fs/food-disease/news/sep2112scan.html

Novel coronavirus identified in Saudi Arabia
A doctor involved in the care of a patient with pneumonia in Saudi Arabia has isolated a novel human coronavirus, according to a report he posted on ProMed Mail, the online reporting system of the International Society for Infectious Diseases. Dr Ali Mohamed Zaki, a professor of microbiology at Dr Fekah Hospital in Jeddah, wrote that the virus was isolated from the sputum of a 60-year-old man whose pneumonia infection was associated with acute renal failure. The report did not say whether the patient recovered from the infection. The isolate tested negative for a host of respiratory viruses, but testing with a pancoronavirus RT-PCR showed a band appropriate for a coronavirus. Zaki said the virus RNA was tested at the lab of Ron Fouchier, PhD, at Erasmus University in the Netherlands, which confirmed that the isolate was a new member of the beta group of coronaviruses, which are closely related to bat coronaviruses. The virus is undergoing further characterization at the lab. SARS (severe acute respiratory syndrome), which caused a global outbreak in 2002 and 2003 that killed more than 700 people, was caused by a then-novel coronavirus.
Sep 20 ProMed Mail post

**alert** · September 23, 2012, 07:34 AM

Re: Jeddah, Saudi Arabia: Pneumonia patient tests positive for novel animal coronavirus

Hat-tip Mike Coston.

ERROR: The request could not be satisfied

http://www.bna.bh/portal/en/news/525747

Saudi Health Ministry Announces Diagnosis of New Form of Coronavirus

10 : 06 AM - 23/09/2012
Riyadh, Sept. 23 (BNA) - Saudi Ministry of Health announced Sunday that a new form of the coronavirus was diagnosed in three people causing the death of two of them; the third is still undergoing treatment. The Ministry explained that, with the rapidly changing weather at this time of the year and with the start of the Hajj season a new strain of coronavirus has been recovered from three patients.
Coronaviruses are considered to be one of the common etiological agents of the common cold. The first case was a Saudi patient diagnosed in one of the hospitals in Jeddah; the second was a Saudi patient and the third a Gulf State patient both diagnosed in London, England. Two of the patients passed away and the third patient is still under treatment. The Ministry said that the coronaviruses are well known and most of those who are diagnosed with it recover completely with no complications after receiving the needed supportive therapy.

**Michael Coston** · September 23, 2012, 07:35 AM

Re: Jeddah, Saudi Arabia: Pneumonia patient tests positive for novel animal coronavirus

Now three cases, two fatal.

The following report comes from the Bahrain News Agency.

ERROR: The request could not be satisfied

http://www.bna.bh/portal/en/news/525747

Saudi Health Ministry Announces Diagnosis of New Form of Coronavirus

10 : 06 AM - 23/09/2012

Riyadh, Sept. 23 (BNA) - Saudi Ministry of Health announced Sunday that a new form of the coronavirus was diagnosed in three people causing the death of two of them; the third is still undergoing treatment. The Ministry explained that, with the rapidly changing weather at this time of the year and with the start of the Hajj season a new strain of coronavirus has been recovered from three patients.

Coronaviruses are considered to be one of the common etiological agents of the common cold. The first case was a Saudi patient diagnosed in one of the hospitals in Jeddah; the second was a Saudi patient and the third a Gulf State patient both diagnosed in London, England. Two of the patients passed away and the third patient is still under treatment. The Ministry said that the coronaviruses are well known and most of those who are diagnosed with it recover completely with no complications after receiving the needed supportive therapy.

**alert** · September 23, 2012, 07:44 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

OK. The three known cases, while all appearing to be current (one is still ill) appear to have significant geographic spread, reducing the chance that they have had contact with each other. Two of them come from different parts of Saudi Arabia, and the reference to a "Gulf State" likely means a different country, such as Kuwait, Qatar, etc. Notably, the article does not mention any family members of any of the 3 cases as ill.

It is unclear if the two newest reported cases were actually treated in London, or whether their samples were merely sent there for confirmation. Judging by the fact that the original case is reported to have been diagnosed in Jeddah (and not the Netherlands), I'm suspecting two of the cases were actually treated in London.

**Treyfish** · September 23, 2012, 08:45 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

Saudi warns pilgrims of the virus, "Krona"

Saudi warns pilgrims of the virus, "Krona"
Riyadh / Ministry of Health announced Arabia for the discovery of three cases infected with a rare type of the virus, "krona", and advised pilgrims from within and outside the Kingdom to follow all the procedures and preventive instructions for their own safety and health. The ministry said in a statement on Sunday: "The cases detected is a Saudi citizen in one of the hospitals in the province of Jeddah, and the second to a Saudi citizen, and the last Gulf, where two of them died and the third continues to receive treatment."

She explained that as part of its preventive to prevent diseases and continuation for its follow-up and a survey of all transmitted diseases between human and keen to approach transparency to matter of public health, it shows that with the acceleration of climate change and the entry of Hajj and Umrah, it was diagnosed this pattern rare virus. It a seasonal influenza viruses known. statement said that the virus "crowns" known, and most people are recovering after providing treatment pads and simple without complications, and in very rare cases and in style rare virus complications occur respiratory and kidney may lead to death, especially for the elderly and those with heart disease, and chronic chest and HIV. She reassured the ministry citizens and residents that such cases are rare and health status reassuring not to worry. called upon Saudi Ministry of Health who wants Hajj or Umrah from inside or outside the Kingdom of commitment vaccinations and instructions issued by the Ministry of Health and attention to personal hygiene and wash your hands and wearing a mask in crowded places and changed daily. She added that she constantly relay emerging in this regard at the national level, regional and global levels, in coordination with the concerned authorities and international health bodies.

http://www.naseej.net/News/SaudiNews...%86%D8%A7.aspx

**Treyfish** · September 23, 2012, 08:52 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

Sunday 23 September 2012
JEDDAH: Saudi Ministry of Health announced Sunday that a new form of the coronavirus was diagnosed in three people causing the death of two of them; the third is still undergoing treatment.
The Ministry explained that, with the rapidly changing weather at this time of the year and with the start of the Hajj season a new strain of coronavirus has been recovered from 3 patients. Coronaviruses are considered to be one of the common etiological agents of the common cold. The first case was a Saudi patient diagnosed in one of the hospitals in Jeddah; the second was a Saudi patient and the third a Gulf State patient both diagnosed in London, England. Two of the patients passed away (God bless their souls) and the third patient is still under treatment.
The Ministry said that the coronaviruses are well known and most of th

http://www.arabnews.com/saudi-minist...nt-coronavirus

**Treyfish** · September 23, 2012, 09:53 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

The ministry assured the public that such occurrences are rare and the overall health conditions are "reassuring and do not cause concern."

The MoH advised Haj or Umrah pilgrims to abide by the vaccinations and instructions issued by the ministry. It also urges everyone to pay attention to personal hygiene, wash hands and wear a mask in crowded places and change it periodically.

The ministry affirmed that it is constantly following developments in this regard at the national, regional and global levels in coordination with the concerned authorities and international health bodies.

http://www.saudigazette.com.sa/index...20120923137241

**alert** · September 23, 2012, 10:15 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

Hat-tip Crof. This proves it's the patient, not the sample, that went to London.

Two obvious errors: A coronavirus is not an influenza virus, and this appears to be an ANIMAL coronavirus, not related to the human coronaviruses OC43, 229E, and NL63 which cause seasonal respiratory illness.

Saudi Gazette/ Home Page

http://www.saudigazette.com.sa/index.cfm?method=home.regcon&contentid=20120923137241

Global News Website covers the latest and breaking news of saudi arabia and the world all the time, with politics, business, technology, life, opinion and sports news.

The Ministry of Health (MoH) announced Sunday that a rare pattern of the coronavirus, a known seasonal influenza virus, has been detected with the acceleration of climate changes and the advent of Haj and Umrah seasons.
In a statement, the ministry said that two Saudis — one at a hospital in Jeddah — and another Gulf citizen in Britain were recently diagnosed with the said virus. Two of them died and the third is still under treatment.
The MoH said that most people afflicted with the virus recover after simple treatment, although "in very rare cases and in a rare pattern of this virus, complications occur to the respiratory system and kidneys, which may lead to death, especially in elderly people and those with chronic cardiac illnesses and immune deficiency," the statement said.

**Giuseppe** · September 23, 2012, 10:23 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

Human Coronaviruses can cause severe disease without to be an extraordinary public health incident:

[Source: Chest, full text: <CITE cite="http://chestjournal.chestpubs.org/content/138/4/811.short?rss=1">Respiratory Viruses in Adults With Community-Acquired Pneumonia ? CHEST</CITE>. Abstract, edited.]

Respiratory Viruses in Adults With Community-Acquired Pneumonia

1. David Lieberman, MD, 2. Avi Shimoni, MD, 3. Yonat Shemer-Avni, PhD, 4. Ayelet Keren-Naos, PhD, 5. Rachel Shtainberg, PhD and 6. Devora Lieberman, MD

Author Affiliations
1. From the Pulmonary Unit (Dr David Lieberman), Division of Internal Medicine (Drs David Lieberman, Shimoni, and Devora Lieberman), Clinical Virology Laboratory (Drs Shemer-Avni, Keren-Naos, and Shtainberg), and Department of Geriatric Medicine (Dr Devora Lieberman), Soroka Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

1. Correspondence to: David Lieberman, MD, Pulmonary Unit, Soroka Medical Center, Beer-Sheva, Israel 84101; e-mail: Lieberma@bgu.ac.il

Abstract

Background:
Use of nucleic acid amplification techniques has increased the identification of respiratory viruses (RVs) in adult patients with community-acquired pneumonia (CAP). The objectives of the present study were to identify RV in patients with CAP using three different sampling methods and to compare CAP virus proportions and types with two comparison groups.

Methods:
The study population included 183 adult patients with CAP, 450 control subjects, and 201 patients with nonpneumonic lower respiratory tract infection (NPLRTI). Each participant was sampled by oropharyngeal swab, nasopharyngeal swab, and nasopharyngeal washing, and the samples were tested for detection of 12 RVs by multiplex TaqMan Hydrolysis probe-based real-time polymerase chain reaction (Integrated DNA Technology; Coralville, IA).

Results:
At least one RV was identified in 58 patients with CAP (31.7%) compared with 32 (7.1%) in control subjects and 104 (51.7%) in patients with NPLRTI (P < .01 and P < .01, respectively). Coronaviruses were identified in 24 (13.1%) patients with CAP, compared with 17 (3.8%) in control subjects, and 21 (10.4%) patients with NPLRTI. Respiratory syncytial virus was identified in 13 (7.1%), four (0.9%), and seven (3.5%); rhinovirus in nine (4.9%), nine (2.0%), and 15 (7.5%); and influenza virus in eight (4.4%), two (0.4%), and 63 (31.3%) patients with CAP, control subjects, and patients with NPLRTI, respectively.

Conclusions:
The proportion of RV involvement in CAP is higher than previously reported. The proportion of RV identified in healthy subjects is significantly lower than in CAP, but it is not zero and should be weighed when interpreting corresponding proportions among patients.

Footnotes
* For editorial comment see page 767
* Reproduction of this article is prohibited without written permission from the American College of Chest Physicians (http://www.chestpubs.org/site/misc/reprints.xhtml).

#Abbreviations
CAP community-acquired pneumonia
LRTI lower respiratory tract infection
NAAT nucleic acid amplification tests
NPLRTI nonpneumonic lower respiratory tract infection
NPS nasopharyngeal swab
NPW nasopharyngeal washing
OPS oropharyngeal swab
RSV respiratory syncytial virus
RV respiratory virus

* Received November 14, 2009.
* Accepted February 11, 2010.

* ? 2010 American College of Chest Physicians

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**alert** · September 23, 2012, 10:26 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

Originally posted by Giuseppe Michieli View Post

Human Coronaviruses can cause severe disease without to be an extraordinary public health incident:

Yes, but the initial ProMED report indicates the virus is a bat coronavirus, not a human one.

**Giuseppe** · September 23, 2012, 10:33 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

Originally posted by alert View Post

Yes, but the initial ProMED report indicates the virus is a bat coronavirus, not a human one.

Like this?

Source: mBio, full text: <CITE cite="http://mbio.asm.org/content/1/4/e00208-10.short?rss=1">Identification of a Severe Acute Respiratory Syndrome Coronavirus-Like Virus in a Leaf-Nosed Bat in Nigeria ? mBio</CITE>. Abstract, edited.]

Identification of a Severe Acute Respiratory Syndrome Coronavirus-Like Virus in a Leaf-Nosed Bat in Nigeria

1. Phenix-Lan Quan a, 2. Cadhla Firth a, 3. Craig Street a, 4. Jose A. Henriquez a, 5. Alexandra Petrosov a, 6. Alla Tashmukhamedova a, 7. Stephen K. Hutchison b, 8. Michael Egholm b, 9. Modupe O. V. Osinubi c, 10. Michael Niezgoda c, 11. Albert B. Ogunkoya d, 12. Thomas Briese a, 13. Charles E. Rupprecht c, and 14. W. Ian Lipkin a

Author Affiliations
1. Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USAa;
2. 454 Life Sciences, Branford, Connecticut, USAb;
3. Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USAc; and
4. Department of Veterinary Surgery and Medicine, Ahmadu Bello University, Zaria, Nigeriad

1. Address correspondence to Phenix-Lan Quan, pq2106@columbia.edu.

1. Editor Anne Moscona, Weill Cornell Medical College

ABSTRACT

Bats are reservoirs for emerging zoonotic viruses that can have a profound impact on human and animal health, including lyssaviruses, filoviruses, paramyxoviruses, and severe acute respiratory syndrome coronaviruses (SARS-CoVs). In the course of a project focused on pathogen discovery in contexts where human-bat contact might facilitate more efficient interspecies transmission of viruses, we surveyed gastrointestinal tissue obtained from bats collected in caves in Nigeria that are frequented by humans. Coronavirus consensus PCR and unbiased high-throughput pyrosequencing revealed the presence of coronavirus sequences related to those of SARS-CoV in a Commerson?s leaf-nosed bat (Hipposideros commersoni). Additional genomic sequencing indicated that this virus, unlike subgroup 2b CoVs, which includes SARS-CoV, is unique, comprising three overlapping open reading frames between the M and N genes and two conserved stem-loop II motifs. Phylogenetic analyses in conjunction with these features suggest that this virus represents a new subgroup within group 2 CoVs.

IMPORTANCE

Bats (order Chiroptera, suborders Megachiroptera and Microchiroptera) are reservoirs for a wide range of viruses that cause diseases in humans and livestock, including the severe acute respiratory syndrome coronavirus (SARS-CoV), responsible for the global SARS outbreak in 2003. The diversity of viruses harbored by bats is only just beginning to be understood because of expanded wildlife surveillance and the development and application of new tools for pathogen discovery. This paper describes a new coronavirus, one with a distinctive genomic organization that may provide insights into coronavirus evolution and biology.

Footnotes

* Citation Quan, P.-L., C. Firth, C. Street, J. A. Henriquez, A. Petrosov, et al. 2010. Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria. mBio 1(4):e00208-10. doi:10.1128/mBio.00208-10.

* Received 25 August 2010
* Accepted 3 September 2010
* Published 12 October 2010

* Copyright ? 2010 Quan et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

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**Giuseppe** · September 23, 2012, 10:36 AM

Re: Saudi Arabia: 3 cases, 2 deaths due to novel animal coronavirus

Above paper full text is available at: http://www.ncbi.nlm.nih.gov/pmc/arti...tool=pmcentrez

Announcement

Worldwide: 24 confirmed cases due to novel animal nCoV coronavirus - 16 fatalities - September 20, 2012 - May 2, 2013

Worldwide: 24 confirmed cases due to novel animal nCoV coronavirus - 16 fatalities - September 20, 2012 - May 2, 2013

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