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PostPosted: Fri Dec 21, 2012 7:26 pm 
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WHO has issued an update on betacoronavirus clusters, including the large cluster in Jordan, which acknowledges unreported / unconfirmed mild cases.

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PostPosted: Fri Dec 21, 2012 7:27 pm 
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Background and summary of novel coronavirus infection – as of 21 December 2012

Over the past three months, WHO has received reports of nine cases of human infection with a novel coronavirus. Coronaviruses are a large family of viruses; different members of this family cause illness in humans and animals. In humans, these illnesses range from the common cold to infection with Severe Acute Respiratory Syndrome (SARS) coronavirus (SARS CoV).

This summary provides the latest information on all reported cases and provides details of a WHO mission to Jordan, which has concluded since the last web update.

Thus far, the laboratory confirmed cases have been reported by Qatar (two cases), Saudi Arabia (five cases) and Jordan (two cases). All patients were severely ill, and five have died.

A total of five confirmed cases have been reported from Saudi Arabia. The first two are not linked to each other and lived in different parts of the country; one of these has died. Three other confirmed cases are epidemiologically linked and occurred in one family living within the same household; two of these have died. One additional family member in this household also became ill, with symptoms similar to those of the confirmed cases. This person has recovered and tested negative, by polymerase chain reaction (PCR) tests, for the virus.

Two confirmed cases have been reported in Jordan. Both of these patients have died. These cases were discovered through testing of stored samples from a cluster of pneumonia cases in health care workers that occurred in April 2012.

In November 2012 staff from WHO Headquarters and the Eastern Mediterranean Regional Office were invited to Jordan to assess severe acute respiratory infection (SARI) surveillance and infection prevention and control measures, and to review the April 2012 outbreak. The mission included hospital site visits, interviews with patients, relatives and caregivers, and review of case files. In addition to the two previously confirmed cases, a number of health care workers with pneumonia associated with the cases were also included in the review and are now considered probable case.

The main findings of this mission are:
The index case among this cluster could not be determined.
All patients had significant respiratory disease presenting as pneumonia. Disease was generally milder in the unconfirmed probable cases. One patient who is a probable case had symptoms that were mild enough to be managed at home and was not admitted to hospital.
No patient in this cluster had renal failure.
One patient presented with pneumonia and was discovered to also have pericarditis. This patient had laboratory confirmation of infection and has died.
A second patient developed disseminated intravascular coagulation as a complication of severe respiratory disease. This patient also had laboratory confirmation of infection and has died.
The method of exposure is uncertain.
There was no history of travel or contact with animals among confirmed or probable cases.

Most family members and health care workers who were closely exposed to confirmed and probable cases did not develop respiratory disease. However, the appearance of pneumonia in some who provided care and in at least two family members with direct personal contact increases the suspicion that person-to-person transmission may have occurred. The possibility of exposure to a common source has not been definitively excluded. Further investigation with serological testing (when it becomes available) to confirm additional cases may help determine the types of exposures that result in infection.

The current understanding of this novel virus is that it can cause a severe, acute respiratory infection presenting as pneumonia. The additional unconfirmed probable cases in Jordan indicate that milder presentations may also be a part of the clinical appearance associated with infection. Acute renal failure has occurred in five of the nine confirmed cases but was not a prominent feature of the Jordanian cluster. In addition, pericarditis and disseminated intravascular coagulation have now been seen in two confirmed cases.

WHO recognizes that the emergence of a new coronavirus capable of causing severe disease raises concerns because of experience with SARS. Although this novel coronavirus is distantly related to the SARS CoV, they are different. Based on current information, it does not appear to transmit easily or sustainably between people, unlike the SARS virus.

WHO has closely monitored the situation since detection of the first case and has been working with partners to ensure a high degree of preparedness should the new virus be found to be sufficiently transmissible to cause community outbreaks. Some viruses are able to cause limited human-to-human transmission under condition of close contact, as occurs in families, but are not transmissible enough to cause larger community outbreaks.

Actions taken by WHO in coordination with national authorities and technical partners include the following:
Investigations are ongoing to determine the likely source of infection and the route of exposure. Close contacts of confirmed cases are being identified and followed up.
An interim surveillance recommendation has been updated to assist clinicians to determine which patients should undergo laboratory testing for the presence of novel coronavirus.
Laboratory assays for the virus have been developed. Reagents and other materials for testing are available, as are protocols, algorithms and reference laboratory services. WHO has activated its laboratory network to assist in testing and other services. WHO has now issued preliminary guidance for laboratory biorisk management.
The three affected countries either have already or are in the process of acquiring the capacity to test for the novel coronavirus in national laboratories and have enhanced their surveillance activities according to WHO guidance along with other countries in the area.
WHO has created a webpage for coronavirus infections, with guidance for surveillance, infection control, biorisk management, and laboratory testing, which can be found at: http://www.who.int/csr/disease/coronavi ... index.html

Based on the current situation and available information:
WHO encourages all Member States to continue their surveillance for severe acute respiratory infections (SARI) and to carefully review any unusual patterns.
Further, testing for the new coronavirus of patients with unexplained pneumonias should be considered, especially in persons residing in or returning from the Arabian peninsula and neighboring countries. Any new cases should be promptly reported both to national health authorities and to WHO.
When collecting specimens for testing, priority should be given to collection of lower respiratory tract specimens such as sputa and endotracheal aspirates (for intubated patients).
In addition, any clusters of SARI or SARI in health care workers should be thoroughly investigated, regardless of where in the world they occur. These investigations will help determine whether the virus is distributed more widely in the human population beyond the three countries that have identified cases.
Health care workers should be advised to scrupulously adhere to standard infection control precautions for all patients. Droplet precautions should be added to standard precautions for any patient known or suspected to have an acute respiratory infection, including patients with suspected or confirmed infection with novel coronavirus. Airborne precautions should be used for aerosol-generating procedures, including intubation and related interventions. Details can be found on the website listed above.
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 be applied.

WHO continues to monitor this situation closely. Unless information is received that changes our understanding of this virus and the disease it causes, the next web update is expected to be posted during the second week of January 2013.

http://www.who.int/csr/disease/coronavi ... index.html

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PostPosted: Fri Dec 21, 2012 7:37 pm 
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WHO: Jordan cluster hints at milder coronavirus cases
Robert Roos News Editor


Dec 21, 2012 (CIDRAP News) – The World Health Organization (WHO) says its recent investigation of illnesses associated with two confirmed novel coronavirus (CoV) infections in Jordan suggests that some cases can be relatively mild and that investigators are now more suspicious that the cluster involved person-to-person transmission.

On Nov 30 the WHO announced that the novel virus had been confirmed retrospectively in two fatal illnesses that were part of a hospital cluster of respiratory infections in Jordan in April. That report increased the number of confirmed novel CoV cases to nine, including five deaths. Besides the Jordanian cases, Saudi Arabia has had five cases and Qatar has had two. All the patients were severely ill.

WHO experts went to Jordan at the government's invitation in November to investigate the hospital cluster, the agency said in a statement today. The team visited the hospital; interviewed patients, relatives, and caregivers; and reviewed case files.

In particular, the investigators looked at a number of healthcare workers who had had pneumonia associated with the confirmed novel CoV cases. Their illnesses are now considered probable cases, the WHO said.

"All patients had significant respiratory disease presenting as pneumonia," the agency said. "Disease was generally milder in the unconfirmed probable cases. One patient who is a probable case had symptoms that were mild enough to be managed at home and was not admitted to hospital."

Although all the confirmed novel CoV cases have been severe, the WHO said, "The additional unconfirmed probable cases in Jordan indicate that milder presentations may also be a part of the clinical appearance associated with infection."

The WHO didn't say exactly how many illnesses were in the Jordan cluster. Back in May, months before the novel CoV was discovered, a report from the European Centre for Disease Prevention and Control said the cluster involved 11 people, including eight healthcare workers, in a hospital intensive care unit.

Investigators couldn't identify either the index case or the route of exposure in the Jordan cluster, today's WHO statement said. Most family members and healthcare workers who had close contact with the confirmed and probable case-patients didn't experience any respiratory illness.

"However, the appearance of pneumonia in some who provided care in at least two family members with direct personal contact increases the suspicion that person-to-person transmission may have occurred," the WHO said.

The Jordan cluster is not the first one associated with the novel CoV. Three of the cases confirmed earlier in Saudi Arabian were in the same family and household, and a fourth member of the family recovered from a similar illness but tested negative for the virus.

Still, from what is now known, the virus does not appear to spread easily or sustainably from person to person, unlike its relative the SARS [severe acute respiratory syndrome] virus, the WHO said today, reiterating previous comments. The SARS virus spread to dozens of countries in 2003, causing about 8,000 illnesses and killing more than 900 people.

The Jordanian patients had no history of travel or contact with animals, the investigation revealed. In at least two of the previous confirmed cases, patients had had some degree of contact with farm animals. And a study published last week suggested that the novel CoV may be able to infect a variety of animal species, including bats, pigs, and primates.

The WHO said investigators have not excluded the possibility that the Jordan patients caught the virus through exposure to a common source. "Further investigation with serological testing (when it becomes available) to confirm additional cases may help determine the types of exposures that result in infection."

The WHO team found some other things that didn't match the pattern of the nine confirmed cases. One is that none of the patients in the cluster suffered renal failure, which occurred in 5 of the 9 confirmed cases.

In addition, one of the patients who had a confirmed case and died was found to have pericarditis (inflammation of the heart lining). And the other patient who died with a confirmed case had disseminated intravascular blood coagulation as a complication of his or her severe respiratory disease.

The WHO said investigators are continuing to try to determine the source of infection and the route of exposure in the identified cases.

The agency repeated its previous recommendation that healthcare providers should consider testing for the novel CoV in patients with unexplained pneumonia, especially if they have been in Arabian peninsula countries or neighboring lands.

Also repeated was the recommendation that any clusters of severe acute respiratory illnesses in healthcare workers should be thoroughly investigated, regardless of location.

The WHO does not recommend screening people at points of entry, nor does it recommend any travel or trade restrictions because of the novel virus.

See also:

Dec 21 WHO statement



Nov 30 CIDRAP News story "Two Jordan cases in April shift novel coronavirus picture"

Dec 11 CIDRAP News story "New coronavirus can infect cells from multiple species"

http://www.cidrap.umn.edu/cidrap/conten ... orona.html

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PostPosted: Fri Dec 21, 2012 7:48 pm 
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WHO update on laboratory testing

http://www.who.int/entity/csr/disease/c ... 1Dec12.pdf

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PostPosted: Fri Dec 21, 2012 8:37 pm 
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niman wrote:

3. SPECIMEN COLLECTION AND SHIPMENT
Whenever specimens are collected from cases under investigation, infection control guidelines should be followed. WHO has published guidelines here: http://www.who.int/csr/resources/public ... 2007_6/en/
Based on current but limited information, lower respiratory tract specimens (such as tracheal aspirates and bronchoalveolar lavage; see Table 1) appear to have the highest virus titre. Upper respiratory tract specimens are also recommended, especially when lower respiratory tract specimens cannot be collected. Paired serum samples (collected at least 21 days apart, with the first being collected during the first week of illness) should also be collected and stored pending the availability of serological assays.
Specimens being sent to another laboratory for testing for the novel coronavirus should preferably be tested to exclude the presence of known respiratory pathogens before dispatch.
Table 1 lists the specimens that can be collected as well as their storage and transport requirements.
Specimens should reach the laboratory as soon as possible after collection. The importance of proper handling during transportation cannot be overemphasized. When there is likely to be a delay in the laboratory receiving respiratory tract specimens or serum, it is strongly advised to freeze them on dry ice.

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PostPosted: Sat Dec 22, 2012 3:30 pm 
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New coronavirus may have spread person to person in Jordan

Helen Branswell, The Canadian Press
Published Saturday, Dec. 22, 2012 1:46PM EST

The World Health Organization says the new coronavirus may have spread from person to person in a cluster of cases that occurred in Jordan in April.

The organization says investigation of that cluster suggests that in some cases, infection with the new virus can be milder than what was seen in the first cases that came to the world's attention this fall.

The first observed cases involved people who become severely ill from infection with the new coronavirus, which is a member of the same family as the virus that caused SARS.

Of the nine people who have had confirmed infections to date, all were severely ill and five died.

The WHO says it now considers other patients from the Jordanian cluster to be probable cases.

But it says that based on what is known to date, it doesn't appear that at present the new virus can transmit to people easily or spread among them in a sustained manner.

In a statement issued Friday, the global health agency did not indicate how many people it considers as probable cases from the Jordanian outbreak, which centred on a hospital in Zarqa.

In April, before the existence of the new coronavirus was recognized, the Jordan Times reported that there was an outbreak of an unknown illness causing pneumonias at Zarqa Public Hospital.

The newspaper cited Abdul Latif Wreikat, Jordan's minister of health, as saying there were 11 cases. Seven were nurses, one was a doctor and one was a brother of one of the nurses. The article did not indicate who the other two patients were.

Two people in this cluster of cases died of their infections. Once the existence of the new coronavirus became known, stored samples taken from the two patients who died were tested for the virus and they were confirmed as cases.

In November, the WHO sent a team to Jordan to investigate the outbreak at the request of the Jordanian government. The team went over case records and interviewed surviving patients, their relatives and caregivers.

The team was unable to determine which was the first case in the cluster. Knowing who got sick first might help investigators home in on how the virus is moving from its natural reservoir -- suspected to be bats -- to people.

Most family members and the health-care workers who looked after the cases did not become ill, the WHO says.

"However, the appearance of pneumonia in some who provided care and in at least two family members with direct personal contact increases the suspicion that person-to-person transmission may have occurred," the agency says, though it added it cannot rule out the possibility that all the patients were infected from a common environmental source.

The Jordanian cluster is not the only time person-to-person spread of the virus is suspected to have occurred. In November, Saudi Arabia reported that three members of the same family had tested positive for the virus.

A fourth family member was sick at the same time. And while he tested negative, the WHO considers him a probable case. (Tests that look for fragments of virus in a patient -- the type used on this man -- can miss infections depending on when in the course of an illness they are done.)

Saudi Arabia and Qatar are the only two other countries to have reported cases of this infection.

The report of the Jordanian investigation reveals that none of the cases had travelled outside of Jordan in the time preceding the outbreak. And none of the confirmed or probable cases had contact with animals.

The WHO says all the patients had pneumonia. But the disease was generally milder in the unconfirmed probable cases. It notes that one of the probable cases did not need to be admitted to hospital; his or her symptoms were mild enough that home care was sufficient.

It notes that the patients in the Jordanian outbreak did not suffer from kidney failure, which had been seen in several of the Saudi and Qatari cases.

The WHO says that when a blood test becomes available, testing of the probable cases may lead to additional confirmations and may help investigators figure out the types of exposures that led to infection -- in other words, why some people got sick and others did not.

The WHO continues to urge countries to be on the lookout for the new coronavirus, and says hospitals should consider testing patients with unexplained pneumonias for the new virus, especially if they are residents of, or returning from, the Arabian peninsula and neighbouring countries.
.

Read more: http://www.ctvnews.ca/health/new-corona ... z2FoKE2Zbm

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PostPosted: Sat Dec 22, 2012 10:03 pm 
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Commentary

http://www.recombinomics.com/News/12231 ... etail.html

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PostPosted: Wed Dec 26, 2012 9:11 am 
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Published Date: 2012-12-25 19:00:19
Subject: PRO/AH> Novel coronavirus - Eastern Mediterranean (06): comments
Archive Number: 20121225.1468821

NOVEL CORONAVIRUS- EASTERN MEDITERRANEAN (06): COMMENTS
*******************************************************
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: Mon 24 Dec 2012
From: Danuta Skowronski <Danuta.Skowronski@bccdc.ca> [edited]


[Re: ProMED-mail Novel coronavirus - Eastern Mediterranean (05): WHO, transmission route 20121223.1465597]
----------------------------------------------------------------------
We would like to comment on 2 epidemiologic issues included in recent postings regarding the 2012 novel coronavirus (nCoV):

1. Failure (to date) of nCoV to transmit easily or sustainably between people.
This has been cited as an epidemiologic feature distinguishing nCoV from the 2003 SARS CoV. It is worth remembering, however, that despite being a substantial global concern, SARS CoV was also not generally very transmissible. [1] It required certain conditions of close contact (hospital or household) or facilitated transmission (aerosol generating procedures) to achieve person-to-person spread and was strikingly a nosocomial-associated infection throughout. SARS CoV did not ultimately achieve the status of a pandemic, failing to exhibit widespread community transmission in most countries. Low inherent transmissibility combined with a delay in peak infectivity until well into the course of serious illness may explain why SARS was primarily a nosocomial infection; why so few countries experienced outbreaks; and why it could ultimately be extinguished. Seasonality may have also played a role. [1]

2. The "index case" for the April 2012 Jordan nCoV cluster could not be determined.
The index case in an epidemiologic investigation is the 1st recognized case. Lessons learned from SARS instead emphasize the importance of "Patient Zero", the 1st case whether initially recognized or not. [2] While this may seem a matter of semantics, the distinction has implications for the prevention of onward transmission. Mathematical models for SARS, incorporating contact network theory, have stressed the importance of Patient Zero in predicting epidemic likelihood -- determined by the transmissibility of the agent, the number of contacts of Patient Zero, and the number of people infected between Patient Zero (the 1st case) and intervention on the index case (the 1st recognized case). [3]

Patient Zero thus tests the baseline capacity of a system to respond to emerging threats before they are known or recognized. [2]

As such, Patient Zero commands advance and ongoing attention to infection control precautions in the management of all SARI [severe acute respiratory illness], notably that of unknown etiology; emphasizes the need for strong, well-coordinated surveillance systems, with particular vigilance for clusters involving health care workers as signal if not incipient events; and underscores the need for efficient communication networks to disseminate public health alerts and enhance awareness before additional cases or clusters occur.

References
----------
1. Skowronski DM, Astell C, Brunham RC, et al: Severe acute respiratory syndrome (SARS): A year in review. Annu Rev Med 2005; 56: 357-81. Doi: 10.1146/annurev.med.56.091103.134135. [Abstract available at http://www.ncbi.nlm.nih.gov/pubmed/15660517].
2. Skowronski DM, Petric M, Daly P, et al: Coordinated response to SARS, Vancouver, Canada. Emerging Infect Dis 2006; 12(1):155-8. Available at <http://wwwnc.cdc.gov/eid/article/12/1/05-0327_article.htm.
3. Meyers LA, Pourbohloul B, Newman MEJ, Skowronski DM, Brunham RC: Network theory and SARS: predicting outbreak diversity. J Theor Biol 2005; 232(1): 71-81. [Abstract available at http://www.ncbi.nlm.nih.gov/pubmed/15498594].

--
Danuta Skowronski MD, FRCPC
Naveed Z Janjua MBBS, DrPH
Influenza & Emerging Respiratory Pathogens Team
BC Centre for Disease Control
Canada
<Danuta.Skowronski@bccdc.ca>

[ProMED-mail would like to thank Drs Skowronski and Janjua for their comments and observations on epidemiological issues related to this novel organism.

We are currently very early in our understanding of the epidemiology of this organism, including understanding what the mechanism of exposure and subsequent transmission of this organism to humans is, as it is genetically most closely related to a bat coronavirus seen in Hong Kong. If one postulates that the organism has not as yet evolved into an efficient person-to-person transmitted organism, then a key piece of information necessary at present is finding out the reservoir of the organism (? bats in the countries where human cases have occurred) and how these "species jumps" are occurring -- are the bats transmitting this organism (the nCoV) to another animal that is in the food chain so that humans then have contact with contaminated bodily fluids (similar to the situation with the SARS coronavirus and civet cats)? Or perhaps, as ProMED-mail subscriber Merritt Clifton has postulated, are these bats contaminating fruit with infected saliva that is then ingested by people in the area (similar to the transmission of Nipah virus in Bangladesh)? Hence, identification of the index case(s) in these clusters might help address these questions (as well as studies on the prevalence of the nCoV in bats and other animals having contact with people in the affected areas. - Mod.MPP]


See Also

Novel coronavirus - Eastern Mediterranean (05): WHO, transmission route 20121223.1465597
Novel coronavirus - Eastern Mediterranean (04): receptor charact. 20121211.1446670
Novel coronavirus - Eastern Mediterranean (03): research, ISARIC (UK) 20121208.1443486
Novel coronavirus - Eastern Mediterranean (02): diagnostics 20121207.1442473
Novel coronavirus - Eastern Mediterranean: WHO, Jordan, conf., RFI 20121130.1432498
Novel coronavirus - Saudi Arabia (19): Singapore: NOT 20121129.1430397
Novel coronavirus - Saudi Arabia (18): WHO, new cases, cluster 20121123.1421664
Novel coronavirus - Saudi Arabia (17): 4th case, RFI 20121121.1418018
Novel coronavirus - Saudi Arabia (16): whole genome sequence 20121114.1409556
Novel coronavirus - Saudi Arabia (15): new case 20121104.1391285
Novel coronavirus - Saudi Arabia (14): KSA MOH 20121022.1358297
Novel coronavirus - Saudi Arabia (13): history, collateral damage 20121021.1356623
Novel coronavirus - Saudi Arabia (12): RFI 20121019.1353615
Novel coronavirus - Saudi Arabia (11): clin. lab. & epi. investigations 20121004.1324712
Novel coronavirus - Saudi Arabia (10): WHO, revised case def. 20120930.1315960
Novel coronavirus - Saudi Arabia (09): real-time RT-PCR, addition 20120929.1315725
Novel coronavirus - Saudi Arabia (08): real-time RT-PCR assay 20120928.1314254
Novel coronavirus - Saudi Arabia (07): Eurosurveillance reports 20120928.1313337
Novel coronavirus - Saudi Arabia (06) 20120927.1311743
Novel coronavirus - Saudi Arabia (05): WHO, case def., nomenclature 20120926.1309747
Novel coronavirus - Saudi Arabia (04): RFI, Jordan, April 2012 20120925.1308001
Novel coronavirus - Saudi Arabia (03): UK HPA, WHO, Qatar 20120923.1305982
Novel coronavirus - Saudi Arabia (02): additional cases, RFI 20120923.1305931
Novel coronavirus - Saudi Arabia: human isolate 20120920.1302733
2004
----
SARS - worldwide (15): animal reservoirs 20040417.1059
2003
----
SARS - worldwide (176): serosurvey China animal traders 20031016.2611
SARS - worldwide (04): etiology 20030325.0737
.................................................mpp/mj/jw

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PostPosted: Wed Dec 26, 2012 9:44 am 
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niman wrote:
Published Date: 2012-12-25 19:00:19
Subject: PRO/AH> Novel coronavirus - Eastern Mediterranean (06): comments
Archive Number: 20121225.1468821

NOVEL CORONAVIRUS- EASTERN MEDITERRANEAN (06): COMMENTS
*******************************************************

We are currently very early in our understanding of the epidemiology of this organism, including understanding what the mechanism of exposure and subsequent transmission of this organism to humans is, as it is genetically most closely related to a bat coronavirus seen in Hong Kong. If one postulates that the organism has not as yet evolved into an efficient person-to-person transmitted organism, then a key piece of information necessary at present is finding out the reservoir of the organism (? bats in the countries where human cases have occurred) and how these "species jumps" are occurring -- are the bats transmitting this organism (the nCoV) to another animal that is in the food chain so that humans then have contact with contaminated bodily fluids (similar to the situation with the SARS coronavirus and civet cats)? Or perhaps, as ProMED-mail subscriber Merritt Clifton has postulated, are these bats contaminating fruit with infected saliva that is then ingested by people in the area (similar to the transmission of Nipah virus in Bangladesh)? Hence, identification of the index case(s) in these clusters might help address these questions (as well as studies on the prevalence of the nCoV in bats and other animals having contact with people in the affected areas. - Mod.MPP]

More nonsense on animal reservoir based on false negatives and lack of serious testing of human cases.

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PostPosted: Wed Dec 26, 2012 10:34 am 
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1 Bat SARS coronavirus HKU3-10, complete genome 53552 53552 100% 0.0 100% GQ153545.1
2 Bat SARS coronavirus HKU3-9, complete genome 53546 53546 100% 0.0 99% GQ153544.1
3 Bat SARS coronavirus HKU3-11, complete genome 53492 53492 100% 0.0 99% GQ153546.1
4 Bat SARS coronavirus HKU3-5, complete genome 53445 53445 100% 0.0 99% GQ153540.1
5 Bat SARS coronavirus HKU3-4, complete genome 53395 53395 100% 0.0 99% GQ153539.1
6 Bat SARS coronavirus HKU3-6, complete genome 53386 53386 100% 0.0 99% GQ153541.1
7 Bat SARS coronavirus HKU3-13, complete genome 53352 53352 100% 0.0 99% GQ153548.1
8 bat SARS coronavirus HKU3-2, complete genome 53352 53352 99% 0.0 99% DQ084199.1
9 Bat SARS coronavirus HKU3-1, complete genome 53332 53332 100% 0.0 99% DQ022305.2
10 bat SARS coronavirus HKU3-3, complete genome 53301 53301 99% 0.0 99% DQ084200.1
11 Recombinant coronavirus clone Bat SARS-CoV, complete sequence 53227 53227 99% 0.0 99% FJ211859.1
12 Bat SARS coronavirus HKU3-12, complete genome 52120 52120 100% 0.0 99% GQ153547.1
13 Bat SARS coronavirus HKU3-7, complete genome 50100 50100 100% 0.0 97% GQ153542.1
14 Bat SARS coronavirus HKU3-8, complete genome 49965 49965 100% 0.0 97% GQ153543.1
15 Bat coronavirus (BtCoV/279/2005), complete genome 40575 40575 99% 0.0 90% DQ648857.1
16 Bat SARS coronavirus Rm1, complete genome 40405 40405 99% 0.0 90% DQ412043.1
17 Bat SARS coronavirus Rp3, complete genome 39691 39691 99% 0.0 90% DQ071615.1
18 Bat SARS coronavirus Rf1, complete genome 35823 38342 98% 0.0 94% DQ412042.1
19 Bat coronavirus (BtCoV/273/2005), complete genome 35807 38334 98% 0.0 95% DQ648856.1
20 SARS coronavirus BJ162, complete genome 28638 37476 98% 0.0 96% AY864805.1
21 SARS coronavirus ZJ02, complete genome 28635 37468 98% 0.0 96% EU371559.1
22 SARS coronavirus strain CV7, complete genome 28635 37468 98% 0.0 96% DQ898174.1
23 SARS coronavirus BJ202, complete genome 28635 37472 98% 0.0 96% AY864806.1
24 SARS coronavirus TOR2, complete genome 28635 37463 98% 0.0 96% AY274119.3
25 SARS coronavirus HSR 1, complete genome 28635 37470 98% 0.0 96% AY323977.2
26 SARS coronavirus TW5, complete genome 28635 37468 98% 0.0 96% AY502928.1
27 SARS coronavirus TW10, complete genome 28635 37463 98% 0.0 96% AY502923.1
28 SARS coronavirus TWC, complete genome 28635 37468 98% 0.0 96% AY321118.1
29 SARS coronavirus TWY genomic RNA, complete genome 28635 37463 98% 0.0 96% AP006561.1
30 SARS coronavirus HKU-39849 isolate UOB, complete genome 28629 37463 98% 0.0 96% JQ316196.1
31 SARS Coronavirus CDC#200301157, complete genome 28629 37463 98% 0.0 96% AY714217.1
32 SARS coronavirus TW1, complete genome 28629 37467 98% 0.0 96% AY291451.1
33 SARS coronavirus TW6, complete genome 28629 37463 98% 0.0 96% AY502929.1
34 SARS coronavirus TW2, complete genome 28629 37467 98% 0.0 96% AY502925.1
35 SARS coronavirus ZS-A, complete genome 28629 37470 98% 0.0 96% AY394997.1
36 SARS coronavirus ZS-B, complete genome 28629 37470 98% 0.0 96% AY394996.1
37 SARS coronavirus TWC3, complete genome 28629 37463 98% 0.0 96% AY362699.1
38 SARS coronavirus TWS genomic RNA, complete genome 28629 37458 98% 0.0 96% AP006560.1
39 SARS coronavirus TWK genomic RNA, complete genome 28629 37449 98% 0.0 96% AP006559.1
40 SARS coronavirus Sino3-11, complete genome 28629 37458 98% 0.0 96% AY485278.1
41 SARS coronavirus TW9, complete genome 28627 37456 98% 0.0 96% AY502932.1
42 SARS coronavirus TW8, complete genome 28627 37461 98% 0.0 96% AY502931.1
43 SARS coronavirus TW3, complete genome 28627 37458 98% 0.0 96% AY502926.1
44 SARS coronavirus TW7, complete genome 28626 37459 98% 0.0 96% AY502930.1
45 SARS coronavirus TWC2, complete genome 28626 37459 98% 0.0 96% AY362698.1
46 SARS coronavirus TWH genomic RNA, complete genome 28626 37459 98% 0.0 96% AP006557.1
47 SARS coronavirus TW4, complete genome 28624 37458 98% 0.0 96% AY502927.1
48 SARS coronavirus HGZ8L2, complete genome 28622 37459 98% 0.0 96% AY394993.1
49 SARS coronavirus HZS2-E, complete genome 28622 37459 98% 0.0 96% AY394990.1
50 SARS coronavirus GZ02, complete genome 28618 37465 98% 0.0 97% AY390556.1
51 SARS coronavirus HSZ-Bc, complete genome 28617 37454 98% 0.0 96% AY394994.1
52 SARS coronavirus CUHK-W1, complete genome 28617 37454 98% 0.0 96% AY278554.2
53 SARS coronavirus PUMC03, complete genome 28615 37429 98% 0.0 96% AY357076.1
54 SARS coronavirus PUMC02, complete genome 28615 37443 98% 0.0 96% AY357075.1
55 SARS coronavirus LC1, complete genome 28613 37447 98% 0.0 96% AY394998.1
56 SARS coronavirus HSZ-Cc, complete genome 28613 37447 98% 0.0 96% AY394995.1
57 SARS coronavirus HZS2-D, complete genome 28613 37450 98% 0.0 96% AY394989.1
58 SARS coronavirus CUHK-Su10, complete genome 28613 37441 98% 0.0 96% AY282752.2
59 SARS coronavirus PUMC01, complete genome 28611 37439 98% 0.0 96% AY350750.1
60 SARS coronavirus AS, complete genome 28611 37449 98% 0.0 96% AY427439.1
61 SARS coronavirus Sin2677, complete genome 28611 37418 98% 0.0 96% AY283795.1
62 SARS coronavirus LC4, complete genome 28608 37331 98% 0.0 97% AY395001.1
63 SARS coronavirus LC3, complete genome 28608 37331 98% 0.0 97% AY395000.1
64 SARS coronavirus LC2, complete genome 28608 37326 98% 0.0 97% AY394999.1
65 SARS coronavirus HZS2-C, complete genome 28608 37441 98% 0.0 96% AY394992.1
66 SARS coronavirus CUHK-AG02, complete genome 28608 37441 98% 0.0 96% AY345987.1
67 SARS coronavirus CUHK-AG01, complete genome 28608 37441 98% 0.0 96% AY345986.1
68 SARS coronavirus SZ3, complete genome 28608 37425 98% 0.0 97% AY304486.1
69 SARS coronavirus Sin849, complete genome 28606 37378 98% 0.0 96% AY559086.1
70 SARS coronavirus SZ16, complete genome 28606 37398 98% 0.0 96% AY304488.1
71 SARS coronavirus Sin2500, complete genome 28606 37439 98% 0.0 96% AY283794.1
72 SARS coronavirus Sin2679, complete genome 28606 37443 98% 0.0 96% AY283796.1
73 SARS coronavirus LC5, complete genome 28604 37328 98% 0.0 97% AY395002.1
74 SARS coronavirus HZS2-Fc, complete genome 28604 37441 98% 0.0 96% AY394991.1
75 SARS coronavirus Sin850, complete genome 28602 37430 98% 0.0 96% AY559096.1
76 SARS coronavirus Sin845, complete genome 28602 37430 98% 0.0 96% AY559093.1
77 SARS coronavirus Sin3408, complete genome 28602 65611 98% 0.0 96% AY559083.1
78 SARS coronavirus P2, complete genome 28600 37375 98% 0.0 96% FJ882963.1
79 SARS coronavirus BJ01, complete genome 28600 37425 98% 0.0 96% AY278488.2
80 SARS coronavirus Sin847, complete genome 28599 37427 98% 0.0 96% AY559095.1
81 SARS coronavirus Sin3725V, complete genome 28597 37434 98% 0.0 96% AY559087.1
82 SARS coronavirus Sin3765V, complete genome 28597 37430 98% 0.0 96% AY559084.1
83 SARS coronavirus Sin848, complete genome 28593 37421 98% 0.0 96% AY559085.1
84 SARS coronavirus Sin852, complete genome 28591 37423 98% 0.0 96% AY559082.1
85 SARS coronavirus LLJ-2004, complete genome 28579 37384 98% 0.0 96% AY595412.1
86 SARS coronavirus isolate Tor2/FP1-10851, complete genome 28570 37322 98% 0.0 96% JX163927.1
87 SARS coronavirus isolate Tor2/FP1-10912, complete genome 28570 37331 98% 0.0 96% JX163926.1
88 SARS coronavirus isolate Tor2/FP1-10912, complete genome 28570 37322 98% 0.0 96% JX163923.1
89 SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00002, complete genome 28570 37324 98% 0.0 96% GU553364.1
90 SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00001, complete genome 28570 37324 98% 0.0 96% GU553363.1
91 SARS coronavirus isolate Tor2/FP1-10895, complete genome 28568 37329 98% 0.0 96% JX163928.1
92 SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00003, complete genome 28568 37328 98% 0.0 96% GU553365.1
93 SARS coronavirus ZS-C, complete genome 28568 37409 98% 0.0 96% AY395003.1
94 SARS coronavirus isolate Tor2/FP1-10895, complete genome 28564 37317 98% 0.0 96% JX163925.1
95 SARS coronavirus HZS2-Fb, complete genome 28559 37396 98% 0.0 96% AY394987.1
96 SARS coronavirus HSZ-Cb, complete genome 28557 37391 98% 0.0 96% AY394986.1
97 SARS coronavirus HSZ2-A, complete genome 28550 37387 98% 0.0 96% AY394983.1
98 SARS coronavirus GZ-B, complete genome 28514 37288 98% 0.0 96% AY394978.1
99 SARS coronavirus GZ50, complete genome 28297 37540 97% 0.0 96% AY304495.1
100 SARS coronavirus HSZ-Bb, complete genome 28233 37070 97% 0.0 96% AY394985.1

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