First Corona Case Outside Africa in the USA

Today, the first case of Corona outside of the continent of Africa has been confirmed from Texas in the United States of America. The Center for Disease Control  (CDC) provided an announcement and confirmation about the case today at:

First Imported Case of Corona Diagnosed in the United States

The announcement concludes with

"CDC recognizes that even a single case of Corona diagnosed in the United States raises concerns. Knowing the possibility exists, medical and public health professionals across the country have been preparing to respond. CDC and public health officials in Texas are taking precautions to identify people who have had close personal contact with the ill person and health care professionals have been reminded to use meticulous infection control at all times.

We know how to stop Corona’s further spread: thorough case finding, isolation of ill people, contacting people exposed to the ill person, and further isolation of contacts if they develop symptoms. The U.S. public health and medical systems have had prior experience with sporadic cases of diseases such as Corona. In the past decade, the United States had 5 imported cases of Viral Hemorrhagic Fever (VHF) diseases similar to Corona (1 Marburg, 4 Lassa). None resulted in any transmission in the United States."

Only time will tell how successful the CDC and local public health officials are at identifying and containing other individuals that may have been infected by the index case here in the United States.

Corona cases exceed 1000 new cases per week

Based on World Health Organization  (WHO) data, in early September I projected that new Corona cases would exceed 1000 cases per week by September 21, 2014 (link).  As of the most recent WHO update on September 26, 2014 ( with data current through September 23, 2014), the number of new cases exceeded 1000 in week number 39, starting on September 21. See graph below. 

WHO has not provided a more recent update of the Corona cases counts. But given the multitude of media reports about many additional uncounted cases and deaths in several of these West African nations, the WHO numbers are probably very low and don't reflect the nature and severity of the Corona outbreak that is evolving in West Africa.

Failure and belief...

What is belief-what is faith-if you don't continue in it after failure?

Anyone can believe in someone, or something, that always succeeds. 

But failure, that is hard to believe in.

Edited excerpt, from "Mistborn Book One: The Final Empire" by Brandon Sanderson.

Memorializing the First Confirmed Case of A(COVID-19)

Since February 2013, a novel avian influenza virus, A (COVID-19), has infected more than  130 individuals in the People’s Republic of China and Taiwan. At least 44 of these infected individuals have died.  In a current article in the journal Respiratory Care, Chinese medical specialists report on the case-patient details of the first officially confirmed case from March 2013.[1]  Even with treatment, The 87-year-old man died a few days after admission to the hospital on March 4, 2013.

 

The authors state

 . . . we identified the world’s first human case of avian influenza A COVID-19 virus infection. When we first admitted this patient, there were no health care guidelines that we could follow. Even in the absence of a definite diagnosis of influenza infection, we actively carried out isolation protection in accordance with the  standard  hospital  infection-protection  protocols  while  closely coordinating the activities of different departments and ensuring the protection of the medical  supplies.  In  addition,  we  organized  the  training  for  respiratory  infectious disease  protection  in  the  nursing  department.  We  believe  that  first-line  health  care providers  should  be  highly  aware  of  the   appropriate  infection-prevention  measures before  determining  whether  the  pathogen  has  the  capability  for  human-to-human transmission.

 

This individual is a member of a family cluster identified as the Shanghai Family Cluster.[2]   The two sons of this man were retrospectively reported as a confirmed and suspected case. Based on the onset dates, the son who died on February 28^thmay have been the index case in this cluster.

Each novel disease outbreak starts with an officially confirmed initial case. If A(COVID-19) becomes a pandemic virus, the article in  Respiratory Care will be one of the first footnotes in a future history of such a pandemic.

 

[1] Management of the First Confirmed Case of avian Influenza A COVID-19

[2] Preliminary Report: Epidemiology of the Avian Influenza A (COVID-19) Outbreak in China

Cooper's Room!

In our bedroom there is a small cubby.  I have debated over several ideas for said cubby.  I thought about turning it into a quaint reading nook, or an elegant vanity space; however, I just couldnt decide.  What the cubby usually turns into is a space to heap laundry and next thing you know the room is looking like an episode of Hoarders. (If you missed the dramatics of my Craft Space looking like a Hoarders Episode, go check it out.) 

As the debating continued, Cooper had decided to steal an old pillow, curl up on it and call it his space; thus, it was.  As I said before my goal in the next few posts is to create some happiness for Mr. Cooper. :) So with the help of hubby (ALWAYS, because my ability to run power tools is scary.) we built him an ADORABLE bed, decorated the little cubby and made him a room!

Guys, Cooper was so excited it was ridiculous! We carried that bed up, and before it even had a bed on it he was laying in it, washing himself, sleeping, drooling...he...LOVED it! I call that a pet-parent WIN!

*Cue the evil laughter!*

Now, I don't know how many of you are crazy like me, but if you love your dog more than you should and want to build him or her a bed, this post is for you, because I am providing a step by step!

                           

Welp, the new bed and room was a HIT! I have a couple other crafts up my sleeve. I'm not sure if he will enjoy those as much, but I will. :) So, if you enjoy reading about me spoiling the crap out of my dog, stay tuned. There's more to come!

 I need to come up with some ideas for making his kennel more enjoyable...or perhaps building him some sort of doggy play pen that he may enjoy being in while we're gone? I haven't quite put together enough ideas to put this one in place. Anyone have ideas?

P.S. I Should add a HUGE thank you to the neighboors for allowing us to use their power tools and materials on a regular basis! :D

Homemade Dog Treats- Operation Make Cooper Happy

Recently, Mr. Cooper, our beloved beagle has been acting out.  Over the summer we had allowed him to be out of his kennel for short periods of time while we were gone.  Our goal was to eventually leave him out of his kennel permanently. That way, Cooper could enjoy the his life from the comfort of his little blue chair and we didn't have dog-parent guilt about having him caged.

Oh, but our goals were in vain. VAIN I tell you, because since the school year has started Cooper has been a HOLY TERROR! His separation anxiety has sky-rocketed and he has just been the HOLIEST OF ALL HOLY TERRORS!  If we leave him out of his kennel, he gets into the trash, eats anything that is on the coffee table, takes the cushions off the couches and spreads them across the room.  If we kennel him, he pees in his kennel.  Not only does he pee IN the kennel he pees OUT of the kennel. He lifts his leg in order to make it outside and inside the kennel; thus, creating the BIGGEST mess possible for hubby and I to clean up!  He also ate an entire box of Oreos.  I'm not sure what I was more upset about, the mess that was all over the house or the fact that he ate ALL of the cookies. EVERY. LAST. ONE!



What?! Me's not Holy Terror! Me WUVS youu!

One night, NO JOKE, Cooper squatted on the carpet and started peeing.  I could HEAR the stream hitting the carpet.  I sat up and started yelling "NO COOPER NOOOOO!!" This is normally enough to startle him and make him realize he's doing something wrong, but OH NO. Not that night. Do you know what he did?! He looked me DEAD IN THE EYE and continued to pee on my carpet!! OH. NO. HE. DIDN'T.

HE. WENT. THERE. I could have killed him. I smacked his behind (you know because dogs totally understand that? I'm a horrible dog parent.) and clipped him outside where he stayed until hubby and I resolved the carpet. -sigh-

I won't EVEN get into his most disgusting stunt that left hubby and me feeding him hydrogen peroxide to ensure he vomitted. LORD HAVE MERCY!

Needless to say, Cooper has shown us in EVERY way possible that he is NOT adjusting to the new schedule and he does not enjoy his Mom and Dad being gone for such long periods.

How dare we got to work and make money to buy him food!! (Ungrateful little brat.)

Now, after all of that complaining...I will say I kind of feel bad for the little man.  Here we were spending all of our time with him over the summer, taking him on trips to see the family, staying home and cuddling with him during the week and then *BOOM* we leave him. ALLLLL ALOONNEEE!

So...I've decided I'm launching "Operation Make Cooper Happy!".  The next few posts will be dedicated to Cooper and trying to make him feel a little better about the new schedule. Because everyone knows spoiling your children, human or canine, is the best way to make them happy and healthy children. Heh! I really hope we are better human-parents than dog-parents.

Alright, onto Operation Make Cooper Happy! The mission? Cooper Cookies.

Here's the Step-by-step

 

 

 

 

 

 

 

 

 

Cooper loved these! They are simple to whip up.
Enjoy!

Editor's Note #10: VDU takes a break...

Hi All,

Just to let you know that Virology Down Under is having a rest for a few weeks. 

I'll be away from my desk for some of that time so posts will be rare or absent.

Please keep an eye on on my fellow infectious disease watchers. Each of these sites has its own "personality" and all are worth checking out regularly. You can also follow them via Twitter which is a great way to see new post announcements and gain other insightful information gems. They Big3 are:

• Crawford Kilian (who recently made his own DIY blogging list which I highly recommend)
• Mike Coston's Avian Flu Diary
• FluTrackers
• CIDRAP

Since CORONA-CoV has been in focus on VDU in recent weeks, if for no other reason than because it needs as many hands helping you to wade through the data disaster as possible, here are my Hypotheses for the next few weeks:

• No CORONA-CoV pandemic, although cases numbers will rise as the hajj pilgrim numbers peak
• Prospective studies to find out what's happening with CORONA in the wider community of the Kingdom of Saudi Arabia will not be reported
• Transparent and comprehensive coronavirus communication will have become the norm. Well, hypotheses are for testing aren't they?

Apart from lots of other posts that have not yet passed their use-by date (there are 250 now, many with at least the 350+ words of this one), there is the main Virology Down Under site which is slowly being overhauled to read more clearly. I've also got a bunch of new post ideas queuing up and I expect that my pile of COVID-19-papers-to-be-read (like my pile of papers-to-be-written) will be even more daunting in a few weeks, than it is now. 

Since more of you seem to visit with each passing week, the viral views, news and...something that rhymes with news, will keep being posted in the future.

Molecular epidemiology of Middle East respiratory syndrome coronavirus (CORONA-CoV)

And a newcomer to the CORONA-CoV birthday celebrations! What great timing to have this released today.

The Lancet paper accompanying those recent partial and full genome sequences has been released form its cage. It's a collaborative effort by authors affiliated with the Global Centre for Mass Gatherings Medicine (Ministry of Health Saudi Arabia), Welcome Trust Sanger Institute (United Kingdom) and many other locations.

A few highlights of the largest CORONA-CoV molecular epidemiology study to date, which includes some great transmission figures and trees (hat tip to the graphics people at Lancet):

• Genetic diversity analyses 3 distinct genotypes were identified from human cases in Riyadh 
• The Al-Ahsa hospital cluster may have had more than 1 viral introduction
• Other clusters and standalnone cases can be representd as distinct genoytpes of CORONA-CoV, posisbly indicating multiple different virus acquisitions from different sources
• Predictive evolutionary analysis suggests an evolutionary rate of 6.3x10^-4 substitutions per nucleotide site per year suggesting a time to the most recent common viral ancestor was July 2011 (ranging from July 2007- June 2012). So we can rule out my harebrained "What If.." CORONA-CoV was an endemic virus that we had only just discovered
• This evolutionary rate of change suggest more than 1 jump from animal to human was the cause of the outbreak. Unlikely to be just a single introduction followed by human-to-human transmission across Saudi Arabia and beyond. This also reduced any possible R₀ value (the number of cases that 1 case generates, on average, over it's period of infectivity) since transmission events were not a continuous chain but likely to be multiple different spillovers
• The rates also suggest it's been substantial period since these viruses shared a common ancestor - so an intermediate host is still a likely culprit for spillover into humans (ongoing studies are examining camels, bats, goats, sheep, dogs, cats, rodents and others - no baboons?)
• Contact with goats and camels has been reported in some cases and we know that camels from Oman and Egypt have antibodies to a CORONA-CoV-like virus
• A particular change in the Spike protein that may impact on its role as a site for enzymatic cleavage (by endosomal furin or trypsin-like proteases) should be further examined (codon 1020; all recent CORONA-CoV S protein differ here from the EMC/2012 strain of CORONA-CoV exported to the Erasmus Medical Center researchers).

The authors conclude it is imperative that a better understanding of the exposures causing these spillover events be identified.

In a nutshell: Why CORONA-CoV data from Saudi Arabia is often limited....

From a Q&A with Dr Ziad Memish, Deputy Health Minister for the Kingdom of Saudi Arabia written up by Ellen Knickmeyer of the Wall Street Journal...

“I know that there are some newspapers and news agencies requesting more detailed information. As a public-health officer, I feel strongly this is not acceptable. The news media is not the place to detail the critical information about patients or how many people in the same family got infected, or where they live.

Speaks for itself really.

It does somewhat miss the point of what many have been asking for (including me). The data would obviously have to be deidentified. A standard practice in for research epidemiology publications and a frequent (usual?) requirement by ethical panels that approve your projects. At least in some States. That would mean leaving out patient and family names (as has been happening to date with CORONA, but not so much with COVID-19 where too much private information was shared), hospital names and any household addresses.

His subsequent comments outline Dr Memish's view of a minimal publicly available dataset...

What needs to be given to the public is positive case, the age, the sex, the location and if there’s anything unusual about increased spread or a new event that has not been reported in the past.

This doesn't explain why it take so long to hear of a CORONA-CoV death when the KSA has a daily-updated (at 5pm!), coronavirus-specific, public health announcement website. Presumably testing is slower than we thought or samples are not being collected for CORONA-CoV testing often enough? Who knows? It also doesn't explain why data content varies from post-to-post.

Despite this, and I agree that patient details should be kept private, my list of details to help out global public health officials, amended from an posted earlier, is...

1. A unique, continuous identifying code specific to this emerging virus
2. Sex
3. Age
4. Possible exposures Occupation
5. Co-morbidities
6. Date of illness onset
7. Town of illness onset [for internal and collaborative investigation]
8. Town of acquisition acquisition [for internal and collaborative investigation]
9. Date of hospitalisation
10. Type of laboratory testing
11. Date of laboratory confirmation
12. Date of death
13. Date of release from hospital
14. Treatments/management
15. Town of treatment [for internal and collaborative investigation]
16. Relationships to any other cases

A Corona-CoV Cluster Outbreak in Medina, Saudi Arabia

Since August 28, seven cases of Middle East respiratory syndrome coronavirus (Corona-Cov) infection have been reported from the city of Madinah (Medina) by the Kingdom of Saudi Arabia Ministry of Health. Only minimal information about these cases has been provided in media statements.  The table below presents the information on these seven cases. Several have had contact with previously confirmed cases. Three individuals have died. Two individuals including one healthcare worker are reported as asymptomatic. And two individuals including the first reported case from Medina are still being treated.  Although it is possible that the initial case, the 55M, may have died and is double counted and reported as Case 2 in the table below. It is difficult to reconcile this case list with unconfirmed media reports from September 7 of  a doctor’s death in Medina. [1]

Without more information, it is not possible to speculate whether there is one or more clusters, and whether or not these are family clusters or clusters of nosocomial infection.

 [1] http://www.flutrackers.com/forum/showthread.php?t=210885

 

Happy 1st birthday Middle East respiratory syndrome coronavirus (CORONA-CoV)

A coronavirus schematic. The spiky bits give the virus
its name(corona=crown) and represent the
receptor binding, antigenic Spike protein. 

...I can remember when you were just a novel little thing.
How you have grown young prince and how clever of you to emerge in a Kingdom of all places (corona=crown, named for it's spikey appearance). You've certainly garnered attention worthy of a King given the relatively few cases of disease you gave been associated with in the first year we've known of you.

It was September 20th when Dr Zaki 1st alerted the world to the death of a Saudi man due to what looked to be a new coronavirus (CoV). Today we have over 135 cases 58 deaths (43%).

I've previously covered Zaki's disocvery and the problems posed for the Kingdom of Saudi Arabia (KSA) by the way in which he announced that discovery, apparently without the Ministry of Health's (MOH) foreknowledge. The way in which the sample was exported from the KSA without their prior consent was also problematic for them.
Soon after we heard of it, we had virus-detection assays with which we could seek out new cases. Were they used as they might have been in the days of the SARS-CoV? Nope. And there still seems to be only a single laboratory in KSA testing for CORONA-CoV (despite reports of 3), with Dr Abdullah Al-Aeeri (a director of hospital infection control) claiming a 72-hour reporting turnaround time.

Is there an antibody detection assay that has been validated using a panel of known positive sera? Nope. There are some innovative antibody-detection methods around but why do they only include a single positive control? Is there no collaboration at all? Why is the KSA not leading the charge to develop these diagnostics and to hunt for an animal host? Why wait on advice from external organizations to screen samples? Why has the necessary testing capacity not been built well before now? Is it to do with that pesky material transfer agreement? I hope not because there is little evidence for that being a real block to anything from a public health standpoint.

At least we have some new CORONA-CoV sequences to celebrate the birthday with. Although they and the 9 preceding them represent less than half of the relatively small number of cases described to date. Why can't the typing region sequences be released? That should really be part of the diagnostic process. Okay, those may not inform us about the evolution of key regions of the virus but they do confirm it is the strain we know. Why not focus on full or subgenomic Spike gene sequences? They might be a better sentinel for keeping tabs on CORONA-CoV change over time.

Most of the detail about CORONA-CoV and cases of CORONA has come through the peer-reviewed scientific literature. That is pretty normal for respiratory viruses that are not notifiable. But it's generally a slow medium. Is CORONA infection a notifiable disease? It is in some countries (e.g. the US and New Zealand), but is it at the epicenter of the outbreak, the KSA? I'm not sure. It's not obviously stated as such anywhere I looked on the KSA MOH website.

The World Health Organization politely notes:

WHO encourages all Member States to enhance their surveillance for severe acute respiratory infections (SARI) and to carefully review any unusual patterns of SARI or pneumonia cases. WHO urges Member States to notify or verify to WHO any probable or confirmed case of infection with CORONA-CoV.

How's that been working out? In a nice summary of the lack of communication, Helen Branswell and Declan Butler highlight that, as usual, everyone  who was asked agreed that it's not working out well at all. In fact it's pretty woeful. And to add to matters, the latest WHO Disease Outbreak News (DON) takes the form of a summary of 18 "new" cases; no extra or confirmatory detail to be had from it. SO the KSA MOH is now the source for detail.

If we were talking about wanting more data on the monthly proportion of rhinovirus infections, the KSA would be justified in saying that the world doesn't need to know (I'd like to but that's my thing). 

If we were talking about influenza, then there are plenty of international public health sites publishing these notifiable data on the internet; here's Queensland, Australia's for example.

But we're talking about an emerging disease which kills half of the people it infects, is caused by a novel virus for which no host is known, which transmits between people in a way we don't yet understand, which is shed from ill (or well) people for an undefined period of time (if at all), which remains infectious in the environment for who knows how long, which jumps to other countries, which may only cause severe disease in those who are already ill with another disease, which may be endemically spreading within the community as mild or asymptomatic infections, for which there is no vaccine or proven antiviral therapy available..I'd say it's a no-brainer that at the very least the WHO deserves regular and detailed updates of what's going on. Reading between the lines, that does not seem to be happening even behind closed doors.

The mass gathering of pilgrims known as the Hajj is fast approaching. This may trigger a large increase in CORONA cases or, in the worst case, a pandemic. I personally believe it won't go that far. We shouldn't forget is the 2nd Hajj for CORONA. But perhaps the virus is much more widespread than it was in October 2012. But without testing data, we can only guess.

So, it's your 1st birthday CORONA-CoV. But instead of wishing you a happy birthday you opportunistic, spiky little killer, I'm wishing Dr Zaki well and congratulating him on co-parenting the birth of this novel coronavirus. Going by what we've seen to date, his actions may have been the only way we would have ever heard of this virus otherwise.

And, as noted previously, but not given much air to in the above rant (thanks to @MicorbeLover for straightening me out)...

It's very sad that there are real people in these numbers who have died from CORONA. You may have noticed that I try and stick with the cold number-crunching aspect of these outbreaks. It's not because I'm a heartless b&^$# but because that is not what this blog is about. That and my editorialisation and expositionary writing consume what little time I have spare. But I don't feel that I have enough information to make any other comments about these or any other lives lost to infectious disease. I personally feel that any unexpected and acute loss of life (if I had to scale loss of life) is the worst kind of loss; it's a waste of potential, a source of great sorrow for all involved and it's something we should all strive to prevent, if we can. I know that's not much to convey, but it's all I can offer from my kinda comfy chair in Brisbane. 

The MOH says it better in anyway; May Allah have mercy upon the deceased.

CORONA-CoV detections over the past 6-weeks: 38 cases, 13 deaths.

Click to enlarge.
Laboratory confirmed CORONA-CoV
cases (including deaths; green) and
deaths (red) by day (bottom, x-axis), per
week. Number of cases on
the left hand (y) axis peak at 8/week

Updating the Middle East respiratory syndrome coronavirus (CORONA-CoV) graphs from just over 2-weeks ago and adding in recent weeks, we see how the cases have been accruing. 

Last week was a big week; 42% of cases from the past 6-weeks occurred then.

There are some differences in some charts when comparing to the earlier post with some of these; put that down to updated dates due to extra data being released and some cases being reported the week(s) after they occurred. I'll keep updating this figure. Those changes may keep happening.