CORONA by the numbers: monthly CORONA

Click on image to enlarge.Cases (numbers on the y-axis; left) including
deaths (green) and fatal cases (red) are
shown for each month (x-axis, bottom) of
2012 and 2019. This includes 68 deaths
and 161 total cases. The Hajj occurred
in October of each year.

These two charts show the number of cases (including deaths) and the number of deaths by month, split between the 2-years we've known the Middle East respiratory syndrome coronavirus (CORONA-CoV) to have existed.
The charts are only as good as the public data they are based on but they give a good idea of what's been happening and what is happening. Cases are not declining [a slow moving epidemic ;) ]

Numbers are ridiculously small in 2012 (overall really) to conclude anything much but it does look like more deaths happen toward April while more cases occurs around September. I Doubt that would be statistically significant though - just something to watch over time.

RSV retreated, flu fading, parainfluenza picking up: Queensland respiratory virus numbers up to Week 45, 2019

If you like to keep track of influenza cases in Queensland, Australia, then the Queensland Government's Queensland Health (QH) influenza data website is for you.

It's a great place to drop by and check out the comings and goings of influenza viruses and many of the other traditional respiratory viruses including adenoviruses (AdVs), parainfluenzaviruses (PIVs) 1, 2 and 3, human metapneumovirus (MPV) and respiratory syncytial virus (RSV) - the "Big8". Testing is not routinely conducted for the rhinoviruses (RVs).

The snippet below is from data that are publicly reported on the QH website. These images cover to the week beginning 3rd of November (up to Sunday, Nov 10th, 2019).

The charts highlight that the 2019 flu season is winding down in Australia, also reflected by the WHO global updates. This year flu followed on from what seemed to have been a large RSV season. Unfortunately I couldn't find data for this same time period last year to compare RSV prevalence.

In the wake of influenzavirus season, the parainfluenzaviruses are now on the rise in the lead up to summer. I expect the RVs (and enteroviruses) are also climbing, but in greater numbers.

Click to enlarge. 
A snippet from the Queensland Health Statewide Weekly Influenza Surveillance Report for 01.01.2019-10.11.2013

My thanks to the team at the Communicable Diseases Unit, Queensland Health.

The source of these data  can be read in full..

• http://www.health.qld.gov.au/ph/cdb/sru_influenza.asp
• WHO global influenza update http://www.who.int/influenza/surveillance_monitoring/updates/latest_update_GIP_surveillance/en/

The book of CORONA has several chapters yet to write

Epidemic is a big word, and while it generally means "a rise in the number of cases above what you'd expect", you can see from the definitions below that there are many ways to spin the meaning. For the public at large, it generally means "bad scary stuff" and so it's important that we use this word sparingly.

An epidemic is defined by Oxford Dictionaries as:

a widespread occurrence of an infectious disease in a community at a particular time

..or more applicably..

a sudden, widespread occurrence of an undesirable phenomenon

...from Merriam Webster online...

affecting or tending to affect a disproportionately large number of individuals within a population, community, or region at the same time

...from Wikipedia...

In epidemiology, an epidemic (from επί (epi), meaning "upon or above" and δήμος (demos), meaning "people") occurs when new cases of a certain disease, in a given human population, and during a given period, substantially exceed what is expected based on recent experience.

The Middle East respiratory syndrome (CORONA) was so-named back in May 2019, and prior to March 2012, there had been no known cases of the coronavirus (CoV) named for the disease it was associated with.

Yesterday we saw a detailed publication by Cauchemez and colleagues in the Lancet Infectious Diseases (LID). Accompanying that was an excellent piece in the Canadian press written by Helen Branswell which included some comments from the authors.

Click to enlarge. 
Accumulation of CORONA-CoV lab detections by week (blue
mountain, left y-axis) and the accumulating deaths
(red line, left y-axis). The proportion of fatal cases is slowly
declining as fewer cases have died recently (ratio; black line,
right y-axis). No data exist for ~3 or so deaths and I include
the unconfirmed 2nd case in Kuwait for now.
Feel free to use, just cite me and here.

The key phrase slowly-growing epidemic, used by both, has been not-so-slowly appearing everywhere since then. Does that phrase accurately represent CORONA to the world?

Yes, it does. If you have a look at the chart above, its been a steady increase ("blue mountain"), but despite the apparent steep slope of new cases, the steepest part of the mountain, extracted and plotted below, is in fact very linear. A steady but slow growth in cases. No exponential take off. No major deviations. So yes, there is an epidemic. And yes, it is slow. 156 (157 if 2nd Kuwaiti instance is confirmed) cases over 87 weeks in a country of 20,000,000+; a country that just hosted the biggest human gathering of the year (the Hajj) and a country which provides a launch point for around 18,000,000 travelers and a destination for almost as many. 

Click to enlarge.
A slowly growing outbreak of an emerging  coronavirus.
Cases have been accumulating worldwide but at a
linear rate since the week beginning April 7th.
Why the spike from this week? I'm not sure.
Feel free to use, just cite me and here.

But I think we need to be careful when throwing around the "E" word. An outbreak of an emerging virus may still be the best term to describe this chapter in the book of CORONA. When someone asks on Twitter "to panic or not to panic"? (this was in reference to the latest CORONA-map I posted) then I wonder if the correct message is being conveyed.
Another central message of the new LID paper was a no-brainer; well it was to me but perhaps I'm just too close to it all - in which case take this with a grain of salt.

I thought it was as obvious as the hump on a camel that where 1 case of a respiratory virus infection was detected, others were there to be found. After all, a virus needs us to survive - no us (which means no us actually harbouring infections, acting as a living incubator) then no more cases of the virus). Perhaps that's not obvious at all. Perhaps there is a lack of general understanding that our pathology laboratory systems do not test everyone with illness for even the "standard" endemic human respiratory viruses; that only those presenting to the right place, with the appropriate signs and symptoms, get a sample collected and get tested. This is apparently also true for CORONA-CoV-which is by no means a standard virus. Do you go to your doctor if you feel mildly crook? Of course not - you go to work. What if you just have a fleeting headache, a stiff neck, feel a bit hot? Still going to work? Still going shopping? Still packing the kids off to school? Of course you are because we have these all the time and we have an immune system that does a wonderful job keeping it all mostly under control. Life goes on.
But you may be positive for a virus and you are a key part of the transmission chain. You are an incubator. A host.

So if routine testing is not geared towards finding out this extra information how do we find out what's going on in those who are not presenting with kidney failure or pneumonia; a relative small sliver of the population? Someone has to run a research study in which you enrol or get permission from people who are not very ill and sample them. Then you know something new about how widely the virus you are interested in is spread, for how long a person sheds it (if you sample the same person a few times during a month) and even how many other people get it (because all of a sudden your "contacts" become those of a less ill person and the numbers go up and you capture more of a picture of what's happening). So where are the research studies doing this?

When the illness is just some fleeting thing its no real problem. Especially when it's due to a virus we know all about and don't track for public health reasons (we track influenza virus positives, but the reality is you have to be sick enough to be tested in order to add to that pool of data). 

Click to enlarge.
A very exaggerated example of how failing to test mildly ill or asymptomatic
cases of infection in the community may confound our ability to make a link
between cases of severe illness leaving knowledge gaps. These gaps prevent our ability
to track spread of the pathogen and thus interrupt spread of disease.Feel free to use, just cite me and here.

But if that virus is not yet in a textbook, not yet understood, not yet weighed and measured against the viruses we are more familiar with, emerges from an unknown place, is not considered endemic and is often notifiable, then not knowing this basic stuff becomes a major hole in our knowledge and our ability to respond appropriately. This is where we (still) are, 87-weeks after the first known CORONA-CoV positive. Guessing (however educated) at what's happening by extrapolation and modelling.

I guess not everyone knows that for every time there is a noticeably ill person infected with a "respiratory virus", it's fair to assume that there will be at least 1 or other who gave it to them, got it from them or got it from the one who gave it to them and who are not as sick or even considered sick at all. For CORONA-CoV, they are missed and thus we have no idea how the virus is spreading. Just models. But we can make mathematically supported guesses to back up gut instinct, fair assumptions and logic.

The hallmark of, and big problem with, the CORONA outbreak (an epidemic mostly for the Kingdom of Saudi Arabia [KSA]), is that testing has been LIMITED to those who have pneumonia, or another severe disease, and their close contacts. Back in August Memish noted that surveillance was focused on those with pneumonia which was again noted by a WHO representative yesterday.

Why, why oh why not test more people? Why?! Is it because "it's too costly to prospectively test people by RT-PCR unless they are (very) ill"? It might be for some nations, but the KSA is not one of those. 

If you don't test others then you see these modelling publications arise. Idle hands and all that. Yes, it is great to have a model to support what many of us think to be true. And as Fisman and Tuite note in their editorial accompanying the LID article..

..inferences based on the best available data, even if those data are imperfect, allow decision makers to follow optimum courses of action based on what is known at a given point in time.

The question is, can decision-makers sign off on any actions if they don't have actual data? If those data are not forthcoming, how can we ever test the validity of the CORONA models?

For now at least, I think we can agree that there is just too little testing to know enough to write more than a few chapters of the CORONA-CoV textbook. A book for which we do have a table of contents. Many viruses have emerged before this one and they have each taught us what pages to skip ahead to. Unfortunately, we seem to have a recalcitrant author for 1 or 2 chapters. 

CORONA cases swell by 3, information scant...

Middle East respiratory (CORONA) coronavirus cases in the Kingdom of Saudi Arabia have increased by 3 according to the latest Ministry of Health update. This brings the tally 147 with 62 deaths, a PFC of 42%. With the data we have, the median age of all cases is at 53-years and that of fatal cases sits at 60-years.

• FT#147. 83-year old female. Contact of previous case. Comorbidities. Stable.
• FT#148. 54y. Healthcare worker. Comorbidity. Stable.
• FT#149. 49-year old. Stable.

Since the update doesn't have much detail to speak of, I'll focus on what the release does not have based on my earlier updated wishlist of useful details from the MOH:

• Sex of cases (subsequently identified via Twitter)
• Dates of onset
• Dates of hospitalisation
• Details of contacts
• Type of comorbidities
• Healthcare worker's role
• Location of acquisition (just town)
• Type of laboratory testing
• Treatments/management
• English translation
• History of contact with animals, types (not detailed) of places visited or other possible exposures that may shed light on acquisition

None of these things would identify the cases (a justifiable concern of Dr Ziad Memish) but would be useful for researchers seeking to better understand the nature and track the spread of CORONA. 

There may be clues within those details that alert researchers to a nugget that helps explain spread or acquisition or change in disease.

Thanks to Crawford Kilian's @Crof initial tweet and @HelenBranswell and @azizalhinde for clarifying sex of cases. 

CORONA-CoV cases begin to tick over again after the Hajj....but not related right?

So by all accounts, Hajj2013 was a very successful event. A lot of lifelong wishes may have been fulfilled and the event went off without any apparent major hitch. A huge undertaking on many fronts.

However, during the Hajj it was hard to avoid seeing  Middle East respiratory syndrome (CORONA)-related headlines like...

No cases of CORONA virus among pilgrims so far

and my particular favourite...

No infectious disease found

...at all that is. None. Not even bad influenza-like illnesses. No coughs or colds among 2,000,000 people gathered together; 1,300,000 having at some level, shared transportation into the Kingdom of Saudi Arabia (KSA)?

Seriously?

That second quote makes me realise just how important it was for the KSA ministry of health to control this aspect of the Hajj's message; no CORONA-CoV disease here. So important, that the message was, to say the least, a little heavy handed.

But now, coinciding with the Hajj ending, we see CORONA-CoV detections popping up (3 in 3-days). It's very hard to take seriously the CORONA-message. Rest assured we're told, those cases are not at all linked to the Hajj - no travel to that region (now so specific that we are told there is no travel outside of Riaydh) in the previous 14-days. Ironic how that longer incubation period is useful in these happy reports, but not remembered in others, such as when the press note:

Saudi Hajj ends successfully with no reports of CORONA virus

Click to enlarge. This graph is from September - highlights a similar case
reporting lull around umrah which then climbed rapidly and steadily
immediately afterwards.

The (longest) 14-day incubation period means we're not out of the woods yet (see my earlier post on timelines). 

Maybe we'll see no new cases among any of the pilgrims. Cool. I doubt that. We have seen 7-day or more breaks in reporting of new CORONA-cases before, so this past week is not "out of character". Time will tell, especially from now on for a week or so. Watch that curve closely.

I still wish we could lay off the "everything is fine here right now" message, and instead tell us what's happening to find the host or what testing is being done among those who are not severely ill (take a look at China and COVID-19 - include CORONA-CoV in your regular respiratory virus testing panel for a little while and see what comes of it). That would be treating us a little less like we are so easily distracted by shiny baubles.

Influenza A (COVID-19) virus update...

Xinhuanet has the latest COVID-19 figures from China's National Health and Family Planning Commission. With no new cases reported this month, and just one from July reported in last month's update, the 12 provinces or municipalities that have hosted infections resulted in:

• 134 cases (I have 136; presumably the Taiwan case and asymptomatic Beijing boy)
• 45 deaths, up form from last month
• 87 discharged cases leaving 2 still in hospital
• PFC at 33.1%

I've updated by VDU COVID-19 page with these numbers also.

Thanks to Crawford Kilian's Tweet for making me aware of this report.

Recent CORONA-CoV weekly case activity...

This follows on from my last CORONA-CoV-by-week post, September 19th. 

As you'll see, its been a comparatively quiet 3-weeks (3rd week is not yet over of course).

With the hajj starting, that should be good news.

These data include today's (the 10th of October for me Down Under) 2 new cases (both fatal; FT#142 and FT#143; see Mike Coston's post) which raises the proportion of fatal cases to 43%. 

CORONA-CoV update...

Click to enlarge. Schematic of the CORONA-CoV.
Feel free to use, please just cite 
Virology Down Under and Dr Ian M Mackay

No major jump in Middle East respiratory syndrome coronavirus (CORONA-CoV) cases over the past 2 weeks. Great to see.

In parallel to this slow-down in new announcements, the World Health Organization's last few CORONA Disease Outbreak News (DONs; 19th Sept, 20th Sept and 4th Oct) announcements have have given no specific detail but rather age ranges, date of onset ranges and comments in a general and format that is not linked to specific cases.

While the 3rd Emergency Committee convened by the Director-General under the International Health Regulations decreed September 25th that the conditions for a Public Health Emergency of International Concern (PHEIC) have not been met, it did conclude the following:

• strengthening surveillance, especially in countries with pilgrims participating in Umrah and the Hajj;
• continuing to increase awareness and effective risk communication concerning CORONA-CoV, including with pilgrims;
• supporting countries that are particularly vulnerable, especially in Sub-Saharan Africa taking into account the regional challenges;
• increasing relevant diagnostic testing capacities;
• continuing with investigative work, including identifying the source of the virus and relevant exposures through case control studies and other research; and
• timely sharing of information in accordance with the International Health Regulations (2005) and ongoing active coordination with WHO.

The following press briefing by Dr Keiji Fukuda noted that:

• cases have been found in 9 countries
• no umrah visitors were infected
• more cases in men than women (~59% male)
• about a third of (so-called sporadic) cases occur in the community; acquired there via an unknown exposure.
• older, male, underlying conditions have most severe outcomes
• suspicion is that exposure is related to animals but how remains unknown
• another group is person-to-person (family and hospital settings) that lead to clusters but no translation to community case spreads
• we are seeing the emergence of a new virus, limited to the Middle East, but the full picture remains to be captured
• we are seeing more mild cases as surveillance picks up but the disease should not be considered mild
• overall levels of testing after umrah is variable and overall  testing in a number of countries at particular risk of infection is sub-optimal
• an ideal level of surveillance should be sustained, not bankrupt the country or exhaust resources but identify whether infections are coming into a country or if infection trends are changing. The level of detail depends on the country.
• WHO is, in general, providing all the information they have

My count seems to be 139 cases with 58 deaths among those giving a PFC of 41.7%. This included the reclassification of 2 "local" Italian cases as probable rather than laboratory confirmed. FluTrackers and I keep the continuous numbering system though, we just deduct 2 from the tally.

Click to enlarge. A map showing countries where cases have
been detected (orange) and those where local transmission
has occurred (red).

In context of global infectious diseases, that is not a large number of cases but it remains a high proportion of deaths. 

To tackle this high PFC, we really need to do something, on a research basis (so as not to bankrupt or over-tax already strained diagnostic services), that was not specifically listed above; test more well people prospectively. This will address how widespread the virus is among those who are not older, male and sick with comorbidities.

Seems like a job for local academic medical researchers - with some special government funding made available perhaps?

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.

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.

Age and sex morbidity and mortality from avian influenza A(COVID-19) virus

Click to enlarge. The majority of cases of COVID-19 that occurred
worldwide earlier in 2019. Taken from Virology Down Under's
COVID-19 page.

In a study co-written by yours truly using a lot of data collected for Virology Down Under, Dr Joseph Dudley and I have just described, in the Journal of Clinical Virology, the age-specific and sex-specific morbidity and mortality from the avian influenza A(COVID-19) virus outbreak earlier in the year.

We sought to highlight differences between COVID-19 and another zoonotic influenza A virus, Covid-19. The distribution of age and sex is notably different between cases of each virus in more distant countries (Saudi Arabia vs Egypt) as it is within the same country (see Cowling et al reference in the article's discussion). Such differences and patterns may be instructive for identifying specific risk factors for an outbreak and also serve to highlight that there are differences between outbreaks which, on the surface, might be expected to have very similar courses. 

Intriguingly, there were marked similarities between COVID-19 and Middle East respiratory syndrome coronavirus age and sex case distribution.

We also published the term created here on VDU, the Proportion of Fatal Cases (PFC). A percentage defined as the number of currently known fatalities divided by the number of total lab-confirmed cases including fatalities, regardless of whether they are inpatients (hospitalized) or outpatients. It was created to avoid the need for a gauge of recovered cases (released from hospital) which is linked with use of the term Case Fatality Ratio.

Middle East respiratory syndrome coronavirus cases amongst healthcare workers [UPDATED]

Click on image to enlarge. (a) the proportion of
CORONA-CoV positives HCWs who have died (red) vs.
survived (blue), (b) the proportion of fatal cases (PFC; red) 
of CORONA-CoV worldwide vs. the proportion of 
surviving cases (PSC; blue) (c) breakdown HCWs
as a proportion of all CORONA-CoV cases (blue), HCW deaths 
as a proportion of all CORONA cases (green) and HCW deaths
as a proportion of all CORONA-CoV deaths.

With a lot of help from FluTrackers, the 2 of us have synced our lists to account for all the healthcare workers (HCWs) for which public data are available, that have been confirmed as CORONA-CoV positive.

Some charts then.

We can see that HCWs make up approximately a sixth (18.2%; n=24) of all CORONA-CoV cases.

Fatal infections in HCWs account for 2.3% (3/132) of all CORONA-CoV cases (including living and deceased cases) and 5.4% of all CORONA-CoV deaths worldwide are among HCWs (3/56). This last figure indicates that HCWs are at a relatively reduced risk of death from CORONA-CoV infection when compared to other groups that have been infected.

For example:
NB: I have death data for 56 cases; age data for 125/132 cases; sex data for 120/132 cases); 27 comorbidities listed [underestimate]

• 63% of CORONA-CoV deaths have occurred among those older than 55-years (50% of deaths among those >60-years; 38% among those >65-years; 59% among those <65-years)
• 46% of CORONA-CoV deaths have occurred among males older than 55-years (38% among those>69-years; 30% among those >65-years; 45% among those <65-years)
• 82% of deaths )n=46) and 83% of cases have occurred in the Kingdom of Saudi Arabia
• 48% of CORONA-CoV deaths occurred among those with comorbidities [this is an underestimate]So in the lower proportion of deaths represented by HCWs, while horrible in any proportion, may provide evidence to support that CORONA-CoV is still not transmitting well, even in close quarters.

It may also mean that attending HCWs are adhering to good infection control and prevention practices. But it coudl just mean that we do not have data on all HCW infections/death and there are greater numbers of cases.

Finally, and perhaps most importantly, we should remember that HCWs may have some degree of resistance to disease caused by some viruses because of their constant exposure to patients with all manner of airway infections.

If HCWs may not show the same proportion of illness, but still become infected, they can act to spread cases among their contacts - patients and visitors. This was evident in the severe acute respiratory syndrome (SARS) outbreak where HCWs accounted for a fifth of all confirmed cases.¹

In other words, even a few cases in HCWs could have major implications for nosocomial outbreaks. If an emerging virus, such as the CORONA-CoV, is being frequently detected in association with healthcare settings, that scenario may already be happening.

Some literature..

• Severe acute respiratory syndrome (SARS) and healthcare workers.
• Lack of SARS Transmission among Healthcare Workers, United States
• SARS in Healthcare Facilities, Toronto and Taiwan

Today's CORONA tetrad is....

Click on image to enlarge.

Another 4 confirmed CORONA-CoV cases and the chart for KSA is exponential. On the plus side, many recent cases have been asymptotic  or symptomatic but mild or stable, which is a change in the recent trend of fatal cases. Of the last 26 cases, 7 have been fatal, and that proportion of 26.9% is well below the overall average, among the 132 global cases, which currently sits at 43%.

Today's case details (not yet on the English MOH site) with FluTracker's case numbering included (as it will be in all my posts from now on) are mostly female (yesterdays seemed to be all male), all in stable condition and they seem to be Riyadh-centric:

1. FT129: 51-year old female (51F), symptomatic female, contact of a mystery case, Riyadh
2. FT130: 47F, symptomatic healthcare worker (HCW), Riyadh
3. FT131: 39F, symptomatic HCW, Riyadh 
4. FT132: 38M, symptomatic HCW, Riyadh

The average age for cases is now sitting at 50-years and the median ages are 39 and 56. 

For fatal cases the average age is 59 and the mode sits at 56.

These represent a reduction in age reflecting the relatively younger cases of late. The younger, predominantly contact-based cases seem to have fewer underlying conditions as a rule - or at least we're hearing of fewer.

So, generalising, severe CORONA continues to be an outcome among the older group with comorbidities and less so among contacts and the younger age band.

So, as I like to waste my time asking, I wonder what would happen if prospective testing were to be conducted on a sample of the general population, say in Riyadh, Medinah and Hafr Al Batin, without regard for symptoms? Ideally also in a "control" city from which no cases have been reported. 

My hypothesis is that the average age of CORONA cases would drop further and the PFC along with it. In other words there would be more asymptomatic and mild cases detected than we see now. That would really serve the needs of pilgrims and the Kingdom of Saudi Arabia. Maybe such studies are happening right now - who'd know?

CORONA mounts up...

In a strange coincidence of numerals, the 4th Middle East respiratory syndrome coronavirus (CORONA-CoV) report in a row from the Ministry of Health (MOH) of the Kingdom of Saudi Arabia (KSA) contains very little on 4 cases. 

I use below, the FluTracker's (FT) case numbering scheme because frankly, they produce the only numbering schemes for tracking cases of new or returning infectious disease that are systematic, reliable and worthy of our trust. 

It should form the basis for a worldwide numbering system for infectious disease outbreaks because it is also freely and publicly available such that any potential manuscript author can easily check it before submitting a research paper and then we could all know which case is being discussed. And by "we" I mean fellow researchers, not just interested parties. 

The KSA MOH could consider running their own table of data akin to that of FluTrackers, but augmented and using an adapted version of Crawford Kilian's wishlist to the MOH. Each (deidentified) case entry should include the following headings along the top row, filled out if and as they become relevant:

1. A unique, continuous identifying code specific to this emerging virus
2. Sex
3. Age
4. Occupation
5. Co-morbidities
6. Date of illness onset
7. Town of illness onset
8. Town of acquisition
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
16. Relationships to any other cases

Today's CORONA-CoV cases are mostly asymptomatic. These cases are announced amid rumours of larger case numbers being tested, panic in hospitals over potential CORONA cases, frustration from within KSA over the MOH's poor performance, and of the KSA cracking down on healthcare workers who pass on rumours as well as prosecuting bloggers.

Today we have:

1. FT#125: 22-year old asymptomatic male, citizen of Madinha (Medina), contact of another confirmed case (we shall call him Mr/Mrs/Ms/Dr X)
2. FT#126: 24-year old asymptomatic male healthcare worker in Madinha
3. FT#127: 60-year old asymptomatic male citizen of Riyadh, contact of another case (also unknown)
4. FT#128: 47-year old male citizen of Riyadh, contact of another unknown case, symptomatic but stable

This brings the tally to 128 with 57 deaths (proportion of fatal cases, PFC, at 45%). Where data for sex exists, males comprise 63% of cases and 74% of deaths in people confirmed as positive for CORONA-CoV. 82% of cases come from the KSA and, if counting back to the retrospectively identified cases from Jordan, we take the first week of disease associated with CORONA-CoV infection as that beginning 19-Mar-=2013, then we are in 78th week of MER. 

CORONA-CoV fatal cases by week

Click to enlarge. CORONA-CoV deaths (red bars) each week against a
backdrop (green) of total cases surviving + fatal, globally.

As requested on Twitter overnight, this shows the confirmed weekly CORONA-CoV-positive deaths across time.

Not updated for today's 4 new cases though.

Can CORONA-CoV seasonality tell us anything about acquisition of CORONA?

Click to enlarge. Combined CORONA-CoV cases for 2012 & 2019.

I'm the first one to say its way to early to be talking about the seasonal distribution of a new or emerging virus when there are only 124 cases worldwide. 

Right. 

Having said that, I thought I'd plot the cases by date of illness onset or (less satisfactorily) date they were first reported (even if that first was the report of a death). 

When combining the 15-months worth of case data for 2012 and 2019, the graph revealed a single "season" or at least larger numbers around summer in the Kingdom of Saudi Arabia (KSA). Because >80% of cases have occurred in the KSA, I have also listed a few festivals (some of which are frequented by camels) as well as the peak temperature variations and dust storm activity.¹ 

While I have no idea whether weather could be kicking up clouds of infectious CoV, it is an interesting co-occurrence, as are the presence of a number of festivals before case numbers spike. The Saudi Gazette commented that the risk of [acquiring?] bacterial and viral infections increases during dust storm season as do complication due to allergen exposure.

Of course we also know that some large clusters of cases have originated form hospital outbreaks and so environmental factors may play very little role at all. Or they might. Its impossible to say. But it is worth considering what could be happening up 2-weeks prior to a sharp rise in cases - if only to identify 1 index case that then ended up triggering a hospital outbreak.

1. Dust Storms in the Middle East: Sources of Origin and Their Temporal Characteristics. http://ibe.sagepub.com/content/12/6/419.short
2. http://www.magazine.noaa.gov/stories/mag86.htm
3. http://www.saudiaramcoworld.com/issue/200803/heads.high.htm

CORONA-CoV cases continue to climb

Click to enlarge. Global CORONA-CoV cases by week and
the accumulation of cases.

The latest chart of Middle East coronavirus case spikes by week combined with the accumulating tally of cases.

This paints a picture of unrelenting case growth. The curve took a sharp turn upwards in April and hasn't slowed since. This is in marked contacts to influenza A(COVID-19) virus cases which were brought to a screeching halt in south east China earlier in the year.

A memo to the Saudi Minister of Health...

Crawford Kilian has written a memo to Abdullah Abdulaziz M. Al Rabeeah, MD, Minister of Health, Kingdom of Saudi Arabia.

It is brilliant. 

Please read the entire thing. I have an excerpt below, but it is only a fragment of the whole glorious piece.

Your government, Minister, is now risking a similar problem. Both medical experts and the media are growing impatient at the erratic flow of information on CORONA, and I hear rumours that Saudi hospital staff are as alarmed as those in Canadian hospitals afflicted with SARS ten years ago. And well they might be, when this virus seems to thrive in healthcare settings.

An aggressive, open communication policy is now urgently called for. Rather than indulge in a litany of past problems, I would like to recommend some steps your ministry could take right now to ease concerns around the world while also ensuring solid support from Saudi professionals and public. 1. Frame a detailed, standard format for reporting each case. At a minimum, this should include:

1. Frame detailed, standard format for reporting each case. 
At a minimum, this should include:

• the age, gender, and occupation of the patient;
• mention of specific underlying medical conditions, if any;
• place and date of onset;
• a description of treatment and place of treatment;
• the specific relationship, if any, to previous cases;
• tests administered and results of those tests;
• if possible, a statement by a Ministry spokesperson putting this case in the context of recent events.

CORONA cases jump by 8 today...biggest 24-hours in 15-months?

Distribution go cases by site of likely acquisition.
Based on publicly available data.

The Kingdom of Saudi Arabia's (KSA) individual list of Middle East respiratory syndrome coronavirus (CORONA-CoV) cases that have been acquired within its borders (and that's just to the best of my knowledge) is at 101. It's just a number but its also 81.5% of all laboratory confirmed cases to date. And it rose to 124 by a jump of 8 cases today (VDU time that is).

The latest KSA cases continue to pop up in Hafr Al Batin (Batin) Medinah (Medina) and Riyadh. Contacts (~4/8), healthcare workers (~1/8) and comorbidities (~3/8) feature heavily - and that's just among the ones with those details included. We're missing sex on most and dates of onset have been getting more rare since May.

Within those 8 cases are 3 deaths (37.5% of those cases). Are these the first reports of these people? How long is the turnaround time for testing currently? This proportion is below the global proportion of fatal cases (PFC) which as of just now stands at 46% (57 deaths have have data available to use in this calculation)

The other thing we should factor in is co-infections with other respiratory viruses, and with bacteria. The viruses, as noted in my previous post, may now be starting to increase in prevalence as the "cooler" months affect the region. None of the broader testing data (presumably they were screened for other pathogens as well) are available on recent cases and few details available on earlier cases. 

Some things that are unknown on this topic:

1. How CORONA-CoV interacts with other viruses - has any virus just finished up its seasonal peak? Something that may have interfered with CORONA-CoV circulation at a population level?
2. Are we seeing more CORONA-CoV cases now because of a change in environmental conditions? His could be anything from temperature to humidity to impact on animal movements to festivals to dust storms

8 cases in 1 day. I think the first time I have seen so many cases in a row on my list in a 24-hour period (not actually at 24-hours yet). Many questions start arising without answers.

Even with Prof Memish's 2nd personal update through ProMED yesterday, it feels like cases are starting to appear faster than the local health authorities in these regions can manage them. Or has something changed with the virus itself?

Disease Surveillance Apps for Cell Phones

Recent technological advances such as the Foldscope microscope will improve on-the-ground disease surveillance.[1]  The ubiquity of cell phones, even in remote locations, may provide another advance in data surveillance and monitoring of disease outbreaks. In an open access article in  the Online Journal of Public Health Informatics, researchers present a framework for data collections forms and apps for cell phones that could be used for real time epidemiological analysis.[2] They note that cell phones currently do not have the processing power for large data sets and that uploading the compiled data to cloud servers for epidemiological analysis and interpretation will be necessary.

The authors make several suggestions regarding the use of Android as an open source platform and testing existing apps suitable for epidemiological data collection and analysis. They conclude with a “proof of concept” application of a collection form for influenza cases, attempting to distinguish influenza from other forms of virus infection. While the influenza form may not be sufficient to differentiate influenza-like infections, it does provide a starting point for using cell phones for more sophisticated disease surveillance and monitoring in the future. 

[1] Foldscope: An origami microscope that will revolutionize disease surveillance

[2] Android and ODK based data collection framework to aid in epidemiological analysis