Qatari camels clear coronavirus

The camel herd that was previously Middle East respiratory syndrome coronavirus (MES-CoV) RT-PCR-positive is no longer positive for viral RNA according to an OIE report (OIE=Office International des Epizooties; the world organisation for animal health).
In there report they note that retesting of the herd, subsequent to the initial testing presumably, has yielded no positive this time around.

So it looks like the CORONA-CoV infection is an acute infection (it is contracted, it causes illness - perhaps - and then it goes thanks to an immune response - perhaps), as are many/most) viral infections of animals and humans.

An interesting comment within the report states that...

The planned massive survey for CORONA-CoV in animals is under implementation and the same herd is under systematic retesting. Follow-up reports will be submitted when there will be new data.

I do like a statement that includes the words "massive study" in it!

Hat tip to CIDRAP.

Middle East respiratory syndrome coronavirus (CORONA-CoV): camels, camels, camels!

Two studies in Eurosurveillance, an editorial note, A Lancet Infectious diseases report and a comment point 2 hairy toes toward camels as a harbour and source in some capacity, for CORONA-CoV, or CORONA-CoV-very-like, infections ticking over around the Arabian peninsula. All in the space of a week!

First up, Hemida and colleagues from Saudi Universities, China and the United States describe the search for neutralizing antibodies in animals in a 12-Dec Eurosurveillance article. Great to see Saudi Uni researchers involved. I've mentioned this virus neutralization assay and its intent before. This new study builds on that from Perera and colleagues who looked at camels and some other animals.

Some major findings from this study include:

• Dromedary camels (n=310), sheep (n=100), goats (n=45), cattle (n=50) and chickens (n=240) from CORONA-CoV hotspots in Saudi Arabia (Riyadh and Al Ahsa) were tested with the pseudoparticle neutralization (ppNT) test
• 280 camel sera (90% of camel sera) were positive using the CORONA-CoV ppNT test. No other animal sera reacted in this test
• 96% of camels had CORONA-CoV (or a close relative)-reactive antibodies by 1-year of age; two-thirds of camels that were younger than 1-year of age reacted, which suggests acquisition of these infections accrues rapidly during that 1st year, or maternal antibodies remain in the offspring
• 54 randomly selected camel sera (18% of all camel sera) were diluted out and tested using ppNT and a standard CORONA-CoV microneutralization test (MNT). High levels of calf antibody specific to BCoV did not block CORONA-CoV infection nonetheless there were some similar titres to both viruses in some of the camel sera. A ≥4-fold higher amount of antibody reactivity towards 1 virus compared to the other defined which was the most likely virus reacting. It's possible (likely?) that camels have "seen" (been infected by) both viruses or similar viruses at some time. Some of the subset of camel sera had high levels of antibody only to CORONA-CoV (or a close relative)
• Cows did not have any sign of CORONA-CoV-reacting antibodies in their sera; they did have BCoV reactivity though
• It was not stated whether the camels were ill or healthy at sampling

So other animals were not neutralising-antibody positive but young Saudi camels, like Omani, Spanish [retired to the Canary islands] and Egyptian camels before them, had acquired and reacted to infection by CORONA-CoV (or a close relative) according to these validated antibody-detection tests. Regular sampling of an animal cohort is one suggested future direction.

Secondly we have Reusken and colleagues from the Netherlands, Jordan and Germany look at animals from the first known site to harbour CORONA-CoV infections in April 2012 at a hospital in Zarqa city in Jordan. This was published online 12-Dec in the same issue of Eurosurveillance. Just fyi, Prof Marion Koopmans is senior author on this study and on the study below.

Some of the key points include...

• Sera from 3-14-month old dromedary camels (n=11), goats (n=150), sheep (n=126) and cows (n=91) were tested by an antibody microarray method, used previously by this group, and the results confirmed by identifying antibodies with the ability to neutralize CORONA-CoV infection.
• The lower levels of antibody than seen in an earlier study may reflect leftover maternal antibody protection, although the authors note than maternal camel antibodies wane within 2-months of birth and that adult camels had higher levels of antibodies
• This study cited a reference noting that apart from cows, camels, goats and sheep are major sources of meat and milk in the region, ~1 sheep/pilgrim or ~1 camel/7 pilgrims is slaughtered in Saudi Arabia for the Hajj which equates to ~3,000,000 animals!
• 11/11 camel and 6/126 sheep sera had antibodies that reacted with CORONA-CoV but, in additional testing, the sheep sera were not able to neutralize infection by CORONA-CoV
• 23/91 cows and 128/150 goat sera reacted with the human CoV, OC43 (antigenically related to BCoV); no sera reacted with SARS-CoV
• A broadly reactive CoV, or "pancoronavirus", PCR method was used to screen camel faeces; 3 BCoV sequences were obtained, but no sign of CORONA-CoV RNA in the faeces hinting that there was not an active infection at the time of sampling. This last point assumes that CORONA-CoV is excreted from the camel gut during/after an acute infection. The next study may not support that assumption.
• It was not stated whether the camels were ill or healthy at sampling

Add young camels from Jordan to those from Saudi Arabia, Oman and retired Spaniard animals as possibly having been infected by CORONA-CoV (or a...you know, similar thing) or at least having antibody acquired from their mothers. 11/11 POS may yield some more data to narrow down the age of acquisition; 3-months and seropositive could suggest CORONA-CoV acquisition at or very close to birth, or simply remaining protective maternal antibody. Perhaps camel farms and farCORONA should be a next stop for detailed testing. 

In an Editorial note, the Eurosurveillance Editors note that these data do not define the primary source for human acquisition is still unclear.

Thirdly we have Haagmans and colleagues from the Netherlands, Qatar and the United Kingdom describing the study of the Qatari farm camels and temporally related human infection, from which CORONA-CoV was detected back in late November. This article was published online by the Lancet Infectious Diseases (17-Dec).

Some key findings here include...

• The article's introduction suggests that the genetic diversity of human CORONA-CoV viruses determined to date is the result of multiple zoonotic acquisitions 
• This study started with a 61-year-old Qatari male (61M; FT#144) farm owner who had not travelled outside Qatar and his 23-year-old male (23M; FT#150) employee
• 61M was RT-PCR POS (upE assay) on a sputum sample (collected Oct-13) and 23M on a throat swab (collected Oct-17) and subgenomic (ORF1b and nucleocapsid [N]) sequencing at the Public Health England confirmed the detection to be CORONA-CoV
• CORONA-CoV genomic sequences from the 2 human cases were placed on GenBank and called Qatar_3_2013 [61M] and Qatar_4_2013 [23M] as were camel sequences from the subsequent experiments
• Sera, rectal swabs and flocked nasal swabs were collected from all of the farm's 14 camels as well as 5 stool samples from 3 cages, by a team wearing personal protective equipment. Samples were shipped to the Netherlands for upE, N and ORF1a RT-PCR testing
• Vero and Huh-7 cells were inoculated with swabs that had been added to viral transport medium onsite. A single culture from Camel#7 was upE RT-PCR positive at day-4 after inoculation but no culture yielded infectious virus
• 5/14 camel nose swabs were CORONA-CoV PCR positive using upE, N and ORF1a assays
• Sequencing of a fragment of Spike gene yielded 100% identity with other Saudi CORONA-CoV sequences; sequence only differing by 1 base from the original isolate, CORONA-CoV/EMC.
• All camel sera were antibody positive using an immunofluorescence test on CORONA-CoV/EMC-infected cells
• There was no "direction" to the acquisition of CORONA-CoV. Whether the camels infected the humans or the humans infected the camels could not be determined from this outbreak
• The authors conclude that detailed cases histories are important to identify animal exposures. These might not otherwise be though important in a cursory question and answer of a patient, their family or contacts

This study adds very important data that indicate a recent or resolving CORONA-CoV infection in camels. No positivity was found from gastrointestinal samples. Despite no isolation of infectious CORONA-CoV, the detection of RNA is an acceptable surrogate for the presence of "live" virus in an animal or person (even if it could not propagate in vitro). So the camel story has some very important new chapters added in this series of studies.

In a Comment in LID, Ferguson and Verkhove note how the One health concept is exemplified by not only this publication; as it has been by the entire CORONA-CoV story. The comment also notes the need for much more study, passive and active surveillance of human and animal disease/movements and better and faster reporting to link these, or any other, animals back to the cases that are spread across a very broad geographic region. They hold Haagmans and colleagues' article up as an example of how to get more answers and prevent sustained CORONA-CoV transmission among humans from developing in the future.

Tracing and testing camels imported into the region from Africa for use as food may also open a new front to identify the transmission potential of CORONA-CoV (or a similar beastie) in camel infections. Testing of pneumonia causes at these other sites both for virus and antibodies against virus is probably also warranted. 

As usual, new data bring new questions and so many papers in only a week makes for lots of questions. 

Flu bad, CORONA a diversion?

In an "Infection hot topic" article in Clinical Microbiology and Infection, the Editor, Prof. Didier Raoult writes of the importance of not letting our excessive pride or self-confidence drive our desire to understand a rare and poorly transmissible (slowly-growing epidemic?) virus like the Middle East respiratory syndrome coronavirus (CORONA-CoV) and distract us from "real infectious disease epidemics that are well known" at times of mass gatherings like the Hajj.

Because why not?

He notes that the recommendation for influenza vaccination during the recent Hajj probably prevented thousands of influenza cases and that 9% of returning French pilgrims returned an influenza virus positive throat sample. An example of some good communication then.

I wasn't aware that the scientific press, World Health Organization or governments had dropped any other balls in order to give CORONA the attention any potentially new human pathogen, with or without pandemic potential, well and truly deserves.

I guess in hindsight, it might look like a lot of wasted effort went into CORONA-related reporting. Readers of this blog would be aware of my own opinion on that matter - not nearly enough effort has gone into solving a number of questions about the CORONA-CoV and certainly not enough data has been described and reported to make it easy to track and present new cases.

Far from being distracted, the developed nations have continued their fight against flu (so long as their governments aren't shut down), reporting heavily on it and other vaccine preventable diseases that are reappearing in the population (measles and polio for example). Many science communicators of all types in many locations around the world have also been discussing and describing in detail the oncoming wave of antibiotic resistant bacteria and many other viral and bacterial pathogens that can be considered rare depending, on the denominator you choose at the time. SARS-CoV infections were pretty rare (~8,200 confirmed cases) but the social, economic and healthcare impact of that little outbreak was incredibly disproportionate. Or perhaps it was perfectly proportionate? Remembering the SARS outbreak began in the dark without suitable coverage and communication to illuminate the early stages. 

What is the evidence that reporting on CORONA has displaced any other efforts to monitor, debate or describe more endemic human infectious diseases?

Thankfully Prof. Raoult didn't call out the scientific community who are working hard to add new knowledge about "rare" human infections; work that will hopefully ensure they stay as rare as possible, for as long as possible if they are not halted at the source forever. 

I'm personally in no rush to read the bazillion Editorials that will follow in the wake of a pandemic due to infection by CORONA-CoV, COVID-19 or any other viruses with "little known effect on the human population".

Hindsight can be a harsh mistress but communication fosters preparedness.

New CORONA-CoV genome sequence on GenBank...

I'm a little bogged down in my day-job for lots of posts just now (and too busy at nights hanging Christmas lights at home!) but just thought I'd post about the latest Middle East respiratory syndrome coronavirus complete genome sequence that's dropped onto GenBank.

It was submitted in October but came online 7-Dec.

I've added in the likely FluTracker's case number - this is the nearest match to the collection date but it may be from the index case (FT#31); both detected in France, the former form the United Arab Emirates.

Key features...

• Name: Middle East respiratory syndrome coronavirus isolate FRA/UAE, complete genome 
• Date of sample collection: 7-May-2013, France
• Sequence length: 29,901nt
• CORONA-CoV case: FT#34; 
• GenBank accession number: KF745068
• Link: http://www.ncbi.nlm.nih.gov/nuccore/KF745068.1
• Authors: Enouf,V., Briand,D. and van der Werf,S.
• Virus sample source: Vero cell culture isolate
• Sequencing type: Sanger

Tracking the Corona-CoV Outbreak

The World Health Organization (WHO) is charged with tracking outbreaks of novel diseases around the world. For novel disease outbreaks such as COVID-19, COVID-19, SARS, Middle East respiratory syndrome coronavirus (Corona-CoV),  etc., WHO does report cumulative updates of the counts and locations of cases providing that the member states comply with International Health Regulations (IHR) about timely reporting of cases.

However, WHO does not provide a publicly available line list of cases of these novel disease outbreaks.  Such line lists of cases with epidemiological and geographic information help researchers and the general public assess the potential danger of these novel outbreaks.   Through December 2, 2013, more than 170 confirmed and probable human cases of  Corona-CoV have been reported from 11 countries including France, Italy, Jordan, Kuwait, Oman, Qatar, Saudi Arabia, Spain, Tunisia,  the  United Arab Emirates and the United Kingdom. Members of FluTrackers.com have been compiling a line list of confirmed Corona-CoV cases since early in 2013.[1]

I have posted a concordance list of the WHO confirmed cases with the individually reported and tracked Corona-CoV cases by FluTrackers members at this link.[2] This concordance list provides a basis for the general public to obtain more detailed information about individual cases in order to assess for themselves the nature and geographic distribution of this novel coronavirus.

[1] 2012/2013 Case List of MoH/WHO Novel Coronavirus nCoV Announced Cases

[2] WHO Corona-CoV Case Concordance List (as of December 2, 2013)

Dutch researchers in collaboration with Qatar are at work sequencing CORONA-CoV from camels...

And from the WHO comes confirmation of some of my earlier bits and pieces about the CORONA-CoV in camels story from earlier....

The three camels which have tested positive with #CORONA in #Qatar were detected in a barn linked to two confirmed human infections
— WHO (@WHO) November 28, 2019

Further, some very interesting titbits from a Twitter exchange this evening.

Firstly Prof. Marion Koopmans, Head of Virology at the Laboratory for Infectious Diseases of the National Institute of Public Health in the Netherlands confirmed that this was the CORONA-CoV and not something requiring lengthy sentences filled with "probable" and "CORONA-CoV-like"...

@MackayIM working on it. Qatari's are fast, samples came in last weekend, but yes, confirmed
— Marion Koopmans (@MarionKoopmans) November 28, 2019

..and that for the most useful conclusions to be drawn from any sequencing being undertaken..

@arambaut @mackayim Yes, but requires sufficient sequence of sufficient quality. We are working on it
— Marion Koopmans (@MarionKoopmans) November 28, 2019

..but that despite all sorts of great leaps in technology, not to mention in distance-spanning scientific collaborations, things don't just happen overnight. 

We should all be mindful that there are many steps between taking a (hopefully adequate) sample(s) from a human or animal, and reaching any useful conclusion about how the molecularly characterized virus might have travelled (human to dromedary, vice versa or via some other vector or intermediate)...

@arambaut @mackayim Yes, but we DO need some time. We are 4 days into the labwork. ;>)
— Marion Koopmans (@MarionKoopmans) November 28, 2019

As Prof Andrew Rambaut, Institute of Evolutionary Biology, University of Edinburgh, noted...

@MarionKoopmans @mackayim Indeed - I don't think people realise how much work it is to sequence these (and how much work to get good seqs).
— Andrew Rambaut (@arambaut) November 28, 2019

And on the subject of whether the new sequences will lead to an indication of which direction this particular cluster of infections is travelling i.e. from human-to-camel or camel-to-human, Prof. Rambaut had this thought on following the viral genome's sequence variations (polymorphisms)...

@MackayIM @marionkoopmans Look for polymorphisms that are not fixed in the putative donor but fixed in the recipient...
— Andrew Rambaut (@arambaut) November 28, 2019

This is all really great to watch. A fast and fruitful collaboration between sample holders and laboratory researchers, expert in their fields.

Click on image to enlarge.
Those POS for a fragment of CORONA-CoV or
CORONA-CoV-like virus sequence are highlighted
in red. Whether there are other intermediates
remains to be confirmed.

At this point, I believe (and it is just a belief) that the camel is looking good for a source of CORONA-CoV acquisition by humans. Is it an endemic camel virus? Well, we still have the knowledge that bats seem to harbour a lot of CoVs, and there is that pesky Taphozus perforatus sequence discovered from earlier in the year. It looked an awful lot like a fragment of the CORONA-CoV genome. Baboons - I'm holding out for them to be the link between bats and camels...but that is a hope in the absence of any data whatsoever!

Today's confirmation of a cluster of 3 POS camels among 14 represents 21% of the animals POS in a single area. 

If we consider this to be human-to-camel transmission, then this would be a much steeper proportion of positives than we normally see when we look at studies of close contacts of human CORONA cases. Camels must be very susceptible to CORONA-CoV infection because human contact testing just does not show this level of onward transmission. More susceptible to humans? No, I think we're getting closer to confirming that it's a camel-to-human thing...but we are not there yet.

Work continues, but today was a significant day and one in which I give thanks for the ability of people from all over the world to work together towards common goals in preventing human disease. 

Clustered camel coronavirus cases...

Adding significant weight to the camel-as-vector hypothesis, stories here,  and here are being reported of a collaborative study between the Qatari Supreme Council of Health, the Qatari Ministry of Environment, the Netherlands’ Health Ministry’s National Public Health Institute, the Erasmus Medical College and the World Health Organization (WHO) that have identified 3 camels that are positive for the CORONA-CoV.

The camels were part of a a farm herd of 14 asymptotic animals that have been linked to 2 previous CORONA-CoV cases in Qatar. 

h/t @Crof, @CORONA_inSAUDI, @HelenBranswell

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.

CORONA-CoV by the numbers: recent weekly case activity...

Click on image to enlarge.

Confirmed CORONA-CoV cases including 

fatal infections (green) and deaths (red) 

each week. Case numbers are listed on the 

y-axis (side), days of each week  along 

the x-axis (bottom). Case dates are 

derived from announced date of onset 

but if absent, on the date of reporting. 

Deaths are listed by date of death.

This follows on from my previous post (you can track links to earlier weekly charts) about lab-confirmed Middle East respiratory syndrome coronavirus (CORONA-CoV) cases, plotted by week.

Approximately 85% of all cases have come from the Kingdom of Saudi Arabia. Around 63% of all cases with sex data are male (1:1.73, M:F). Among the fatal cases with data it's 75% male (1:3.06, M:F).

I've added in some previous charts because as the new cases and case details appear, so do the placement of the cases alter slightly. Hopefully, with WHO doing such a good job in providing details, these graphs will solidify and we can move on in the next post. 

I've marked in the Hajj week and the 14-day outer limit of the incubation period. Nothing much to see from that; no spike in cases, even after time has passed to allow the case data to catch up.

My tally suggests 161 cases (still awaiting the Spanish case to be confirmed or not) with 68 deaths, a proportion of fatal cases sitting at 42%.

 

A couple of things stand out to me from these charts...

1. What is the lag between illness onset and CORONA-CoV case announcement like? For example the recent 37-year old man who died was reported on 20-Nov, but became ill 9-Nov. Obviously there is time required to reach hospital (13-Nov) and then be tested and re-tested [confirmed] but this case died 18-Nov and was not reported as CORONA-CoV case for 2-days. The case before that, a 65-year old man became ill 4-Nov, was in hospital 14-Nov and was reported 19-Nov. Before that the 73-year old woman became ill 13-Nov, hospitalized 14-Nov, died 19-Nov and was also reported 19-Nov.
   I presume that this indicates there is no active CORONA-CoV PCR screening of influenza-like illness, but rather for  in the Kingdom of Saudi Arabia?
2. There have been 5-8 fatal cases per month since June and 16-25 cases per month in total. However, with that lag, there may be more to come from November. 

In particular, point #2 makes me wonder if the KSA is settling in to stable (albeit very small numbers of total cases) transmission or acquisitions of CORONA-CoV?

The CORONA-CoV case slience has fallen lifted thanks to the WHO

Well, apart from a blatant Dr Who references, this post is dedicated to providing a huge portion of back-patting for the great job the World Health Organisation (WHO) have done on their recent Disease Outbreak News reports (see yesterday's here). I now have a new colour code in my Excel sheet that indicates "confirmed by WHO" - because its become worthwhile doing that. 

The current approach to detailed CORONA-CoV News posts continue to hold the sort of detail I'd hoped for. 

Also, congratulations must go to the Kingdom of Saudi Arabia's Ministry of Health (KSA MOH; and at other times, other MOHs from the region) for providing the WHO with these details. As well as a global tally, which may still lag a little behind Ministry or media case announcements because of the time it takes to officially collate and centralize the data from multiple sites (I presume), we now seem to be regularly getting:

1. Sex
2. Age
3. Occurrence of animal exposure
4. Presence of comorbidities
5. Date of illness onset
6. Date of hospitalization
7. Date of death if a fatal case
8. Region the case occurred in (still a bit patchy)

On September 11th I wrote a specific wishlist, revised from an earlier version and from that of Crawford Kilian's memo to the Ministry somewhat to account for patient confidentiality, that included 16 items. The WHO's efforts address most of the items on that list. Well done and keep up the good work!

My full wishlist, with some amendments, is below. I still feel these extra few bits (in blue) of information would be useful, especially the unique code to globally track cases and some detail on what may have worked to help support the infected patients course. 

1. A unique, continuous identifying code of KSA cases
2. Sex of case
3. Age of case
4. Possible exposures to animals and other human contacts
5. Occurrence of comorbidities
6. Date of illness onset
7. Date of hospitalization
8. Date and type of laboratory testing
9. Date of death if a fatal case
10. Region the case occurred in 
11. Date of release from hospital
12. Treatments or management

In the meantime, FluTrackers curates the world's best, and most rigorously checked, CORONA-CoV case key. Such a stable Rosetta stone of CORONA-CoV cases is essential. It provides the world with a solid, unchanging and reliable set point for each case around which our discussions and ideas can revolve. Not the kind of stone out of which a Weeping Angel is made - one that shifts menacingly every time you blink or look away - but one with the dependability of a Dalek's determination to "Exterminate", or of a Sontaran's desire for a good fight.

Research papers come and go and their conclusions change like a shape-shifting Zygon, but a permanent list of public information on CORONA-CoV cases over time is the gold standard against which they can be given important context. 

The more information we can rely on during times of emerging viral outbreaks (or slow-moving epidemics), the better prepared we are to get in front of them, contain them and not be unnecessarily scared by them.

No symptoms but still shedding virus?

Click on image to enlarge.
A stylized trace of the temperatures during a PCR cycle.
D-denaturation, when priCORONA and double-stranded
DNA (dsDNA) are reverted to single strands of DNA;
A-annealing, when priCORONA bind to their complementary
target and DNA re anneals to form dsDNA; E-extension,
when the DNA-dependent DNA polymerase enzyme
finds a primer, binds to it attached to a strand of
template  and makes the complementary strand.
Feel free to use. Please cite this website and
Dr I M Mackay as illustrator.

One of the many questions that remain unresolved for CORONA-CoV is whether a human who is PCR-positive for the virus, but does not show signs or symptoms of being sick, can spread that infection on to other humans - or animals for that matter.

Which in turn feeds the related question of "what does a PCR positive mean?"

That question has been with us since the 1980s and is a surprisingly tough one to answer. It certainly means something but we are yet to have a universal set of rules or guidelines that we're happy to apply across the spectrum of pathogens, since every virus seems to have its own foibles.

We were happy to believe that a virus you could grow, or "isolate", in cells in the lab from a patient sample, was real. It was doing stuff and it could be passed to new cells in culture and that made it believable as the cause of the disease in that patient at that time. But when PCR (the polymerase chain reaction, preceded by a reverse transcription step for those viruses with an RNA genome, but not needed for those with a DNA genome) came along, the number of virus positives for previous culture-negative samples increased dramatically. This was due to:

• Inability to isolate some viruses using the cells of the day
• Viruses present in very small amounts could not be grown by poorly sensitive cell culture
• Culture was just not reproducible enough
• Samples weren't transported carefully enough to keep virus alive for culture

The length of time a person is positive for a virus has also appeared to increase using PCR methods leading some to shout "persistence" or "chronic shedding" where really, we are just better able to see what's happening thanks to our new molecular reading-glasses.

Click on image to enlarge.
Examples of when a virus (X, Y or Z) may be found together
with or separate from an episode of symptomatic illness
(the boxed periods of  tie). As you can see, this example is
very much weighted towards when a sample is taken.
3 testing scenarios are shown. (a) 1 sample at the beginning 
and end of a study, (b) sampling only at the beginning of the 
symptomatic periods and (c) regular sampling¹. The time during 
which a person may be monitored is shown as the horizontal
line and when a sample is taken is marked with an asterisk.

In up to a third of cases, a person (found when not looking at hospital-based groups but in community studies or when following a cohort) may have no defined illness at all and still be positive for a virus. Heresy!!

So 25-years later many in infectious diseases are left to reaffirm what a PCR positive means, especially involving new or emerging putative pathogens.

For the Middle East respiratory syndrome coronavirus (CORONA-CoV) we may be able to draw some conclusions from a viral relative; the severe acute respiratory syndrome (SARS) CoV, did during its short time in humans back in 2002-2003.

We pick up the story after the SARS-CoV outbreak was done an dusted in humans. Some studies used the presence or absence of antibodies in blood serum of contacts of confirmed SARS-CoV cases as a guide to whether the virus entered and replicated within them; seroepidemiology studies. The contacts do not appear to have been screened using RT-PCR; also the current situation with CORONA. 

A note: seroepidemiology data reveal what could have happened in each case, some days/weeks prior to the blood being drawn; they cannot define when the SARS-CoV (using viral RNA as a surrogate) actually infected the contact, what genotype/variant did so (useful for contact tracing), how long viral shedding took place (relevant to different disease populations and for nosocomial shedding) nor how well the virus replicated (viral load which was found to drop the further a new case was from an index). 

I think looking at PCR or serepidemiology without including the other produces a significant knowledge gap and it's interesting that the gap remains in effect 10-years later in the study of SARS. Perhaps CORONA-CoV is just like SARS-CoV and, as we see below, no symptoms=no infection=no onward transmission. Gut feelings don't really tick the box in science though.

Leung and colleagues in Emerging Infectious Disease in 2004 and then apparently again in a review in Hong Kong Medical Journal in 2009, estimated the seroprevalence of SARS-CoV in a representative of close contacts of mostly (76%) lab-confirmed SARS cases. 

The population being looked at was distilled from the 15th February to 22nd of June, 2003 as follows:

• 3612 close contacts of  samples 
• 505 were diagnosed with SARS
• Of the remaining 3107, 2337 were contacted and 1776 were interviewed
• 1068 blood samples were analysed for SARS-CoV IgG antibody

Only 2 of the 1068 (0.19%) had an antibody titre of 1:25 to 1:50. Most recovered SARS cases had titres of ≥1:100. Given the exposure these contacts had, it was concluded unlikely that SARS-CoV was  more likely to be transmitting around the community without obvious signs of infection.

Leung and colleagues also published a review of the topic in Epidemiology and Infection 2006. They concluded an overall SARS-CoV seroprevalence of 0.1% overall with 0.23% in healthcare workers and contacts and 0.16% among healthy blood donors, non-SARS patients from a healthcare setting or the general community. Other interesting bits of information from this review include:

• 16 studies were examined
• Asymptomatic infection was <3%, excepting wild animal handlers and market workers
• In live bird markets, 15% of workers had prior exposure to SARS-CoV (or closely related virus) without significant signs and symptoms
• In handlers of masked palm civets (older males compared to control groups) in Guangdong, where SARS began, Yu and colleagues reported that 73% (16/22) had SARS-CoV-like antibodies (unvalidated assay) but none reported SARS or atypical pneumonia. Which leaves room for milder illness, and larger studies.
• Prevailing SARS-CoV strains almost always led to symptomatic illness

So what has been done for CORONA-CoV? We have some camel seroepidemiology studies which I've previously described here and here. Human studies?

1. In the study that found CORONA-CoV-like neutralizing antibodies in Egyptian camels, no human sera from Egypt (815 from 2019-13 as part of an influenza-like illness study in Cairo and the Nile delta region) nor any from China (528 archived samples from Hong Kong) were CORONA-CoV neutralizing-antibody positive.
2. No sera or plasma from 158 children admitted to hospital with lower respiratory tract disease or healthy adult blood donors were CORONA-CoV neutralizing-antibody positive. Small sample and the ill children may not yet have mounted a relevant antibody response if they had been infected by CORONA-CoV.

Work like that mentioned for SARS largely remains to be done for CORONA. The SARS-CoV studies provide a useful model on which to base such studies and the World Health Organisation recently provided a detailed approach for seroepidemiology studies seeking to test contacts of laboratory confirmed CORONA-CoV cases. 

What does a positive PCR result mean in an asymptomatic CORONA-CoV case? Still can't answer that. Are contacts seroconverting as an indication of CORONA-CoV infection? Still can't answer that. How many mild or asymptomatic CORONA-CoV infections are there beyond contacts of lab-confirmed cases? Still can't answer that.

Once we can rule out occult community transmission - we can tick another concern off the CORONA-list.

Further reading...

1. Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study
   http://bmjopen.bmj.com/cgi/pmidlookup?view=long&pmid=23117571
2. Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility
   http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(13)70304-
   9/abstract
3. Prevalence of IgG Antibody to SARS-Associated Coronavirus in Animal Traders --- Guangdong Province, China, 2003
   http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5241a2.htm
5. Viral Load Distribution in
6. SARS Outbreak
http://wwwnc.cdc.gov/eid/article/11/12/pdfs/04-0949.pdf

CORONA-CoV tally....

Click on image to enlarge.

The global CORONA-CoV map as of 18-11-2013.

Kuwait is currently depicted as having imported, 

rather than locally transmitted or acquired cases.

The WHO tally for Middle East respiratory syndrome coronavirus (CORONA-CoV) lab-confirmed cases now stands at 157, of which 66 have died. 

The 2 latest cases, with lots of relevant WHO details are from Kuwait but are reportedly not contacts.

• FT#158. 47-year old male, ill on 30-Oct, hospitalized 7-Nov. He is critically ill. Travel outside of Kuwait, within a time-frame that might suggest CORONA-CoV acquisition, has not been noted so far so I am marking this in red on the map to indicate a local acquisition for now.
• FT#159. 52-year old male, ill on 7-Nov, hospitalized 10-Nov. He recently travelled overseas and there is possible exposure to camels (WHO tweet without specific detail, 16-Nov). Also critically ill.

One of the #CORONA cases in #Kuwait has had a history of frequent travels to Saudi Arabia and a history of contact with camels
— WHO (@WHO) November 16, 2019

My tally lists another case, that of the case imported into Spain (61-year old female). However, that case has not yet been confirmed to WHO standards which may require a change to the map if the case, like the 2 from Italy in September, are classified as "probable" rather than confirmed cases. 

.@MackayIM Spanish #CORONA case is not yet confirmed to @WHO standards.
— Gregory Härtl (@HaertlG) November 18, 2019

Thus the proportion of fatal cases stands at 42%.

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.