Wednesday, 30 October 2013

New MERS-CoV laboratory test: takes 10-minutes but what can it tell you?

Back in June we heard of a quick test for MERS-CoV to add to the diagnostic armamentarium. I posted on it here.

Now that the Abu Dhabi Medical Congress & Exhibition it was presented at is over, we are hearing about it again through a story at The National. 

Still no details though, so my original concerns about sensitivity (how often will it miss true positive cases because it is not sensitive enough?) linger on.

Further, it's a "blood test" that also uses DNA amplification so the patient will presumably need to be sick enough to have a viraemia (virus spilling over into the blood) so it may not help at all for screening contacts or less ill people with lower viral loads. It is being described as useful for "identifying the virus in its early stages". 

Another assay that looks similar, described in PLoSONE by these researchers earlier in the year, does not appear comparable to PCR-based methods in terms of its sensitivity. 

For MERS-CoV, as for any newly emerging pathogen with unknown characteristics spreading in ways we are yet to understand, detection sensitivity is a key factor.

I look forward to seeing same real-world evaluation data.

French "probable" case pas vraiment so probable after all

FluTracker's and Mike Coston is busy keeping us up-to-date on the latest with MERS-CoV concerns around the world post-Hajj.

Last night's probable case has tested negative for the MERS-CoV according to media - the Health Ministry website has not released this yet.

The surviving case of MERS-CoV in France, is still hospitalized.

First case of MERS-CoV in Oman...home of antibody-positve camels...[UPDATED]

A new country has described, via the media (quoting Mohamed bin Saif al Hosni, Under-Secretary for Oman's Health Affairs), its first Middle East respiratory syndrome coronavirus (MERS-CoV) case, the sultanate of Oman. 

It seems that the case was acquired locally from someone infected outside Oman.

  • 68-year old male with diabetes
  • Still no detail on the supposed confirmed case he was in contact with or the test type or date of hospitalization
  • The Oman Ministry of Health website has not officially confirmed the case at this stage. 
  • When confirmed, this will be the 149th confirmed case ("probable" FluTrackers #151)

Oman's Centre for Public Health Laboratory (CPHL) has been testing for MERS-CoV from suspect cases since October 2012 and while prospective laboratory screening of returning Hajj pilgrims was not being undertaken, observation for signs and symptoms of disease was ongoing.

If we remember back to early August, - 50 of 50 retired racing camels from Oman had antibodies to something that was closely related to the MERS-CoV. 

Thanks to Mike Coston, @makoto_au_japon and @Crof for tweets and posts
Thanks to FluTrackers for tweeting & posting the AFP updat

Tuesday, 29 October 2013

Latest confirmed cases and a probable new MERS-CoV case(s) in France [UPDATED]

It's been a couple of days since the last report of a new MERS-CoV case, that of an expatriate, 23-year old asymptomatic male contact of another case in Doha, Qatar (the 7th seemingly acquired on Qatari soil). 23M (FT#150) was mildly ill and was diagnosed through routine screening of contacts. The man worked with animals in a barn owned by a previous case according to the latest WHO update. Once again this highlights that the MERS-CoV can move on from an infected person and it can do it stealthily. However, the next "round" of infection seems to be (a) milder in severity and (b) the end of the transmission event.

Unfortunately the recently described MERS-CoV-positive 83-year old woman in Jubail on the eastern coast of Saudi Arabia, has reportedly died. Apparently she was hospitalised a month ago.

Buzzing around on Twitter (thanks to @makoto_au_japon) and the web nothing is the story of a probable case in a 43-year old in France. The man returned from a stay in Saudi Arabia and he is currently described as stable. There areno more details on France's Department of Health and Social Affairs website but they have noted it on their Twitter feed (@Minist_Sante) and have the media release. The various translations mention the plural, "cases" (machine glitch?). An article in the Khaleej Times notes it is unclear whether this person was a pilgrim to the Hajj. My Form 3 French is very rusty and didn't covered public health so I eagerly await laboratory confirmation. 

If this imported case is confirmed [UPDATE: it was not] it will be France's 3rd detection, only 1 of which has been transmitted locally.

The MERS-CoV laboratory confirmed count currently stands at 148 cases with 63 deaths (PFC of 45.6%) .

Why palm tress in the MERS-CoV acquisition model...?

Click to enlarge. See more at earlier post.
I have palm trees drawn in as a sort of focus for my hypothetical acquisition model for the Middle East respiratory syndrome coronavirus (MERS-CoV). 

I first posted this graphic back in late August. It shows ways in which humans might acquire/have acquired the (probably) occasional MERS-CoV infection from an (suspected) animal host/intermediate host.

You can probably see from that paragraph, that this is just some crazy thoughts and there are no data that link them together.

I was recently asked why the palm trees? My thinking here was that date palms, and perhaps other flowering trees, may attract insectivorous bats as well as providing shade, and perhaps water if nearby, for animals and humans. This could create a point of cross-over between species - even if they don't directly co-mingle there may be opportunity to come in contact with contaminated excreta, saliva or partially eaten fruit or bugs.

Monday, 28 October 2013

Influenza deaths amongst children...

Influenza-associated paediatric mortality data.
US CDC FluView. Click to enlarge.
I'm a little bogged down in feeling sorry for myself (no new grants in 2013), paper writing, grant planning/duck aligning just now - but I'm keep an eye on Twitter for gems like this one.

Over on his blog, Avian Flu Diary, Mike Coston has a great summary of some papers and a recent study that serve to highlight the importance of vaccinating children against influenza virus. It's a virus that can kill especially among, but not limited to, those with comorbidities. Influenza is a vaccine-preventable disease.

Have a read of the whole article at

Sunday, 27 October 2013

MERS-CoV antibodies not found in children in 2010-11 or adults from 2012

Gierer and colleagues from the German primate center and the University of Dammam in Saudi Arabia, have presented the findings of their study of antibodies to the Middle East respiratory syndrome coronavirus (MERS-CoV).

The publication, in Emerging Infectious Diseases (ahead of print - you can find it here, at least until it's other link here starts working), measured the antibodies capable of blocking infection by MERS-CoV, called "neutralising antibodies" with a method they have described before. The assay was not validated with multiple MERS-CoV-positive patient sera, but appeared specific in the testing completed. None of the sera stopped the MERS-CoV Spike protein coated virus-like particles (VLP) from entering the Caco-2 cell line. Entry of the lentivirus/Spike hybrids was measured by enzyme activity inside the cells if infection is successful. Less or no activity if the VLP could not enter the cell because the VLP's Spike proteins were bound after pre-incubation with anti-MERS-CoV-containing patient sample. 

Patient samples from the area served by King Fahd Hospital were obtained from:

  1. Children (158 sera, 77 female, mean age 12 months) admitted to hospital with lower respiratory tract infections during 12-months form May 2010. 
  2. Adult (110 plasma samples, all males, mean age 28-years, upper limit of 52-years) blood donors 
No sera or plasma had neutralising MERS-CoV antibodies.

The authors conclude that <2.3% of children and <3.3% pod adults were seropositive though, because that accounts for the upper limit of the confidence intervals. They also note that their sampling of hospitalized children could have missed an antibody response (because it takes time to develop) if they had only just been admitted to hospital for MERS-CoV. 

Additionally, its a pretty small sample on which to be base too many conclusions when considering a virus that is spread across a 2,100,000kms2 and reportedly caused notable disease in <200 of 28,000,000 people.

MERS case-control study during the Hajj

Dr Ziad Memish, Deputy Minister of Health, Kingdom of Saudi Arabia, has made a welcome comment about some analysis of ill cases that went on during the Hajj. In the Saudi Gazette..

He added that in addition to detailed investigations of every suspected case, case-control studies for index cases and intensive follow-up of contacts with serological testing to improve understanding of the critical features of MERS-CoV infection were carried out.

I'm not clear on whether that indicates there were MERS-CoV cases during the Hajj, or if he is referring to probable cases that were not confirmed (no contacts then?) or to respiratory illnesses in general. He unfortunately wasn't quoted as saying whether any of those results were positive for MERS-CoV infection. 

Given that 997,3709 pilgrims apparently partook in some degree of medical healthcare service while in the KSA for Hajj, this study should provide some very useful information about what MERS-CoV was doing both in the ill and the healthy in mid-October. I might even be able to stop whingeing about lack of testing of all but those who are severely ill (or their contacts)!

The case-control study protocol is likely to follow that defined by the WHO in July - which can be found here.

The controls (best if >1 per case) will be randomly selected people of equal age (leeway varies with age band) and sex ("matched"), living in the same neighbourhood (to ensure try and capture the same environmental exposures; difficult for visiting pilgrims so general are of pilgrimage might suffice) that are not presenting with the same illness as the confirmed "case" at the time of sampling. Sampling (described in the lab testing WHO document here) which is recommended to include material from the lower respiratory tract - which may prove difficult from otherwise well controls. Informed consent is recommended as part of the (any such) study so controls will know what they are in for ahead do time.

Interestingly the WHO document comments that...

Currently, circulation of this virus in the community is thought to be nonexistent or minimal at most and the numbers of infections low. For that reason, prospective controls who have not had recent respiratory illness can be enrolled without laboratory

This study will address whether this is an accurate premise.

MERS cases swell by 3, information scant...

Middle East respiratory (MERS) 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 MERS. 

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

Saturday, 26 October 2013

Influenza A(H7N9) vaccine approved by Chinese food and drug administration for use...[UPDATED]

CNTV English language newshour reports that the home-made first influenza vaccine from China has met local safety standards and is ready for mass production. The vaccine was a collaborative development between the First Affiliated Hospital under the School of Medicine of Zhejiang University, Hong Kong University, Chinese Center for Disease Control and Prevention, National Institute for Food and Drug Control, and Chinese Academy of Medical Sciences.

It will be interesting to read about what the virus is comprised of (seems to use the older influenza PR8 strain as a backbone, employing a reverse genetics approach to add in H7N9) and how the vaccine makers got around H7N9's predicted low immunogenicity issue, what the dosing regimen is and what was used as adjuvant (mentioned here, earlier). As Mike Coston notes on Avian Flu Diary, the announcements don't detail much of the preceding safety trials that should have been carried out for a vaccine to have reached this level of development. 

Mike has an earlier post over on Avian Flu Diary that reminds us about the few that are sick enough to be obviously ill....and perhaps the many that do not seek medical attention because infection resulted in relatively mild disease. Largely, as Mike notes, any numbers assigned to infections that result in milder or even asymptomatic disease are guesstimates for now - at least until some actual testing is reported. History supports that mild infections are likely, but every zoonosis is its own beast.

More coming soon on the vaccine's development path and on testing to understand H7N9's reach.

Thanks to @makoto_au_japon for identifying the vaccine story through Twitter

Friday, 25 October 2013


A troup of Hamadryas Baboons (Papio hamdryas) outside
of Riyadh, Saudi Arabia. Hamadryads live for 30 to 35-years
Monkeys I tell ya, monkeys! notes that baboons are such a problem in the Kingdom of Saudi Arabia's southwest that electric fences are being erected to keep them out of certain areas.

Is anyone testing baboons for MERS-CoV? Or any other virus hunting going on in them for that matter? 

I've posted on the movements and interactions of these furry troublemakers before, and they also feature in the VDU model of MERS acquisition.

If they are even infrequently in contact with humans, bats and camels - then perhaps we should give them the laboratory once-over. 

Some serology and some next generation sequencing would be a good place to start.

Thanks to FluTracker's Tweet and post on this.

MERS update: WHO catches up but passes along no detail - and Hajjis look clear

The World Health Organisation updated it's MERS-CoV tally. The total (144 cases) is the same except for the confirmation of 2 deaths (to 62) hinted at in my last update

Disappointingly and once again, the update doesn't allow any analysis because there are no specific details with which to cross-check against our case lists.

Even CIDRAP is heading to the newspapers to try and identify which existing cases have died.

With my arbitrary deadline for emergence of new MERS cases being the 27th of October (this Sunday)  only 2-days away, I think its pretty safe to say that there has been no major symptomatic MERS-CoV transmission event associated with the peak assembly period of the Hajj in 2013 (just like there was none in 2012 when MERS-CoV was already in play). 

The United Arab Emirates is reportedly not checking pilgrims for symptoms, although they have their own 2-week clock running to monitor for signs and symptoms of new cases of flu-like illness in pilgrims.

Thankfully, there are studies performing actual laboratory testing, although the details remain unclear. Such studies will tell us whether MERS-CoV is among us already, but not causing the serious disease we've become used to associating with the virus.

Dr Jake Dunning (@OutbreakJake) noted on Twitter...

He also went on to say that...

ISARIC - the International Severe Acute Respiratory and emerging Infection Consortium- can be read about at
So my next question becomes, have we been watching the emergence of a new endemic human coronavirus? That question is based on a hypothesis that we have a lot more undetected cases and on Dr Ziad Memish's earlier assertion that MERS-CoV cases are already out and about in other countries. Time, and some testing, will tell.

Influenza A(H7N9) in Zhejiang, Dutch DURC and dogs..

With the second H7N9 case (see FluTracker's thread) in Zhejiang, located only 13km from the earlier case, things seem to be picking up where they left off in late April. Poultry exposure seems key to this latest case who was a farmer who engaged in poultry trading. That word, trading, also sparks concern. It suggests that the farmer was exposed to poultry coming from, or going to, somewhere else. H7N9 is on the move. Both patients are very unwell.

Zhejiang province had the steepest rate of case acquisition back then and reached the highest H7N9-confirmed case number as well. 

Looks like this province is going to be a key battleground for the next wave of H7N9.

Meanwhile, Eurosurveillance continues its fantastic coverage of this and the Middle East respiratory coronavirus  and H7N9 outbreaks. It already has a paper online (less than a week turnaround) of the earlier Zhejiang H7N9 case in a 35-year old male (35M) which includes a note about the subsequent Zhejiang case! Outstanding work to the researchers and the publishing team. Quality publication almost in the time it takes to write blog post!

This journal certainly highlights how quickly detail research results and analysis, when submitted to peer review, can be published. 

Click to enlarge. The laboratory turnaround
times for H7N9 detection (where suitable date
data exist) since the outbreak began in early 2013. 
  • 35M was identified though the surveillance system for unexplained pneumonia
  • He was not a farmer and had not had close contact with another probable case. The laboratory turnaround times on this case was 7-days. A 2.2 day improvement on the rolling average I stopped calculating May 6th.
  • The most likely source of exposures was a trip to rural region of  Ningbo city where he may have been in contact with animals. But that was 10-days prior to onset which would make it a long incubation period. 35M remains unconscious so further detailed tracking of exposures is not possible
  • The virus was >95.5% identical to H7N9 from earlier in the year but with 5 hitherto unreported mutations in the neuraminidase (NA) gene. 2/9 bird market samples were also H7N9 PCR-positive but could not be sequenced due to low viral load
Meanwhile, Reuters reports on Albert Osterhaus and Ron Fouchier at the Erasmus Medical Center who are firing up the "gain-of-function" studies to look at what would be required for H7N9 to become a pandemic virus; essentially changing the virus to look for increased transmission. This work will be performed in an highly secure, enhanced biosafety Level 3 lab. Which of course doesn't change the subject matter - but does define how difficult it would be for that to escape. It's not convincingly clear why this virus needs to be given an evolutionary push, rather than "reverse-engineering" those influenza viruses that have previously been pandemic viruses - or some other approach with less risk of creating a virus that if it escaped, would cause a pandemic. Well, to me at least...but I'm no flu expert. You can find much more on dual-use research of concern (DURC) in Laurie Garrett's latest writing over at Foreign Affairs.

And to add to general influenza virus concerns, Sun and colleagues report in Infection, Genetics and Evolution, that infectious H9N2 (isolated using embryonated chicken eggs), strains of which has been implicated in providing genetic material to H7N9, can be isolated from dogs. The isolate was called A/Canine/Guangxi/1/2011 (H9N2). Between 20% 45% of dogs were found to be antibody-positive to H9N2. A range of dogs seem to have been virus-positive with signs and symptoms including loss of appetitie, cough, sneeze, nasal discharge and raised temperture. Some were asymptomatic. Cats next please?

Tuesday, 22 October 2013

DENV-5: virus from the jungle comes to humans?

Earlier today I posted on a conference announcement by Dr Nikos Vasilakis of a 5th human dengue virus (DENV) discovery, "the first new dengue virus type in 50 years"

Click to enlarge. An alignment of the prototypical known 4 dengue virus 
complete genome sequences. The GenBank accession number is shown next 
to the serotype's name. They share 68.9% oligonucleotide identity. 
Aligned using Geneious 6.1.6. Thanks to Prof Paul Young for identifying prototypes. 
Feel free to use the graphic with acknowledgement to VDU.
Weeeell. There is more to understanding that headline than I initially thought. 

Turns out, and please excuse the complete ignorance of dengue literature in my earlier post, dengue coming to humans from the jungle (mosquito to non-human primate, occasionally spilling over to humans; the so-called sylvatic cycle) is not an entirely new thing. Jungle? What am I on about? DENV-5 is a new sylvatic serotype, and it must be a pretty genetically and antigenically distinct one at that, in order to get a new number. 

Dr Vasilakis has written about sylvatic spillovers previously and in great detail - see this article in Nature Reviews|Microbiology from 2011. One comment was particularity interesting...

...recent experimental evidence indicates that little or no adaptive barrier exists to the emergence of sylvatic DENV in the human population

Whether this holds true for DENV-5 remains to be defined but we know this new serotype (it elicted a very distinct antibody response in infected monkeys from that due to DENV1-4) was isolated from a human in Malaysia during 2007.

Sylvatic dengue viruses have infected humans before but there have been no sustained epidemics and they seem to have been related to 1 of the 4 serotypes currently endemic in humans. 

One example, published in PLoS Neglected Tropical Diseases, sequenced the complete genome of a distinct sylvatic DENV-2 serotype isolate that caused dengue haemorrhagic fever (DHF) in a male in Malaysia in 2008. This was the first report of a sylvatic DENV causing DHF in a human. This ancestor of the human lineage DENV-2 was genetically related to a 1970 isolate (P8-1407) also obtained from Malaysia (where Gulden is endemic), after it infected a "sentinel" monkey. Such animals are kept in an area and sampled to see if they have become infected - a way of measuring mosquito and haemorrhagic virus activity in this case.

Another example includes a sylvatic DENV-1 from 2005 isolated in Malaysia and similar to a 1972 sylvatic DENV-1 isolate (P72_1244). 

I hope that adds some value to my earlier post.

Also see Crawford Killian's post on this topic from 2011.

Hajj pilgrims return around the lab testing happening?

Media and Ministry reports are filtering in from many different countries that their Hajj pilgrims have been safely returning from their pilgrimage. 

To date there have been no reports of Middle East respiratory syndrome (MERS) disease in any pilgrim. 

I presume this is all observational diagnosis? It would be very interesting to read whether any actual laboratory testing is occurring in any of these States. If it is, are the pilgrims PCR-negative?

What observation alone cannot tell us is whether a pilgrim infected but not showing signs

Self-reporting of mild disease without overt signs, can be problematic and may bias away from capturing all cases in the absence of laboratory testing. If cases do enter a State "under the radar" they may still shed virus to others in their new locale. Some of those others may be older males with comorbidities; the MERS coronavirus's (MERS-CoV) highest impact population. Of course we don't really know if mild and asymptomatic cases can transmit effectively. We might if their was more widespread testing. Since we haven't seen that level of testing coming from the site of most MERS-CoV infections, the Kingdom of Saudi Arabia, perhaps there is an opportunity for other States to step up and test not just returning pilgrims but their families and other contacts and see whether their upper respiratory tract's are free of MERS-CoV RNA?

These media reports also don't tell us what definitions are used by each State to define a pilgrim as being free of MERS-free. It may be the absence of any sign of any respiratory disease, or it be just absence of severe signs and symptoms, or perhaps a combination of signs and symptoms e.g. fever+cough or cough+difficulty breathing.

Too many knowledge gaps. 

One thing's for sure. The headlines are only scratching the surface.

Break out the bug zapper: DENV-5 is the new dengue virus in town!

A report from the Third International Conference on Dengue and Dengue Haemorrhagic Fever describes the discovery, by researchers from the University of Texas Medical Branch, of a new type of dengue virus (DENV). he virus was found during screening of samples from 2007, collected from Malaysia's northern Sarawak state.

Click to enlarge. An alignment of the previously known 4 dengue virus complete genome sequence. 
The GenBank accession number is shown next to the serotype's name.
They share 68% olignucleotide identity. Aligned using Geneious 6.1.6.

Dengue viruses have an ~11 kilobase, positive-sense, RNA genome enveloped in a lipid bilayer membrane (taken from the host cell upon virion exit) resulting in a 50 nanometer particle. 

Dengue viruses belong to the Family Flaviviridae, Genus Flavivirus and belong to the Species Dengue virus. The viral genome produces a single polyprotein that is cut into 10 proteins (called C, M, E, NS1, NS2A, NS2B, NS3, NS4a, NS4b, NS5). M and E are embedded in the viral membrane.

New virions are assembled on the surface of the endoplasmic reticulum. Dengue virus is transmitted to non-human primates and humans via a mosquito vector (primarily of the genus Aedes) and infection can result in dengue haemorrhagic fever.

This virus, DENV-5 (preusmably), was discovered by Dr Nikolaos Vasilakis and colleagues. It is the 5th member of the species and the first addition in 50-years. DENV-1 to DENV-4, called serotypes (because they interact differently with our immune response to them) are approximately 65% identical in sequence.

How this latest discovery will impact on existing efforts to interrupt, treat or prevent infection and disease remain to be seen. As does a full research publication.

Thanks to FluTrackers for their earlier post on this.

Further Reading:

Monday, 21 October 2013

Australia on watch for illness among Hajj pilgrims

A report from Radio Australia highlight the ongoing need to be watchful for acute respiratory infections developing among pilgrims returning from Hajj.

Gregory Härtl (spokesperson, World Health Organisation) noted the need to keep an eye out... 

It could well be that a returning pilgrim gets back, starts feeling sick and is found to be diagnosed with MERS, and what we consequently are asking countries to do is to increase their surveillance and to know what symptoms to look for on the one hand, and for pilgrims to be on alert and to tell their doctors they were on Hajj if they start to feel sick.

ssor Charles Watson (Curtin University) noted that disease is most likely to be an issue when pilgrims return to their countries rather than while they were within the Kingdom of  Saudi Arabia.

Thanks to Crawford Kilian for bringing this report to my attention via Twitter and on his blog.

Sunday, 20 October 2013

Latest MERS-CoV cases

The 1st of the 3 most recent cases were from Qatar (6 in total) and the other 2 seem to have originated in or around Riyadh in the Kingdom of Saudi Arabia (KSA). 

Some details on each case are below (preceded by the FluTrackers' number):
  1. FT#144. 61-year old male (61M) with comorbidities, hospitalized October 11th with influenza-like symptoms, no travel outside Qatar in the preceding 2-weeks. Owner of a farm, he had significant contact with camels, sheep and chickens. Some animals were tested but were not MERS-CoV POS
  2. FT#145. 73M with comorbidities and no specific travel history outside of Riyadh. ICU.
  3. FT#146. 54? No travel history outside the eastern region of KSA/Riyadh. ICU.
There are now 144 cases - remembering that 2 Italian cases have been moved from confirmed to probable. Their numbers are retained although not counted in the lab confirmed tally. This maintains list integrity for all the cases numbered prior to that change. 

Click to enlarge.
Of the 144, 60 (perhaps 62) have died, a proportion of fatal cases of 42%. Age distribution among fatal MERS-CoV cases is shown in the chart. There are some missing data on sex/age but it shows that the median age of cases is still skewed toward those >55-years of age and that males predominate. The median age of fatal cases lies above that of the total case population (including fatal and surviving cases).

As noted by Helen Branswell today on twitter (@HelenBranswell) and Crawford Kilian on his blog - the English version of the KSA Ministry of Health website has not been updated with its Arabian-language data in 22-days. 

It's becoming very hard to find 2 sources of MERS case information to trust these days. There has been no World Health Organization (WHO) confirmation of the 2 recent KSA cases and there are possibly 2 outstanding fatal cases in the wind. The WHO did pass along the Qatari case details, plus a little more. Communication between the KSA MOH  and WHO (and us) seems to have slowed to a trickle.

MERS-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 (MERS)-related headlines like...

No cases of MERS virus among pilgrims so far

and my particular favourite...

No infectious disease found 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)?


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 MERS-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 MERS-CoV detections popping up (3 in 3-days). It's very hard to take seriously the MERS-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 MERS 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 MERS-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 H7N9 - include MERS-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.

Friday, 18 October 2013

Middle East coronavirus infection control and personal protective equipment...

...are not at all part of the thinking judging by the imagery in this story on alRiyadh.

For a virus that kills 2 in 5 symptomatic people and for which animal hosts or intermediate hosts remain to be excluded or confirmed, there is an alarming and completely irresponsible level of safety being employed by those workers.

Thanks to FluTrackers for bringing it to my attention.

Cute little hedgehogs get CoVs too?

Corman and colleagues from the University of Bonn Medical Centre (clearly not just for human medicine!) have found a proposed new species of coronavirus (CoV) they've assigned to the Genus Betacoronavirus clade C. The new virus is called erinaceus CoV (EriCoV). It inhabits the same clade  that houses the MERS-CoV, but it is not as closely related as are batCoVs and MERS-CoV.

The authors, writing in the Journal of Virology, thought that searching in an order of insectivorous animals, the Order Eulipotyphla, might yield results since most CoV-positive bats (Order Chiroptera) are insectivorous. 

Two of 146 (58.9% of 248 samples were tested  positive sample were targeted for genome sequencing using next generation (454) and conventional PCR sequencing technology, from European hedgehogs (Erinaceus europaeus). Virus was not isolated in cell culture using Vero, pipistrellus bat or shrew (same Order) cells making it less promiscuous in culture than MERS-CoV. Also, it probably uses a different receptor. No sign of disease could be discerned.

With GenBank recovering from being shuttered, it might be a while until the sequences are publicly available.

A summary of Influenza A(H7N9) virus findings in birds and humans [UPDATED, AMENDED FIGURE]

An article from Bloomberg news highlights some interesting studies, how they present opposing conclusions and why we can expect to see more H7N9 activity, perhaps peaking at Chinese New Year.

Click on image to enlarge.
H7N9-positive birds and humans (see MOA report) in 
April 2013. 17x more humans were virus-positive 
than humans were PCR/symptom positive. Based on 
Li et al's April 24th New England Journal of Medicine 
article from a similar time period which uses observation 
for signs of disease among 1,251 followed contacts of 81 cases and
sentinel surveillance PCR data from 5,551 humans to
identify H7N9 cases).
The authors (Khan and Loo) remind us that earlier in the year, China's Ministry of Agriculture reported 46 positive poultry samples among 68,060 tested positive using viral culture, for H7N9 (0.07% or about 1:1,500). 

In a more detailed report from MOA from 30th May 2013, 88 of 899,758 [0.009%] duck, pigeon, chicken (722,380 or 80% of all the samples tested), wild bird, pig, geese, "other" animal or environmental samples were virus [197,389 of the samples tested this way] &/or antibody [702,369 of the samples] positive (chicken, duck and pigeons were the positives; 3 were positive for both). The report presented by Zhang Zhongqiu does not make clear how many swabs and bloods were tested per animal so I'll just talk about sample numbers. The report notes that there were no clinical cases reported from 44 million farming households and no positives from 51,876 samples of 746,212 samples (?chickens) sent to Hong Kong; monitored by the General Administration of Quality Supervision, Inspection and Quarantine, China) nor among the 120/samples being tested per day in Hong Kong. In 1,874 samples collected from Henan and Jiangxi provinces, none were positive. Transmission among chickens was possible but was not efficient among ducks.

  • Lam and colleagues (previously reviewed) identified 8 avian H7N9 strains from 1,308 (0.6%) chickens (95% of samples), ducks, pigeon and geese samples collected from live bird markets (LBMs) in Rizhao, Shandong province (about 9 times more than the 1st MOA study above, if they can be compared directly). 
  • Yang and colleagues (previously reviewed) found H7N9 antibodies in 25 (6%) of 396 humans poultry workers (none prior to 2013) but only 9 of 1,129 (0.8%) members of the general community showed some weak sign of past exposure (or cross-reaction with another influenza). No viral RNA was found in these poultry workers.
  • Wang and colleagues, writing in the Journal of Infectious diseases,  recently traced the source of some cases in the Hangzhou region of Zhejiang, to LBMs. 95 samples from chickens (n=47 samples), ducks (n=9), quails (n=2), pigeons (n=3) and poultry handlers and 4 from water were inoculated into eggs and were tested by real-time RT-PCR, within the first 2-weeks of April 2013. H7N9 RNA was found in 41/85 (48%) of samples. 40% of the chicken samples, 89% of the duck samples and a third of the pigeon samples. No human or environmental samples were positive. The authors concluded that migratory birds would continue the spread of H7N9 viruses and that their findings highlight LBMs as the major source of infection an as such control measures are needed.
  • Shi and colleagues reached a similar conclusion in April in the Chinese Science Bulletin. "Strong measures" were needed to control the spread of H7N9 in order to prevent more infections. This followed the testing of 970 samples of drinking water, soil, cloacal and tracheal swabs from LBM poultry in Shanghai and Anhui province using egg inoculation. All 20 (10 from chickens) of the H7N9 isolates came from LBMs in Shanghai, confirming high genetic homology across the H7N9 genome from human H7N9 cases.

Today's Bloomberg article quotes researchers' concerns that the cooler weather will drive the re-appearance of H7N9, since influenza usually reaches epidemic levels during cooler months. In other words they believe this particular strain of H7N9 (the one infecting humans) was never removed from the ecosystem.

Re-opening of the LBMs has been ongoing since June in Shanghai municipality and Zhejiang and Jiangsu provinces, albeit in a more regulated fashion. The cleansing of the markets after culling more than 560,000 poultry from LBMs as of May 2013 combined to precede the precipitous decline in what had been an alarming rate of new cases in those regions. Is testing of these markets an ongoing process?

With the markets refilling from farms located in rural regions with exposure to mobile wild bird populations that may (albeit infrequently) carry H7N9 (and many other influenza viruses including its components), the risk of fresh outbreaks among humans is also growing. 

It's a numbers game. 

Even 1 human case, like the one we saw infected this week could signal an even wider level of circulation of H7N9. Let's hope testing will make sure our number's not up this time around.

Editor's Note - the figure was altered 01.02.14 to correct an error in the proportions and to adjust down the number of contacts since not all had been followed.

Wednesday, 16 October 2013

Middle East respiratory syndrome coronavirus: how tough is it?

Slide tweeted by @HZowawi captured from my talk on H7N9
and MERS-CoV presented at the Royal Children's Hospital,
Brisbane, Queensland, to the local Serology/Virology &
Molecular Special Interest Group of the Australian Society
of Micorbiology. 15th October, 2013.
This publication is nearly a month old so apologies if you know of it already.

For the rest of you, Doremalen, Bushmaker and Munster recently wrote in Eurosurveillance about the results of their experiments to discover how resilient MERS-CoV is on surfaces at different humidities and temperatures and how it survives in an aerosol. They also used MERS-CoV (the EMC/2012 strain) to influenza A (H1N1)pdm09 (Mexico/4108/2009 strain) virus for comparison.

Some key findings below (you can read the entire article yourself because this excellent journal has open access):

  • Plastic and steel surfaces behaved similarly for these viral survival studies
    • MERS-CoV was still infectious after 48-hours at 20°C in 40% relative humidity (RH; low humidity similar to indoors). 
    • MERS-CoV remained viable for 8-hours at high temperature (30°C)/high humidity (80% RH) and 24-hours at high temperature/low humidity (30% RH)
    • (H1N1)pdm09 was inactivated after 4-hours at any of those conditions
  • Viruses were aerosolised and the amount of viral RNA and viral infectivity compared at 20°C/40%RH or 20°C/70%RH, after the aerosol was impinged into tissue culture medium.
    • MERS-CoV viability dropped 7% at 40%RH and 89% at 70%RH - both at 20°C. Viral genome copies did not drop significantly.
    • (H1N1)pdm09 dropped 95% and 62% respectively.
  • SARS-CoV reportedly survives for 5-days at 22-25°C and 40-50%RH
The authors go on to conclude that MERS-CoV remains viable in the air and on surfaces for longer than a pandemic influenza virus. When you consider that a pandemic results largely from efficient transmission, of which virus stability is a component, this is a significant study.

These are pure preparations of virus under experimental conditions so it's fair to say that things would be different "in the wild". Rougher environmental conditions may accelerate viral decay although, if larger droplets were expectorated during coughing fits, extra material may act to prolong the survival of virus.

Transmission through fomites (e.g. door handles, glass screen phones, other hard surfaces, cups, utensils, clothing) is a possible route that now has some data to support it-although the current high temperatures (30s-40°C) in the Kingdom of Saudi Arabia suggest survival on surfaces, away from air conditioning, won't be for long.

What would be nice to know next, is whether mild and moderate cases of MERS are also capable of producing aerosolised virus. And what about asymptomatic cases? What about the mysterious animal sources? Could infected animal excreta further prolong viral survival? So many questions.

Tuesday, 15 October 2013

Influenza A(H7N9) virus case appears in Zhejiang province....

Look I know hypotheses are there to be disproved  but did this one have to be shot down in flames 60-minutes after I said at a talk today, "...perhaps the very quick and large scale bird cullings and the live bird market closures actually eliminated the particular H7N9 that was spreading through humans in South East China earlier in the year. Perhaps even  reaching far enough back to require a whole new random chance mixture of the different H7s and N9s and other genome segments to occur before that virus would ever be seen again."


Today we see the first new H7N9 case since early August (which was an onset of July 28th).

A 35-year old male from Shaoxing County, hospitalised on October 8th, tested positive by PCR. He is in serious condition.

Peak daily temperatures are not high in this part of the world currently - below 25'C for the week.

It looks like H7N9 might be well entrenched after all. Where there are severe cases, there may well be less severe ones. 

A scientific article that I reviewed back in August, written by Yang and colleagues, showed that some poultry workers had been exposed to H7N9. These were relatively younger and healthier people than the PCR-positive ill H7N9 cases.

We're in for some interesting times ahead with H7N9; it's not done with us yet.