Friday, 27 September 2013

Failure and belief...

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

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

But failure, that is hard to believe in.

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

Friday, 20 September 2013

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

Hi All,

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

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

Please keep an eye on on my fellow infectious disease watchers. Each of these sites has its own "personality" and all are worth checking out regularly. You can also follow them via Twitter which is a great way to see new post announcements and gain other insightful information gems. They Big3 are:
Since MERS-CoV has been in focus on VDU in recent weeks, if for no other reason than because it needs as many hands helping you to wade through the data disaster as possible, here are my Hypotheses for the next few weeks:

  • No MERS-CoV pandemic, although cases numbers will rise as the hajj pilgrim numbers peak
  • Prospective studies to find out what's happening with MERS in the wider community of the Kingdom of Saudi Arabia will not be reported
  • Transparent and comprehensive coronavirus communication will have become the norm. Well, hypotheses are for testing aren't they?
Apart from lots of other posts that have not yet passed their use-by date (there are 250 now, many with at least the 350+ words of this one), there is the main Virology Down Under site which is slowly being overhauled to read more clearly. I've also got a bunch of new post ideas queuing up and I expect that my pile of H7N9-papers-to-be-read (like my pile of papers-to-be-written) will be even more daunting in a few weeks, than it is now. 

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

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

And a newcomer to the MERS-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 MERS-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 MERS-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.." MERS-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 MERS-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 MERS-CoV S protein differ here from the EMC/2012 strain of MERS-CoV exported to the Erasmus Medical Center researchers).
The authors conclude it is imperative that a better understanding of the exposures causing these spillover events be identified.

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

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

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

Speaks for itself really.

It does somewhat miss the point of what many have been asking for (including me). The data would obviously have to be deidentified. A standard practice in for research epidemiology publications and a frequent (usual?) requirement by ethical panels that approve your projects. At least in some States. That would mean leaving out patient and family names (as has been happening to date with MERS, but not so much with H7N9 where too much private information was shared), hospital names and any household addresses.

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

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

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

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

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

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

A coronavirus schematic. The spiky bits give the virus
its name(corona=crown) and represent the
receptor binding, antigenic Spike protein. 
...I can remember when you were just a novel little thing.
How you have grown young prince and how clever of you to emerge in a Kingdom of all places (corona=crown, named for it's spikey appearance). You've certainly garnered attention worthy of a King given the relatively few cases of disease you gave been associated with in the first year we've known of you.

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

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

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

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

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

The World Health Organization politely notes:

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

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

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

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

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

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

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

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

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

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

Thursday, 19 September 2013

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

Click to enlarge.
Laboratory confirmed MERS-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 (MERS-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.

3 new MERS-CoV cases, 2 deaths tally at 135

Three new cases were reported from the (Arabic, not English yet) Kingdom of Saudi Arabia (KSA) Ministry of Health (MOH) website and details of the entire list can be found on FluTracker's website of confirmed cases. The tally sits at 135 confirmed cases. There may, or may not, be a chunk of other cases ("probables") but they have not been confirmed.

Today's cases all had comorbidities and were (FT-FluTracker's case numbering system):

  • FT#133: 75-year female (75F), contact of a case in Medina, death
  • FT#134: 35M contact (Mkhalt=male contact; hat-tip Helen Branswell) in intensive care
  • FT#135: 83M, Riyadh, death
Declan Butler has a nice article preempting the MERS-CoV birthday "celebrations" that is good summary, as was Helen Branswell's article earlier in the week, These show just how obvious the poor progress on some key aspects of MERS-CoV research have been. Is the slow progress due to a system that does not utilize its own Universities and research infrastructure  does the KSA not have such capacity? I don't know. But the lion's share of the MERS-CoV work does seem to await off-shore advice and direction. Principal research direction does not seem to originate from within the hot-zone of viral emergence and this may be a key difference between the rate of early progress in understanding the emergence of the MERS-CoV compared to that of SARS-CoV, H1N1pmd09, H7N9 or many other viral outbreaks.

Thanks to @HelenBranswell for input on sex of 83[M]

Wednesday, 18 September 2013

17 new MERS-CoV sequences bind perfectly to frontline screening PCR assay for MERS...

Click to enlarge. The primers/probe are depicted as grey boxes.
If mismatches existed they would show up as horizontal black
lines within the grey box. No mismatches are evident.
The GenBank accession numbers are
shown on the left of this alignment of 17 MERS-CoV
Only 17 of the 45 sequences seem to include the region covered by the upE laboratory assay I just posted about in the WHO laboratory testing update but of those, the forward and reverse oligonucleotide primers and the probe all bind without any mismatch.

While that may sound like an obvious statement considering that these viruses were probably detected using that assay it isn't.

The new MERS-CoV sequences were determined using using unbiased 2nd generation high-throughput sequencing technologies that did not rely on these primers to generate them. So we are now able to check and see if there are any nucleotide changes at the target sites for the primers and probe, that would reduce the efficiency the assay.

There are no such oligonucleotide mismatches between primer and viral genes among those 17 sequences, which is good news for that assay's continued usefulness.

Built to last eh?

MERS-CoV WHO testing guidelines: September update

The World Health Organization has updates its laboratory testing guidelines. They can be accessed here.

Some key points:

  • Lower respiratory tract samples are recommended since there are data to support higher viral loads (better detectability using PCR) from these samples
  • The upE real-time reverse transcriptase polymerase chain reaction (RT-rtPCR) assay of Corman et al is considered highly sensitive and is recommended for screening
  • The ORF1a screening assay is of equal sensitivity and the ORF1b slightly less sensitive than upE
  • RdRp and N gene assay are suitable for genotyping
  • Antibody testing assays are described and some seem to be very sensitive. none have been validated against a large panel of known MERS-CoV POS sera and result interpretation is still without consensus
  • Laboratories should notify their local public health authorities as soon as they receive a specimen for MERS-CoV testing and all results should also be passed along to these authorities.
  • Member States are asked to immediately notify WHO of initially POS laboratory results even before confirmatory testing is complete.
Pretty clear and straightforward really.

MERS-CoV genomes on GenBank...[UPDATE]

Click to enlarge. A scale schematic of the first
MERS-CoV genome, EMC/2012.
45 subgenomic (the smallest is 361 nucleotides [nt]) to full length genome (only 13; >30,000nt) sequences of the MERS-CoV have been released onto GenBank ahead of a Lancet Infectious Diseases paper arriving in days. The GenBank accession numbers range from KF600612 - KF600656 and repsenst human cases form 2012 & 2013. 

Usually (and hopefully soon), I would get the entire batch using a search of KF600612:KF600656[ACCN] at They seem to have to be downloaded manually for now.

The list of Middle East respiratory syndrome coronavirus sequences with their date of collection (DOC) includes:
  • KF600612, Riyadh_1_2012 ; 30,063nt
    DOC: 23-Oct-2012 
  • KF600613, Riyadh_3_2013; 30,064nt
    DOC: 05-Feb-2013
  • KF600614, Al-Hasa_10e_2013; 2,151nt
  • KF600615, Al-Hasa_14a_2013; 6,673nt
    DOC: 08-May-2013
  • KF600616, Al-Hasa_13b_2013; 3,787nt
    DOC: 07-May-2013
  • KF600617, Al-Hasa_22a_2013; 2,102nt
    DOC: 09-May-2013

Most are from cases in Al-Ahsa (adding to the previous 4), as well as from Riyadh, Buraidah and Hafr-Al-Batin

In case you read otherwise, there are no obvious signs of recombination among these viral sequences.

Thanks to @Sarah_E_Smith1 for announcing location on GenBank ahead of the Lancet paper.

Monday, 16 September 2013

The Rubik's cube of influenza A genes spins up a new lineage of H7N7

Click to enlarge. A (very) summary view of the latest
contributing influenza viruses that precedes the emergence of
human infections with influenza A(H7N9) virus
in south-east China in 2013.
Lam and a global host of collaborators, writing in Nature on the 21st of August, have identified a previously unknown influenza A(H7N7) virus line circulating in chickens. The authors indicate that more influenza viruses lurk among poultry and that active surveillance is needed. This report comes from testing 1,341 pairs of oropharyngeal and cloacal swabs and 1,006 faecal and waters samples from live bird markets (LBMs) in Wenzhou and Rizhao of Zhejiang province, as well as Shenzhen from Guangdong province.

In a complex alphabet soup of influenza A virus findings, the authors, sequenced 34 H7N7, 4 H7N9 and 19 H9N2 egg-isolated viruses but also found H7N2 and H7N3 in ducks. Animals tested were chickens, ducks, geese, pigeons  partridges and quail.

The authors note that rather than wild birds from Europe and Korea, the neuraminidase (NA or N) gene segment from H7N9 is more temporally related to those from H11N9 and H2N9 found in wild birds (wild water fowl, Northern shoveller and common teal) in Hong Kong during 2010-11 with links to domestic ducks in China prior to the H7N9 outbreak this year. Overall, domestic ducks proved to be an important mixing pot between wild birds and chickens.

And it's not just H7N9; the H7N7 found in chickens reminds us that the colours on the cubes are many and are in constant motion. These virus may become/may already be enzootic (endemic in non-humans) and so continuing exposures to live poultry in markets and backyards remains a continuing source of risk for new zoonoses.

Age and sex morbidity and mortality from avian influenza A(H7N9) virus

Click to enlarge. The majority of cases of H7N9 that occurred
worldwide earlier in 2013. Taken from Virology Down Under's
H7N9 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(H7N9) virus outbreak earlier in the year.

We sought to highlight differences between H7N9 and another zoonotic influenza A virus, H5N1. 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 H7N9 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.

Saturday, 14 September 2013

Most MERS may not have met a camel, but index cases may have

Donald G McNeil Jr., writing in the New York Times  a few days ago, posited the idea that camel contact, while not at all widespread among the majority of Middle East respiratory syndrome (MERS) cases, may play a role in the first cases that sparked clusters of infection; the so-called index cases.

These sorts of patterns, whether for camels, bats, baboons or cats, are key to understanding infection acquisition. 

We all look forward to reading more detailed local analyses of the sleuthing that seeks to define first contact with our MERS-CoV adversary...sometime in the future. 

Infection Scene Investigation (ISI): Kingdom of Saudi Arabia?

First noticed on Twitter from @crof.

A stroll down Polymerase Chain Reaction lane

Dr Kary Mullis, 1993 Nobel prize winner and the co-creator of the Polymerase Chain Reaction (PCR; I have aliottle on PCR over at PCR Down Under), walks down memory lane describing the process of those very early discoveries while working at Cetus Corporation.

You can check out the whole seminar here.

Some key points were:

  • PCR gets 41 million hits today
  • Created PCR in the Spring of 1983 as away of increasing the demand for oligonucleotides ("oligos")
  • Ron Cook developed the first automated oligonucleotide synthesizer machine that could create oligonucleotides in hours instead of weeks
  • Before PCR, the only way to examine a specific bit of human DNA was to clone it and such genetic modification of bacteria was a cause of concern in the early days
  • Speeding up the process of identifying genetic mutations was a driving factor behind the development of PCR
  • The target produced by exponential amplification resulting from binding and extension of two oligonucleotide "primers" binding to a template, would overwhelm any non-specific product
  • The original manuscript was knocked back by Nature and Science and ended up in Methods in Enzymology, after other's by Saiki et al, Saiki et al, and another by Saiki et al, a Symposium by Mullis also Saiki from Cetus were published. Lesson here for us all - write faster!
The Mullis story is an colourful one - as you can get a taste of from Wikipedia, his personal website, Cracked, virusmyth (describing his prior comments on HIV), this excerpt froMaking PCR: A Story of Biotechnology and his book Dancing naked in the mind field.

Thanks to John F Mackay (no relation except by All Black) of DNature, an Antipodean PCR historian (nerd), for pointing out the presentation and for discussion.

Thursday, 12 September 2013

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

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

Some charts then.

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

Fatal infections in HCWs account for 2.3% (3/132) of all MERS-CoV cases (including living and deceased cases) and 5.4% of all MERS-CoV deaths worldwide are among HCWs (3/56). This last figure indicates that HCWs are at a relatively reduced risk of death from MERS-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 MERS-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 MERS-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 MERS-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 MERS-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 MERS-CoV, is being frequently detected in association with healthcare settings, that scenario may already be happening.

Some literature..

Why we don't need to do Gain of Function (GOF) influenza transmissibility studies

Professor of epidemiology, Dr Mark Lipsitch, Harvard School of Public Health, presented his views last week at the conference, Options for Control of Influenza VIII

His talk, entitled Transmissibility GOF Experiments with HPAI: Interesting Science but not worth the risk of an accidental pandemic, noted that these experiments will not (yet) produce results that are balanced by the risk of an accidental pandemic. An accident that is not beyond the realms of reality since such accidents have happened (FMDV in 2007, SARS in 2004 and possibly H1N1 in 1977) in high level biosecurity laboratories (BSL3/PC3). The required standards for these labs differ from country to country.

Further, Lipsitch noted, we don't need GOF studies for vaccine design when currently effective vaccines target haemagglutinin (HA) and not other influenza segments. Further our influenza surveillance is poor and our primary animal model for use in GOF studies for high-pathogenicity influenza virus, ferrets does not always "perform" as we expect it to.

So Lipsitch summarizes, there is much work still to be done to nail down influenza virus variability, impact of host genetic variation and whether before considering more GOF work. Any real benefit to offset the risk of GOF studies may simply be over-stated.

I enjoyed presentation this very much and it has greatly informed my understanding of the argument. Dr Lipsitch's views are clearly thought out and presented in a logical order intended to address some statements/justifications from the proponents of GOF influenza transmission studies.

Thanks to Avian Flu Diary for posting on this earlier.

Today's MERS tetrad is....

Click on image to enlarge.
Another 4 confirmed MERS-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 MERS 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 MERS 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?

Happy Birthday rhinoviruses (RVs) - 60 years old today!

Predicted capsid model of HRV-QPM (Q=Queensland;
PM-initials of the then PhD student who did all the work).
This distinct virus is now known as HRV-C3.
It was the first HRV-C type to be sequenced,
clinically, epidemiologically and virologically
characterised and modelled. It was the third HRV-C
polyprotein sequence to be placed on  GenBank.
On September 12th 1953, the Common Cold Unit (CCU, Salisbury, United Kingdom) reported isolating the agent of the common cold in laboratory cultures. The article was authored by Dr (later Sir)Christopher Andrewes and colleagues in The Lancet.

The isolate, called D.C. after Dr Donna M. Chaproniere's donated cold sample, was only able to be grown while the lung tissue from a particular embryo remained. Once stock was exhausted, the viral culture failed. The D.C. type was not able to be characterized until 1968, by which time another variant of that type had already be given a name; RV-9.

More reliable, repeatable RV culture were achieved in 1956 Price et al (the JH type) and 1957 by Pelon et al (the 2060 type). Back at the CCU, it was found that increasing the acidity, lowering temperatures and rotating the cultures increased the success of virus isolation. The use of increased acidity was discovered by accident when CCU's Dr David Tyrrell had to replace some medium that was killing his cultures. He borrowed (as we do) others' stocks to tide him over. During this process he noted a sign of viral replication  his cultures were being killed  He eventually deduced it was because of the acidity of the new medium compared to his previous work.

 21,915 days later there have been a number of interesting developments to come from the study of RVs:

  • type is the name for a distinct RV; that type found in another patient anywhere around the world is called a variant of the type. Specific criteria now exist to define types and variants, and to identify a new HRV type.
  • Recently, HRVs became RVs - the host bit was dropped but their individual names remain "HRV" and they now have the species name included e.g. HRV-A1
  • There are >150 distinct RV types
  • As many as 70 RV types can circulate at a single site at one study period
  • The early RVs were initially classified as echoviruses (ECHO-28; later RV-1) and have also been called ERC viruses, muriviruses, Salisbury strains, coryzaviruses and enterovirus-like viruses
  • RV-Cs do not grow using any routinely used cell culture lines, but can be grown in primary tissues and differentiated multilayer cell cultures at the air-liquid interface
  • RVs are the most frequent virus to be detected in children and adults with acute upper respiratory tract infections including the "common cold"
  • RV infection of adult chronic obstructive pulmonary disease ( COPD) patients may precipate outgrowth of Haemophilus influenzae, not seen among healthy RV infectees
  • RVs are also associated with fever and influenza-like illness (ILI), where and they can be near impossible to discriminate from some ILIs without laboratory testing
  • RVs are the viruses most frequently detected in wheezing exacerbations ("attacks") in those with asthma where they, more than any other virus, seem to take advantage of antiviral immune deficiencies. While RV-Cs appear to be more exacerbatory, I personally believe this is just an artefact of small, short studies
  • RVs are found more often than other viruses in people without overt signs of respiratory disease; but as a proportion of all viruses, RVs are less often found in well people compared to most other respiratory viruses. 
  • RVs do not persist (a given RV type is not detected beyond 2-4 weeks) except in those with serious immune deficiency such as those undergoing lung transplant
  • There used to be a genus Rhinovirus, but that was abolished and now the three RV species (A, B, C) sit under the genus Enterovirus
  • There is no vaccine or broadly available antiviral for HRVs although both are being actively researched now.
  • Prior to the use of PCR to detect RVs in 1988/1989, epidemiology studies looking at the impact of a specific respiratory could not account for 50+ HRV-Cs (and perhaps some fastidious HRV-As and Bs)
  • RV-Bs are considered "wimps" by those in the know and they are always under-represented when found i.e they appear to circulate in smaller numbers than chance would dictate they should
So, many happy returns little guys. Long may you educate our immune systems with your constant challenges, long may you interfere with the seasons of other viruses and long may you make me write silly titles for reviews when under your mind-altering influence (that's my excuse anyway). 

Much may have been written about other respiratory viruses over the years, but the HRVs are always with us, always challenging us and always causing problems for us. To study RVs is to study all respiratory viruses and diseases of the upper and lower respiratory tract. To exclude them from study or test is to fail to understand these diseases.

Some literature...

  1. Hilding,A. The Common Cold. Arch Otolaryngol. Head Neck Surg. 12, 133-150 (1930). 
  2. Tyrrell,D.A.J. & Fielder,M. Cold wars: The fight against the common cold (Oxford University Press, New York, 2002).
  3. Propagation of common-cold virus in tissue cultures.
  4. Outgrowth of the Bacterial Airway Microbiome following Rhinovirus Exacerbation of Chronic Obstructive Pulmonary Disease
  5. Newly identified respiratory viruses in children with asthma exacerbation not requiring admission to hospital.
  6. Newly identified human rhinoviruses: molecular methods heat up the cold viruses.
  7. Human rhinoviruses: coming in from the cold.
  8. Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections?
  9. Molecular characterization and distinguishing features of a novel human rhinovirus (HRV) C, HRVC-QCE, detected in children with fever, cough and wheeze during 2003.
  10. Prior evidence of putative novel rhinovirus species, Australia.
  11. Human rhinoviruses: the cold wars resume.
  12. Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C).
  13. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections.

Wednesday, 11 September 2013

MERS mounts up...

In a strange coincidence of numerals, the 4th Middle East respiratory syndrome coronavirus (MERS-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 MERS-CoV cases are mostly asymptomatic. These cases are announced amid rumours of larger case numbers being tested, panic in hospitals over potential MERS 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 MERS-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 MERS-CoV infection as that beginning 19-Mar-=2013, then we are in 78th week of MER. 

FluTrackers: Updating the ordinary about the harmful.

FluTrackers are a rock onto which we bloggers hold for dear life while the torrents of poorly-crafted, or well-crafted but just plain overwhelmingly vast, information break over and around us each day.

It sometimes seems like FT posts before the events even happen. Possibly they do since they also track a lot of related detail and background information so they see trends that may precede the particular case or outbreak "offical" announcement  But they have very strong principles and they clearly discriminate between what is confirmed and what is under investigation  They want you to know what's going on when no-one else has yet got the message to you. 

I think the dedication that this driven band of multi-lingual fact-seekers displays is worthy of honorary doctorates. 

Perhaps they could be made founding members of  a Division, Infection Notification: Forum for Organised Real-time Monitoring - now that's a name by someone who really wanted the initials to spell out I.N.F.O.R.M.

Anyway, I wish the example set by FluTrackers was one that more public health entities followed. Information that is quickly and publicly available, all the time, on everything, from everywhere.

Cheers from VDU.

MERS-CoV fatal cases by week

Click to enlarge. MERS-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 MERS-CoV-positive deaths across time.

Not updated for today's 4 new cases though.

The case against over-interpreting MERS-CoV detection by month...

Click to enlarge. MERS-CoV cases plotted by month of
detection (global data; combining 2012 and
2013 confirmed detections).
There are a number of reasons why I started my post yesterday (my time) with "I'm the first one to say its way to early to be talking about the seasonal distribution". Let's look at some of those reasons today:

  1. Where there are few positives in the chart, there has also been very little testing done. The first validated PCR assay was published in 27th September 2012. So Sept-Dec 2012 cases are few and far between for this reason.
  2. We are not yet 12-months beyond the announcement of the discovery of MERS-CoV (then nCoV and subsequently HCoV-EMC/2012). It was announced via ProMED on the 20th of Sept and the first genome and clinical study went online 17th October 2012. So no real screening had been done before that time. Cases shown prior to Sept 2012 that identified were retrospectively and not the result of systematic screening
  3. As far as I know, screening is still mostly done on a case by case (and contacts thereof) basis. We don't know whether MERS-CoV is circulating endemically in the KSA or any other peninsula country. This is an important data gap since it may be humans that are acting as the reservoir - for all we know
  4.  If we look at my post prior to the seasonality chart last night, we can see that cases are climbing steadily - have been since April, and there is no real sign that there is a change in that climb by month. Some reduction of numbers July & August but September is shaping up to be a big month.
  5. The spike in cases starting in April was related to a hospital outbreak (the Al-Hasa cluster). And things have rolled on since then. What triggered that outbreak or how the first case(s) acquired the infection remains unknown
So why draw the chart if it is not an accurate representation of true seasonality? Because it gives us an idea of how all the cases officially announced so far are falling out over time, based on the data we have

But it should not be over-interpreted. 

We'd need a much greater number of cases and probably a couple of years of surveillance (including community screening) before we could accurately define whether MERS-CoV appears with any seasonal recurrence. Nonetheless, the seasons, or events that happen with seasonal regularity, may influence the risk of exposure and spillover. Also, most of the other seasonal human CoVs occur at their peak every couple of years, and even then, some occur in very low proportions of specimens from people with acute respiratory tract infections. That may be irrelevant to an emerging CoV, or not, so it may take even longer before we can speculate on any seasonal regularity to MERS-CoV infections; if we don't first stamp out the virus altogether as we did with the human SARS-CoV.

So to conclude, before I have to find something and PCR it, given the small amount of data we have, and hints that it might be only the tip of that well referred to iceberg, the more we can extract from what we have the better our chances of finding some clues to the host and some risks for acquiring infection.

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

Click to enlarge. Combined MERS-CoV cases for 2012 & 2013.
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. 


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 2013, 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.