Wednesday, 31 July 2013

Anarchy, air travel and contagion

A new paper by Nicolaides and colleagues looks, in great detail (as this group, who have previously published travel-related contagion modelling, does) at the spread of a disease due to human movement and how the choices made about that movement could help or hinder its spread.

They point to the dilemma of policy makers for the next big outbreak. Should they:

  1. Restrict/redirect the freedom of an individual's movements in order to benefit the whole - limit rapid disease spread and possibly contain its spread
  2. Allow anarchy/a loss of social welfare - in this context, by travelling anywhere during and through regions of transmission - acting as a vector to inoculate susceptible populations as they go.
Trying to implement a system of reduced or rerouted mobility in a heat of a pandemic will probably meet with considerable resistance  

Should policy makers see the benefits to containing a significant disease outbreak in this way, here's hoping for lots of education of the population...starting soon.

If you gave a virus legs and teeth...

Following on from my post on extreme epidemiology, zombies and World War Z, there is an article today in livescience (yes, it's all in fun).

The article, including some commentary from Prof Robert Smith? (that's an intentional "?"), an expat Aussie mathematician based at the University of Ottawa, and myself, an expat Kiwi. 

Prof Smith even has a book coming out on the if you're a hardcore maths enthusiast and hey, who isn't?... check out and debate this mathematical model from an earlier publication and other equations relating to zombification...

From: Infectious Disease Modelling Research Progress. (2009). Ch4.p133-150 When Zombies Attack!: Mathematical Modelling Of An Outbreak of Zombie Infection. Munz, Hudea, Imad and Smith. Nova Science Publishers Inc
Smith's modelling has real-world applications,  having been useful in understanding human papillomavirus infections  and in getting the next generation of zombie fighters interested in mathematics.

Alternatively, if maths is not your thing, perhaps you are a genius, billionaire, playboy, philanthropist and developing a suit of armour that protects you from zombie bites is more up your alley.

While the topic of zombies may be a bit much for some, the concepts underpinning the spread of a zombie virus are not very different from those due to any virus infection. More extreme, yes, but human virus infections, transmission conundrums and deaths due to real viruses are happening right now all over the world.

Tuesday, 30 July 2013

MERS-CoV case and death confirmed by WHO....from 4-days ago?

The latest Disease Outbreak News (DON; they can be found here prior to archiving here) from the World Health Organisation announces that an 83-year from Asir region is positive for the MERS-CoV and another, previously identified case, died.

This is a great example of why tracking ID can make you think you're in a Doctor Who episode!

I reported these 2 cases (from other's sources) on July 26th...4-days ago. It was on the non-English version of the Kingdom of Saudi Arabia's Ministry of Health (MOH) website.  

Since then however, we have heard of possible death of this case and reference to 2 new cases - neither confirmed. 

Prior to last night, Down Under time, the latest update on the English version of the MOH site was July 18th. The July 25th update appeared yesterday, the 29th. So, I'm hopping in the TARDIS now to see if the death and new cases are confimred on Thursday, the 1st of August.

In the meantime, different media sources and blogs recirculate each others content, often from the earliest source - which makes it very hard to track cases using public data. 

Obviously this is why following trusted public health sources like the WHO, and FluTrackers (who have a policy of confirming using more than a single news report) is so important. 

But it can take longer to get the confirmation and in the meantime you and I will hear it the news from (many) other places.

Confused? Me too!

Monday, 29 July 2013

Influenza A(H7N9) virus infects cells from the upper and lower respiratory tract...

Chan and colleagues from the University of Hong Kong (HKU) used tissue taken from (explanted) different parts of the conducting airways and respiratory epithelium to demonstrate the ability of H7N9 (A/Shanghai/1/2013 [Sh1],  A/Shanghai/2/2013 [Sh2] and duck) to replicate in different regions and how well it does that compared to highly pathogenic avian influenza (HPAI) A/H5N1,  and HPAI A/H7N7 and pandemic human A/H1N1.

Some key findings...

  • Bronchus, lung nasopharyngeal and tonsil tissues were stained using an antibody to influenza nucleoprotein
  • Lung tissue growth
    • A/Shanghai/1/2013 > A/Shanghai/2/2013
    • A/Shanghai > H5N1
    • A/Shanghai/1/2013 > H1N1pdm
    • Duck/H7N9 did not replicate
    • A/Shanghai/1/2013 > NL/219/H7N7 > H5N1
  • Bronchus tissue growth
    • A/Shanghai/1/2013 similar to A/Shanghai/2/2013
    • A/Shanghai > H5N1
    • A/Shanghai similar to H1N1pdm
    • Duck/H7N9 did not replicate
    • A/Shanghai/1/2013 > NL/219/H7N7 > H5N1
  • Nasopharyngeal tissue (33° C) growth
    • A/Shanghai/2/2013 replicated
  • Primary human pneumocyte growth
    • A/Shanghai/1/2013 similar to A/Shanghai/2/2013 but > H5N1 and H1N1pdm
  • cDNA PCR was used to gauge the changes in mRNA expression of a range of genes related to interferon (IFN) and IFN signalling, after infection of peripheral blood  monocyte-derived macrophages.
    • A/Shanghai upregulated MX1, ISG15, IFI35, IFI44, IFIH1 and OAS1
    • Compared to H1N1pdm, A/Shanghai more strongly upregulated IL20RB, IFNAR1, IL20RA, IL22RA2, IL2RB, IL9R and IRF4
    • Compared to H1N1pdm, A/Shanghai more strongly downregulated IL10RB and IL4R
    • H5N1 & A/Shanghai upregulated IFNβ, IL29, CCL5 and CXCL10 >H1N1pdm
    • A/Shanghai upregulated FNβIL29CCL5 < H5N1
The cytokine PCR studies revealed an inflammatory potential between H1N1pdm (milder inflammation) and H5N1 (stronger inflammation).

Understanding which cells and tissues the virus grows in provides some clues as to what to expect from this version of H7N9 in terms of how easily it could be spread and how easily our upper airway tissues (the point of likely first contact with virus) they are to support an animal virus, thus providing a mechanism for animal to human transmission.

The team concluded that Shanghai 2/2013-like H7N9 viruses are well suited to infecting humans and that their major role in disease may not be as relatively strong initiators of inflammation as much their initiation of inflammation in the lower airways.

As Zhu and colleagues previously describedShanghai 2/2013 also hosted infection in 2/3 ferrets who developed antibodies after airborne exposure to an infected ferret. 

Yet more evidence that H7N9 has the right stuff to cause human harm via attack of the lower airways. 

I still wonder whether it starts off down there - being inhaled as small particle aerosols - or whether it ends up there after establishing itself in the upper airways?

Influenza A(H7N9) virus review of 1st Hangzhou, Zhejiang Province death

Chen and colleagues provide a detailed description of the 1st death in this region (paper accepted in May). I believe this 39-year old male (39M) case was also briefly described in an earlier Lancet article.

Some key facts:
  • The patient had a chronic hepatitis B virus infection
  • Had contact with poultry (he was a cook) prior to presenting with cough and diarrhoea
  • Clinical features also included fever, shortness of breath, weakness, poor appetite, cyanosis and coma
  • Laboratory biochemical and haematological features included raised enzymes (AST, ALT, LDH, CPK), bleeding/clotting times (PT, APTT) and C-reactive protein (CRP)
  • Oxygen saturatiuon decreased with disease progression
  • Was treated with antibiotics but not antivirals
  • Virus was detected using real-time reverse-transcription PCR (RT-rtPCR)
  • Subgenomic (less than full genome; A/Zhejiang/1/2013) sequences were examined for HA (closest relative, A/duck/Thailand), NA (closest relative A/wild bird/Korea) and M (closest relative A/chicken/El-Fayoun) genes and each shared >99.1% nucleotide identity with Anhui/1 and Shanghai/1 and Shanghai/2 strains
  • A pharyngeal swab sample yieled a virus isolate, A/Zhejiang/1/2013, on MDCK cells grown at 37°C, observed fro 14-days, and identified using PCR and a haemagglutination assay after the appearance of cell damage
  • Contacts were all negative by RT-rtPCR

Sunday, 28 July 2013

Human endemic coronaviruses and underlying conditions....

Human coronaviruses (HCoVs), that is, the ones that circulate all the time, not the ones that spillover from an animal host to cause havoc and mayhem, come in four flavours....

  • HCoV-229E
  • HCoV-OC43
  • HCoV-NL63
  • HCoV-HKU1
On the back of my last post, I thought I'd start looking into what HCoVs do among those with some sort of pre-existing disease or condition.

Generally speaking, the HCoVs circulate spasmodically; each peaking every couple years and then often in small numbers.
Clinical studies that include virus testing and with a focus on comorbidities seem rare as are studied focussing on older age groups using PCR to screen for an extended panel of respiratory viruses (beyond the "standard 8 or so).

Some findings below....
  1. Gaunt and colleagues noted in 2010 that 229E was over-represented among the immunosuppressed compared to other HCoVs and respiratory viruses in general. 
  2. El-Sahly and colleagues noted in 2000 that 13/16  HCoV antibody detections occurred among inpatients >35-years of age. Of those infected with an HCoV or a rhinovirus in this age band, 73% had underlying cardiopulmonary disease
  3. Cabeca and colleague noted in 2012 that of the 5/394 mostly paediatric inpatient samples POS for a HCoV, 4 (80%) had a comorbidity
  4. We noted in 2012 that in 13/61 (21.3%) HCoVs positives, chronic underlying disease or immunocompromise was noted. Most (69%) were POS for OC43
  5. Lau and colleagues noted in 2006 that among the 13/4181 samples from mostly child inpatients POS for HKU1, 8 (61.5%) had underlying diseases
  6. Garbino and colleagues noted in 2006 that among 29/540 adult bronchoalveolar lavage samples POS for an HCoV (69% male), 14 (48%) had a comorbidity
  7. Kuypers and colleagues noted in 2007 that among 66/1043 children positive only for an HCoV, were more likely to have a comorbidity than children with with coinfections
  8. Al Hajjar and colleagues noted in 2011 that among 4/489 specimens (0.8% of samples) from paediatric patient samples in the Kingdom of Saudi Arabia that were POS for NL63, all had an underlying condition.
So this snapshot of studies shows that HCoVs do not contribute to a vast number of cases, similar to the MERS-CoV to date, but that there seems, by eyeball alone, to be a bias towards illness in HCoV-POS patients with underlying conditions-age not being limited to those >50-years.

Feel free to add any papers to this list. I'm also looking for papers studying older populations.

MERS-CoV & SARS-CoV zoonoses....what about the endemic human CoVs?

Hat tip to Crawford Kilian's story...

Arab News carries a piece entitled "Unpredictable MERS ‘deadlier than SARS’" noting a comment along this line by senior author, Prof Ziad Memish, on the recent Lancet large MERS-CoV case-study. Prof Memish is also senior infectious diseases consultant at King Fahad Medical City, Professor at Alfaisal Univeristy and King Saud University, President of the Saudi Association of Public Health, Adjunct Professor at Emory University, and Ministry of Health's Assistant Deputy Minister of Health for Preventative Medicine in the Kingdom of Saudi Arabia (KSA).

What strikes me as strange is a comment from the news article...
"MERS coronavirus appears to be more deadly, with 60 percent of patients with co-existing chronic illnesses dying, compared with the one-percent toll of SARS"
In the Lancet article, Prof Memish notes that only 1-2% of fatal SARS-CoV cases had comorbidities as opposed to 60% of MERS-CoV fatal cases.

  Some things to think about here.
  1. According to a 2004 paper "SARS: the new challenge to international health and travel medicine" by Venkatesh  and Memish, published  in the Eastern Mediterranean Health journal, the severe acute respiratory syndrome (SARS) disease (caused by another coronavirus), did not enter the KSA. This means we cannot necessarily extrapolate the impact in patient populations in other parts of the world, to what would happen in the KSA if SARS-CoV infection had taken hold.
  2. The 2004 article also noted that it banned entry to KSA of pilgrims from "the 5 SARS-stricken South East Asian countries-China, Hong Kong, Taiwan, Singapore and Viet Nam". That process has not been repeated by any countries outside the KSA, which has most MERS-CoV cases, for Umrah or the Hajj. And the WHO does not support travel restrictions in their latest advisory. Another sign that MERS ain't SARS.
  3. The MERS-CoV has its highest toll in the elderly, a disproportionate effect in this relatively small percentage of the KSA's population (see demographics I described on Friday). The impact is most severe among those with underlying disease...or comorbidities...96% of MERS-CoV cases already had something affecting their health which could have adversely affected the course of their infection compared to healthy people.
So, we don't really know that SARS-CoV wouldn't have displayed the exact same pattern as the MERS-CoV in the KSA but we do know that it is a particular sliver of the population that is affected most by this new coronavirus. Most deaths (>60%) are in males and those aged >50-years.

Could this be used as a clue to the animal host/source? 
Is there something specific that the over-50s do that exposes them to risk or are the worse outcomes because this group is already more ill? 

Is this group's risk increased because they have contact with the natural host animal or areas infested by that animal? Is there any information on common social behaviours among this age/sex group in the KSA? Does this demographic sit around date palms in the evening (fruit bat "hang-outs"?)? Eat certain foods, drink particular drinks? Prepare food or drink a certain way? Do things that they won't talk about because its a taboo subject - that could be putting them at risk? Keep certain animals as pets (a secondary host-intermediate vector?). Kill or have close contact with certain animal?

When you look at MERS-CoV as a virus that mostly causes death in a specific segment of the population, the next question might be, what do the endemic human coronaviruses (HCoV) 229E, OC43, NL63 and HKU1 do to people in the same age and comorbidity-laden populations? 

Stay tuned.

Possible death of existing MERS-CoV case (83M from Asir) and 2 new cases

Crawford Kilian has an article from the press about the death of an existing case (83M) and 2 new cases - #2 is "a man" and #3 a 63F. 

I'll update this as any detail becomes available. If confirmed by the KSA MOH and WHO will bring the tally of cases (including deaths) to 93 and the deaths to 47.

The Wolverine: the rebuttal's inner animal?

If World War Z is a tale of extreme epidemiology, then perhaps The Wolverine gives screen-time (and claws) to some of the feelings a Chief Investigator may cycle through, just after reading their Assessment Letters around June each year (Down Under at least). 

Then we put them in a drawer for a day or two while we put the animal away again. 

Or Bruce Banner (The Hulk) said in the Avengers...

"...I'm always angry..."

Friday, 26 July 2013

Biggest Middle East Respiratory syndrome coronavirus (MERS-CoV) case study to date

Assiri and colleagues from the Kingdom of Saudi Arabia (KSA) today described, in The Lancet, the clinical characteristics of 47 cases of MERS-CoV. The largest detailed analysis of MERS-CoV cases to date.

This report includes 20 cases more than that 27 reported previously by these authors, along with additional information on the first 27. 

The paper opened by noting that clinical data are scant and suggest that's because of the small number of cases since it appeared 15 months ago. The case numbers include all 90 known MERS-CoV cases. 1 new case was announced today.

Some key points from the paper...
  • Nasopharyngeal swabs, tracheal aspirates and bronchoalveolar lavage specimens were taken by attending doctors
  • Since June 15,  MERS-CoV has been detected in 16 ( 17.5% of the current tally of 91 cases) asymptomatic people as a result of screening contacts
  • The authors note the need for rapid and accurate antibody tests to apply to case-control studies
  • 45/47 (96%) of  cases had 1 or more comorbidities with diabetes, chronic kidney/heart disease and hypertenstion the most common among surviving cases
  • All but 2/47 were citizens of the KSA
  • Fever and cough were found in >83% of cases with shortness of breath in 72%
  • Nausea, vomiting  abdominal pain and diarrhoea were present in 17-26% of cases
  • Runny nose was rare (4%), sore throat (21%) and cough were occasional (dry-47%; productive-36%) and headache, chest pain and coughing blood were present in 13-17% of cases
  • Chest X-Ray was abnormal in all cases
  • Neither blood nor respiratory sample from any case had another virus or bacterium detected. That's an extraordinary finding. Co-detections around 20% or more are the norm, not the exception. This might indirectly flag the extent of the antiviral inflammatory response being mounted to MERS-CoV
  • Time between symptom onset and sampling averaged  about 72-hours
  • Real-time RT-PCR threshold values fro 37/45 samples ranged form 20-40
  • Cellular laboratory findings revealed mostly normal neutrophil counts while just over a third had low platelet and/or white blood cells; lactate dehydrogenase and aspartate aminotransferase levels were raised in half of the cases
  • The authors identify a large number of knowledge gaps and some that require urgent research including finding the host, source of exposure to it, what are the excretion and transmission dynamics, how best to sample, contain and manage patients

The authors write of a current absence of clinical and laboratory features to distinguish MERS-CoV cases from other respiratory infections. We have had very good viral detection methods for a while now, so its unclear which other tests they mean when they say "no tests are available" to exclude MERS (the disease) among patients with fever. That could also be said of any respiratory disease due to virus infection. For example, we know much about HCoV-NL63 and HPIV-3, but if a child presented with croup (associated with both viruses), we could not reliably distinguish which caused the disease using signs and symptoms alone. This is a problem common to all respiratory viral infections, not simply those due to MERS-CoV, and is best addressed using an extended panel of assays. Resources permitting.

Could anything biochemically, haematologically or clinically distinguish a patient as being infected by MERS-CoV rather than any other virus? Surely we are beyond trying to do that?

The paper does not mention whether there are sera available from all these cases to address the stated need for good, and well-validated, antibody-detection (serological) assays. As stated by others previously, KSA has the best sample population to make this happen. Without validation (testing antibody-detection assays using known positive as well as negative patent sera), the delay in producing a reliable assay and in getting a better grasp of who has been previously exposed to the MERS-CoV, what the real proportion of fatal cases is and the efficiency with which an infected person to pass on the virus (basic reproduction number, R0).....remains out of reach.

Belated Happy Birthday to Rosalind Franklin (1920-1958)

The 25th would have been Dr Franklin's 93rd birthday.

In 1952 while working at King's College in London, Dr Franklin captured images (including Photo 51) of the patterns made by DNA scattering X-Rays...which revealed a helical structure. 

The photo was the basis for James Watson, Francis Crick and Maurice Wilkins chemical model of DNA as double helix structure.

We who follow owe much to her hard work and devotion.

MERS-CoV: new case and a death in previous case both from Asir Province

Hat tip to crofsblogs and FluTrackers

The Kingdom of Saudi Arabia (KSA) Ministry of Health (MOH) website announces a new case (83, no other details) and the death (no details at all; FluTrackers believe it could be case 66M1, announced 26.07.13) in a previously confirmed case. Both from Asir province (population 1.9 million).

The KSA MOH website is having some issues just now though.

Cases now at 91 / Deaths at 46
PFC2: 50.5%

The MERS-CoV page on VDU has been updated with these numbers.

For general info, The World Bank lists the 2012 population of Saudi Arabia (2010 census) as 28.29 million.

 In 2007, the proportion of the KSA population:
  • 65-years and older: 2.8%
  • 0-14-year old: 32.4%
  • 15-16-year old: 64.8%
  • 1.37 males for every female.
For MERS-CoV cases (with data available) :
  • Average age of cases (including deaths) is 53-years
  • 65-years or older: 29%
  • 3:1 males aged 65-years or older
  • Males: 61.9% of cases; 77% of deaths are in males

166M-"M" means "year old Male"
2 PFC - see earlier post

Thursday, 25 July 2013

Allergy to a Transformer's garbled signals

Transforming growth factor-β (TGFβ) is a protein we secrete throughout most of our body which controls the growth, function and future employment of cells through binding to its receptor on them and creating a specific response inside the cell. It's also one of many very important managerial proteins called cytokines. It is involved in immunity (calms it down, stops it from over-reacting to foreign things) and asthma, among other things name a few.

Frischmeyer-Guerrerio and colleagues found that patients with a genetic disease called Loeys-Dietz syndrome (LDS), had high IgE antibodies, eosinophil numbers and TH2 helper cells...all markers of and contributors to allergy. LDS is a genetic disorder in which TGFβ receptor proteins are a bit wonky. LDS patients had incidence of asthma, food allergy, eczema, allergic rhinitis and eosinophilic gut disease.

In the case of asthma, I wonder if LDS patients also had more exacerbations. These are greatest burden of disease in those with asthma. Asthmatics are also known to have a predisposition to worse outcomes after viral infections, which reach higher viral loads, as if they were not being suitably attacked by the antiviral arm of the immune system.

The authors note how changes in just one gene can lead to complex changes that manifest as disease, because the altered, reduced or absent gene products can't partake in their normal activities further down its chain of action.

A drug called Losartan may be useful to alter the signalling due to TGFβ. However, it has not been tested on LDS yet.

Drug resistant bacterial terrorists worthy of alarm

Hat tip to Namraj for the education.

Maryn McKenna describes the rising alarm over our inability to stop infections by bacteria, because we have essentially run out of drugs to which they are sensitive. This is despite Doctors keeping in reserve the important drugs like carbapenems. But carbapenem-resistant Enterobacteriaceae (CREs) continue to spread, and kill.

Okay, so this is VDU - but viruses have a hand here too - one of the historic reasons behind overuse of antibiotics has been for  the (ineffective) treatment of  infections that were actually due to viruses-bad colds for example. Of course there are many other sources for antibiotics being flushed into the environment.

In on editorial in Nature, you can read of the rarity of new antibiotic discoveries in parallel with previous widespread use of antibiotics to aid growth of livestock.

And as we just spoke of bacteriophages earlier today...what ever happened to their use as bacteria-specific drugs? This was, and continues to be, a popular area of research in Eastern Europe according to the 2011 review by Harper and colleagues. Chemicals (antibiotic drugs) This overtook this area, as did regulatory and quality issues and the need for more comprehensive characterisation of them because some of the early work may have been rushed. 

Bacteriophage are looking like an ever more viable option in light of the growing crisis stories like those above highlight.

For example, there are recent papers describing the ability of bacteriophages to kill CREs including Klebsiella species - members of the Enterobacteriaceae. Recent phage success stories include killing of K. pneumoniae that mediate liver disease in mice and being superior to more traditional antimicrobials in treating burn wound infections in mice.

Oh, and Holmfeldt and colleagues just described the discovery of 12 new genera of phage comprising 31 phage from aquatic bacteria.

Time to get serious and turn the less conventional into conventional antibacterial options?

You think you're under pressure?

The human herpesviruses (HHVs) have their DNA genomes poised to be fired into the cell with which they are docked, under pressures equivalent to 10s of atmospheres. These are the recent findings of Bauer and colleagues.  

Those protein capsids must be pretty tough.

So at least the early stage of DNA entry is a passive process; just relies on good old force.

This is the same way, and with a similar degree of pressure, that the bacterial viruses called bacteriophage, inject their genetic material through the much stronger cell wall and into a bacterium.

Big fleas have little fleas,
Upon their backs to bite 'em,
And little fleas have lesser fleas,
and so, ad infinitum.

And the great fleas, themselves, in turn
Have greater fleas to go on;
While these again have greater still,
And greater still, and so on.

"The Siphonaptera", from Wikipedia

Wednesday, 24 July 2013

Editor's Note #9: End of a (very short) era - beginning of a much longer new one!

...and the beginning of a new one! For the first time in 6021-days (or 16-years, 5-months and 26-days since 28-Jan 1997 in fact), part of Virology Down Under (VDU) has moved off the University of Queensland's servers. 

*sniff*But its only this relatively new format, the blog bit, not the rest of the site. For some reason, actual blog professionals want to be able to link to some of my ramblings. Go figure! I hope this new format helps.
This move allows a better record of the articles....for me as much as you...and it definitely speeds up the process of writing...a lot as I don't have to edit all the blog entry's HMTL and CSS by hand. Phew.

Perhaps it will free up some more time to revamp the older pages too.

You will now be able to leave comments: perhaps ideas, corrections or suggestions and you can get update alerts via sites like bloglovin'.

There will still be search capability through a Google search box, and I'll leave The Freezer (old blog entries) intact. I will endeavour to move all the old blog entries onto this Google-based Blogger platform...but it may take a while.

The original core business of the VDU site - its pages providing more relaxed information on different viruses, DNA and PCR - will remain on the University of Queensland server, thanks to the Sir Albert Sakzewski Virus Research Centre. Only the blog component will be moving.
It's been a long time and lot of tech since I started VDU on my home 486DX Gateway Pentium II (128Mb RAM and 6.4Gb HDD). Let's hope this new home for the blog has the same legs.

Thanks to Crawford Kilian for the nagging impetus to make the blog more citation-friendly, to my wife, Kat, for the idea of a dedicated blog site for VDU (and much more) and to my boys Corin and Ronan for being brilliant...and for giving me the time during their school holidays in March to get this blog started! 

Many thanks for reading. Returning to normal blogging tomorrow.

Editor in Chief, Virology Down Under

Open a box of mystery.

The newest jaw dropping viral discovery is a big one - literally. Philippe and colleagues describe 2 protozoan-infecting megaviruses (possibly part of a proposed group, the family Megaviridae, in the future?).

These guys are not tiny, simple or only subtly different. One virus, Pandoravirus salinus (from marine sediment at the mouth of Tunquen river, central Chile) was 1,000nm long (shaped like an amphora), 500nm wide, has a genome of 2,473,870-base pairs and potentially encodes 2,556 protein coding sequence (CDSs), 93% of which were novel. They do not seem to have a capsid, rather a trilayered tegument.

The second discovery was named P. dulcis and was found in the bottom of a freshwater pond near Melbourne in Australia; it's genome was 1,908,524-bp, encoding 1,502 CDSs.

Some more info at the Megavirus page

Yeesh. The stuff we don't know...

Tuesday, 23 July 2013

Ferrets are not small furry humans.

Zeng Guang, Chief epidemiologist at the Chinese Center for Disease Control and Prevention (CDC), commented on the recent H7N9 study from his own country (covered here)...
The findings are mainly based on animal tests in the lab that have not been witnessed or substantiated among the H7N9 human cases reported. So it shouldn't affect current intervention efforts or strategy at all

So far, no substantial evidence of H7N9 spreading among humans has been detected

And Zeng, back in April, made other comments about H7N9 transmissibility...

Humans' susceptibility to the H7N9 virus is only a little bit higher than to that of H5N1

Sure. I think we all understand that a tad over 130 cases in an area with 10s of millions people living in it, does not indicate a great deal of human-to-human transmission. As I noted yesterday, I wonder what active PCR screening of well human populations would yield?But ferrets are not supposed to be used for direct comparisons: 1 infected ferret in 3 exposures, under experimental conditions, probably does not equal 1 infected human in 3 exposures. Ferrets have tails, are much shorter, have a lot more body hair and a tendency to bite - not the usual description of a human. So there are other differences.

Ferrets are however, meant to be a great alternative to placing two humans in a cage separated by 7cm with one downwind of the other, inoculating one then harvesting tissues from them both to see where the virus ended up. Such human infections (reviewed here), acceptable for some viruses (e.g. rhinoviruses), would most likely yield the most relevant data to wild human infections. But we can't do that sort of thing for a virus we know to be detected in people who die. The risks to the participants are too high.

Also, we can and do inoculate ferrets and other animals with "unnatural" amounts and unnaturally pure preparations of virus to get the results we are this case infection to let us observe transmission. Sure ferrets are not tiny humans, but we still have work to do to prove they are not a very useful indicator of what might be happening in the transmission of H7N9.

Let's turn Zeng's question around then: What evidence is there that 33% of ferrets being infected in various H7N9 studies, is not what happens to humans in the context of previous exposures, underlying diseases, the human immune system, chance encounters with animals and people, exposure to lower amounts of virus etc?

Monday, 22 July 2013

New Influenza A(H7N9) case in Hebei, 1st for this province.

Hat tips to Crawford Kilian, FluTrackers and Mike Coston for extensive coverage.

In what is one of the most thoroughly reported single cases since we heard of H7N9, the weekend saw the confirmation of an H7N9 infection in a 61-year old female from Hebei province. I don't mean that flippantly, such a ferocious reporting response highlights just how jumpy this virus, and influenza in general, makes those who watch the webs.
The patient, from Lanfang city, is now in a Beijing hospital, on extra-corporeal membrane oxygenation (ECMO) - this indicates severe disease with a need to support the heart and lungs in their task of providing oxygen to the body.  
The patient had not travelled outside of Hebei but lives near a poultry market.

No close contacts have tested H7N9 positive. She was reportedly situated in 2 different hospitals in Lanfang, before being sent to Beijing and tested for H7N9.

I've updated some key charts at the H7N9 page.

This raises a lingering question for me though. Many, many, many samples, both animal and human have been tested for H7N9 in China. As I understand it though, the human samples are mostly from those exhibiting signs or symptoms of illness or from contacts of those doing so. Would it not be a very useful study to add to these data a prospective PCR-based screening study of samples from "normal healthy" community populations/cohorts to see if H7N9 is circulating stealthily?

I respect the resources that it would take, but I also acknowledge the huge laboratory testing capacity currently available in China. It's phenomenal. These data would certainly add another piece to the puzzle.

Sunday, 21 July 2013

Thoughts and (many) questions on the 4 MERS-CoV UAE cases. [AMENDED]

Thanks to Prof Andrew Rambaut for pointing out my incorrect usage of R0

4 new infections were detected from health-care workers (HCWs) in contact with a previously confirmed 82-year old male MERS patient-we've covered this previously.

My main question is: Does that mean the basic reproduction number (R0) for MERS-CoV is creeping towards being greater than 1? If in fact 4 new infections arose from every case, on average, that would put the MERS-CoV up there with influenza, SARS-CoV and mumps.

While the 
R0 is not >1, this was an informative small cluster of human infections. Basic protective measures may not have been taken in this cluster and presumably we can exclude pre-existing immunity as a moderating factor (although do we know that yet?).

I'm also assuming these 4 are otherwise "normal healthy" people, not suffering any major underlying disease(s), and so I'm having trouble imagining what stops this from happening all the time. Perhaps co-infections in which the MERS-CoV is the super-infecting (2nd) virus such that an innate and moderating immune response is already underway?

Perhaps the virus has recently changed to become more easily transmissible - we need more sequences from recent strains and more isolates in animal studies to confirm that or course. I'm not holding my breath that either of those will be achieved rapidly-although perhaps I should be holding my breath.

To me, and feel free to educate me on any of this post via Twitter (@MackayIM), this means we should expect to see more viral RNA-positives (regardless of symptoms since 2/4 here were asymptomatic) in contacts...doesn't it? What is the status of testing "less close" contacts? How far does the testing net get thrown I wonder?

Nonetheless, we don't see 4 new community infections from every case in the KSA. I'm assuming that the KSA MOH lab(s) uses the same PCR assay as that recommended by the WHO. 

Others have already noted that, on the data we have, MERS-CoV is unlikely to cause a pandemic.The most recent announcement of 2 cases of MERS-CoV provides an answer to that, one that is a typical KSA MOH site's communication:

It is worth mentioning that, the MOH has tested 64 samples recently, given that, all of such samples have been proved negative, May Allah be praised, except the cases that have been published.

No contacts positive there. So, at the end of the day, we can't extrapolate much from clusters, because when we consider the entire MERS-CoV population and all of it's tested contacts, we have an R0 value <1. Still, the clusters do happen and this does highlight that numbers, tools and hypotheses are good as guides - they should not to be used without full regard to each specific pandemic, epidemic, outbreak, cluster or even individual case.

Saturday, 20 July 2013

World War Z: a study in extreme epidemiology.

I saw this at the movies Thursday night. I really enjoyed the movie - really delivers on its zombie promise and adds the story of a father trying to look after his family.

It struck me though that it's also a great story of what would happen if, instead of anthropomorphising viruses into beings that wish to do gave them a pair of legs and let them decide what to do...which it turns out is to transmit, transmit, transmit! So, some irreverent thoughts on how a Z virus might fit in the current context of virus outbreaks..

  1. Diagnosis would be a doddle. No need to painfully design, optimise and validate a catch-all PCR for the virus based on one sequence you got from the internet, or to keep that assay ahead of mutation-defeating viral evolution. There would be pathognomonic signs of disease - eyes rolling back into the patient's head and turning white, a strange web-like pattern of blood vessels under a pallid skin tone, very bad teeth, spasmodic limb and jaw movements, disregard for personal safety when colliding with objects at speed, an ability to rapidly accelerate, disregard for heights, a hideous squeally noise on inhalation (which also prevents the virus from spreading stealthily) and the very urgent need to bite any piece of you that it can. Any 3 of these should be a diagnostic triad.
  2. Molecular epidemiology won't be necessary to track viral change. Nor will it be possible in the time you have left. No need to find the best and most diverse gene segments to sequence, no reason to use next generation/high throughput sequencing to characterize the entire genome, create phylogenetic trees and look for the impact of a multitude of tiny amino acid changes....because, you know, who cares how much worse could the virus get!?
  3. Monitoring virus transmission will be much easier. Turn on the TV or radio and follow how many countries have not yet been over-run. Oh, and that banging on your door is probably not someone asking you to switch your power company or coming to talk to you about religion.
  4. Calculation of the basic reproduction number (R0) should be made much simpler. It would be any number >1, rising continually until someone can successfully enact sufficient cranial damage upon the infected case. Definition of a super-spreader becomes much more obvious. Oh, and there are no asymptomatic cases.
  5. The need to argue about and decide upon the best way to calculate a Case Fatality Rate\Ratio would be relaxed. Every case dies...unless they already have a fatal disease. There is no time for hospitalisation...and anyone left in the hospitals wants to bite you.
  6. No need for arguments about, and delays due to, Material Transfer Agreements. Every country has its own cases, no-one wants to claim sovereign rights over the virus and there is no longer a biotechnology or manufacturing industry left to profit from diagnostic kit or antiviral developments down the track. The track has been eaten.
  7. Some of the variables needed to grow the virus for in vitro study are well defined: inoculation period-12 seconds to 10 minutes; favoured temperature-your body's; preferred cell type: does it really matter at this point?!
  8. Animal models are no longer needed for disease studies. Human models are plentiful. Unfortunately there won't be time for ethical approvals and no way to get informed consent. Additionally, your lab will need a large plexiglass-enclosed holding chamber in the middle of it. No real need to study transmission methods through. Generalising to "transmission occurs via a bite" is probably enough - the number or bites or whether a small bite is as effective a transmitter as a big one may be a study for another day.
  9. Treatment options are limited to removal of the bitten area along with 10cm of the neighbouring tissue. Do so within 5 seconds of infection or else look for a source of acute cranial trauma.
  10. Prevention is also limited to inoculation with a deadly micro-organism...or having a pre-existing terminal condition. The former will be easy to find in any WHO research facility apparently, just look for a cold room vault. Any vial of serum-coloured, non-frozen liquid, adjacent to a drawer of syringes, should do the trick. Probably best if you can find an antibiotic or functioning antiviral somewhere first.
  11. Detailed date data on illness onset and death are unnecessary - they will likely be the same day and probably today, or perhaps yesterday. This also removes frustration that your only information on new infections comes from cases being published through the scientific journals...rather than mainstream or social media.
Make you wonder?

Friday, 19 July 2013

Two new MERS-CoV cases in the Kingdom of Saudi Arabia.

I'll have to update the numbers and graphs again as a second announcement from KSA today identifies a 41M from Riyadh and 59F from Al-Ahsa governate, both in intensive care units.

This brings the total to 90 cases, 78.9% from KSA (also claims 86% of deaths, of those with identifying data) 7.8% from UAE, 61.9% with data are male and the PFC falls further to 50.0%

MERS-CoV proportion of fatal case chart.

Finally got around to this graph, one of my favourites from those I made for H7N9.

It shows the change in "Case Fatality Rate" (or PFC as I've taken to calling it here) over time. You will be able to see the graph more clearly on the MERS-CoVpage later today. It shows the very changeable PFC. Currently it is declining as death reports have slowed while the number of laboratory detections, including more that are mildly ill or with no signs and symptoms at all, continue to rise.

Latest article from CIDRAP: new H7N9 animal studies & comment from VDU EiC.

Shameless self-promotion - but very cool when someone asks for your opinion about something you are interested in.The CIDRAP article by Lisa Schnirring covers the newly released paper by Zhang and colleagues of the Prof Hualen Chen's uber-group at the Harbin Veterinary Research Institute, China.

To quote myself....

The study reinforces that even 'lowly' or inefficient transmission-only 33% of ferrets, for example-is still transmission," Mackay said. "That proportion would lead to a lot of human cases in densely populated or frequented areas.

And just look at these numbers: 10,703 samples from 30.03.13-02.05.13, collected from poultry markets in all the key H7N9 provinces and municipalities. All (I said all!) were inoculated into eggs. 238 influenza viruses (136 Newcastle disease viruses as well) of which 52 were influenza A(H7N9) virus. They then sequenced the complete genome of 37. Phenomenal work.

While I am no expert on what each and every influenza mutation does (I'm thinking about making a table on the flu page), I was interested in how closely related all the genomes were (<4% nucleotide difference between them all) and that the major differences are at the level of amino acid changes. Also, there were no amino acid changes noted after animal inoculation or transmission. Does this mean the virus is already happy in its own skin?

Although highly similar, the most diverse genomes (those with <99.5% identity to the H7N9/Anhui/1 strain) came mostly from the Shanghai principality. Does that mean anything in terms of site of ground zero? The site of "youngest" viruses perhaps? PB1 seemed to be the most variable H7N9 segment in terms of nucleotide differences.

In the future it might be informative to look at genetic comparisons of complete H7N9 genomes from mild/asymptomatic cases and those from moderate/severe/fatal cases. As well as considering what other viruses and bacteria are in these two groups and whether virus:virus or virus:bacteria interactions may play a role in more severe outcomes.

And this study confirms that of Belser (see below) - if you're a mouse, don't get H7N9!

I haven't looked myself, but it would also be useful to know whether the recommended H7N9 PCR-based assay targets remain conserved in the latest genomes.

MERS-CoV count reaches 88 [UPDATED].

The addition of 2 new cases in the KSA and 4 in the UAE (2 asymptomatic and 2 mild illness) lowering thePFC to 51.1%.

[UPDATE] According to Crawford Kilian's latest info, the four UAE cases are all Doctors caring for the recent 82M case (FluTracker's Case #82 coincidentally). Does this qualify as a super-spreader, 1 case and 4 transmitted infections?

Thursday, 18 July 2013

MERS-CoV cases #82 and #83 are mildly ill outpatients.

Hat tip to Crawford Kilian.

Two new MERS-CoV cases reported on the Kingdom of Saudi Arabia's Ministry of Health website.

Both cases are from Asir (Southwestern KSA), the 42F (F=female) is possibly a healthcare worker and the other, a 26M, had contact with another MERS case. No dates. No details of which case.

The KSA has now hosted 86% of known MERS-CoV cases. 64% of all cases with data being male. The new PFC is 53.6%.

The first MERS-CoV novel is almost written!

And Crawford Kilian, in releasing his inner editor, has the complete framework.

All that's missing is one monkey with a disproportionately amount of blood from which we can purify vast quantities of antibodies to cure new and existing cases...and reverse any existing tissue damage, and remove the likelihood of any sequelae. Okay. So this is why I'm not a writer. Expository dialogue indeed.

Now go read this entertaining article - Crawford is a writer.

(formerly pandemic) H1N1 is a seasonal influenza virus these days.

Some people look aghast when I suggest a pandemic virus could now be "just" a seasonal virus...but here is the word from the Härtl's mouth...

Printed words from the mouths of others, including some good points, can be found here.

WHO declares no eMERSgency?

Hat tip to Master Corin Mackay for title help.

The 2nd meeting of the International Health Regulations (IHR) Emergency Committee concerning MERS-CoV, convened by the WHO Director General with a new special advisor added (Ms Karen Tan, Senior Director, Public Communication Division, Ministry of Communications and Information, Singapore) and several affected State Parties (France, Germany, Italy, Jordan, Kingdom of Saudi Arabia, Qatar, Tunisia and the United Kingdom) on a party line, unanimously decided not to declare a Public Health Emergency of International Concern (PHEIC)

The Committee will reconvene in September, or earlier if needed. By September we'll have given the MERS-CoV every chance to spread by providing it with millions of people to jump to, from wherever it comes, at the hottest zone of infection, the KSA. If cases do not take off after the Hajj, one would think the immediate risk for a MERS-CoV pandemic would drop significantly.

Based on these views and the currently available information, the Director-General accepted the Committee’s assessment that the current MERS-CoV situation is serious and of great concern, but does not constitute a PHEIC at this time.

A drug to stop rhinovirus (HRV) infections in patients with chronic obstructive pulmonary disease (COPD)?

For those who don't know, the HRVs are the most frequent infecting agents (that we know of) of the human upper (and perhaps lower but that work is not done) respiratory tract (URT).The first HRV was isolated in 1953 in the UK and the viruses were soon burdened by the label "common cold viruses". This was largely because early studies were conducted in adults who generally have milder outcomes.
There are about 77 genetically distinct HRV-As, 60 HRV-Cs and 30 HRV-Bs - that's nearly 170 distinct viruses (includes serotypes and genotypes)! Imagine 170 distinct coronaviruses.

In the past they were classified by the type of cell they infected/receptor they used into major (most of them used ICAM-I as the receptor) and minor (the rest; use VLDL-R as the receptor) groups. Sequencing is the preferred method to classify them today.

The receptor for the HRV-Cs remains unknown and they do not grow in routine cell lines instead needing more advanced culture methods. Because of this, studies predating 1988 (the first published PCR primers) generally don't account for the HRV-Cs, even though they were there and causing infections.

A.Prof Eva Kathryn Miller and I recently reviewed the HRV-Cs in some detail. Around 70 distinct HRV genotypes can circulate at a single place over a year...depending on the population being studied. I and others have found that to be the case in both the community and in hospital-based populations.

A recent article from Yamaya and colleagues suggests that a mucolytic drug (stimulates surfactant production and release to help the airways clear themselves of gunk) might be of use in treating HRV infections in COPD patients at least.

Exacerbations, which are mostly due to viruses, are the main contributor to disease burden in patients suffering from COPD, as they are in those with asthma.

The drug, ambroxol hydrochloride is already thought to reduce the frequency of URT disease and may reduce ICAM-I expression. The authors tested this using a major group HRV, HRV-B14 and found reduced release of virus, ICAM-I levels and reduced viral RNA levels.

Prophylactic use may inhibit HRV-B14 infection and modulate the inflammatory response to infection. Many of the differences were moderate (mostly arithmetic rather than logarithmic), albeit statistically significant.

It would be interesting to see what effect the drug has on other major group HRVs, minor group HRVs and on the hard to culture HRV-Cs.

Tuesday, 16 July 2013

MERS-CoV numbers by area - UPDATE.

Let me preface this release with the statement "I hate doing this!" "This" being the use of data that are the best I can find, but not the best we could have. I've been spoilt by H7N9 which, at least initially, but not lately, was filled with dates. Seems like the only dates being publicly discussed in relation to MERS-CoV cases are those the bats may be contaminating.

However, the number of cases without any obvious dates of illness is steadily climbing towards half of all cases so I've decided to bite the bullet and make a second graph of MERS-CoV cases by site of infection to highlight the increases.

The new update uses Dates of Onset (DOO) where available but is augmented by Dates of Reporting (DOR) for the remainder (still missing 1 case). While this is inaccurate, it does serve the purpose of showing where the cases are accumulating from, and roughly how quickly that is happening, at each location.

As an example of how the two datasets compare, I've excised a part of my Excel sheet to show you that the trends (left column = new chart data DOO+DOR; right column = DOO data only) remain, even if the numbers change. It also highlights the biggest cluster of missing DOOs which dramatically to increase in number after the week beginning June 9th. Anyone know why or what changed?

The new chart, produced with my thanks for the extra dates found at Flu Wiki's MERS-CoV page, will be placed, in a larger size, above the current version that uses only DOOs, on my MERS-CoV page, and both will be kept updated.