Friday 28 February 2014

Editor's comment: Biomolecular Detection and Quantification...

I've been invited to be a section Editor for Biomolecular Detection and Quantification (BDQ).

BDQ is an Elsevier-based, open access, peer-reviewed journal dedicated to championing excellence in molecular study design, measurement, data analysis and reporting. 

BDQ's Editor's-in-Chief are Stephen Bustin, Jim Huggett, Justin O'Grady, Michael Pfaffl, Carl Witwer and Ron Cook. Quite the line up huh?

My role will be one of attracting, reviewing and shepherding manuscripts relating to BDQ in infectious disease, but particularly related to viruses.

Our two main aims
  1. to provide a forum for discussion and recommendation of guidelines designed to improve the accuracy of molecular measurement, its data analysis and the transparency of its subsequent reporting;
  2. to publish molecular biology based studies that adhere to best practice guidelines, both current and future.
So, if you have any ideas for future articles or would like to publish in our little baby right now (once they become toddlers things get more rowdy), please contact me or one of the other Editors as soon as you can.


Thursday 27 February 2014

Editor's Note #14: VDU in the scientific literature

Virology Down Under gets a 2nd citation (1)!

Dr Anne S De Groot and colleagues used a VDU graphic for a recent paper and cited VDU for it. Many thanks!

To read the paper entitled Cross-conservation of T-cell epitopes: Now even more relevant to (H7N9) influenza vaccine design hop over to..

  1. 1st citation for VDU at

Snapdate: Middle East respiratory syndrome coronavirus (MERS-CoV)

Click on image to enlarge.
Chart update time for human cases of the MERS-CoV.

Chart #1: lab confirmed(Ministry announced) human cases of MERS by region of acquisition. MERS is a disease with its activity firmly rooted in Saudi Arabia.

Chart #2: age and sex distribution pyramid. MERS is a disease of older males.

Click on image to enlarge.
Chart #3: here we see total and just the fatal MERS-CoV cases in humans, by month and year. I've kept the same value on the y-axis (left side) for ease of comparison. This chart highlights that there is no obvious seasonality for cases. In 2014 we're seeing more in Jan and Feb than we did in 2013 and in 2013 cases trickled along at similar levels from April onwards. This, if anything, supports the sporadic acquisition of cases and rejects the idea that, at least among the hospital-based population that is the main one to have been tested to date, MERS-CoV is not a seasonal virus.

Click on image to enlarge.
Chart #4: this one shows as the slowly spreading outbreak. More disturbingly, it shows the very gradually increasing PFC. Currently, 43% of MERS cases have died; 2 in 5. Guess its worth remembering that MERS-CoV may a puny virus in camels and in terms of transmission efficiency; but not at all puny in regards to what it does to the older usually male and mostly already ill people it infects. It is quite an efficiently lethal virus in that sub-population.

Coming back to MERSerable data...

A grab of the past 20 MERS-CoV positive human cases reported
by a Ministry and listed over FluTracker's if you want to look in
more detail. Even though the tally goes to 191 - there are 186 total
(some have been removed after being reduced in status to
probable cases). Under the FluTracker Case # banner, a pink fill
indicates a death. A pale blue fill under the Sex column indicates that
the World  Health Organisation (WHO) have reported the cases through
their Global (GAR) Disease Outbreak Notice (DON) website.
Click on image to enlarge.
I'm preparing a brief invited talk on MERS and MERS-CoV for next week at the Molecular Microbiology Meeting in Sydney

So I'm updating MERS-CoV data - 4 cases since last I did this. And the data remain as horrible as the last time I complained

The figure above highlights just how horrible. Have a look at:

  • How many data gaps there are for sex (a very basic piece of demographic information to provide without comprising patient identity)
  • How many data gaps there are for date of illness onset
  • The absence of any KSA unique identification codes (there were 4 provided in August...and that was that)
  • How many dates of hospitalisation there are
I'll throw up some new charts shortly but really, they will reflect these data gaps.

But really, this has all been said before so I won't rehash my disappointment too much. 

Except to say..

It isn't at all surprising to read a comment like that from Prof Ian Lipkin recently. This being in the context of his unreciprocated collaboration with the Kingdom's Deputy Minister of Health, Dr Ziad Memish...
We've gone our separate ways, and I wish him well
...which may also inform us about why the collaboration between the MOH and the World Health Organisation (WHO) produces such spartan data on MERS cases, at least when you compare the quality of data to that which China provide WHO on avian influenza A(H7N9 virus cases; a much larger undertaking involving a more populous State and many more geographic and political boundaries.

Vale Dr. Albert Z Kapikian

Others will no doubt write more cogently and personally than I can about Dr Kapikian's >56-years of medical and virology expertise, skills, discoveries and personality but I wanted to make a just a few quick comments on his passing in relation to a group of viruses for which he is not as often associated; the rhinoviruses (RV).

Dr Kapikian was an expert with electron microscopy (EM), learning the use of it from June Almeida at the Royal Postgraduate Medical School, University of London in 1970. His use of immune EM led him to discover the viruses we now call noroviruses in 1972; a major cause of gastroenteritis. He also found instances of rotavirus (RoV) in the United States and went on to lead the development of an oral vaccine to prevent the serious diarrhoeal disease associated with infection by RoVs. 

He has over 200 publications listed on PubMED.

I exchanged a couple of eMails with him in 2009 (which Al graciously replied too in excellent detail) but never got to meet him, much to my disappointment. My first knowledge of him was from my work with rhinoviruses. While these were not his research focus, he Chaired the group that published the 1st (and 2nd in 1972 and co-authored the 3rd in 1987) formal description in 1967. This report gave the largest group of distinct respiratory viruses their 100 names. He helped to bring together RV researchers and their often identical isolates from around the globe and helped to create the 1 key to link them all in a single unifying scheme; HRV-1 to HRV-100. Having had a tiny role in doing that for the latest species, RV-C, I can more than imagine how much of a challenge that must have been at the time. Dr Kapikian also used his immune EM expertise to visualize the rhinoviruses in 1972.

That Dr Kapikian is so highly regarded, described as warm-hearted and the smartest and nicest guy in the room, speak volumes of him as a human. His track speaks to his role as a leader and medical virologist of huge impact.

Another trailblazer has moved on.

Dr Albert Z. Kapikian, Chief, Epidemiology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health in the United States, died 24-Feb at 86-years of age.


  1. National Institutes of Health statement on the death of Dr Albert Z Kapikian
  2. Seeing the new calicivirus: norovirus
  3. Context for the discovery of norovirus
  4. Sabin Gold Medal
  5. Dr Kapikian's publication list on PubMED
  6. NIH on the Sabin medal
  7. Children's Vaccine Initiative Pasteur award summary at NIH
  8. Alumni Award of Distinction from Weill Cornell Medical College where Dr Kapikian got his MD
  9. Awarded Fellowship of The American Academy of Microbiology
  10. Visualising rhinoviruses by immune electron microscopy
  11. First rhinovirus numbering system report
  12. A collaborative report: rhinoviruses--extension of the numbering system from 89 to 100.
  13. A collaborative report: Rhinoviruses-extension of the numbering system

Wednesday 26 February 2014

Dromedary camels are a host of MERS-CoV...

Yes. Not a "MERS-CoV-like" virus or "something very closely related to but slightly different" from MERS-CoV. Camels. Are. A. Host. 

There was already plenty of evidence to suggest this (see some of my previous posts on this linked below), and none to really dissuade me from thinking otherwise. And yesterday we saw a new paper by Ian Lipkin and his collaborating crew from King Saud University in Saudi Arabia that make this issue more obvious than ever. 

So let's stop messing around. There is an elephant in the MERS-room...and its a camel! 

The Middle East respiratory syndrome coronavirus, does in fact look to be a camel virus that causes few symptoms in that host, is acquired by young camels and has been for at least 22-years, and then people somehow get infected, probably from proximity to camels or due to habits involving camels. the keeping of camels or at gatherings in which grumpy slavering camels are congregating. 

Yes, there is little evidence for any contact with camels among the 186 human cases as Dr Ziad Memish, deputy health minister of the Kingdom of Saudi Arabia (KSA) points out, but as Prof Marion Koopmans noted to NPR"few people [with MERS] have had the kind of follow-up you would want". So we take denial of any contact with a grain of salt.

There is definitely some contact however; some that is pretty solid. For example, the owner of a camel in Jeddah (4) that both tested positive for MERS-CoV or the Qatari farm camels and owner and an employee that were all MERS-CoV positive (5,7). 

And there is far less evidence against camels as a source of  some/many/most human cases and for anything else. 

So in the new paper in mBio published online 25-Feb, we read of the most comprehensive KSA camel study to date. Camels from 2013 were sampled and camel sera collected and frozen since 1992-2010 were tested and many were found to be MERS-CoV antibody positive. From the more recent dromedary camels, nasal swabs were also found to be viral RNA positive; RNA that is definitely from MERS-CoV.

Some key findings...

  • No sheep or goats were MERS-CoV antibody or RNA positive; a routine finding now. Bovine CoV antibody reactivity was identified in these animals however, and in 17% of camels
  • Antibody was detected using infected cells and also using a method that employs a specific portion of a MERS-CoV protein (part of the nucleoprotein)
  • 150/203 (74%) of camels from all over the KSA had MERS-CoV antibodies in a pattern reminiscent of any endemic human respiratory virus
    • 95% in camels older then 2-years (adults)
    • 55% in those ≤2-years (juveniles)
    • The south west had the lowest proportion of positive camels (5%)
    • Higher proportions were found in central KSA (Riyadh)
  • 3 rectal swabs were positive for MERS-CoV RNA using real-time reverse transcriptase polymerase chain reaction (RT-rtPCR). 2/3 camels were also nasal swab POS
    • 36/104 juvenile camels were nasal swab POS
    • 15/98 adult camels were POS
    • 66% of samples from the west (Taif) were POS but none from the south west
    • no RNA was detected in a sampling of camel blood/sera and so the archived samples from earlier years could not be sequenced to verify that they had MERS-CoV sequences in them
  • Amplification and sequencing of a 1,044nt portion of the Spike gene, 2,004nt ORF1ab region found that less than 1% difference from previous published MERS-CoV sequences and the nucleocapsid gene region was identical. Great to see a move away from recent reliance on complete genome sequences and a more practical and rapid subgenomic, multi-target molecular epidemiology approach used. 
    • 11/13 higher viral load samples could be amplified and sequenced
It was interesting hear the TWiV (this week in virology) podcast interview with Prof Lipkin [IL] and Assoc. Prof Thomas Briese (TB) in which they noted:

  • MERS-CoV is a "puny" virus causing little overt disease on camels [IL]
  • The MERS-CoV genome seems to be fairly stable; its not influenza virus and does not seem likely to evolve rapidly
  • Baboons[!], dogs, cats, rodents are on the list to test when the team return to KSA
  • There has been a previous report on limited human antibody levels to MERS-CoV in at least the east of the KSA
Sources and previous posts on camels and MERS-CoV...

  1. mBio paper by Alagaili and colleagues
  2. NPR's Richard Knox: excellent story
  3. CIDRAP Story
  4. Camels owner in Jeddah
  5. Two Eurosurveillance studies reporting MERS-CoV antibodies in camels
  6. MERS-CoV antibodies in 10-year old UAE camel sera
  7. More on the Qatari camels and some MERS-CoV sequencing and social media chatting
  8. MERS-CoV antibodies in camels from the Canary islands and Oman
  9. Early cautionary thoughts from the WHO
  10. Thoughts about MERS-CoV acquisition
  11. Querying whether there is a better possible source for human cases
  12. Summing up the first 100-days of (human) MERS-CoV infections
  13. MERS-CoV antibodies in camel sera dating back to 2005 in the UAE
  14. Gatherings and acquisition/transmission of MERS-CoV between animals and humans
  15. Qatari camels clear the MERS-CoV from their systems
  16. TWiV podcast

Using human volunteers to understand influenza virus behaviour and its impact....

This will be the first in a long term project to catalogue the literature's record of volunteer infection studies using influenza virus (IFV). Much like the one I started on rhinovirus transmission back in Nov-2013...see those posts here and here, so far.

I don't guarantee it will be done before I'm too old to type, but I'll be adding to it as time allows. ;)

So first up is a paper.

Author: Frederick Hayden et al
Journal: J Clin Invest 101(3):643-9
Year: 1998
IFV strain used: A/Texas/36/91 (H1N1)
Inoculation route/amount/viral titre: intranasal/0.25ml/105 TCID50

Volunteers included: 19 healthy susceptible males (26%) and females, median age 21-year
Antibody levels: ≤1:8, haemagglutinin-inhibition (IH)

Some key results...

  • Volunteers were kept in isolation for 1-day prior to inoculation.
  • Most (74%) volunteers shed virus on day 1 (1 day after inoculation) as determined by viral growth from recovered nasal washings
  • All volunteers developed symptoms with scores peaking at day-2 and returned to normal by day-8
  • 12/19 (63%) developed fever, peaking at day-2
  • Upper respiratory tract signs of illness (runny nose, sore throat occurred in 15/19 (79%), peaking at day-2
  • Lower respiratory tract symptoms (cough, hoarseness) peaked on day-5
  • Systemic symptoms (muscle aches, fatigue) also peaked on day-2
  • Proinflammatory cytokines in nasal washes revealed several patterns:
    1. Interleukin (IL)-6 and interferon (IFN)-α increased (day-2), decreased, then increased again (day-5) - a biphasic pattern
    2.  IL-8 tumour necrosis factor (TNF) began rising at day-2, peaking at day-4; IL-8 (peaking when nasal mucous turbidity increased) not decreasing as rapidly as TNF
    3. IL-1β, IL-2 and tissue growth factor (TGF)-β did not rise
  • Cytokines in plasma and serum
    • IL-6 and TNFpeaked weakly but at the same times as in the nose 
    • IFN-α and IL-8 were not detectable
    • IL-1βIL-2 and TGF-β did not rise
  • Nasal lavage virus levels (titres) correlated with fever, total symptoms, systemic symptoms and upper respiratory symptoms, TNF, IFN-α and IL-6 on day-2. Total symptoms, viral titre, IL-6 and TNF all correlated on day-5
  • Lower respiratory tract symptom scores peaked in correlation with IFN-α and IL-6 on day-5 & day-6 (also when IL-8 peaked)
As you'd expect given the inoculation route, signs and symptoms of disease occurred first in the upper respiratory tract and then progressed to the lower respiratory tract over time. This is obviously not a "natural" infection as we do not get 0.25mL of flu-containing liquid flying up our noses when someone sneezes on/near us. So the value of this study lies other than in studying natural transmission.

The authors note a few things in the discussion...

  • The response to infection at the site likely leads to the local (runny nose,cough) and the systemic (fever, myalgia) signs and symptoms. 
  • Cytokines are produced by a variety of cells; monocytes/macrophages, bronchial epithelial cells, CD4+ and CD8+ T cells and the infected epithelial cells themselves.
  • Mouse models seem to have more severe lower respiratory tract disease after influenza virus infection than do human volunteers
  • Other cytokines may be involved during more severe natural influenza infections of humans
  • TNF-α, although rising earlier, peaked later perhaps acting to control inflammation after virus has been contained (in the upper respiratory tract at least; what's happening in the lower respiratory tract?)
  • TNF-α and IL-8 were part of the 2nd wave of cytokines and may be better markers of more severe lower respiratory tract influenza disease
Cytokine background information...
  • IL-6
    • A proinflammatory cytokine
    • Secreted by T cells and macrophages
  • IL-8
    • Also known as neutrophil chemotactic factor
    • A chemokine secreted by macrophages and epithelial cells and anything with tool-like receptors
    • Attracts neutrophils and other granulocytes and indices phagocytosis in them
  • TNF-α
    • Also called cachexin or cachectin
    • Mostly secreted by macrophages,but also CD4+ lymphocytes and natural killer (NK) cells
    • It is a pyrogen, inducing fever, apoptotic cell death, cachexia (weight loss) and inflammation
  • IFN-α
    • A Type I interferon secreted by leukocytes, macrophages, epithelial cells, endothelial cells etc
    • Involved in the innate immune response against viral infection by triggering many other antiviral proteins and processes

Sunday 23 February 2014

Live bird market closures continue...

Changsha, capital of Hunan province has had its live poultry markets closed since 21-Feb (1).
H7N9 case map.

So that can be added to Shanghai, major markets in Hangzhou, Ningbo and Jinhua cities in Zhejiang (15), markets in Guangzhou, Guangdong ((3); plus a previous 2-week pause for disinfection in Shenzen (15) ), Hong Kong recently extended its ban (4) on live poultry imports from mainland China and Fujian provinces markets were closed fro disinfection back in 21-Jan. 

No word, that I can find anyway, on market closures in the Jiangsu province (11.8% of all H7N9 cases), other sites in Fujian province (5.5%) or Anhui province (2.5% but over-represented in cases recently).

And yet with no cases announced yesterday - the latest in a recent precipitous decline in total human cases per day - it's tempting to wonder whether market shutdowns in regions that have had the highest case activity (Zhejiang and Guangdong provinces) and which produce or trade a lot of the nation's chickens, have had enough of a flow-on effect to stem the tide in other regions supplied by these. 

Aside #1: Poultry eggs are mainly produced by >1-billion birds in Henan, Shandong, Hebei, Liaoning, Jiangsu, Sichuan, Hubei, Anhui, Heilongjiang and Jilin (7,8) whereas >4-billion broiler chickens (bred for meat) are more concetrated in Shandong, Jiangsu, Guangxi, Liaoning, Guangdong, Anhui, Sichuan and Henan provinces  (2,6,8,9,10,11,12,13).
Aside #2: An interesting to read (5,9) that the volume of chicken consumed per capita has risen by 9-fold or more in recent years - it has not always been the staple but is part of the tradition.



H7N9 snapdate: nothing new to report

No new human cases of avian influenza A (H7N9) virus yesterday.




Friday 21 February 2014

H7N9 appears in a new north eastern Chinese province: Jilin

Click on image to enlarge.
...and the map expands a little more. 

It would be interesting to know if this case was acquired from a live poultry market stocked with birds sourced within the province or from the vast network of poultry movement that links the provinces and their markets across thousands of kilometres.

As I write this, there are 365 cases and 113 deaths, if I can add the latest Guangdong fatality to the 112 I wrote about, earlier today.

H7N9 deaths jump significantly....

Click on image to enlarge.
Twitter was buzzing this morning with news that several sources had announced a new total number of deaths in human cases of H7N9 infection.

It was not a total surprise that there were more deaths than we had heard about, and that is for several reasons:
  • In Wave 1, Spring 2013 in South east China, there had been a greater proportion of deaths than we have seen in Wave 2. That's seemed unusual.
  • After Wave 1, the proportion of fatal cases (PFC; see background here) sat up as high as 33%. Wave 2's high case numbers but few reported deaths had lowered that to 18% at one point. If the virus hadn't changed and human-to-human transmission had not changed then that was incongruous
  • The media were reporting higher numbers than we had data for in early Feb and in late Jan, Xinua reported 26 deaths in Zhejiang alone for 2014 - this far outstripped any publicly data available
So now we see that the tally is 112 fatal H7N9 cases among people infected with a laboratory confirmed H7N9 virus, since the outbreak began in 2013; that tally includes both waves of human cases. That makes the PFC among the 361 confirmed human cases at 31%. 

So this one new piece of news has bumped up the PFC by 10%. From 1:5 (22% last week) to nearly 1:3 cases dying after acquiring infection. 

Thankfully, H7N9 is not spreading efficiently among humans (or chickens according to reports). But these are numbers to care about.

For comparison, my Excel sheet has 64 cases with data that I can cross-check (I believe that agrees with the FluTracker's count also). 

The last media update I looked at had a tally of 77 fatal outcomes

So we have between 35-48 people have died without any ability for anyone outside China to link them to:
  • their age
  • when they became ill
  • where they were
  • how they may have acquired their infection
  • their sex
  • time to hospitalization and diagnosis
  • length of stay in hospital 
  • what contacts they had and how they have fared. 
I think that this is a ball that has been not just been dropped, but buried in a hole and covered over with feathers. I'm disappointed by such a gaping data loss. And don't get me started about the absence of H7N9 sequences from 2014 cases!

  1. SCMP with higher death tallies than public data indicated
  2. Xinhua lists 26 deaths in Zhejiang alone for 2014
  3. VDU blog on missing deaths
  4. Mike Coston's Aviann Flu Diary take one the new data, with other sources
  5. FluTracker's thread with links to eth WHO report
  6. China's Ministry of Agriculture report of enlarged H7N9 death tally|en&tbb=1&ie=UTF-8
  7. The WHO report under the "vaccines" section

H7N9 snapdate: epidemic curve as Wave 2 looks to be ending...

Click on image to enlarge.
This image is another way of showing that the current wave of human cases of avian influenza A(H7N9) virus is ending and that we are solidly within a period of "tailing" (cases only ticking over at low levels in the lead-in or lead-out of the main peak).

BUT: These data are based on figures that are publicly available. As we learned overnight, those numbers can come in fits and starts, if at all. The addition of a large number of deaths without any identifying information linking to the case onset, supports what some have been suspecting for a while; we don't have a full picture of what's happening with H7N9. 

There are now up to 48 more deaths due to H7N9 infections, depending on where your base count is taken from (verified updates or or the media) than we knew about 12-hours ago.

More on that topic later today.

Thursday 20 February 2014

Allergy and viral infection: wheeze and more wheeze

I really liked this Letter by Karta and colleagues from the University of Wisconsin. Not just because it makes some sense to me but because it's not a long drawn-out immunology study written in alphabet soup with multiple 12-panel figures that make me cry.

Trying to understand how viruses (my thing) trigger asthma exacerbations (a clinical thing) via activation of multiple inflammatory pathways (an immunology thing designed to be impossible to follow unless you love keeping tract of tiny little initialisms and what each of them do, did and used to be called 5-minutes ago) is heavy going. This Letter somehow adds to the field without all of "that".

The authors obtained mononuclear cells from the lower respiratory tract of 10 volunteers with mild atopic (allergic) asthma, by bronchoalveolar lavage. That was Day zero (D0). At 48-hours (D2) the donors were given an allergen and cells were collected by BAL again. 

Macrophages were obtained from the D0 and D2 cells (they stick to the plastic culture flasks, other blood cells don't) and they were then challenged with 1 of 3 rhinoviruses (RV); either RV-A16, RV-B14 or RV-A2. I say challenged because rhinovirus doesn't replicate within macrophages (also written in shorthand as MΦ) but they do interact with them.

The team then looked at a bunch of initialisms which represent some potent chemicals called chemokines:

  • CXCL10 (IP-10)
    • C-X-C motif chemokine 10; formerly interferon gamma-induced protein 10
    • secreted by macrophages that have been activated by RV interaction
    • also secreted by endothelial cells and fibroblasts
    • secreted from cells in response to interferon gamma (IFN-γ)
    • signal the recruitment of immune cells  (monocytes/macrophages, T cells, natural killer [NK] cells and dendritic cells) that take charge of getting rid of virus
  • CXCL11
    • C-X-C motif chemokine 11; formerly known as Interferon-inducible T-cell alpha chemoattractant (I-TAC) and Interferon-gamma-inducible protein 9 (IP-9)
    • also secreted by macrophages that have been activated by RV interaction
    • secreted in the pancreas and liver
    • secreted from cells in response to IFN-γ and IFN-β
    • interacts with cell surface receptor, CXCR3
    • recruits activated T-cells
  • CCL2 
    • Chemokine ligand 2; formerly known as monocyte chemotactic protein-1 (MCP-1) or small inducible cytokine A2
    • can also be secreted by macrophages after RV exposure
    • also secreted by monocytes and dendritic cells and expressed by neurons, astrocytes and microglia
    • recruits monocytes and basophils
    • binds to the cell surface receptors CCR2 and CCR4
  • CCL8
    • Chemokine ligand 2; formerly known as monocyte chemoattractant protein-2 (MCP-2) 
    • can be secreted by macrophages after RV exposure
    • recruits mast cells, eosinophils, basophils, monocytes, T-cells and NK cells
    • binds to cell surface receptors CCR1, CCR2B and CCR5
Some key findings...
  • D2 samples that were not challenged with virus made less CXCL10, more CCL2 and nothing much changed in levels of CXCL11 or CCL8.
  • D0 samples incubated with RV saw a statistically significant rise in the amount of all 4 chemokines
  • D2 samples incubated with RV saw a rise in CCL2 but a drop in CXCL10 and CXCL11 but no effect on CCL8 
So the first batch of findings indicate that RV infection does not induce the same chemokine response from lower airway macrophages of people with allergy that have just been exposed to an allergen (think pollen or dust mite).

Further, it identified that in macrophages, a key immune cell in controlling viral infections in the airways, may not respond as effectively to RV infection in the body if such infection follows an allergen hit. At the same time, increasing CCL2 may increase inflammation by attracting those types of cells (eosinophils, neutrophils and more macrophages).

The team also went on to look at the levels of the 2 known RV cellular receptors, intercellular adhesion molecule I (ICAM-1) and the low density lipoprotein receptor (LDLR) and LDLR-related protein-1 (LRP-1). Receptors have been used as a way to categorise RVs in the past and some adhere to this when making choices in the design of their immunology research relating to RVs.
  • D2 macrophgaes had raised levels of ICAM-1 on the cellular surface but lowered levels of LDLR and LRP-1
  • Other blood cells showed no difference in receptor levels
  • Allergen-induced effects on RV receptor expression are distinct from its effects on chemokine levels
Great to know that RVs are ubiquitous and so are allergens!

  1. Information on some cytokines and cell signalling following viral infection
  2. Wikipedia as a starter for detail on cytokines

Wheezing after respiratory virus infection...

Takeyama and colleagues from Japan delved into the viruses present among young children (≤ 3-years of age) hospitalized with a clinically defined lower respiratory tract infection.

This exemplifies what many such studies do; sample from the upper respiratory tract to find signs of replicating virus in order to study a disease of the lower respiratory tract

It's a stretch but if you go along with it you are implying that an upper respiratory tract infection either triggers the symptoms from afar or that the virus travels into the lower respiratory tract to directly cause inflammation and/or cell destruction.

Viruses were detected by PCR-based methods.

Some key findings...
  • Respiratory syncytial virus (RSV) was the virus detected most often (51/102 samples from 153 children) in children who were admitted with wheezing followed by rhinoviruses (RV; 21 or 14%), RSV+RV (12 or 8%) and then parainfluenza virus 3 (PIV3; 8 or 5%), influenza virus (IFV; 5 or 3%) or human metapneumovirus (hMPV; 5 or 3%)
  • A similar pattern was observed in 259 children who were admitted without wheezing (RSV-25%; RV 9%; IFV 7%; RSV+RV-4%; PIV3-3%; hMPV-1%)
  • 67% of children with wheezing were virus positive (POS)
  • Children with an allergic predisposition (IgE antibody levels >30IU/mL at admission and a parental history of asthma) POS for RSV more often had wheezing later
  • Children who were wheezing & RV POS when they were admitted were more likely to wheeze again than were those who were RV POS without wheeze at admission.
So [allergic predisposition + RSV] or [wheeze/clinical severity + RV] were 2 factors related to subsequent wheeze.

The authors also raised the spectre of RV positivity occurring in asymptomatic individuals in other studies. However, that can happen to some extent with all respiratory viruses. No other virus has 160 distinct type like the RVs...but that's another story.


Humans unlikely to infect poultry with H7N9? Data please!

The United Nations Food and Agriculture Organization (FAO) has said that poultry is not at risk of being infected by humans carrying H7N9 virus.
In fact, we have no evidence that affected people could transmit the virus to other species, including birds. The highest risk of virus introduction is uncontrolled live poultry trade between affected and unaffected areas.
But absence of evidence is not evidence of absence.

We have seen studies, like this one, that use a human H7N9 virus and use it to successfully infect chickens. So the virus is capable of replicating even if it is inefficient at spreading to other chickens or even ferrets ( a human surrogate of influenza infection). But then we do know that humans get infected from exposure to something in poultry markets.

I agree (for what that's worth), that the risk of spreading virus is more in the area of moving infected birds around, as well as their own migration movements. But I think it is too early be early to issue strong denials that humans may infect poultry until we find some data to support them.


Why I think the 2nd wave of human influenza A(H7N9) virus infections has broken...

If you look at the chart above, it shows declining:

  • Average cases per day (blue data points) in 2014
  • Less noticeable but consistently declining average cases per day when calculated across all of Wave 2 (oranges data points)
  • And importantly, a drastic decline in the number of new cases being announced after the 27-Jan peak. 

From 5-Feb, we have not seen more than 2 cases/day whereas in Jan we were regularly seeing 5-6 cases/day (peaking at 12/day).

The last time we saw this steep a drop in cases was 19-Apr 2014; the end of H7N9's 1st wave of human infections. 

That doesn't mean the virus has gone away or that the outbreak has been "solved". I learned that lesson last year. H7N9 is still out there. 

If these latest case numbers accurately reflect what is happening in China, then it looks like closing poultry markets did the same job in 2014 that it did in halting the 2013 Spring outbreak in southeast China. It will be down to the poultry industry and perhaps the Ministry of Agriculture in China to find evidence that specifically disproves a role for poultry in human infections; and it seem clear that changing from fresh to processed poultry has some even more safety data to support it.

We still have no data that lets us point the finger at chickens, or ducks or song birds or pigeons or geese or some other animal in the markets as the source. 

We just know there is a strong association between humans getting infected after being in the presence of "live poultry" usually in a market setting. With reports suggesting better growth of H7N9 in song birds compared to chickens as well as poor spread of virus between infected chickens, there is much work to be done outside of chickens to track the source of the virus down.

Wednesday 19 February 2014

I care what the H7N9 numbers are...

This was the Tweet from Crawford Kilian (hereafter "Crof") a couple of days ago. 

I respect Crof. He has been as much of a mentor in my year doing this as has anyone. He even sent me his book on "Writing for the Web". I immediately changed a few things that I did after reading parts of it. Unfortunately nothing can help my appalling typing skills.

So when I saw that Tweet I thought it must have been a hook to get people to come read the full story. Twitter is a great way to attract readers to my blog; its a top referring site. Among other things, it's an important tool for promoting what we write to a wider audience. Sometimes a catchy title can be as good a bait as something more straight down the line. So, hooked, I dutifully read on.

What I found has been disappointing me ever since I read it 2 days ago, because I care about these numbers, and I thought you did too, Crof.

The article is of a type that I have read several times from Crof. It reminds those of us getting carried away with small, confined disease outbreak that hey, it's a great big world of misery out there and many more people are suffering and dying of all manner of diseases, a lot of which we forget about. Sometimes we don't forget though, we just focus on other things for a time.

I think it is a very valid point to make; and to make it over and over again is also fine with me. Points made in a blog post are very quickly forgotten, if they are ever read in the first place. At least a search engine may lead some back to that post or online newspaper story, unlike a printed newspaper which if not read may never have existed.

What really disappointed me I think...and I've been trying to work out why this has stuck with me for 2-days now, even causing me to give up on writing this last night or on blogging about viruses at that Crof's post never did back away from the message of that original Tweet. Who cares about those numbers? It continued to hammer home that to follow such small numbers of deaths needed a special kind of justification, even for Crof. He said....
When I see WHO's H7N9 updates extending to 10 or 15 cases, it looks a bit alarming, I grant you. But let's put it in proportion.
Yes, I pay more attention to avian flu than to lung cancer and malaria. So, unfortunately, does everyone else...if you define "everyone else" as affluent, educated, vaccinated individuals living in countries with excellent public health systems and drinkable tap water.
For us, it's the implicit threat of some clever virus that holds our attention: we don't have a vaccine for this one, so we ourselves are as vulnerable as some kid in Cité Soleil or Asunción or Gorakhpur.
I suppose we can justify our interest by arguing that by studying these new diseases, we learn more about other diseases, and ourselves, as well. And that's a plausible argument.

Finishing with
Meanwhile, since I posted a few minutes ago that 768 mothers died in childbirth today, the number has risen to 775.

So Crof, are there so few people on the planet that some cannot keep an eye on one disease, some on another? I get that we do have to prioritise certain diseases over others. We have limited resources and human nature seems such that we never get everyone to pull in the same direction for long enough to truly solve our problems. But there is no definition of a suitably attention-worthy number of lives lost to infection. Every infection that takes a life, or even those that make life miserable, are worthy of our attention, our study, our understanding and eventually, our efforts in defeating it. I care about those numbers.

You cited a number of examples of other causes of far greater human death and disease. I remember a post or comment of yours with similar information that has always sat in the back of my mind as a check and balance of over-reacting.  Yet I have also read many other posts from you that champion the need for better information about MERS and MERS-CoV cases, for example. You often provide "granular" (my word of the month) detail on individuals with infections. You followed the story of a single French MERS patient for many weeks. And so did we because of you. So I simply don't "get" how this post fits, if not to remind us that ALL the numbers are always worthy of our care. 

Yes. There are very few cases of H7N9 compared to the world’s population. But there could be many more, as I know you are more aware than many, with only a few bits of bad luck and circumstance lying between "sporadic" and "sustained". Why not have more eyes rather than fewer on such risks?

There were very few cases of SARS, H5N1 or even now, few new cases of polio or measles compared to such a huge denominator. But each and every one of those diseases has been and should be watched, followed, tracked and its every aspect quantified. 

Every death that could be prevented now with vaccination or in the future by better education, better research, better understanding of the patterns and changes to those patterns, and better awareness by the public themselves, is one more person who remains a living family member. I don't dwell on every death I've reported but I know what it would be like if it happened to someone close to me.  

So I leave you with these 2 thoughts...

And if a little pandemic porn helps all of us protect our health, and outgrow the need for such porn, then maybe it's worthwhile.
..the attention we pay to these fringe viruses is certainly worth the effort..

...and I hope to read many more like them in the future Crof. 

Just like you care about the words that you masterfully write, I think you like me, also really do care about what the H7N9 number are.