Housekeeping on VDU blog: 145 posts and counting

Only 2-days of May 2013 left to copy across from the old blog format. 

Lots of still-pertinent posts during May so if you haven't seen them already have a browse.

And somehow, I missed my 100-blog-post party! Definitely a cake for 500 posts.

Back to some paper summaries tomorrow.

Speculation Into Darkness.

As part of my crippled USS Vengeance-like crash course into the workings of influenza viruses over the past nearly 6 weeks, I've been doing some reading. 

A Science Policy Forum article I'm skimming through tonight, from Lipsitch and colleagues in 2012, makes a nice comment: 

We contend that predictions about how particular influenza strains will behave in humans or, even more important, how they will evolve, remain highly speculative. 

While this was written with H5N1 as the subject, it is clearly applicable to H7N9. It nicely sums up my understanding on this late Friday evening as well! And who needs a colon anyway?

Losing control of the numbers?

That's how it was described to me by my esteemed colleague, the Editor in Chief of FluTrackers. 

For the past 5 week we've had fairly detailed data coming out of China about avian influenza A(H7N9) cases; dates, places, names, deaths, discharges., All these placed into the public domain and not just reported to Health officials through less public channels. 

Sure, I've griped about a missing number here and there in the past, but its not like I have a right to this information. Are these the data I'd like to see? No, I'd like to have seen prospective real-time RT-PCR-based (couple of assays targeting different regions) screening hospital outpatients, the community and including asymptomatic people, of all ages. I'd like to see serology on the vendors and those who frequently visit markets versus those who do not. And I'd like it all done yesterday. But that's flippant, and easy to say from my desk in my environment of instant gratification, some 7,330km away. Are these data from every single H7N9 case? Probably not, for a number of reasons. So, for some pure speculation. 

It just doesn't feel right. 130 cases spread over such a wide area, steep onset curves that suddenly halt, patents like Lee from Taiwan and others who claim no bird contact, so few severe cases among market vendors, evidence for asymptomatic and suspected clusters. 130 cases seems too low. More unreported cases may exist simply because we don't have all the results yet. Those may be coming down the pipeline. The time and effort to conduct screening and sequencing, collate data, cross-check and report results for humans and animals on the scale that is necessary to answer the questions being posed, is vast. China needs to juggle many other social and political issues around the reporting of deaths, illnesses and human-to-human transmission of this new virus. It has its own way of doing that. Most states do.

Nonetheless, scientists, policy makers, healthcare officials and vaccine producers (traditional and cutting edge) already have the information they need to get started on preparing for any future H7N9 pandemic.

• Vaccine seed strains have been circulated worldwide
• WHO influenza collaboration centres have positive H7N9 RNA controls for their RT-PCRs
• More RT-PCRs have since been developed to overcome the (not unexpected) deficiencies in first-generation assays
• Serological reagents are in use in China and in preparation elsewhere
• Key global health bodies have updated their pandemic plans
• We have estimates of incubation periods, clinical signs and symptoms indicating that severe acute respiratory disease cases look like....severe acute respiratory disease cases would be expected to look
• We know transmission may be happening between humans but inefficiently
• We know closing down wholesale poultry markets seems to correlate with a decrease in severe H7N9 cases in humans
• We've dusted off (ineffective) heat sensing cameras and (pointlessly) ill-fitting face masks again
• We have a good idea of what the wild host is (a bird...like it is for all influenza A viruses) just not evidence for which one or where it all started
• We've officially named our viral nemesis.

So all in all, we're not too badly off.

However Week 6, so far, has provided confirmation that publicly available case details have almost dried up.
The data we've had have been interesting and have allowed me to plot the detailed charts and graphs you've been viewing on the H7N9 page. Half of those views are from repeat visits. 

Today, my last hope faded for an update on those details for the recent 6 H7N9 deaths and the missing details on about 15 discharged patients. The WHO update had no new information in it at all. Perhaps other lists will be updated soon?

Here's hoping for some new data in the future, especially if that data should signal to the rest of the world that H7N9 has changed genetically, or a return of exponential rises in new H7N9 illness onsets such as we saw in Shanghai and Zhejiang. 

I think we have what we need to know that an H7N9 pandemic could emerge, but that one hasn't emerged yet.

Anger over anti-vaccination comment.

The entirely confusingly named Australian Vaccination Network (next month they will face a court battle to retain their misleading name), actually a cabal of anti-vaccination advocates, has encouraged parents to avoid vaccinating their children and do not rely on your GP's opinion. You know, those experts in community ills who often have there own children and have trained and worked for over a decade to ensure the community is healthy.

Instead, consult books, especially those penned by fringe writers who may have not knowledge or expertise in the science and medicine of infectious disease whatsoever.
As Australian Medical Association president Dr Steve Hambleton suggested, you can obtain facts from the Immunise Australia website and there is an excellent publication, produced by the Australian Academy of Science, The Science of Immunisation: questions and answers. 

The documents on these sites are fully up front about their being some risks, its just that these risks are generally very minor things like redness, soreness and swelling - probably nothing like that bruise little Johnny is sporting from school today or that bite Jenny inflicted on herself when she bit her own cheek at dinner last night.

 In comparison to acquiring the unadulterated disease against which these vaccines protect, its nothing to be unusually worried about.

H7N9 Weekly wrap-up. Bird flu, what bird flu?

We finished Week 5 with astonishingly few new notifications and a lot more difficulty finding key dates for hospitalization, death and discharge. For example, a 55-year old male named Jiao from Hunan province has been variously cited as being the 25th or 27th death associated with H7N9. No-one seems to have a name for the 26th death. Just 1 disease onset and 2 deaths deaths during that period (see the many charts on the H7N9 page) making it the least fatal week of the outbreak. A total of 26 cases have been discharged from hospital (see Case chart on H7N9page, with perhaps another 9 unnamed discharges from Zhejiang. No new cases reported from Shanghai, Beijing, Anhui, Jiangsu, Henan or Shandong. Lab confirmations for cases with dates of onset preceding Week 5 appeared for Jiangxi, Fujian, Hunan and Zhejiang. 

Considering how steep the rate of confirmations was for Zhejiang in particular, the drop off is quite remarkable. The wet market closures seem to be the most popular factor in the decline of new (severe) human cases but there is still no word on prospective PCR screening for H7N9 among non-severe cases or among those without chronic underlying conditions.

So, as far as we know, pneumonia remains the most frequent indicator of H7N9 infection and that seem to be among mostly males with a constellation of underlying disease and infection. 

Week 5 saw a flurry of peer-reviewed scientific papers emerge. Some better-defined the clinical cases, other reported risks based on what we know from past influenzaviruses and others described the avian and genetic pathways for the parent and grandparent H7 and N9-containing viruses that seem to lead to the creation of H7N9. Intriguingly, there are still very few reports of H7N9 in the ducks, chickens and wild birds proposed as the hosts from which humans catch the virus.

While markets have been found to contain H7N9-positive birds, there are remarkably few human cases among market vendors or those working with the feather plucking machines (another proposed transmission route proposed during Week 5). Could vendors have pre-existing immunity? 

So another curious week with plenty of questions raised, but cases and deaths declining.

Influenza virus transmission.

An interesting blog post from 2006 by Revere on some aspects of what H5N1 virulence (in terms of disease severity), transmission and preconceptions. 

Do we put too much stock in believing that recently emerged viruses eventually settle in to their new hosts, seeking a perfect balance between virus replication, transmission and host mortality? 

In other words, do viruses adapt over time so that originally severe infection outcomes (like pneumonia) become mild illnesses (like the common cold or just feeling a it crook). 

There may be some parallels to be drawn with H7N9 as we continue down its path. 

Or perhaps H7N9 has been adapting to humans for longer than we think?