Thursday, 9 January 2014

H5N1: 1st fatal case in North America...[UPDATED x4-FINAL]

An otherwise healthy resident of Alberta, Canada, died 3-Jan after contracting influenza A(H5N1) virus during a visit to Beijing ,China. The person did not leave the Beijing area and did not visit live bird market. The victim returned on Air Canada flights (according to a Tweet from @HelenBranswell), showing signs and symptoms on admission to hospital 1-Jan which included high fever and lethargy without cough or other signs of acute respiratory tract illness. The patent died of meningoencephalitis. The lab confirmed H5N1 7-Jan. 

Canadian officials will not be describing the patients age, sex or occupation. Giving the region would be enough to identify the patient given there is only 1 case.

A highly pathogenic avian influenzavirus (HPAI or "high-path) that can kill the birds it infects, H5N1 has been confirmed in 648 people across 15 countries since its identification in a 3-year old boy in Hong Kong in May 1997 (first identified in a goose in 1996). There were 38 cases identified globally in 2013, with 24 deaths. A slow-burn that seems comparable to H7N9's current spread. How often H5N1 is considered in the screening of influenza-like illness I do not know; another similarity might be under-reporting/limited prospective PCR-based screening.

As ever, these sporadic imported cases also serve to highlight that the pathogen is circulating at the source. The route of acquisition for this case is unclear at this stage. H5N1 does not readily transmit among humans requiring close contact with birds and there has been no sustained human-to-human transmission.

When a human does become infected by the virus, severe acute respiratory distress syndrome can result. This is ascribed to the availability of receptors in the deeper airways and lungs, which bind the virus and trigger the person's own immune-mediated disease via a "cytokine storm"; a large scale release of the chemicals our bodies usually employ to keep virus infections in check, but on a larger scale with more severe consequences to the host. Such a storm does not commonly occur following infection by a seasonal influenza virus (e.g. H3N2) infection, 

The WHO does not list any H5N1 cases in the area around Beijing on its 2013 map (18-Dec-2013). An out-of-date timeline of "major" H5N1 events lists human cases in Beijing in Nov-2003 and Dec-2008. Major outbreaks among birds in China have centered around Qinghai lake.

There is no H5N1 component in the current seasonal influenza vaccine, but then there is no significant risk to the Canadian public health from H5N1.

The current WHO phase of pandemic alert for H5N1 is ALERT:
This is the phase when influenza caused by a new subtype has been identified in humans. Increased vigilance and careful risk assessment, at local, national and global levels, are characteristic of this phase. If the risk assessments indicate that the new virus is not developing into a pandemic strain, a de-escalation of activities towards those in the interpandemic phase may occur.

As the Public Heath Agency Canada recommend, Think-Tell-Test....
THINK
  • implement best practices for triage, infection control and patient management as indicated
TELL
  • Consult your local Public Health for assistance in SRI/severe ILI patients with the following:
    • Recent travel or contact with travelers to an affected area with confirmed H5N1 activity in humans and/or domestic poultry
TEST
  • Consult your local Public Health for guidance on appropriate testing, recommended procedures and prioritization for H5N1 investigation IF significant exposure history has been established which may include:
    • Close contact (within 1 metre, i.e. touching distance) with a confirmed human case of H5N1 or
    • Close contact with sick or dead domestic poultry or wild birds

Other news and related information sources include...

Monday, 6 January 2014

From birds to humans....

Reports indicate 2 new cases of human infection with influenza A H7N9 in Guangdong. The 47-year-old (Foshan) and 71-year-old (Yangjiang) males are both hospitalized and in bad condition.

It was only a matter of time since the market testing has been revealing signs of H7N9 circulating.

For 47M...

"The Guangdong health authorities have on patients 60 close contacts under medical surveillance, not currently found exception."

For 71M...

"The Guangdong health authorities have on patients 65 close contacts under medical surveillance, not currently found exception."

So the contacts are under surveillance but I strongly suspect that if that surveillance was to extend to actual RT-PCR testing, then we would likely see some detections amongst those cases. Symptoms alone do not the full story tell.

My source was Twitter via @pandemic_news and associated blog post here.

H7N9 in Guangdong; Market #2

As the tally of H7N9 cases passes 150 (n=151 since Feb-19-2014, 321-days), crofsbogs has picked up on an environmental sample from a second live bird market (Nanchao market) that has been confirmed as positive for H7N9 by Center of Disease Control and Prevention (CDCP).

This time we learn that nucleic acids were detected so RT-PCR methods are in use, at least in Zhuhai city, a prefecture-level (between less populated than a Province but more than a County) city on the coast of Guangdong province bordering with Macau. 

Was RT-PCR in use during those huge poultry screening events last year? Tracking back to a post on some of the vast numbers of animals tested (hundred's of thousands) earlier in 2013 it looks like the testing back then was virological (trying to grow virus I presume) and serological (detecting antibody to recent infection by the virus) rather than molecular (PCR-based). I stand to be corrected on that.

Just thinking out loud, but it seems to me that 800,000+ birds had been tested using RT-PCR then we would have had a much better idea of the extent to which H7N9 was distributed across China.

As an aside, the 3 most recent human cases also read like a who's-who of 2013's H7N9 hotspots; Jiangsu province, Shanghai municipality and Zhejiang province. 

I'm making some more lines available on my Excel sheet.

Editor's Note #13: 2014 thoughts...

Virology Down Under.
What does Virology Down Under's (VDU) blog stand for? 

First off, a little background.

The idea of VDU the website, was to provide some useful info on viruses; the type of info that could be used to help less expert people get an idea of what they are and what they do to us. It had its beginnings in 1996 as the website for the Sir Albert Sakzewski Virus Research Centre (SASVRC), my workplace. It then accrued enough mutations that it evolved into VDU.


That endeavor truly started online in 1997; 16-years, 11-months and 9-days ago. Last year VDU spawned a blog. This. 

The VDU website, while in need of sprucing up (still), exists more as a fixed point in time while the blog aims to keep readers abreast of some of the goings on in virology. The blog's focus is on respiratory virology because that's what I know most about, but other things get dropped in on occasion. The focus is also on my take on things, hopefully with some humour thrown in. I initially commented in April 2013 that I'd stay away from blather and keep the opinion related to hard data. That's still my intent, but opinion being what it is I may rant on occasion, I may drift away from citable evidence and I may collect thoughts in a way that cannot be verified by any one single study. Hopefully I'll make that clear but it will all be part of VDU's DNA...probably RNA given its focus on respiratory viruses...and nerdy little comments like that will continue to pop up too!

I've noticed during my short time in "flublogia" (I think that's a hard 'g') that each blog/site/newsboard has a distinct personality. Apart from spending a large slice of their own time collecting, collating and writing about infectious diseases for a largely intangible audience; page hits and comments being key proof-of-life beyond the keyboard. Some key authors I have learned from in 2013 produce a "vibe" through their blogs. I often read the same new piece of information but on multiple sites to see a wide range of interpretations - each one telling me something different, each a specialized cell contributing to the tissue. 

Crawford Kilian emphasizes the human cost to infections, Mike Coston emphasizes ways to personally protect yourself from infection and manages to place new news in superb context thanks to his blog's back-catalogue of posts while FluTrackers emphasize the spotting of information before it even occurs (yes, they are that fast!) and lays the groundwork for trends that are often only visible after their subject matter has emerged. If I want to actually be interested in what's happening in the world of not-viruses, I'll go to Maryn McKenna's Superbug because it's the only bacterial text I enjoy reading (and she posts funny Tweets). There are others but correcting all these typos means that I write slowly and this has already taken a while.

So what about VDU's blog? It aims to identify, define and add opinion to patterns seen during virus infections, epidemics and outbreaks. It's a part-time thing so I post when I can. My opinion may not be bleeding-edge expert or informed by decades of specific literature and research (sometimes it is)- virology has many, many aspects to it and I don't claim to be across them all - but I am most happy to be educated so please do leave comments here or on Twitter, LinkedIn, ResearchGate or anywhere else I've left an avenue for contact.

Another of the VDU blog's intentions is present its data pictorially and certainly to create a reference of somewhat "softened" science for you and also for me; it now serves me as a literature review repository and I hope some of its graphics can also be useful to you in your talks, blogs or whatever. VDU's images remain free to use - I just ask that you link back to the blog.

I won't dwell on the misery caused by virus infections (and there is much), in fact I deliberately keep VDU faceless and focus on the virus rather than the host. Others do a much better job of conveying the human cost than I can anyway. It's not because I don't care (I have written on this topic previously) so I apologize if it all seems a little devoid of humanity.

The VDU blog is not yet 1-year old; still an infant in human terms. It's been crawling along okay so far but it's still got a lot to learn and hopefully some more readers to pick up as it grows. In its 1st year VDU's blog has driven 2 publications, been cited in the scientific literature, under-pinned a lot of interviews with the media and been the reason for few local and interstate seminars (another coming up next month). More than I could have possibly imagined. It has also  created a lot of new links to good people both in science research and in science writing. I have learned much thanks to the help and mentoring these people have provided.

I hope that gives you an idea of what to expect from the blog in 2014. All the best for the New Year.

IanM


Sunday, 5 January 2014

H7N9 in the water and the goose stalls, in Guangzhou

Via Twitter, Xinhuanet posted a story this evening that tests have identified influenza A(H7N9) virus in 2 poultry booths selling goose meat and an environmental sample of sewage water in a wet market in Zengcheng, Guangzhou, Guangdong Province. 

The nature of the testing, reported bye the local Center of Disease Control and Prevention (CDCP) is not specified so whether live virus was detected or viral nucleic acid is unclear. Finding influenza virus nucleic acids in the water of a live bird market in the current climate is not hard to believe - PCR being so sensitive and all - but whether it came from geese is not clear without more information.

There doesn't seem to be anything about this on the Animal Health's OIE latest disease alert list.

Disinfection of the market has been carried out and there is a suggestion that slaughtering of birds will occur soon.

Of course, FluTrackers had this a day ago!

Friday, 3 January 2014

Antibodies in 10-year old UAE camel sera suggestive, but not evidentiary, of the presence of MERS-CoV a decade ago

Click on image to enlarge. 
I've cobbled together a graphic of the assays
that have come from Prof Christian Drosten group and
colleagues, mostly for the detection and
confirmation of MERS-CoV in human samples.
632 of 651 (97.1%) dromedary camel serum samples collected in 2003 and 2013 in the United Arab Emirates (UAE) have been found to react with Middle East respiratory syndrome coronavirus (MERS-CoV) or key pieces thereof.

Meyer and colleagues from the Netherlands, Germany and the UAE also tested 16 control samples from German zoo camels but none reacted to MERS-CoV in their testing system. This indicates that the camels have not been infected by the MERS-CoV (or something very much like it) leading the authors to suggest that the virus is relatively isolated to Arabian peninsula's eastern edge...as far as we know from the testing performed to date. 


This is a potentially huge piece of good news because it suggests, to me at least, that there is a very strong chance that the spread of MERS-CoV can be contained. It will however, take a collaborative effort to "stamp out" MERS-CoV the same way SARS-CoV was stopped in its tracks (to partly quote Mike Coston) through effective infection prevention and control measures being created, implemented and enforced. 


In the absence of further testing from other regions around the world, we hold information in our hands that suggests a region-specific isolation to the MERS-CoV. And we know that right now it does not seem to be very good at all at transmitting from human-to-human. Perhaps reflecting that it is currently a camel virus and not a human one? Of course, it may never evolve into a human virus.


From what we do know today of the MERS-CoV, stamping out human infections may involve some of the following steps:



  • Being aware of the risk of contact between humans and camels and seeking to limit such contact if it could occur in the absence of suitable precautions including personal protective equipment
  • Testing camels for active infection, which may not result in notable disease in camels, and isolating those camels from other camel herds to try and "burn out" infection in camels altogether. The horse racing industry might have some good advice in this department
  • Learning more about all aspects of MERS-CoV acquisition, spread and disease in camels and perhaps in other animals. This will be influenced by future screening projects results which will hopefully identify any other animals that also a close relative/immediate ancestor that is passed to camels and then humans, or perhaps directly to humans
  •  Implementing ways to break the chain of spread from a putative other animal host to camels to people. 

Hopefully such steps could be achieved without any long term impact to camel interaction in the region as they are an essential source of social, economic and dietary enrichment.


A recombinant MERS-CoV Spike immunofluorescent assay was used to screen samples for reactive antibodies. Vero cell s expressing a recombinant Spike protein from MERS-CoV or HCoV-OC43 (used to detect cross-reactive antibodies) were fixed and then incubated with diluted animal or control serum samples (1:20 - 1:80 at 37'C for 60-min). Captured antibody was labelled with an anti-llama antibody fragment labelled with a fluorescent tag (FITC). A MERS-CoV human protein microarray assay was used to confirm screening results (I've noted this assay previously here). Virus neutralization studies were also conducted using a method I've previously written about


Meyer's study also screened 182 camel's faecal samples collected in 2013 using broad-ranging CoV RT-PCRs which, upon nucleotide sequence confirmation, yielded 2 bovine coronavirus (BCoV) positives, but no MERS-CoV positives. We learn from this that recently stored faecal samples can yield CoV RNA that can also be sequenced.


It's also worth a quick hop back to looking at the bigger picture of animal testing for a moment. Succeeding in detecting MERS-CoV RNA among the relatively small numbers of samples tested to date is akin to finding the Arkenstone among Erebor's piles of gold (even if it looked easy in the movie). Sure, a decent number of different animal species have been tested so far, but only small numbers from each. And even though there is a high proportion of camels with MERS-CoV (or its antigenic kin) antibodies, we still have to strike it lucky enough to sample during what may well be an acute virus replication period lasting only days to a couple of weeks. So far, it looks like luck has been as slippery as a woodland elf on a riverbank. Larger numbers of each animal species, camels especially, should land a hit or two in the near future I'm betting.


There is still much testing to be done, but perhaps it's possible to shut the gate before the camels have truly bolted.


Hat-tip to Helen Branswell on Twitter and her article here.

The weather in eastern China...

Just a random snippet form a paper I was skimming that helps us southern hemispherans get a grip on the seasons and weather elsewhere...


Some studies have claimed that climatic factors, particularly temperature, have a clear impact on seasonal influenza outbreaks [34,35]. The weather in eastern China is very cold between December and January, and temperatures begin to rise in late February. It is usually relatively warm in March and April, and starts to get hot from May. The temporal characteristics of human infections with influenza A(H7N9) virus suggest that temperature has some association with incidence of this disease. The prevailing mild climate may have been particularly suitable for influenza A(H7N9) virus infection since there was an increase in the number of cases in March–April. If there is a relationship, attention must be paid as there could be a potential outbreak in the same period (March–April) in the future.



Thursday, 2 January 2014

H7N9 median time between events: the story of average disease

Click on image to enlarge.
From Clinical Findings in 111 Cases of Influenza A (H7N9) Virus Infection, Gao et al, Volume No 368, Page No. 2277-85. Copyright © (2013) Massachusetts Medical Society. Reprinted with permission from Massachusetts Medical Society.
This is a supplementary figure from the New England Journal of Medicine article entitled "Clinical Findings in 111 Cases of Influenza A (H7N9) Virus Infection" published May 2013 by Gao and colleagues working at a host of Chinese institutions around Eastern China.

It presents key median times between virus acquisition through to death among 62 influenza A(H7N9) virus-infected patients.

It struck me as a very clear way of summarizing the timeline to death among those with this outcome ascribed to infection by H7N9 earlier in 2013.

It is noteworthy that the median time for antiviral therapy to commence was 7-days, ostensibly too late to have an effect on severe infection and disease....but then a definite diagnosis took 8-days on average so antiviral treatment would have to have been commenced without lab confirmation, in order to be most effective. 

It seems that quite a few H7N9 patients present to at least 2 facilities once they become symptomatic. From the figure above, antiviral treatment is usually started at the second, tertiary care facility. Could it be started earlier?

This really stresses the key role of the first Doctor an H7N9 patient presents to, an event which itself occurs 48-hours after symptoms develop. The high end of when antiviral treatment needs to be administered to have its greatest impact.

Wednesday, 1 January 2014

Keeping patient privacy to the fore...

Crawford Kilian (CK; with one "l") and Andrew Rambaut (AR) passed a couple of tweets a couple of evenings ago (my time), and I chipped in my 5c worth (inflation and all) at the time.

I wasn't really meaning to be argumentative, my comment was asking, cynically, whether a suggestion to improve patient privacy suggested by AR would help unstopper the cork of oft-times incomplete and sometimes slow or non-English information on cases of MERS-CoV infection in Saudi Arabia.

Yesterday afternoon CK penned some more detailed thoughts on the issue of patient privacy, stigma and microbial infections. The overall message from all related communication's (including Saudi Ministry of Health's [MOH] Dr Ziad Memish's comments to CK on patient privacy back in September) is that patient personal space was being encroached upon by media who had deduced their identity from the amount of detail in the Saudi press releases
about cases. This may have led to these patients, who had apparently complained to the Saudi MOH, being identified to their community and perhaps being stigmatised just because of their viral passengers. As Dr Memish wrote....


Over the last year we had patients and families complain to us about intrusion of their privacy by media reporters who recognized their identity through the transparency of reporting their case details.

He had said a similar thing a few days earlier in an interview I wrote about here.

I offer some thoughts and arguments below; and yes, this time I am being argumentative. There are a few issues here...
  1. Patient privacy must always be protected
  2. Is patient privacy being breached?
  3. Should we expect to have MERS-CoV data available for hobbyist bloggers and interested scientific parties?
As someone who has worked in a research capacity with patient samples for 2 decades, I've seen the ethical sands shift constantly towards improved patient privacy. I'm painfully aware that the need to ensure the patient's privacy is paramount. I can't pipette from a sample unless I have the appropriate external ethical approval to do so - every funded project in our lab is conducted this way today. I have not one problem with that whatsoever. At the end of the day, whether in a research or public health capacity, I want to try and help sick people - not make their lives more difficult.

When you submit yourself as a patient to a Doctor's care you do not expect to have your results show up in the local newspaper or on a tinpot blogger's column (I'm talking of mine not yours CK or AR!), or to be hounded by the media as you exit your hospital. Of course there may be exceptions to those people - we saw quite a few H7N9 cases wheeled or walked to the waiting press pack earlier this year. Being a patient puts us at a level of vulnerability that none enjoy and for it to be taken advantage of is absolutely unacceptable. I would have thought that keeping a patient's result details private is part of the Duty of Care. 

Still, I do wonder at the extent to which MERS-CoV patients are stigmatised because they are MERS-CoV-positive which was deduced by the media from the "transparency of reporting their case details". Let's take the best case scenario for MERS-CoV case details...age, sex, region, hospital name, underlying conditions, perhaps a couple of other items on a good media release. How does the media find out about that person to the extent that they track them down and hound them for an interview? They don't have access to medical records. Is the media release (see below) enough or should a bony accusatory finger be pointing towards a leak from one of the patients' sources during their travel through "the system"; someone not all that fussed about maintaining patient confidentiality, for whatever reason(s)? 

There is quite a chain of links between the patient and many others when that patient is sampled for disease diagnosis; a chain made longer when the disease is an unknown like MERS, driven by a newly discovered virus like the MERS-CoV. The lab techs will receive and process the sample, matching a patient slip to a specimen which is tested and linked to a result which may then be repeated externally for reliability. The clinical team(s) providing care and the hospital administrative staff, perhaps ambulance services, public health officials, international scientific and clinical experts such as World Health Organization and perhaps a panel of experts in a working group may or may not all have more patient detail than was released to the media. The family and those friends that are told will also be among the knowing. All this is just the same as in other countries around the world. How is it that reporters can identifying the patients? Is it happening differently in other parts of the world to the way it is in the Kingdom of Saudi Arabia; as CK noted, is it a cultural thing?
If you take a look at a recent English language MERS-CoV case media release, from the Saudi MOH, we still see that some key patient details are continuing to be reported...

Within the framework of the constant monitoring and epidemic surveillance of the novel Coronavirus (MERS-CoV), the Ministry of Health (MOH) has announced that five new cases have been recorded.

The first case is for a 57-year-old male citizen, who has been suffering from some chronic diseases. Now, he is at the IC unit, receiving the proper treatment, may Allah grant him speedy recovery. 


The second case is for a 73-year-old male citizen, who has been suffering from some chronic diseases. He passed away, may Allah have mercy upon him.


As for the third (43-year-old resident), fourth (35-year-old resident) and fifth (27-year-old citizen) cases, they work at the health sector. They were in contact with confirmed cases of this virus, and didn’t suffer from any symptoms. May Allah, Almighty, heal the injured cases and bestow upon them the cure they so earnestly desire.

If this little amount of detail is not considered a problem now, then I don't see why a slightly expanded media release should be any more of a patient identifier; expanded along the lines of what I've listed previously here. Extra information is, I firmly believe, useful for "crowd-sourced epidemiology" - that which provides many fresh sets of eyes to perhaps help analyze aetiologies, peruse pathological puzzles and delve diagnostic dilemmas. It also allows for the re-presentation of all manner of complex infection and disease issues, after filtering through the minds of others, some of whom are very good at extracting points of interest for a much wider audience, thus contributing to keeping the world informed. 

But I'm drifting.

What about that "mysterious outbreak" in Montgomery County, Texas, USA back Dec-19? We didn't get each and every case's details and sure, that didn't raise too much ire did it? In fact, I don't think we've officially heard whether all 8 people (50% of whom sadly died) were influenza A(H1N1) virus positive or not. Yet it was assumed by the press and some others to be the case within hours. What then is the "So What" question from such an absence of patient information for you and I and the rest of the world who are not part of the patient chain? It's simply "so what??" We didn't need to know more than that. Yes, its horrible that people should die when they may not have had to. And yes, a US citizen's cultural affiliation with the media may be as different from that of a Saudi Arabian citizen as chalk is from cheese, but so long as the experts on the ground know the details, that's what really matters isn't it? So long as the treatment and management of the patients, the informing of their loved ones and the prevention of further viral spread is being attended to (including reinforcing the message that flu is a vaccine-preventable disease in the Montgomery instance) then people outside the loop of patient-doctor-scientist-admin-loved ones don't need to know anything further do they?

If such data could be released without identifying the patients at all - great, and I would have thought that quite possible in a country of 20+ million. The contents of current media releases seem to support that thinking too. But if it is not possible, then perhaps we should wake up to the fact that no one outside that list above needs to know. I've written about entitlement previously

Personally, I doubt that if the MOH stopped printing these tiny snippets of deidentified case detail, like those quoted above, it would halt the media from seeking interviews with people who had been afflicted with a "mystery" illness. But what do I know?

As we know from Dr Hatem Makhdoom, who accepts the description of an an experienced virologist on the Saudi Ministry of Health team said...
..in other words the experts in the scientific world are getting the knowledge they need, even if we bloggers are not.

At the end of the day, its about current and potential future patients; caring for the former, and preventing illness among the latter.

H9N2 confirmed in 86-year old Hong Kong citizen living in Guangdong province...

Influenza A(H9N2) virus, another "bird flu" but this usually causing mild signs and symptoms of infection, has been confirmed in an 86-year old man reported Dec-30.

The man's underlying illnesses were added to by chills and productive cough from 28-Dec when he was admitted to hospital with a fever.

Sputum tested positive for H9N2. Not sure if an upper respiratory sample was tested.

He had no recent contact with poultry and no contacts have shown signs of illness.

Mild human cases in Hong Kong have previously been reported in 1999, 2003 and 2007 and imported cases in 2008 and 2009.

As ProMED moderator CP (Craig R. Pringle) noted, enhanced surveillance in the region is likely to continue to pick up all sorts of H and N viruses and variants. Interesting watching these pop up - especially if they remain as mild infections, unlike H7N9 has so far.

Sources...