Tuesday, December 31, 2013

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...

Monday, December 30, 2013

Qatari camels clear coronavirus

The camel herd that was previously Middle East respiratory syndrome coronavirus (MES-CoV) RT-PCR-positive is no longer positive for viral RNA according to an OIE report (OIE=Office International des Epizooties; the world organisation for animal health).
In there report they note that retesting of the herd, subsequent to the initial testing presumably, has yielded no positive this time around.

So it looks like the MERS-CoV infection is an acute infection (it is contracted, it causes illness - perhaps - and then it goes thanks to an immune response - perhaps), as are many/most) viral infections of animals and humans.

An interesting comment within the report states that...

The planned massive survey for MERS-CoV in animals is under implementation and the same herd is under systematic retesting. Follow-up reports will be submitted when there will be new data.

I do like a statement that includes the words "massive study" in it!

Hat tip to CIDRAP.

Saturday, December 28, 2013

Influenza A(H7N9) virus case accumulation for 2013...

Click on image to enlarge.
Sure a full 12-months of H7N9 in humans hasn't passed yet, but 2013 is coming to a close. 

I have 148 H7N9 cases worldwide including deaths and the asymptomatic boy from Beijing who seems to still be off the official tallies for some reason. WHO have not had an official tally of fatal cases in their recent 2 disease outbreak news posts, the last with a tally was 6-Nov in which 45 deaths were recorded with 6 cases remaining in hospital and 88 having been discharged. Hong Kong's Centre for Health Protection (CHP) maintains a running tally of mainland China cases With the recent death of a Hong Kong man the tally of fatal cases rest around 46 (PFC of 31.1%).

I've just changed my spreadsheet to a weekly format from the daily version and the first chart it reveals is shown above. 

This includes the lay of the land for all H7N9 cases from the beginning of the outbreak, 11-Feb (date of pneumonia for son of index case), through to 29-Dec. Date data employ dates of reporting if no date of illness onset could be found.

We can see from this 47-week inclusive dataset that the principle period of activity was in late March to late April. Whether that will also be the case in the new year is anyone's guess really.

What we can say from the vast amount of influenza virus research data in the scientific literature, is that each and every new combination of 8 gene segments that comprise a distinct influenza A virus seem capable of their own distinct "personality".

What to watch for with human parechovirus (HPeV) infections...

With HPeV infections generally around during summer (see specific earlier story arising from cases in babies from New South Wales), it's well worth mirroring the advice form NSW health on what to look for. 

The full sources of this information can be visited at the pages listed below.

A brief agglomeration of the information...

HPeV (closely related to enteroviruses) has been detected in a number of neonates and young infants admitted to NSW hospitals during October and November 2013. Infants present very unwell with a rapid onset of acute sepsis-like (whole-body or systemic inflammation to a widespread infection) symptoms and can infect teh central nervous system. This is often followed by an erythematous, often confluent rash. Children under 3 months of age are the group most likely to develop severe disease, but most recover with supportive treatment.

Suspect HPeV infections in neonates (newborn) or young infants can present with a fever (>38.0°C) and:

  • Irritability and appearing to be in pain 
  • Tachypnoea
  • Maculopapular or erythematous rash 
  • Encephalitis
  • Diarrhoea or loose stools 
  • Myoclonic jerks
  • Tachycardia 
  • Hepatitis

How is it diagnosed?

Stool samples, nose and throat swabs, cerebrospinal fluid (CSF), or blood can be tested for HPeV at a specialist laboratory.

Initial Management and Treatment


Children presenting with a fever, sepsis-like signs &/or neurological signs, including irritability, should be assessed and treated for suspected sepsis using local protocols and discussed with an Emergency Consultant or Paediatrician.
There is no specific treatment for HPeV, treatment is supportive only.

How is HPeV disease prevented?


There is no vaccine to protect you from HPeV infection.

Good hygiene is the best protection: wash hands with soap and water after going to the toilet, before eating, after wiping noses, and after changing nappies or soiled clothing
Ensure the mouth and nose are covered when coughing and sneezing. Wipe the nose and mouth with tissues, dispose of used tissues and then wash your hands.

People who are unwell with colds, flu-like illness or gastro illness should stay away from small babies. 

If you are caring for a small baby and are unwell, wash your hands or use an alcohol-based hand rub before touching or feeding the baby.

Further reading...

Tuesday, December 24, 2013

Merry Xmas and Happy Holidays 2013

Hi All,

Just a quick wish from me to you for a Happy Xmas time.

If you are lucky enough to have been born into a wealthy country, enjoy your good fortunes and have a very festive and well-fed time with friends and family over the next few days. 

But please also spare a thought for the many more people on the planet who have a much harder road to travel each and every day. Perhaps add substance to that thought with a last minute present in the name of some of your loved ones, gifted to a charity that can help. This year I am supporting  UNICEF via their excellent range of charity gifts. Polio vaccination kits will be in a couple of Xmas stockings this year!

All the very best for a safe, happy, prosperous (well-funded) 2014.

Ian 
Editor-in-chief,
Virology Down Under

Monday, December 23, 2013

Middle East respiratory syndrome coronavirus (MERS-CoV): camels, camels, camels!

Two studies in Eurosurveillance, an editorial note, A Lancet Infectious diseases report and a comment point 2 hairy toes toward camels as a harbour and source in some capacity, for MERS-CoV, or MERS-CoV-very-like, infections ticking over around the Arabian peninsula. All in the space of a week!

First up, Hemida and colleagues from Saudi Universities, China and the United States describe the search for neutralizing antibodies in animals in a 12-Dec Eurosurveillance article. Great to see Saudi Uni researchers involved. I've mentioned this virus neutralization assay and its intent before. This new study builds on that from Perera and colleagues who looked at camels and some other animals.

Some major findings from this study include:

  • Dromedary camels (n=310), sheep (n=100), goats (n=45), cattle (n=50) and chickens (n=240) from MERS-CoV hotspots in Saudi Arabia (Riyadh and Al Ahsa) were tested with the pseudoparticle neutralization (ppNT) test
  • 280 camel sera (90% of camel sera) were positive using the MERS-CoV ppNT test. No other animal sera reacted in this test
  • 96% of camels had MERS-CoV (or a close relative)-reactive antibodies by 1-year of age; two-thirds of camels that were younger than 1-year of age reacted, which suggests acquisition of these infections accrues rapidly during that 1st year, or maternal antibodies remain in the offspring
  • 54 randomly selected camel sera (18% of all camel sera) were diluted out and tested using ppNT and a standard MERS-CoV microneutralization test (MNT). High levels of calf antibody specific to BCoV did not block MERS-CoV infection nonetheless there were some similar titres to both viruses in some of the camel sera. A ≥4-fold higher amount of antibody reactivity towards 1 virus compared to the other defined which was the most likely virus reacting. It's possible (likely?) that camels have "seen" (been infected by) both viruses or similar viruses at some time. Some of the subset of camel sera had high levels of antibody only to MERS-CoV (or a close relative)
  • Cows did not have any sign of MERS-CoV-reacting antibodies in their sera; they did have BCoV reactivity though
  • It was not stated whether the camels were ill or healthy at sampling
So other animals were not neutralising-antibody positive but young Saudi camels, like Omani, Spanish [retired to the Canary islands] and Egyptian camels before them, had acquired and reacted to infection by MERS-CoV (or a close relative) according to these validated antibody-detection tests. Regular sampling of an animal cohort is one suggested future direction.

Secondly we have Reusken and colleagues from the Netherlands, Jordan and Germany look at animals from the first known site to harbour MERS-CoV infections in April 2012 at a hospital in Zarqa city in Jordan. This was published online 12-Dec in the same issue of Eurosurveillance. Just fyi, Prof Marion Koopmans is senior author on this study and on the study below.

Some of the key points include...
  • Sera from 3-14-month old dromedary camels (n=11), goats (n=150), sheep (n=126) and cows (n=91) were tested by an antibody microarray method, used previously by this group, and the results confirmed by identifying antibodies with the ability to neutralize MERS-CoV infection.
  • The lower levels of antibody than seen in an earlier study may reflect leftover maternal antibody protection, although the authors note than maternal camel antibodies wane within 2-months of birth and that adult camels had higher levels of antibodies
  • This study cited a reference noting that apart from cows, camels, goats and sheep are major sources of meat and milk in the region, ~1 sheep/pilgrim or ~1 camel/7 pilgrims is slaughtered in Saudi Arabia for the Hajj which equates to ~3,000,000 animals!
  • 11/11 camel and 6/126 sheep sera had antibodies that reacted with MERS-CoV but, in additional testing, the sheep sera were not able to neutralize infection by MERS-CoV
  • 23/91 cows and 128/150 goat sera reacted with the human CoV, OC43 (antigenically related to BCoV); no sera reacted with SARS-CoV
  • A broadly reactive CoV, or "pancoronavirus", PCR method was used to screen camel faeces; 3 BCoV sequences were obtained, but no sign of MERS-CoV RNA in the faeces hinting that there was not an active infection at the time of sampling. This last point assumes that MERS-CoV is excreted from the camel gut during/after an acute infection. The next study may not support that assumption.
  • It was not stated whether the camels were ill or healthy at sampling
Add young camels from Jordan to those from Saudi Arabia, Oman and retired Spaniard animals as possibly having been infected by MERS-CoV (or a...you know, similar thing) or at least having antibody acquired from their mothers. 11/11 POS may yield some more data to narrow down the age of acquisition; 3-months and seropositive could suggest MERS-CoV acquisition at or very close to birth, or simply remaining protective maternal antibody. Perhaps camel farms and farmers should be a next stop for detailed testing. 

In an Editorial note, the Eurosurveillance Editors note that these data do not define the primary source for human acquisition is still unclear.

Thirdly we have Haagmans and colleagues from the Netherlands, Qatar and the United Kingdom describing the study of the Qatari farm camels and temporally related human infection, from which MERS-CoV was detected back in late November. This article was published online by the Lancet Infectious Diseases (17-Dec).

Some key findings here include...


  • The article's introduction suggests that the genetic diversity of human MERS-CoV viruses determined to date is the result of multiple zoonotic acquisitions 
  • This study started with a 61-year-old Qatari male (61M; FT#144) farm owner who had not travelled outside Qatar and his 23-year-old male (23M; FT#150) employee
  • 61M was RT-PCR POS (upE assay) on a sputum sample (collected Oct-13) and 23M on a throat swab (collected Oct-17) and subgenomic (ORF1b and nucleocapsid [N]) sequencing at the Public Health England confirmed the detection to be MERS-CoV
  • MERS-CoV genomic sequences from the 2 human cases were placed on GenBank and called Qatar_3_2013 [61M] and Qatar_4_2013 [23M] as were camel sequences from the subsequent experiments
  • Sera, rectal swabs and flocked nasal swabs were collected from all of the farm's 14 camels as well as 5 stool samples from 3 cages, by a team wearing personal protective equipment. Samples were shipped to the Netherlands for upE, N and ORF1a RT-PCR testing
  • Vero and Huh-7 cells were inoculated with swabs that had been added to viral transport medium onsite. A single culture from Camel#7 was upE RT-PCR positive at day-4 after inoculation but no culture yielded infectious virus
  • 5/14 camel nose swabs were MERS-CoV PCR positive using upE, N and ORF1a assays
  • Sequencing of a fragment of Spike gene yielded 100% identity with other Saudi MERS-CoV sequences; sequence only differing by 1 base from the original isolate, MERS-CoV/EMC.
  • All camel sera were antibody positive using an immunofluorescence test on MERS-CoV/EMC-infected cells
  • There was no "direction" to the acquisition of MERS-CoV. Whether the camels infected the humans or the humans infected the camels could not be determined from this outbreak
  • The authors conclude that detailed cases histories are important to identify animal exposures. These might not otherwise be though important in a cursory question and answer of a patient, their family or contacts
This study adds very important data that indicate a recent or resolving MERS-CoV infection in camels. No positivity was found from gastrointestinal samples. Despite no isolation of infectious MERS-CoV, the detection of RNA is an acceptable surrogate for the presence of "live" virus in an animal or person (even if it could not propagate in vitro). So the camel story has some very important new chapters added in this series of studies.

In a Comment in LID, Ferguson and Verkhove note how the One health concept is exemplified by not only this publication; as it has been by the entire MERS-CoV story. The comment also notes the need for much more study, passive and active surveillance of human and animal disease/movements and better and faster reporting to link these, or any other, animals back to the cases that are spread across a very broad geographic region. They hold Haagmans and colleagues' article up as an example of how to get more answers and prevent sustained MERS-CoV transmission among humans from developing in the future.

Tracing and testing camels imported into the region from Africa for use as food may also open a new front to identify the transmission potential of MERS-CoV (or a similar beastie) in camel infections. Testing of pneumonia causes at these other sites both for virus and antibodies against virus is probably also warranted. 

As usual, new data bring new questions and so many papers in only a week makes for lots of questions. 

Little rhino...

To the tune of ‘I’m a little teapot’

I’m a little rhino,
Strain in doubt
Bind with my canyon
Bind without
When I’ve replicated
Just the right amount
You’ll need to get a tissue to blow me out


[alternate: exacerbate your wheezing and cough me out]

Thanks to Cassandra Faux for putting this one together back in 2007.

Sunday, December 22, 2013

Twelve weeks of childcare...

To the tune of the twelve days of Xmas

In the first week of childcare,
some kids got sick with me
The lab said they might have HRV

In the second week of childcare,
some kids got sick with me,
Two had paraflu,
and a few might have had an HRV

In the third week of childcare,
some kids got sick with me,
Three had an entero
Two had paraflu
and a few had uncultivable HRV

In the fourth week of childcare,
some kids got sick with me,
Four had OC43
Three had an entero
Two had paraflu
and a few had untypeable HRVs

In the fifth week of childcare,
some kids got sick with me,
Five had MPV
Four had OC43
Three had an entero
Two had paraflu
and a few had something like an HEV

In the sixth week of childcare,
some kids got sick with me,
Six had HKU1
Five had MPV
Four had OC43
Three had an entero
Two had paraflu
and a few had newly identified HRVs

In the seventh week of childcare,
some kids got sick with me,
Seven had an adeno
Six had HKU1
Five had MPV
Four had OC43
Three had an entero
Two had paraflu
and a few had pleconaril-resistant HRVs (we think!)

In the eighth week of childcare,
some kids got sick with me,
Eight had bocavirus
Seven had an adeno
Six had HKU1
Five had MPVs
Four had OC43
Three had an entero
Two had paraflus
and a few were PCR-positive for HRV

In the ninth week of childcare,
some kids got sick with me,
Nine had RSV
Eight had bocavirus
Seven had an adeno
Six had HKU1
Five had MPV
Four had OC43
Three had an entero
Two had paraflu
and a few had antigenically distinct HRVs

In the tenth week of childcare,
some kids got sick with me,
Ten had NL63
Nine had RSV
Eight had bocavirus
Seven had an adeno
Six had HKU1
Five had MPV
Four had OC43
Three had an entero
Two had paraflu
and a few had more than a single HRV

In the eleventh week of childcare,
some kids got sick with me,
Eleven had Wuv and Kiv
Ten had NL63
Nine had RSV
Eight had bocavirus
Seven had an adeno
Six had HKU1
Five had MPV
Four had OC43
Three had an entero
Two had paraflu
and some came from a clade of HRV (which was distinct!)

In the twelfth week of childcare,
some kids got sick with me,
Twelve had IFAV
Eleven had Wuv and Kiv
Ten had NL63
Nine had RSV
Eight had bocavirus
Seven had an adeno
Six had HKU1
Five had MPV
Four had OC43
Three had an entero
Two had paraflu

and a few had what we call HRV C

Thanks to Katherine Arden and Cassandra Faux for helping me put these together back in 2008.

Saturday, December 21, 2013

You're the virus I got...

To the tune of Grease/You’re the one that I want

I’ve got chills, they’re multiplyin’, and I’ve got a sore throat
Home remedies that I’m tryin’, feels like I’m dyin

Really runny nose, now I cough and ache
and the doctor says its flu
Really runny nose, now it’s in my chest
To my lab I must be true,
There’s nothing  left, nothing left for Doc to do

Chorus:
It’s a rhino I’ve got
(a tiny little rhinovirus), not the flu, Doctor
A rhino I’ve got (a tiny little rhinovirus),
not the flu, Doctor
A rhino I’ve got (a tiny little rhinovirus),
not the flu
It’s all I need (an A or C)
Oh yes indeed (yes indeed)

If you’re filled with secretions
Lungs too hard to inflate
Medicate, must aren’t worth mention, resistance you’ll make

Starting to wheeze, cause of cytokines
I need some air, maybe ’roids will pull me through
Starting to wheeze, is it RSV?
I don’t have two, just an HRV that’s all
Are you sure? Well those PCRs wouldn’t lie


Chorus: (repeats out)

Thanks to Katherine Arden and Cassandra Faux for helping me put these together back in 2008.

The Bocavirus...

To the tune of Copacabana

Its name was boca, it was a parvo
No membrane just a shell, a tiny genome n’ there as well
It was found worldwide, but first in Sweden
And while it might yet be a star, its role remains unclear by far

Around a crowded globe, its mode of spread unknown
It was newly found and yet endemic
PCR helped show

Call it boca, the bocavirus
Quite close to a dog and cow virus
Call it boca, the bocavirus
Coughing and sneezing, expiratory wheezing
But the boca, was it a cause?


Its name was boca, and just this year
It was found in blood and stool, but isolation did not ensue
Although with EM, something was seen
And now systemic is where it’s at, PCR alone is falling flat

And so more questions flow, we still have far to go
Most often found with another virus
Co-detections rule!

Call it boca, the bocavirus
Quite close to a dog and cow virus
Call it boca, the bocavirus
Pneumonia and sneezing, expiratory wheezing
But the boca, its everywhere


Its name is boca, it raises questions
But two years later on, no real answers have been found
It is a virus, on that we’re certain
Still reports from far and near, describe detections everywhere

Sequences don’t change much, although two clades show up
We need more trials and more controls
But will that be enough?

Call it boca, the bocavirus
Quite close to a dog and cow virus
Call it boca, the bocavirus
Gastro and sneezing, expiratory wheezing
What does the boca, do to us?


Thanks to Katherine Arden and Cassandra Faux for helping me put these together back in 2007/8.

Friday, December 20, 2013

FluTrackers needs your help....HELP THEM!!

I've written before about how much we smaller bloggers and interested other parties rely on FluTrackers to be the rock on which we can rely. Have a quick read of that post here.

FluTrackers are a bunch of volunteers who self-fund the computer infrastructure that houses and serves us with the carefully agglomerated rantings of a seemingly endless stream of information sources on all manner of infectious disease happenings, from all over the world; almost instantly in many cases. There's a very good chance that if it made it onto any website anywhere, then that information has been read and filtered and posted by one of the very few super-diligent FluTrackers newshounds.

I cannot imagine, even if blogging was not only a part-time hobby for me, how I would ever manage to do what FluTrackers manages.

Over 50,000,000 page views this year provide ample data to indicate that they perform a service that is of considerable value to many. 

FluTrackers punches very far above its weight in the complex, fast-paced world of infectious disease communication. I frankly don't know how they do it for the price - which, of course, is borne entirely by them.

So it comes to this time of year when we see a request from the crew at FluTrackers for some financial aid from us - some of those millions of page viewers. If only a tiny fraction of us were to donate $10 (that's a tub of Sara Lee ice cream in my neck of the woods), FluTrackers would be able to fund themselves for many a day.

So come on guys - help keep the FluTrackers tracking flu...and rhinovirus...and bocavirus...and respiratory syncytial virus...and parechovirus...and enterovirus (including poliovirus)...and parainfluenzavirus...and adenovirus...and staphylococcus...and unusual spikes in hospital admissions...and pneumonia cases... and emerging diseases...and emerging viruses...and disease outbreaks...and tuberculosis and...far too many more other things to list.

I might now be $10/poorer for each user that reads/uses the data in my own household, but I'll be exponentially more enriched in 2014 for the data I know they will (hopefully continue to) provide to the world's amateur and professional disease trackers and the public-at-large. 

Read more about where this paltry amount of money will go from FluTrackers themselves.

And more from Mike Coston's blog here on the Cost of fluing business.

Randall the red-nosed toddler...

To the tune of Rudolph the red-nosed reindeer

Randall the red-nosed toddler
Had a very runny nose 
Asthma exacerbation 
Fever adding to his woes 

All of the other toddlers 
Didn't have immunity 
They all came down with symptoms 
Differing in severity 

Then one group of researchers 
Virus-hunting was their game 
Swabbed, extracted, amplified
A rhino POS of course was spied 

Randall’s rhino was sequenced 
Turned out to be rhino C
Randall the red-nosed toddler
Just a 'common' cold indeed!


Randall the red-nosed toddler
Had a very runny nose 
Asthma exacerbation 
Fever adding to his woes 


Thanks to Katherine Arden and Cassandra Faux for helping me put these together back in 2008.

More confirmation that rapid influenza diagnostic tests (RIDTs) should be used in context

The Texas Department of State Health Services have a useful couple of paragraphs from an Influenza Health Alert that puts into context reliance on the convenient and rapid, but ultimately intensive rapid influenza tests.


Rapid Lab Tests: Rapid Influenza Diagnostic Tests (RIDTs) can be useful to identify influenza virus infection, but false negative test results are common during influenza season. Clinicians should be aware that a negative RIDT result does NOT exclude a diagnosis of influenza in a patient with suspected influenza. When there is clinical suspicion of influenza and antiviral treatment is indicated, antiviral treatment should be started as soon as possible, even if the result of the RIDT is negative, without waiting for results of additional influenza testing.


Mike Coston also has an excellent article touching on some of the many other viruses that can cause influenza-like illness and on rapid testing, over on his blog, Avian Flu Diary. I highly recommend it.

Cost is always an important factor when hospitals and attached diagnostic laboratories consider how to address infections. Rapid turnaround time is another major cost because, for those small number of viruses with this option available, an antiviral drug can be administered and there seem to be benefits from doing this as early as possible for severe influenza. In some cases of course, a vaccine is available to block severe disease from occurring when you get infected (they don't stop infection, but a response to a vaccine is much safer than a bad response to an actual virus infection, as we've seen in the recent media for H1N1 in Texas. 

During flu season, influenza virus is an obvious cause for a spike in hospital admissions for acute respiratory symptoms - but if confirmation of that pathogen relies on a testing platform that can miss a third of infected individuals (only 17/45 PCR positives were detected by am RIDT in Ref#2) then antivirals may not be used in time. In a more recent comparison of RIDTs using PCR results as the standard, viral load in the upper airway (less virus gave fewer positives - duh), age (the young and elderly were less often positive), presentation time (sampling >2-days after onset of illness reduced the proportion of positivity), virus type (less sensitive for subtype B infections than A) and whether there was pneumonia or not (the former were less often positive perhaps reflecting less viral replication in the upper airway than in the lower airway?) were factors in how well the antibody-based RIDTs performed. Sensitivity ranged from 50% to 94%. These 2 studies used samples from the upper airways (swabs or nasopharyngeal aspirates respectively, as suggested by the BD™ Directigen EX Flu A+B assay, Alere™ Influenza A & B Test and the QuickVue® 117 Influenza A+B test)

In these instances, PCR-based methods (used as the "gold standard" in those published evaluations) shine but they take longer to generate a result and require more expertise to conduct than a rapid test. The slightly longer time is not just because they take hours to conduct instead of the minutes of a rapid test (remembering that viral lab diagnoses used to take days not hours) but because lab testing is only part of a process which also involves paperwork and passing verified and signed off results and information to all concerned clicnial parties and patients. That can take more time-and sometimes be a bottleneck for result release. Its hard for a patient's family and friends to wait, but the results will be that much more reliable when they come.

A feature of influenza season is the concurrently reduced levels of activity of other viruses. Influenza tends to "push out" a lot of other viruses during it's peak season - probably reflecting influenza's ability to dominate the immune response in an infected individual, and by extrapolation, reduces the number of susceptible individuals at the community level, remembering that the majority of influenza cases are acute upper respiratory tract illnesses.

So it looks more like the Montgomery County deaths may have been due to the high levels of influenza A(H1N1)pdm09 virus generally circulating in them there parts. A KHOU news outlet report, also circulated on ProMED, suggest that 4 Montgomery county deaths were due to H1N1, as well as other sine the regions. However, the Montgomery County Public Health District reports only 2 H1N1-confirmed deaths, so things are still a little confusing there. And as for whet other viruses may also be in these patients...so far, who knows?


A brief guide to some terms used in these sorts of discussions (also from Ref #2 below)

Sensitivity
No. of true positives / no of true positives and false negatives

Specificity
No. of true negatives / no of true negatives and false positives

Positive predictive value
No. of true positives / no of true positives plus no. of false positives

Negative predictive value
No. of true negatives/ no of true negatives


References and further reading...
  1. FluTrackers story. http://www.flutrackers.com/forum/showthread.php?p=517368#post517368
  2. Accuracy of rapid influenza diagnostic test and immunofluorescence assay compared to real time RT-PCR in children with influenza A(H1N1)pdm09 infection. http://www.ncbi.nlm.nih.gov/pubmed/23175329
  3. Clinical and Virologic Factors Associated with Reduced Sensitivity of Rapid Influenza Diagnostic Tests in Hospitalized Elderly and Young Children. http://www.ncbi.nlm.nih.gov/pubmed/24285739

Wednesday, December 18, 2013

Texan flu step: flu-like illness outbreak in Montgomery County [UPDATE #2]


Click image to enlarge.
County of Montgomery highlighted in red.
From Wikipedia
While 1,920 influenza-like illnesses (briefly that's measurable fever plus one or more particular symptom usually; includes sore throat, fatigue, body aches and complications including pneumonia) have occurred in this county since the start of the local influenza season, 8 severe infections (all with pneumonia) in adults (41-years to 65-years old) have been admitted to 1 (?) facility. These 8 cases are not all testing positive for the "common" influenza virus types. Initial testing may have been by rapid "bedside" influenza test which are known for their lack of sensitivity. PCR testing would be preferred, if that wasn't used.


According to the US Centers for Disease Control and Prevention website, seasonal influenza's populations at greatest risk of severe disease usually include the very young (under 5-years) and older adults (>65-years), pregnant women and indigenous populations, and those with a range of pre-existing medical conditions.

4/8 cases died and none of the fatal cases were vaccinated against influenza (?survivors were vaccinated). Kidney issues have also been reported according to a video report at the Houston Chronicle.

1/4 surviving case has tested positive for influenza A(H1N1)pdm09 virus, which is circulating locally as the annual flu season is well engaged in the region. 2 other survivors have tested NEG for all influenza viruses and have been sent on to the CDC. Test results are outstanding on the other survivor.

Click on image to enlarge.
2013-14 Influenza season data from FluView, CDC at
http://gis.cdc.gov/grasp/fluview/main.html.
Of those 221 antigenically subtyped by the CDC,
184 are H1N1 2009.
Management steps include staying away from ill people, hand-washing using soap and water/alcohol-based hand rubs, covering coughs and sneezes, staying at home when ill, cleaning linens, eating utensils and dishes used by ill people, and wiping down frequently touched surfaces if likely to be a landing spot for virus from an ill co-habitant/co-worker/school or daycare child.

It would be interesting to know what testing has been employed for influenza and what other respiratory viruses and bacteria have been tested for and excluded because, despite some enthusiastic but highly misleading and inflammatory guesswork, there are not yet enough data to identify an infectious aetiology for this pneumonia cluster. I'm sure in a busy environment like this, work is progressing on many levels to resolve the mystery. Since at least 2 of the 8 patients have tested negative for influenza viruses, it is premature to extrapolate from the 1 positive case that H1N1 is the cause of all cases; it may be but those results are not yet in.

References...