Keep calm and call the lab...without it, you know less than you think you do [UPDATED x2]

This morning there are 2 symptomatic healthcare workers (HCWs) in the United States (of America; I'm just going to use the "US" from from here on) who came into contact with the recently diagnosed MERS-CoV positive 44M (age and sex confirmed yet?) imported case.

The news has driven something of a twitter storm in the #MERS channel. Not unexpected I guess. The implication is that these 2 have acquired MERS-CoV from contact with the imported MERS-CoV-positive person. 

But that link is still far from proven yet. [UPDATE: both HCWs tested negative for MERS-CoV [1]]

This is a slightly revised version of that which I posted 18-March.
Thanks to Dr K Arden for helpful advice.
Click on image to enlarge.
VDU images are free to re-use. I can provide a better quality if needed.
Please just cite Dr Ian M Mackay, and this blog, http://virologydownunder.blogspot.com.au/,
if used elsewhere.

...Something to remember, or become aware of...

There are >200 known human viruses that have at one time or another been linked to patients with signs and symptoms that defined an 'influenza-like illness" (ILI). No-one can predict what these HCWs are infected with, but they have been or currently are infected by something. Lab tests are essential to know this.

I've asked Orlando Health's social media team (@orlandohealth) if these 2 HCWs are also being tested for the more "standard" 8 or 9 endemic human respiratory viruses/virus groups in parallel with MERS-CoV testing. I'll update this post with what I learn.

These standard viruses include influenzaviruses (A and B; red above), respiratory syncytial virus (dark pink), adenoviruses (orange), human metapneumovirus (pale pink) and parainfluenzaviruses 1, 2, 3 (purple). I'd also hope the rhinoviruses (in green above) since they are numerous and a frequent cause of ILI that can confound the very broad ILI tag. This panel of viruses comprise a standard testing menu which may be further extended, or shrunk, depending on the lab and they are included in commercial PCR-based kits. 

Keep in mind too that a positive PCR (if that's what is used) result does not mean the virus found is the cause of the illness. It may be that another virus, that has since dropped below the limit of assay detection was the cause, or a couple of viruses working in series or parallel, or a virus & bacterium working in synergy or a virus that wasn't tested for, or a virus that is not even known yet...pant.

But if these 2 HCWs do test positive for the MERS-CoV, it's not all that unexpected. Respiratory viruses on the scale you see above have not co-evolved with us/been introduced to us recently because they are easy to get rid of or stop from spreading between/to us.

MERS-CoV is just one of a long line of (probable) respiratory viruses that keep taking us to school to teach us just how sneaky and effective they can be at spreading and just how much our preconceptions trip us up, letting them finish with the best grade.

To stop the spread of them in an environment full of sick people, like a hospital, or even a school, a daycare centre, a long term care facility, a cruise ship, a plane, bus, or even a living room, is no mean feat. It's worth remembering that no single virus does only one thing. There is no "pneumonia virus", no "bronchitis virus", there's not a "common cold virus", there's no "droplet-only" spread, there's not "only replicates in nasal cells", there are just respiratory viruses and their very complex multicellular hosts. I'm happy to argue any of these points, but come prepared to show me that every avenue has been exhausted to support your argument beforehand. I'll give you the drum right now, they really haven't.

Respiratory viruses can each do lots of things and the outcome on our health is heavily determined by us; our previous exposures, our age, our general health, our maternal antibody levels, our underlying diseases, our genetic makeup, our environment, our climate, our animal and human contacts, our personal hygiene and our habits.

End of monologue.

Reference...

1. http://www.flutrackers.com/forum/showpost.php?p=534975&postcount=49

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.

You're the virus I got...

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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.

RSV retreated, flu fading, parainfluenza picking up: Queensland respiratory virus numbers up to Week 45, 2013

If you like to keep track of influenza cases in Queensland, Australia, then the Queensland Government's Queensland Health (QH) influenza data website is for you.

It's a great place to drop by and check out the comings and goings of influenza viruses and many of the other traditional respiratory viruses including adenoviruses (AdVs), parainfluenzaviruses (PIVs) 1, 2 and 3, human metapneumovirus (MPV) and respiratory syncytial virus (RSV) - the "Big8". Testing is not routinely conducted for the rhinoviruses (RVs).

The snippet below is from data that are publicly reported on the QH website. These images cover to the week beginning 3rd of November (up to Sunday, Nov 10th, 2013).

The charts highlight that the 2013 flu season is winding down in Australia, also reflected by the WHO global updates. This year flu followed on from what seemed to have been a large RSV season. Unfortunately I couldn't find data for this same time period last year to compare RSV prevalence.

In the wake of influenzavirus season, the parainfluenzaviruses are now on the rise in the lead up to summer. I expect the RVs (and enteroviruses) are also climbing, but in greater numbers.

Click to enlarge. 
A snippet from the Queensland Health Statewide Weekly Influenza Surveillance Report for 01.01.2013-10.11.2013

My thanks to the team at the Communicable Diseases Unit, Queensland Health.

The source of these data  can be read in full..

• http://www.health.qld.gov.au/ph/cdb/sru_influenza.asp
• WHO global influenza update http://www.who.int/influenza/surveillance_monitoring/updates/latest_update_GIP_surveillance/en/

H7N9 is not the only game in town.

Three HCWs who looked after the first H7N9 exported case have developed upper respiratory tract(URTs) infections somewhere during the 15-days between illness onset and lab confirmation. It is well worth noting that H7N9 is not the only virus that can cause URTs.

There are over 200 endemic human "respiratory viruses" that have been associated with URTs including the rhinoviruses (160 of them alone), coronaviruses, adenoviruses, enteroviruses, parainfluenzaviruses, influenza viruses, metapneumovirus, respiratory syncytial virus and bocavirus. Working out what causes a patient's URT is a challenging task, especially when more than one of these viruses can be detected by PCR in a patients airway sample at the same time. 

Differential diagnoses (testing for all the things that may cause the same clinical appearance) is interesting in times of an outbreak. Keep an eye on these HCWs - they could be an important canary in the dark H7N9 mine we've been stumbling about in so far.