Friday, 29 July 2016

Editor's Note #26: Virology Down under gets an award!!

Well this is some pretty cool news to wake up to on a Friday morning!!

Virology Down Under (this blog and its extended presence on LinkedIn and Facebook) has just been awarded one of InfectionControl.tips "Top Innovations of the Year of 2016" awards for global engagement.
 



I'm one proud little blogger!

With the moniker of Join. Contribute. Make A Difference, InfectionControl.tips has been a welcome addition to the field of open, public-speak communication of health information and provides an avenue for health professionals to explain things to an eager and wide audience. 

My partner in crime (and life) @kat_arden and I have written a few pieces for this site now, including our latest effort - The Language of Zika Virus Testing. No doubt we'll contribute more as time allows and needs dictate. 

If you haven't already, it's also a great idea to have a try at writing in a different non-academic style of language too. IC.tips' editors can help you out with that if needed. 

We also love that IC.tips is open-access, free and shares our enthusiasm for wanting to make a difference in some way.

You can see other award winners at: http://infectioncontrol.tips/award-top-innovations-year/




Thanks team - #VirolDU is honoured to be a part of your goals.

Wednesday, 27 July 2016

Public Zika virus data can be volatile Zika virus data...

So it turns out I hadn't had a stroke or started losing my mind. 

....10 hours earlier....

I received an answer to my questions tweeted at the Colombian National Institute of Health asking why Colombia's Zika virus (ZIKV) data had been revised downward. Was it simply data cleaning? How did it happen? Why now? As you can see from the drop in weekly figures (that last red bar), it was a quite a cleanup if so - a drop in 5,000 cases!
Graph No. 1. The cumulative curve of suspected ZVD cases
(pink circles, left-hand axis) and the change in suspected ZVD case
numbers when compared to the preceding week's total
(red bars, right-hand axis) including the original
epidemiological week No. 28 data. Data from [1].
Click on graph to enlarge.

Graph No.2. The cumulative curve of confirmed ZIKV infections 
(lilac circles, left-hand axis) and the change in confirmed ZIKV infection 
numbers when compared to the preceding week's total 
(purple bars, right-hand axis). Now added the reported umber of microcephaly cases 
confirmed as ZIKV infected (yellow bars, right-hand axis) including the original 
epidemiological week No. 28 data. To account for adjustments 
that take cases away when there is no weekly case growth, a negative 
value - the y-axes now allow for negative values. Data from [1]. 
Click on graph to enlarge.










































Dr Fernando Ruiz, the Deputy Minister of Public Health and Service Delivery Colombia kindly engaged me on Twitter, telling me that each week their data get adjusted to account for current and former week's lags. I sent him Graph 1 above to try and reiterate that this past epidemiological week had been a bit different than any other this year. When he bounced some numbers at me something seemed weird - these were different from what I'd recorded. 

Sure enough, my spreadsheet no longer matched up with the numbers I'd harvested on Sunday morning (my time, AEST) from the Week No.28 Colombian Epidemiological Bulletin.

Weird. My usual first reaction - it's all my fault. Had I been daydreaming when I copied the numbers across? Had my Excel formulae betrayed me (never!)? Had the kids edited my blog? Had the cat sneakily deleted and typed a few figures. Had I had a small cerebral incident? Am I having one now?

Am I doomed to never know the answer?

Thankfully, @FluTrackers had a post from @thelonevirologi including charts and numbers from the Colombian data and sure enough a key figure was there that was common to both our datasets - but no longer anywhere to be found on the Colombian bulletin - 7 166 confirmed laboratory cases. And, coming to the rescue of my sanity, @thelonevirologi still had the original PDF - the data had indeed been released wrongly and then corrected and re-released by the National Institute of Health. Phew.

Public data are volatile

This really is a stark reminder that public data are volatile and can change. 

Sometimes that change may not be identified by the publisher - no version numbering and no note to say what changed and why. Simple stuff to add, but sometimes completely absent. 

We bloggers, who live in the 'grey literature' world (and rarely attract citations from the scientific literature), may be better at understanding the need to own our changes and mistakes. We often try to correct them in a way that is obvious to those who use or even rely on our information. This is just good practice.

And what about Colombia's ZIKV numbers this week?

As to the updated ZIKV figures from Colombia, the revised versions show that clinically suspect ZIKV disease cases do in fact continue to rise (+933) and that there were 22 more confirmed cases among pregnant women added this past week. No general ZIKV disease confirmations were reported after the 176 from last week and no new cases of ZIKV-associated microcephaly were added this week after 4 consecutive weeks of growth. Perhaps this is one of those laboratory 'off weeks'.

Colombia notes that it expects ZIKV-related microcephaly cases to increase in September and October 2016 as more pregnant women come to term.[2] A nearly 8% increase in (known) miscarriages has already been reported in Colombia but no rise in the use of abortion clinics which might otherwise "hide" the congenital impact of ZIKV infection not registered as microcephaly.[3] 

Given these ZIKV infections are still being suspected and detected, it seems very strange that Colombia picked now to declare it's epidemic over.[2] For certain, numbers have been slowing each week for at least 6 weeks but they are still being reported (perhaps just lagging older results?). 

A quick summary: sexual events play a role in ZIKV transmission, persistence of virus is real at several sites, we have not yet examined all possible transmission avenues (oral and respiratory epithelium, eyes, ingestion) and we still don't know whether the 80% of cases that are asymptomatic play any role in human-to-mosquito or human-to-human transmission nor whether that 80% figure still holds today. 

Perhaps the Colombians simply mean that the ZIKV numbers per week have fallen below some arbitrary internal epidemic threshold value now. Maybe cases are still being identified, just not at epidemic levels or rates. I'd have thought a threshold would take more than a year and a bit to determine for a new disease with so much still unknown, but perhaps not.

Graph No. 3. The corrected cumulative curve of suspected ZVD cases
(pink circles, left-hand axis) and the change in suspected ZVD case
numbers when compared to the preceding week's total
(red bars, right-hand axis) including the updated
epidemiological week No. 28 data. Data from [1].
Click on graph to enlarge.



 
Graph No.4. The cumulative curve of confirmed ZIKV infections
(lilac circles, left-hand axis) and the change in confirmed ZIKV infection
numbers when compared to the preceding week's total
(purple bars, right-hand axis). Now added the reported umber of microcephaly cases
confirmed as ZIKV infected (yellow bars, right-hand axis) including the updated
epidemiological week No. 28 data. To account for adjustments
that take cases away when there is no weekly case growth, a negative
value - the y-axes now allow for negative values. Data from [1].
Click on graph to enlarge.

References...
  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/Forms/public.aspx
  2. http://www.nytimes.com/2016/07/26/world/americas/colombia-zika-epidemic-end.html?partner=rss&emc=rss&smid=tw-nytimes&smtyp=cur&_r=0
  3. https://www.washingtonpost.com/world/the_americas/colombia-offers-the-possibility-that-the-zika-epidemic-may-not-be-as-bad-as-feared/2016/07/12/d8c91e60-3d78-11e6-9e16-4cf01a41decb_story.html?postshare=8051469159730881&tid=ss_tw


Sunday, 17 July 2016

Colombia Zika virus report, Epidemiological Week No. 27...

The latest epidemiological report from Colombia, which includes data on Zika virus disease (ZVD; 03JUL2016-09JUL2016), has been produced by the Colombian National Institute for Health team.[1]
NOTE: While these data were reported the past epidemiological week, they may not be from that week. See earlier post about possible reporting lag.


Graph No.1. The cumulative curve of confirmed ZVD cases
(green circles, left-hand axis) and the change in confirmed ZVD case
numbers when compared to the preceding week's total
(green bars, right-hand axis). Data from [1].
Click on graph to enlarge.

Graph No. 1 shows that 176 new laboratory confirmed cases of ZVD were reported this week. The total sits at 8,826 or 10% (the highest proportion reported to date-steady for the  past 6 reporting weeks) of all clinically suspected Zika virus (ZIKV) detections.


Graph No.2. The cumulative curve of suspected ZVD cases
(pink circles, left-hand axis) and the change in suspected ZVD case
numbers when compared to the preceding week's total
(red bars, right-hand axis). Data from [1].
Click on graph to enlarge.
Graph No. 2 shows the change in suspected cases. These are not laboratory confirmed. The suspected ZVD cases continue to rise in a linear fashion, adding 984 this week to total 89,962.


Graph No.3. The cumulative curve of confirmed ZIKV infections
(lilac circles, left-hand axis) and the change in confirmed ZIKV infection
numbers when compared to the preceding week's total
(purple bars, right-hand axis). Now added the reported umber of microcephaly cases
confirmed as ZIKV infected (yellow bars, right-hand axis). To account for adjustments
that take cases away when there is no weekly case growth, a negative
value - the y-axes now allow for negative values. Data from [1].
Click on graph to enlarge.
Graph No. 3 shows that to epidemiological week (EW) No. 27, 11,614 suspected (+77 compared to last week) and 5,882 confirmed ZIKV infections (+135) have been identified in pregnant women.

As of this report, 21 (+3 from last EW) live births have been diagnosed with congenital ZIKV syndrome (CZVS; microcephaly/central nervous system disorder), confirmed as being ZIKV positive. That represents 0.36% of all confirmed ZIKV positive mothers-the 4th EW in which this proportion has risen.

Some back of napkin calculations looking at these numbers suggest that there are 3-4 deliveries for every 1,000 ZIKV-positive pregnant women that result in a ZIKV infected baby with microcephaly. This assumes each neonate has been tested for ZIKV as [6] suggests. This figure has no clear understanding of the number of aborted or miscarried foetuses that are also occurring from ZIKV-positive pregnant women. Abortions and miscarriages will need a local baseline to understand the scope of this component of the impact of ZIKV infection.

160  other microcephaly diagnoses (up from 112 last week and the highest value to date) are now under investigation - this value has also been rising very quickly and suggests suspicious CZVS cases in Colombia are accruing faster than the pace of complete investigation can keep up with. 

It now seems very likely that we can expect those bars to keep rising steeply in the coming weeks. The line is well and truly crossed.

Graph No. 4
below focuses on just the ZIKV-positive cases and those that remain under investigation, highlighting how the investigatory total has changed each week and been trending upwards since Epidemiological Week No. 14. 
Graph No.4. The change in confirmed ZIKV infection numbers
when detected in association with a microcephaly diagnosis, compared
to the preceding week's total (yellow bars, left-hand axis). Data are from [1].
Click on graph to enlarge.
It has now been 275 days, or 9 months 1 day, since ZIKV was first confirmed in Colombia on 16th October 2015.[2] Colombia is currently carrying the next biggest load of ZVD cases, after Brazil.[3] Keep in mind that when talking about microcephaly - we have to think back in time to what insult or infection might have occurred in the first or second trimester (probably-still not definitive). The counts of virus occurring this week will have zero impact on what happened back then. Also keep in mind that Colombia may be reporting things differently from Brazil.[5,7]

Brazil first reported positive (but unconfirmed) laboratory tests for Zika virus disease on 29th April 2015. Brazil then started to report a rise in foetal anomalies (an initial 141), in the form of microcephaly on 30th October 2015. This was 184 days - or about 6 months later.[4]

References...

Wednesday, 6 July 2016

Kids are virus factories...

UPDATE #1: 06JUL2016
Ms. Mohinder Sarna and Associate Professor Lambert have just recently published some cool data from a large and very heavily sampled respiratory virus-related study.

The new report comes from a large birth cohort study entitled the Observational Research in Childhood Infectious Diseases (ORChID) study. 

ORChID is a "longitudinal community-based dynamic birth cohort study of ARI [acute respiratory infection] episodes in children from birth to 2 years of age in the subtropical city of Brisbane, Australia". The study followed babies until they were two years old, taking weekly - yes, WEEKLY! - respiratory swabs and dirty nappy swabs and then tested the heck out of them for known viruses and bacteria. 

The testing results are not part of this report so use of the term "infection" is presumptive. For this study I would have preferred ARI=acute respiratory illness; URTI-upper respiratory tract illness; LRTI-lower respiratory tract illness. But infection is being used in the sense of the clinical picture, where a long history of literature and prior knowledge informs a medical doctor's definition of these acute illnesses as most likley due to virus infection

The details of the study's intentions were previously spelt out in Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study.[1]

But the topic of this post is the latest publication from this cohort study: The Burden of Community-Managed Acute Respiratory Infections in the First 2-Years of Life.[2; unfortunately it's paywalled but abstract is visible]. 

I'm not reviewing the whole thing today, I just wanted to pick out a couple of bits and a figure because it really exemplifies how often our little darlings become ill. These are generally mild illnesses and usually without any long term problems. Of course, that doesn't make the grown-ups on the receiving of an infant with a very transmissible virus all that much happier!

A couple of interesting things:

  • this is a community rather than hospital-based study which gives us a real snapshot of what happens in normal life - interpret that with the knowledge that infants were "from families of more advantaged backgrounds, which is common in longitudinal cohort studies"
  • otherwise healthy infants in this cohort had a distinct illness every 2 months on average; fewer during the first 6 or so months but more after that 
  • sampling density is phenomenal - weekly samples. Also a good participant retention rate and 78% of expected days were captured
  • antibiotics were prescribed in 21.9% of all ARI episodes - usually for acute otitis media (middle ear infection), and more often for a LRTI than an URTI
  • when antibiotics were prescribed for upper respiratory tract illnesses (well known to be overwhelmingly viral in nature and this not targeted by an antibacterial drug), it was most often in family physician visit older male doctors
    Note: Table 4 in the paper should not have had "Antibiotics" indented-personal communication with thanks to A/Prof Lambert for clarifying
  • some minor illness may have been missed because symptoms including fever, mood change and poor feeding are hard to measure in this very young age group.
    "I say mother, I'm feeling a tad peaked this morning". Umm, no. More like "Waaah!"


Copyright © 1999-2016 John Wiley & Sons, Inc. All Rights Reserved.
Publication: Pediatric Pulmonology; Content Title: The burden of
community-managed acute respiratory infections in the first 2-years of life;
Content authors: Mohinder Sarna,Robert S. Ware,Theo P. Sloots,
Michael D. Nissen, Keith Grimwood,Stephen B. Lambert.[2]
Reprinted with permission granted by Dr Sarna and RightsLink. License No. 3902730655132. 
Click on image to enlarge.
It will also be really interesting to see how often these children are infected but without a measurable illness resulting. 

What will the total number of infections look like in a year, in the community, among young children? More than a single infection every 2 months is my (highly biased) bet. That paper is coming, but unlike winter, it is not yet here.

Disclosure...

I have also been a little involved with this study during my previous life, as acknowledged elsewhere.[1]

References...
  1. Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study.
    http://bmjopen.bmj.com/content/2/6/e002134.long
  2. The Burden of Community-Managed Acute Respiratory Infections in the First 2-Years of Life.
    http://onlinelibrary.wiley.com/doi/10.1002/ppul.23480/abstract
Updates...
  1. Author title changes

Tuesday, 5 July 2016

Brazil's microcephaly and CNS disorder (M&CD) monitoring: Report No. 32, 2016-Week No. 25...

These graphs are made by me using data obtained from epidemiological week (EW) number 25's Brazil Ministry of Health microcephaly and foetal and infant microcephaly and central nervous system (CNS) disorders (M&CD) report.[1]

Brazil last reported a total of 120,161 suspected Zika virus detections some weeks back. Around one thousand of these have been confirmed.[2,3]

Suspected M&CD cases...

The total number of suspected M&CD cases increased by 126 to 8,165 this EW (compared to last).



The graph above shows the number of suspected M&CD diagnoses in Brazil up to 25-June-2016. The cumulative curve (yellow dots; left hand axis) is growing, but slowly. 

This was another weekly rise (orange bars; right-hand axis). These bars are based on the difference in total suspected cases reported this EW compared to that reported in the last EW. This method may not reflect the diagnoses that occurred during the past EW (some may have come from days or weeks earlier), but that level of detail is not available in the MOH report.

Confirmed and discarded M&CD diagnoses...

M&CD cases under investigation increased by 54 to 3,061 this week.


In the graph above, we can see that 50 (blue bars; right hand axis) suspected M&CD diagnoses were discarded upon closer investigation with a current total of 3,466 removed.

The rate of these resolved diagnoses (line with blue dots, left-hand axis) seems similar to the rate of the smaller overall number of confirmed M&CD diagnoses (red dots, left-hand axis).

As of this EW, 20% of suspected M&CD diagnoses have been confirmed while 42% of suspected diagnoses have been discarded-a percentage that has been steady for 4 EWs.

The cumulative number of confirmed M&CD diagnoses does continue its climb this EW, growing by 22 new diagnoses (red bars; right-hand axis) to total 1,638.


The number of these M&CD diagnoses to be confirmed with a Zika virus infection also grows (green dots; left-hand axis) by 37 new detection (green bars; right-hand axis) to 270 this EW after rising by 7 the preceding EW.

Those confirmed Zika virus infections represent 16% (an increase for the first time about 11 weeks) of all confirmed M&CD diagnoses and 3% of all suspect diagnoses.

References...

  1. http://portalsaude.saude.gov.br/images/pdf/2016/junho/30/Informe-Epidemiol--gico-n---32--SE-25-2016--27jun2016-16h18.pdf
  2. http://combateaedes.saude.gov.br/images/sala-de-situacao/informe_microcefalia_epidemiologico26.pdf
  3. http://combateaedes.saude.gov.br/images/boletins-epidemiologicos/2016-013-Dengue-SE16.pdf