VDU's blog: epidemiology

Showing posts with label epidemiology. Show all posts

Tuesday, 20 June 2017

Working for health can make you sick....

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Saturday, 20 May 2017

Ebola virus disease in the DRC: first graphs...

The World Health Organization have apparently found an outlet for their Ebola virus disease (EVD) reports for 2017's Democratic Republic of the Congo outbreak.

It's not the Disease Outbreak News site. It's not the WHO media page. It's not any of the past EVD outbreak pages on the central WHO site.

Turns out the Situation Reports (SitReps) are to be found on a new page on the WHO African site.[1] Okay. Why not? Found it eventually. I've plotted the first 4 (they started from 15th of May) below. Not much to say about trends at this early stage obviously!

Click on image to enlarge.

Don't go expecting to find how we got to the totals shown on the 15th - those may well be lost details. Or they may come out later. We'll have to wait and see. Outbreaks viewed from the public point of view are very much about patience and trying not to leap to any dramatic conclusions - like those decisions taken by at least one country in Africa to start screening passengers for signs of EVD.[2] It's your budget guys - spend up if it makes you feel safe. At this stage, and perhaps ever, its a pretty wasteful exercise though; apart from your citizens seeing you doing something.

Back to numbers. I'm pretty impressed with the WHOAfro SitRep - the 4th Report carries a detailed table of cases, deaths and locations and also a timeline graphic (below) which is fantastic.

Click on image to enlarge.This image is part of SitRep No.4.[3]

And to wrap up, just for a glimpse of what has come before and where we are now (and because I promised @kristindownie I would!), I've also added an updated "EVD through time" bar graph. Where we are with the current outbreak total is highlighted using a red arrow and the towering totals of West Africa are indicated by yellow arrows.

Click on image to enlarge.

References...

Tuesday, 14 March 2017

SNAPDATE: H7N9 by map...

With the latest numbers out from Hong Kong's Centre for Health Protection, Week 10 marks the second week of around a dozen human spillover cases - likley to be poultry to human infections.

Click on image to enlarge.

While the number of cases at each geographic location within China is small given the millions living in each region, this week's cases are spread across 10 provinces or municipalities. A huge area.

Guangxi province is adjacent to Vietnam. It's always worth remembering that an outbreak anywhere can turn into a threat everywhere.

From these numbers, there is no obvious escalation of human cases to suggest anything has changed in the way H7N9 infections are acquired; they remain relatively rare and from animal-to-human close contact.

While the cases are still coming, the totals (see weekly and daily bars below) shows a levelling off - at last suggesting a slowing of this season's epidemic. But stay tuned.

Numbers of human H7N9 cases.

Image taken from the VDU static H7N9 graphs and numbers page.

Click on image to enlarge.

Sunday, 5 March 2017

Avian influenza A(H7N9) virus in humans: lay of the land...

I'm getting a little more of a grip on the H7N9 numbers thanks to the data from the Hong Kong Centre for Health Protection (CHP) [1] - which have been a solid source in 2017.

Keep in mind that these numbers :

are imperfect because they are reported inconsistently by those who have the data and because they only contain partial detail - death details are impossible to come by. Please keep in mind that there is no global, running-tally of H7N9 cases presented to the public, by any public health entity. There is a great line list from the citizen-run FluTrackers list, ([2]my usual go-to) but in 2017 they got swamped by these unsatisfactory data.
will only represent those cases that have been lab tested. Any people who have met the criteria for being a "Case" [pick from 3-6] - which in most instance means being sick. In some instances a cases is identified because diligent doctors have followed up those people who had contact with a known case - which is called contact tracing. Sometimes these contacts may virus positive by only mildly ill or have no illness at all.

I've graphed these wrangled data using one of my older formats - to show which province, municipality or autonomous region is contributing to the peaks as the site of origin for an H7N9 case.

Sometimes where a case has been detected may not be where they were infected. I prefer to talk about where a case "acquired" their infection.

Click on image to enlarge.
Data for this graph can be downloaded from my static H7N9 graphs page, here.[9]

We can see - perhaps - that the major contributors to the peaks in January and February's 5th Wave are Jiangsu province (green circles) followed by Zhejiang province (orange circles) then Guangdong (brown circles), Anhui (purple circles), Hubei (red squares) and a range of smaller contributor regions.

Guangdong and Zhejiang are familiar to H7N9 watchers as being hotspots for human spillover and while Jiangsu has always had a presence in the outbreaks, it has had a very big season this time around.

It remains to be seen whether a range of market live poultry market (LPM) closures has cut the flow of virus into these markets and to their many, many visitors. These closures have been in response to cases rather than to prevent the outbreaks but no obvious nationwide coordination is apparent. It seems likely that spread of infected fowl will continue until more markets close, the source is contained or the seasons for influenza spread (winter and colder shoulders) is over.

Stay tuned to the CHP update this week - last week's tally was lower than previous weeks; a blip or a trend?

A few things about this graph.

It mirrors the FluTracker's line list numbering scheme up until FT816. From entry No. 817 it uses data from the CHP reports. These are PDFs but as they helpfully told me by email this week - you can extract the data yourself using Adobe Acrobat Pro. If you don't have that - I've already done that extraction and am happy to share an Excel version of it with you. Shoot me an email, leave a message or Tweet me @MackayIM.
The Outbreak numbering - or waves - is based on when cases appeared or stopped. Its imperfect too. There are published schemes but they also differ from each other [e.g. 7,8]. This isn't life or death - you get the idea from the obvious peaks and troughs. FYI - this year I've updated my numbering for previous outbreaks.
Market closures include long term or short term shutdowns or rotating closures for one or more days for disinfection followed by restocking. Each province is a populous place. Often markets are closed here or there but not everywhere in a province and certainly not all provinces at once.
Data are plotted by week of illness onset (hard data to come by) or when the case was reported. The grey peaks indicate totals from all provinces for that week

References...

Friday, 24 February 2017

H7N9 numbers....no-one agrees...

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Tuesday, 21 February 2017

H7N9 virus in humans in China: just how big is this?

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Sunday, 19 February 2017

H7N9 in humans - biggest ever season in humans - most poorly reported as well

UPDATE: No.1 20FEB2017

Below is the best I can do to plot avian influenza H7N9) virus cases in humans against month.

And just to be clear - it's a very big underestimation. WHO is reporting 1,222 cases in humans [3] - but patchy public data exist for about 1,000.

Click on image to enlarge.
NOTE: This is a big underestimate as it only includes cases
with public detail available to identify them. There are
approximately 200 cases missing.

Ideally the charts above woudl be based on the month that illness onset occurred - when each person became ill. But those details just are not publicly forthcoming from China's massive human and animal influenza surveillance and testing system.

I'm sure the data are to hand internally, and they may be on hand at the World Health Organization (WHO) - but you wouldn't know it by looking for them publicly.

The WHO used to be helpful with providing H7N9 data but it seems their latest efforts to provide more detail on MERS cases has exhausted them.

Hong Kong's Centre for Health Protection (CHP) has been valiantly chipping away, but they also fail to provide sufficient detail to link cases with media or other reports. What they do provide are summary totals.

As for fatal outcomes from H7N9 infection - forget understanding who dies when and why. Those numbers have been frankly a pathetic mess for four years.

This week marked the fourth anniversary of our knowledge of H7N9 in humans - the first case became ill February 18th 2013 in as part of a Shanghai family cluster. Since then we've seen less and less detail on cases. And by "detail" I don't mean their names and addresses - just case age, sex, date of illness onset/hospitalization/death, linkage between case and death, poultry or human contact and place infection was likely acquired. Basic and standard stuff.

Meanwhile the mainstream media report every bolus of data that are dumped as if these were new cases and deaths that have just occurred. In reality, the huge January spike below may include many cases and deaths from a month or more earlier. It may mis many cases that have not been detected.

We're definitely having a huge H7N9 season in 2016/17 (n=176 human cases using public case data, but over 400 based on announced totals[3]). We had bigger detailed tallies in 2014 (n=326) and 2015 (n=220), but never a season as big as these totals make it out to be now.

This is the largest H7N9 season ever recorded.

In media interviews over the past weeks, I've put the current season down to lethargy in closing live bird markets as cases and deaths have mounted. The response has been faster in previous years.[1,2] Poultry is a big deal in China.[2] Perhaps the poultry lobby has won out over human life this season.

References...

Updates...

Amended to indicate the scale of the case numbers, based on totals, not individual detailed cases, in the 2016/17 seasons. The largest season of H7N9 in humans...on record.

Thursday, 26 January 2017

WHO sets the table....and lays it with MERS-CoV details

This just made my day. A Tweet from scientist and program manager at the World Health Organization (WHO), Dr Embarek. In the tweet he noted that Middle East Respiratory syndrome coronavirus (MERS-CoV) data will now be presented by WHO in an easy-to-access Mirosoft Excel table...

An example is in this latest update.[1]

Excerpt of new MERS-CoV data from [1]

This will make data collection for scientists, public health teams and researchers looking to follow what's happening with this camel-borne virus as it spills over to humans so much easier. I've been painstakingly entering data from several sources since 2013 - and this will really streamline the process.

Thanks to those at the WHO for making this happen.

Now, could you please also do this for all the other pathogens you keep track of....different influenza viruses (H7N9, H5N6, H5N1), zika virus, dengue virus, yellow fever virus....and make it retrospective....

References...

http://www.who.int/csr/don/26-january-2017-mers-saudi-arabia/en/

Monday, 26 December 2016

Snapdate: influenza H7N9 cases in humans, by the numbers...

An updated chart.
[SNAPDATE'S are snap updates that don't have lots of detail and chat...although they almost always end up having lots of chat!]

A summary of the monthly, weekly and daily data graphing human avian influenza A(H7N9) virus infections in humans reported from the hotzone, China.

Daily weekly and monthly H7N9 numbers, taken from the
FluTrackers curated line list [1] and the World Health
Organization disease outbreak news reports.
Click on image to enlarge.

References...

Sunday, 23 October 2016

Microcephaly cases under investigation for links to Zika virus in Colombia keep accruing...

Diagnoses of Zika virus infection linked to microcephaly continue to very slowly rise in Colombia, rising by 11 since the end of July 2016 - with 1 new case in this most recent reporting week to reach a total of 47.[1]

Brazil reports 2,033 cases of Zika virus congenital syndrome (CZVS) as of 20-OCT-2016, among a background of 109,596 "confirmed" cases.[2] However, a confirmed case listed by Brazil includes confirmed and probable cases as described by the Pan American Health Organization (PAHO) definition.[3]

Meanwhile the number of microcephaly (?CZVS or just head size?) cases that remain under investigation in Colombia continue to accumulate.

Up until mid-June, these numbers used to be in double digits, but they have risen dramatically (yellow dots in graph above) since then to reach over 300 and continue to climb steadily. How many of these will be added to the microcephaly/CZVS total is unclear.

References...

Sunday, 9 October 2016

Zika virus in Colombia is very quiet - but undiagnosed rashy fever disease hasn't gone away...

Just a quick snapdate today.

Clinically suspect cases of Zika virus (ZIKV) infection have increased by 227-933/week for the past 12 weeks (red graph) - but none have been confirmed as ZIKV by the Colombian Institute of Health.

That seems to indicate just how terrible clinical diagnoses is. Otherwise, there's a testing or reporting problem.

The green graph below shows the flat line that indicates no new positives confirmed by laboratory testing.

Thankfully, we also continue to see few new cases of ZIKV-linked congenital syndromes. Although, this is also something of a conundrum.

Pregnant women are not being reported with many new confirmed or suspected ZIKV diagnoses - which makes sens of there is no rise in confirmed cases overall.

Sunday, 28 August 2016

Colombia Zika virus report, Epidemiological Week No. 33...

UPDATE No.1: 29AUG2016

The latest epidemiological report from Colombia, which includes data on Zika virus disease (ZVD; 14AUG2016-20AUG2016), 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 0 new laboratory confirmed cases of ZVD were reported this week; the 6th week of this. The total sits at 8,826 or 9% 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 but have been slowing for weeks, adding 270 this week to total 93,551.

Graph No.3. The cumulative curve of clinically suspect (lilac triangles, left-hand axis) and 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 number of microcephaly cases
confirmed as ZIKV infected (yellow bars, right-hand axis). Data from [1].
Click on graph to enlarge.

Graph No. 3 shows that to epidemiological week (EW) No. 33, 11,752 suspected (+30 compared to last week) and 6,054 confirmed ZIKV infections (-2) have been identified in pregnant women.

As of this report, 34 (+5 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 0.53% of all confirmed ZIKV positive mothers-the 4th consecutive EW in which this proportion has risen.

Some back of napkin calculations looking at these numbers suggest that there are 5-6 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.

209 other microcephaly diagnoses (down from 254 last week) 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 and rising by +5 for 2 weeks in a row.

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 317 days, or 10 months 12 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[2] Colombia is currently carrying the next biggest load of suspected ZVD cases [8] (although more confirmed in Puerto Rico. NB: not all of the "Casos confirmados" are lab confirmed, but I'm told most are).[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...

Updates...

Clarified Puerto Rico has more confirmed cases than Colombia but fewer suspected

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...

Sunday, 19 June 2016

Colombia Zika virus report, Epidemiological Week No. 23...

The latest epidemiological report from Colombia, which includes data on Zika virus disease (ZVD; 05JUN2016-11JUN2016), has been produced by the Colombian National Institute for Health team.[1]
NOTE: While these data are from those reported the past epidemiological week, they may not be from that week. See earlier post about possible reporting lag.

Graph No. 1 shows that zero new laboratory confirmed cases of ZVD were reported this week-this must be an "off" week for laboratory reporting - you can see others in the above graph where the green bars sit at zero. The total still rests at 8,221 or 10% (the highest proportion reported to date) of all clinically suspected Zika virus (ZIKV) detections.

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 2,086 this week to total 85,021.

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 No. 23, 10,704 suspected (+268 compared to last week) and still 5,420 confirmed ZIKV infections (+zero-no lab results this week) have been identified in pregnant women.

As of this report, 6 (+0 from last 2 weeks) live births have been diagnosed with microcephaly/central nervous system disorders and were reported as being ZIKV positive; 81 (up from 69 last week and the highest value to date - could things be picking up pace?) other microcephaly diagnoses are now under investigation.[1] That represents 0.11% of all confirmed ZIKV positive mothers.

Graph No. 4 below focuses on just these ZIKV-positive cases and those that remain under investigation, highlighting how the investigatory total has changed each week, but has also been trending upwards since Epidemiological Week No. 14. This may be a marker of a rise in microcephaly and other congenital disorders.

It has now been 247 days, or 8 months 3 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[2] Colombia is currently carrying the next biggest load of Zika virus disease 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 different from Brazil.[5]

Brazil first reported 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...

Saturday, 18 June 2016

The elephant squeaked...

An interesting new paper came out from Pacheco and colleagues from Colombia's national institute of health (INS or Instituto Nacional de Salud) this week. The INS team have written up their Zika virus (ZIKV) data spanning from 9th August 2015 to 2nd April 2016.[1] ZIKV data were not being regularly collected prior to then.

For me, the main new outcome from this report is that there seem to be no adverse outcomes to babies born to mothers who were infected with symptoms suggestive of ZIKV infection, in the third trimester of their pregnancy. Phew.

I'm not surprised at the low number of ZIKV-related microcephaly diagnoses observed, because I've been following the INS's weekly reports on this which make that issue very clear. I talk a little more about that issue below.

There were quite a few other bits and pieces in this publication. I've tried to capture some of the ones I found interesting in the list below:

The time taken for health care centre ZIKV disease (ZVD) data to be reported by the INS is approximately 1.5 weeks
Elevations 2,000m above seal level are not considered a risk because they are above traditional ZIKV-mosquito habitats, but they may still harbour human cases that have travelled from lower elevations and these may be under-counted
In 2010, half (52%) of pregnancies in Colombia were unintended and condoms were used in the same proportion of sexual encounters reported by women. Any advice aimed at reducing risk of sexual transmission of ZIKV - or other sexually transmitted infectins - will need to innovate to get that message across
Two-thirds (67%) of suspected ZVD cases were reported in females. Incidence per 100,000 population was similar in children but higher in females. This may reflect more testing of, and concern among, women of child-bearing age
Most pregnancies with symptoms suggestive of ZVD were ongoing when this report came out. This supports the thinking that it is still too early to say that Colombia will not have the same ZVD-related congenital disease problems among its pregnant women that Brazil has claimedIn a subset of 1,850 pregnant women who delivered babies, 532 (29%; 16% of pregnancies were not ongoing-why was not made clear) experienced their symptoms in the first trimester, 702 (38%; 29% not ongoing) in the second and 616 (33%; 82% born at term with normal weigh; 2% at term but low weight, 8% preterm, 1% were perinatal deaths and 7% are ongoing) in the third.
Lanciotti primers were used for RT-PCR of serum samples, but they look to have been updated in this study. The names differ-1087 instead of 1086 in the cited publication by Lanciotti et al.[2], 1163 instead of 1162c, 1108-FAM instead of 1107-FAM.
It would be good to see what sequences were actually used here. Most RT-PCR testing (60% of 3,384 samples tested during this period) was on samples from pregnant women (see No. 4) and no testing of urine was discussed which is a shame because urine is reportedly a better sample for RT-PCR because the detection window can be extended beyond that of using serum alone
No antibody testing was available - that means a lot of missed opportunities to confirm suspect ZVD diagnoses
The INS mandates reporting of all symptomatic cases. I had a little hope that perhaps Colombia, because they have been good at reporting throughout this event, might have also looked at whether the "80% asymptomatic" figure from previous outbreaks still holds today. Okay - it was a teensy hope. It will need a specific study
Fever was an integral part of the INS case definition - but fever is absent in 20% to 72% of cases.[1,3] This could mean a lot of ZVD cases were not included in the analysis - with an unknown impact on linkage to microcephaly counts from Colombia
As STATNEWS reported earlier[4], the World Health Organization has indicated that Colombia is not reporting on aborted foetuses or miscarriages that might have been related to ZVD. The impact of this omission is unclear and it would be great to know more about the issues and concerns here
During this period 4 infants (born between weeks 37 and 39) were reported to have microcephaly and confirmed ZIKV infection; 1 had abnormal brain findings and 3 abnormal hearing evaluations and other findings were listed as well. However, none of the 4 mothers reported symptoms of ZVD during pregnancy. Colombia is capturing newborn issues other than head size, at least following that initial diagnosis of microcephaly being made
STORCH (syphilis, toxoplasmosis, other agents [which other?], rubella, cytomegalovirus, and herpes) screens, karyotype analysis and ZIKV virus testing of the subset of 1,850 pregnant women with suspected ZVD were the only other tests described.
Investigations into teratogenic or toxic causes of microcephaly [6] not happening - at least based on the contents of this report
Among 239 ZIKV-negative samples (another 316 were ZIKV positive-all collected within 7 days of symptom onset - 8 (3%) were positive for dengue virus and 23 (10%) for chikungunya virus

The authors conclude that women with symptoms suggesting ZVD in the 1st trimester, may start to deliver affected babies soon after the early April cut-off date that this report covers. It's now the second half of June though and we have only had 6 cases reported by Colombia.[5] This may all be because of those reporting differences and timing issues discussed above and elsewhere on VDU. We await some more discussion about precisely how that would be the case.

We should also remember that clinically suspected diagnoses in this neck of the woods can be fraught with difficulty because fever+rash can be caused by a very wide range of things - including other mosquito-borne viruses known to be co-circulating. Take those totals with a big grain of NaCl and look laboratory confirmed samples for trends. This is also bias because a lot of the Colombian laboratory focus has been on pregnant women.

Click to enlarge.

We really know very little about the incidence of ZIKV in the general population or about the proportion of confirmed ZIKV infections that have little or no disease or about the rate of microcephaly or other congenital disease outcomes from infection. These would be very useful numbers to have to help us understand different risks and they rely on an accurate denominator. By 'accurate' I mean one based on actual testing results, not one based on guesstimates and models that lean on "suspected" data. This knowledge gap equally applies across all of the epidemic countries though, not just to Colombia.

For now, the elephant in the room continues to be the subject of insufficient conversation.

References...

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