Showing posts with label microcephaly. Show all posts
Showing posts with label microcephaly. Show all posts

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...

  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/Forms/public.aspx
  2. http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&Itemid=270&gid=36621&lang=en
  3. http://www.paho.org/hq/index.php?option=com_content&view=article&id=11117&Itemid=41532&lang=en

Sunday, 25 September 2016

Colombia Zika virus report, Epidemiological Week No. 37...

The latest epidemiological report from Colombia, which includes data on Zika virus disease (ZVD; 11SEP2016-17SEP2016), has been produced by the Colombian National Institute for Health team.[1]
NOTE: While these data were reported the past epidemiological week (EW), they may not be from that week. See earlier post about possible reporting lag.

As of this report, 41 (+1 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 0.70% of all confirmed ZIKV positive mothers-the 8th consecutive EW in which this proportion has risen.

Some back of napkin calculations looking at these numbers suggest that there are 7 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 [2] 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.

246 other microcephaly diagnoses (up from 216 last week) are now under investigation - this value had also been rising very quickly until a recent dip and plateau. Its rise once again might suggest suspicious CZVS cases in Colombia are accruing faster than the pace of complete investigation can keep up with. 

The graph below focuses on just the ZIKV-positive cases and those that remain under investigation, highlighting how the investigatory total has changed each week.

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 344 days, or 11 months 8 days, since ZIKV was first confirmed in Colombia on 16th October 2015.[2] Keep in mind that when talking about microcephaly - we have to think back in time to what insult or infection might have occurred during pregnancy. 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.[3]

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] However, the genetic analyses suggest Zika virus was in Brazil from around 2013. It had a lot longer to get established. Perhaps this is the difference between Brazil and Colombia.

But whatever the difference, there is a rise in microcephaly in Colombia compared to Brazil as we can see from the data in this Pan American Health Organization (PAHO) report...

401 cases counted up to EW 33 (now at EW 37) is 2.9X higher than the usual microcephaly figure per year for Colombia.
From PAHO report.[4]
References...

  1. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/2016%20Boletin%20epidemiologico%20semana%2037.pdf
  2. Zika Virus Disease in Colombia — Preliminary Report
    http://www.nejm.org/doi/full/10.1056/NEJMoa1604037#t=article
  3. http://virologydownunder.blogspot.com.au/2016/06/the-elephant-squeaked.html
  4. PAHO Zika-Epidemiological Report | Colombia
    http://www.paho.org/hq/index.php?option=com_docman&task=doc_view&gid=35139&Itemid=270&lang=en

Saturday, 20 August 2016

Tests and temps...

From [10]
It's been about 5 weeks since Brazil updated its microcephaly-related-to-Zika-virus reporting index page. 

The last post listed (a couple of others made their way out via other channels) was from epidemiological week (EW) No. 26. 

For comparison, Colombia is about to post data for EW No. 32. [12]

Interestingly, Colombia's National Institute of Health has not seen any new laboratory confirmed Zika virus disease cases during that same period - so perhaps Brazil is not seeing any either?

Temperature graphs (in Celsius) from 
accuweather.com.
Top-Miami Beach, Florida.
Bottom-Rio de Janeiro, Brazil
Meanwhile, more of the US state of Florida is seeing local Zika virus spread.[4,5,6] If we look at the temperature graphs we can see that Miami Beach (around 32'C)  is certainly a lot warmer and holding more steady than Rio (around 24'C) in August 2916. 

High and fluctuating temperatures are important for flavivirus multiplication in mosquitoes but for the mosquitoes themselves, particularly Aedes aegypti, they can live for about the same period (around 3 weeks) when conditions suit, whether at 26'C or 30'C.[12,13]

As I was recently taught by Rebbeca C Christofferson and Anthony Willson, viral loads do better in mosquitoes living at an optimal temperature. But when more Dengue virus for example, is replicating throughout the mosquito, that can have an effect on the length of their lives, even if not having an immediate impact on mortality.[14]

When you stop and think about it there is a lot going on for a mosquito when it takes a big blood meal. 

There could be a huge rapid weight gain, and there can be a 20'C temperature difference between the host's blood and the insect's temperature - that's a big shock at any size! There is also a big osmotic imbalance (difference in osmotic pressure due to the concentration of dissolved solids in the host's blood versus that in the insect's hemolymph [8,9]) and there's a need to get rid of toxic metabolites.[1] 

Have you seen that big drop of excreted fluid attached to some species of mosquito's butt? It appears once feeding has started and is something they excrete (urine and concentrated red blood cells; a process called prediuresis) to help them balance osmolarity, offset weight gain and sometimes to regulate their temperature through evaporation.[2,7] 

Some mosquito species retain the drop ('drop-keeping') making use of evaporative cooling, some emit new drops.[7] As far as I can tell so far, Aedes species don't make use of the drop for cooling. Male mosquitoes don't heat up because they don't feed on blood so they rely on environmental temperatures for heating and cooling.[7]

So much more reading to be done (apologies for errors above - I'm still learning about mozzies) - just not of data from Brazil.

References...
  1. Thermal Stress and Thermoregulation During Feeding in Mosquitoes
  2. https://en.wikipedia.org/wiki/Insect_thermoregulation
  3. http://www.vanderbilt.edu/hillyerlab/Research__Circulation.html
  4. http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0002190
  5. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961054/
  6. http://www.ncbi.nlm.nih.gov/pubmed/18021028
  7. http://www.cell.com/current-biology/pdf/S0960-9822(11)01311-X.pdf
  8. https://en.wikipedia.org/wiki/Hemolymph
  9. https://projects.ncsu.edu/cals/course/ent425/tutorial/circulatory.html
  10. http://portalsaude.saude.gov.br/index.php/o-ministerio/principal/leia-mais-o-ministerio/197-secretaria-svs/20799-microcefalia
  11. http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/Forms/public.aspx
  12. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961054/pdf/ehi-10-2016-119.pdf
  13. http://journals.plos.org/plosntds/article/asset?id=10.1371%2Fjournal.pntd.0002190.PDF
  14. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961054/pdf/ehi-10-2016-119.pdf

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...

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

Sunday, 12 June 2016

Colombia Zika virus report, Epidemiological Week No. 22...

The latest epidemiological report, which includes data on Zika virus disease (ZVD; 22MAY2016-04JUN2016), 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. 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 639 more laboratory confirmed cases of ZVD were reported this week than last. The total now rests at 8,221 or 10% (the highest proportion reported to date) 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 1,572 this week to total 82,935
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. 22, 10,436 suspected (+17 compared to last week) and 5,420 confirmed ZIKV infections (+529) have been identified in pregnant women.

As of this report, 6 (+0 from last week) live births have been diagnosed with microcephaly/central nervous system disorders and were reported as being ZIKV positive; 69 (up from 48 last week) other microcephaly diagnoses are now under investigation.[1] That represents 0.11% of all confirmed ZIKV positive mothers (as drop from last week). Graph No. 4 below focuses on just these positive cases.
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 239 days, or 7 months 26 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.

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]

Saturday, 11 June 2016

More microcephaly to come..?

The Brazilian Ministry of Health presented some information around Zika virus (ZIKV), June 10. Specifically some good news about its recent steady decline ahead of the Olympics. Good timing, huh?

Its always good to see some data - it's unclear if these are clinically suspected (most probably) or laboratory confirmed cases (highly unlikely given the numbers being so high and lab capacity being reportedly so low) from this graph, but if we look further down at Figure 2, the Pan American Health Organization data, which lists slightly fewer cases each week that Brazil (PAHO figures may need updating?), does not list any confirmed cases, only "suspected". I assume that means rashy febrile people. 

If we add up the weeks listed by the Ministry, there have been 159,914 cases in 2016.

Figure 1. From Brazil Ministry of Health slideset, June 10.
Slides No.12 and No. 13 [1]
Click on image to enlarge.
So, if these are ZIKV and not Dengue virus, Chikungunya virus, an enterovirus or some other acute cause of rash [2], then should we expect to see a new wave microcephaly and central nervous system disorders starting from around July? I've said July because that is about 184 days pr 6 months after the rise starts - 184 being the magic number between when ZIKV was first identified in Brazil (although we are pretty sure it was there much earlier[3]) and when the first 141 microcephaly diagnoses were announced.[4]

Meanwhile, Colombia - the elephant that won't leave the room - reports just 6 ZIKV-linked microcephaly diagnoses despite nearly eight months having passed since they first identified local spread of ZIKV and there already being nearly 5,000 pregnant women confirmed as ZIKV infected.[5] 

Brazil reports just 3,598 pregnant women clinically, epidemiologically or laboratory (presumably a much smaller number) confirmed as infected with ZIKV yet its population is a quarter of Brazil's (48 versus 200 million according to 2013 data via Google). It's a strange one that could be explained by ZIKV alone not being the cause of microcephaly or else by those extra years during which ZIKV was in Brazil but not yet Colombia being somehow key to the occurrence of microcephaly. 

First we need a little more genome sequencing to understand whether ZIKV was also present in Colombia for longer than dictated by its first laboratory confirmed case report. Perhaps a ZiCRA project is required?[5]

Meanwhile, it would be great if Brazil published its national numbers in a weekly report - along with confirmed numbers. The promise of the "Boletins Epidemiológicos de Dengue, Chikungunya e Zika" has not been realised with only two reports over the past 10 epidemiological weeks and no specific listing of laboratory confirmed numbers.[6] 

I can't help but recall that some were very upset at The Kingdom of Saudi Arabia for what was, in hindsight, relatively better epidemiology data for MERS-CoV. Strange why this has not been an issue here. One of the many mysteries of Zikasteria? I have no answer. 

References...

  1. http://portalsaude.saude.gov.br/images/pdf/2016/junho/10/saude-nos-jogos-olimpicos-e-paralimpicos.pdf
  2. http://virologydownunder.blogspot.com.au/2016/01/zika-virus-briefly.html
  3. http://science.sciencemag.org/content/early/2016/03/23/science.aaf5036.full
  4. http://virologydownunder.blogspot.com.au/search?q=184
  5. http://zibraproject.github.io/about/
  6. http://combateaedes.saude.gov.br/situacao-epidemiologica#boletins

Brazil's microcephaly and CNS disorder (M&CD) monitoring: Report No. 29, 2016-Week No. 22...

These graphs are made by me using data obtained from epidemiological week (EW) number 22'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 107 to 7,830 this EW (compared to last).


The graph above shows the number of suspected M&CD diagnoses in Brazil up to 04-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 decreased by 145 to 3,017 this week - the eleventh consecutive decrease.



In the graph above, we can see that 190 (blue bars; right hand axis) suspected M&CD diagnoses were discarded upon closer investigation with a current total of 3,262 removed.
The rate of these resolved diagnoses (line with blue dots, left-hand axis) continues to outpace 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 increased for 18 weeks.

The cumulative number of confirmed M&CD diagnoses does continue its climb this EW, growing by 62 new diagnoses (red bars; right-hand axis) to total 1,551.


The number of these M&CD diagnoses to be confirmed with a Zika virus infection also grows (green dots; left-hand axis) by 1 new detection (green bars; right-hand axis) to 224 this EW after rising by 15 the preceding EW.

Those confirmed Zika virus infections represent 14% of all confirmed M&CD diagnoses and 3% of all suspect diagnoses.


References...

Monday, 30 May 2016

Microcephaly, calcium deposits and eye problems...

What do virologists do when they are holed up at home with a productive cold? No idea. But I'm doing some reading of stuff I don't know much about; some historic literature on microcephaly.

I thought the slightly edited quote below, was interesting.[1]

Historic articles describing eye issues in microcephaly diagnoses are also interesting.[2,5] These are in light of similar language describing Brazilian microcephaly diagnoses as being part of a distinct or a unique syndrome.[3,4] 


This does beg the question of how well we've catalogued microcephaly's features in the past? With new and emerging technologies and techniques always adding new ways of looking at disease, perhaps we're due for an update. 

This is all well outside my area of expertise so take it with a huge grain of salt, but perhaps some of the current event is rediscovery, or even new discovery of something that is not unusual, just not previously captured among microcephaly diagnoses due to genetic issues, other infections or environmental influences?

It would be helpful to see some modern comments/reviews around this topic from experts in this field.

References..

  1. http://jnen.oxfordjournals.org/content/jnen/13/2/318.full.pdf
  2. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2081695/pdf/procrsmed00586-0039.pdf
  3. http://annals.org/article.aspx?articleid=2498549
  4. http://www.pbs.org/wgbh/frontline/article/in-babies-with-microcephaly-unique-damage-wreaked-by-zika/
  5. http://www.ncbi.nlm.nih.gov/pubmed/6777726

Wednesday, 25 May 2016

Brazil's microcephaly and CNS disorder (M&CD) monitoring: Report No. 27, 2016-Week No. 20...

These graphs are made by me using data obtained from epidemiological week (EW) number 20'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 portability confirmed.[2]


Suspected M&CD cases...

The total number of suspected M&CD cases increased by 89 to 7,623 this EW (compared to last).

The graph above shows the number of suspected M&CD diagnoses in Brazil up to 21-May-2016. The cumulative curve (yellow dots; left hand axis) is growing, but slowly.

This was another slower 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 decreased by 75 to 3,257 this week - the ninth consecutive decrease.


In the graph above, we can see that 114 (blue bars; right hand axis) suspected M&CD diagnoses were discarded upon closer investigation with a current total of 2,932 removed.

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

As of this EW, 19% of suspected M&CD diagnoses have been confirmed while 38% of suspected diagnoses have been discarded-a percentage that has increased for 16 weeks.

The cumulative number of confirmed M&CD diagnoses does continue its climb this EW, growing by 50 new diagnoses (red bars; right-hand axis) to total 1,434.




The number of these M&CD diagnoses to be confirmed with a Zika virus infection also grows (green dots; left-hand axis) by 1 new detection (green bars; right-hand axis) to 208 this EW.

Those confirmed Zika virus infections represent 15% of all confirmed M&CD diagnoses and 3% of all suspect diagnoses.

Monday, 23 May 2016

Brazil's microcephaly and CNS disorder (M&CD) monitoring: Report No. 26, 2016-Week No. 19...

These graphs are made by me using data obtained from epidemiological week (EW) number 19'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 portability confirmed.[2]

Suspected M&CD cases...

The total number of suspected M&CD cases increased by 96 to 7,534 this EW compared to last.

The graph above shows the number of suspected M&CD diagnoses in Brazil up to 14-May-2016. The cumulative curve (yellow dots; left hand axis) is growing, but slowly.

This was another slower 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 decreased by 101 to 3,332 this week - the eighth consecutive decrease. This may be occurring for a range of (guessed) reasons including:
  • improved capacity to address a large volume of request for clinical classification of suspect diagnoses.
  • streamlining the confirmation processes
  • retrospective application of changed head circumference definitions resulting in reductions to the number of the microcephaly diagnoses.
    This aspect will not reduce the number of cases with structural brain changes that occur in the absence of a decreased head size - which are reportedly also related to Zika virus and/or other causal influences.
    There is time involved in making these diagnoses because of the need for detailed ultrasound and other diagnostic investigations to identify congenital infection outcomes including intracranial calcifications, dilation of cerebral ventricles or posterior fossa changes and other issues.
In the graph above, we can see that 139 (blue bars; right hand axis) suspected M&CD diagnoses were discarded upon closer investigation with a current total of 2,818 removed.

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

As of this EW, 18% of suspected M&CD diagnoses have been confirmed while 37% of suspected diagnoses have been discarded-a percentage that has increased for 15 weeks

The cumulative number of confirmed M&CD diagnoses does continue its climb this EW, growing by 58 new diagnoses (red bars; right-hand axis) to total 1,384

The number of these M&CD diagnoses to be confirmed with a Zika virus infection also grows (green dots; left-hand axis) by 2 new detections (green bars; right-hand axis) to 207 this EW

Those confirmed Zika virus infections represent 15% of all confirmed M&CD diagnoses and 3% of all suspect diagnoses - but these are not fair comparisons for a range of reasons I won't go on about here.

References...

  1. http://portalsaude.saude.gov.br/images/pdf/2016/maio/18/Informe-Epidemiol--gico-n---26--SE-19-2016--16mai2016-19h00.pdf
  2. http://combateaedes.saude.gov.br/images/sala-de-situacao/informe_microcefalia_epidemiologico26.pdf

Sunday, 22 May 2016

Zika in the mouse...

Just over a week ago there were a few published Zika virus (ZIKV) studies in mice and brain balls (neurospheres and organoids). These were big deals. One was a letter to Nature by Cugola and colleagues, describing defects in the brains of mouse pups after their mothers were infected with virus.[1] This was one big letter and well outside my expertise to review in any sort of depth. But it raised a few questions for me.

Briefly, there were two parts to the letter - in part 1, two lines of pregnant mice (SJL and C58BL/6) were injected with virus and the pups evaluated immediately after birth. In Part 2, cell culture created human progenitor stem cells (hPSCs) and brain balls (neurospheres and cerebral organoids) were incubated with ZIKV.

This study included a ZIKV variant currently circulating in Brazil (ZIKVBR) rather than using the virus from six decades ago, but disappointingly, it did not include dengue virus or Chikungunya virus as control viruses against which to compare the activities described for ZIKV. There was some use of a slow-growing, attenuated (low risk of nerve pathology) vaccine strain of yellow fever virus as control virus - but exactly how wasn't clear to me. There was no virus control in the mouse work though - just the organoid experiments - as far as I can tell.
  1. One big takeaway message was that the C56BL/6 pups did not have any notable differences compared to healthy pups. Virus did not seem to cross the placenta. All the problems found were in the other line of mice - the immunologically defective SJL.[8,9]
    The authors note the C56BL/6 line had a robust antiviral immune response.
    If ZIKV is indeed the cause of congenital disease in humans, there is something to that result that should be of much interest. Whether that is at the level of a genetic immune deficiency, a microbiome-level issue or the occurence/history, absence or order of past infections, among other things, is unclear
  2. The SJL pups were smaller, had lots more ZIKV RNA in the brain than in kidney, liver or spleen, tissues, had eye abnormalities and had elevated markers suggesting that brain cell death was linked to apoptosis and autophagy. The authors remarked how these shared similarities with foetal human disease
  3. I have my usual question about how relevant to a human is a model that directly introduces a dumpload of virus into the blood (40,000,000,000 plaque forming units) by injection when the natural route of infection of a human is considered to be mostly due to a (presumably) much lower load from mosquito bite. Adding the same dose of inactivated ZIKV would have been very interesting to test for non-viral effects from the inoculum (h/t KatA)
  4. Human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs) were also exposed to virus and found to die via apoptosis. But where did these cells originate? I can't tell from the methods and references cited. Was it from human skin cells as other experiments have used? Skin cells are known to host ZIKV [3] Could this be a confounding factor? 
  5. Mock infected NPCs - "pretend" infection in the absence of any actual virus to check whether the method or material carrying the virus caused the observed damage - actually upregulated expression of the likely receptor for ZIKV, AXL, but ZIKV infection didn't.  Does that mean ZIKV down-regulated expression caused by something in the mock inoculum?
  6. High doses (10 MOI) of ZIKV killed NPCs, but a lower dose (1 MOI) did not - what does that mean for the heavily dosed mouse model; and for a human bitten by a mosquito? ZIKVBR and an African lineage ZIKV (ZIKVAF) acted similarly. 
  7. In three dimensional cultures, neurospheres growing in the presence of 10 MOI of ZIKVBR were smaller and cell death was apparent - the effect was not as strong with ZIKVAF suggesting lineage differences. Effects were dose dependent - stronger with higher doses (10 MOI) than lower (1 MOI). Differences between ZIKV lineages is something yet to be fully explored by virology-for some inexplicable reason(s).
You'll possibly have noticed two units used by the authors - plaque forming units and MOI (multiplicity of infection). These are different because of different methods used to determine the endpoints. Briefly (but still technically):

From Sloutskin et al.[6]
  • For plaque-forming units (PFU) - we titrate infectious virus that can damage cells (make plaques) and look at where the effect finishes. By titrate I mean serially dilute and then add each diluted solution to a separate well of the same cells, usually grown in a multiwell plate. The effect is the formation of plaques - areas of clearing due to virus-induced death of cells that had first been grown into a single layer in each plate well before being infected by a virus preparation. The dilution before the effect finishes is the PFU.
    There are also issues around how well PFU value determined using one cell culture model holds up when infecting a cell/tissue/organ/animal that is different from the one you determined your PFU on - you may get different results.
    For example you may find your virus preparation contains 10,000 PFU on the original cells, but if you did that same titration with the same preparation but using a different cell type, it may contain 100,000 PFU or 1,000 PFU.
    In the study above, ZIKV was grown up using a C6/36 mosquito cell line, then titrated using porcine kidney epithelial cells to determine the PFU then that C6/36 preparation was used for the mouse, NPC, neurosphere and organoid incubations. This is normal approach but can raise questions.
  • For multiplicity of infection (MOI) we are talking about the average number of virus particles in a preparation that infect a target cell. 1 MOI means 1 virus particle per cell. An MOI of 10 means 10 virus particles per cell.[4] This works well in cell culture where we often use a single cell type grown in a single layer - conditions, viral density and culture volumes are optimized and we use the same cells as for the PFU.[5] When you take that MOI of 1, calculated on your cell line, and add it to a different and complex tissue, or animal, with lots of different cell types, perhaps spread over a larger or smaller surface, in the presence or absence of an antiviral response, with more or fewer receptors etc...the ratio of 1 virus : 1 cell will probably not hold up. So using a higher MOI makes it more likley that each cell in a different tissue/organ/animal will get infected. Thus an MOI of 1 and 1 PFU are not always the same thing. A virus preparation determined to have an MOI of 1 using one system might require 0.1 or 273.64 PFU of that preparation in another cell/tissue/organ/animal system, because it takes that amount to finally show the desired effect (cell death, PCR positivity, virus protein detection etc) in that target cell/tissue/organ/animal.

    We should also think about how relevant an MOI of 10 is to the thing we originally sought to study. In this case it is the early brain structure of a foetus whose mother was infected from a mosquito bite.
    The bite itself would not have delivered anything like an MOI of 1 to any tissue in that mother's body.
    But how much ZIKV crosses the human placenta in the rare cases that it does at all? Well, we assume placental crossing is a rare event for ZIKV.
    I'd presume it's also not an MOI of 1 for any tissue in the foetus - unless the placenta is where the virus is being amplified. But it does seem like there is a lot of ZIKV in the brain of studied infected foetuses.  So this mouse model might reflect what happens in a forming human brain that amplifies virus it acquired after placental crossing, or that was present from conception (here for more on that theory[7]).  

One of my biggest questions about this study is - so what? 

This is an incredibly dense and impressive piece of work - don't get me wrong. It may well be the definitive result that so many have commented on it being. But I wonder if the same degree of very detailed investigation gone into the study of other mosquito-borne viruses in mouse brains? Have we sought out the congenital infection potential of other arboviruses in mouse pups and investigated arbovirus impact on neurospheres and organoids to this extent? Are these results unique to ZIKV or do the same or similar effects from other viruses, that - to our knowledge - are not considered threats for congenital disease in humans? We should probably establish that, by using more experimental controls, before we continue on our journey along this limb.

I have trouble saying that this experiment equals that disease as much as I am troubled by saying that the (possible) surge of microcephaly diagnoses in north east Brazil is caused by that particular parallel viral epidemic.

References...
  1. The Brazilian Zika virus strain causes birth defects in experimental models
    http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature18296.html
  2. http://jvi.asm.org/content/82/12/6024.full
  3. http://www.ncbi.nlm.nih.gov/pubmed/26085147
  4. https://en.wikipedia.org/wiki/Multiplicity_of_infection
  5. http://www.virology.ws/2014/05/06/virology-question-of-the-week-what-matters-more-multiplicity-of-infection-or-virus-concentration/
  6. http://www.bio-protocol.org/e1295
  7. http://virologydownunder.blogspot.com.au/2016/04/the-three-parent-hypothesis-mum-dad-and.html
  8. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1453197/
  9. http://www.informatics.jax.org/external/festing/mouse/docs/SJL.shtml