VDU's blog: Situation Report

Showing posts with label Situation Report. Show all posts

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...

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. 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 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. 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 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.

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 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...

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 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 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 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.

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]

References...

Saturday, 11 June 2016

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...

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.

References...

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...

Sunday, 15 May 2016

Colombia Zika virus report, Epidemiological Week No. 18...

The latest epidemiological report, which includes data on Zika virus disease (ZVD; 01MAY2016-07MAY2016), has been produced by the Colombian National Institute for Health team.[1]

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 1,116 more laboratory confirmed cases of ZVD were reported this week than last. That's the biggest weekly rise on record. The total now at 4,867 or 7% (reaching the highest proportion reported to date) of all the clinically suspected Zika virus (ZIKV) detections.

Graph No.2. The cumulative curve of suspectedZVD 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 2,665 this week to total 71,299 suspected cases of ZVD. This is far from the biggest weekly rise suggesting the figure above may indicate more testing or improved laboratory capacity or reporting (clearing a backlog?).

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. 18, 11,417 suspected (-307 compared to last week) and 2,948 confirmed ZIKV infections (+941 - biggest rise to date) have been identified in pregnant women.

As of this report, 5 (same as last week) live births have been diagnosed with microcephaly/central nervous system disorders and were reported as being ZIKV positive; 43 (up from 32 last week-fourth week to increase in total number) other microcephaly diagnoses are now under investigation.[1] That represents 0.17% of all confirmed ZIKV positive mothers (down from 0.25% last week).

It has now been 210 days, or about 7 months, 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. 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]

References...

Wednesday, 11 May 2016

Colombia Zika virus report, Epidemiological Week No. 17...

The latest epidemiological report, which includes data on Zika virus disease (ZVD; 24APR2016-30APR2016), has been produced by the Colombian National Institute for Health team.[1]

Graph No. 1 shows that 1 fewer laboratory confirmed case of ZVD was reported this week than last. That's different. The total now at 3,751 or 5% of all the 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 2,671 this week to total 68,634 suspected cases of ZVD.

Graph No. 3 shows that to Epidemiological Week No. 17, 11,724 suspected (+418) and 2,007 confirmed ZIKV infections (-1) have been identified in pregnant women.

As of this report, 5 (an increase (+1) from last week) live births have been diagnosed with microcephaly/central nervous system disorders and were reported as being ZIKV positive; 32 (up from 26 last week) other microcephaly diagnoses are now under investigation.[1] That represents 0.25% of all confirmed ZIKV positive mothers.

It has now been 207 days, or about 7 months, 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]

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...

Sunday, 1 May 2016

Colombia Zika virus report, Week No. 16...

The latest epidemiological report, which includes data on Zika virus disease (ZVD; 17APR2016-23APR2016), has been produced by the Colombian National Institute for Health team.[1]

Graph No. 1 shows that 460 new laboratory confirmed cases of ZVD reported this week. The total now at 3,752 or 6% of all the 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 3,752 this week to total 65,963 suspected cases of ZVD.

Graph No. 3 shows that to Week No. 16, 11,306 suspected (+207) and 2,008 confirmed ZIKV infections (+305) have been identified in pregnant women.

As of this report, 4 (no increase from last week) live births have been diagnosed with microcephaly/central nervous system disorders and were reported as being ZIKV positive; 26 (up from 22 last week) other microcephaly diagnoses are now under investigation.[1]

References...

http://www.ins.gov.co/boletin-epidemiologico/Boletn%20Epidemiolgico/2016%20Boletin%20epidemiologico%20semana%2016.pdf

Friday, 29 April 2016

Brazil's microcephaly and CNS disorder (M&CD) monitoring: Report No. 23, 2016-Week No. 16...

These graphs are made using data obtained from Week 16's Brazil Ministry of Health microcephaly and foetal and infant microcephaly and central nervous system (CNS) disorders (M&CD) report [1] and media report.[2]

Suspected M&CD cases...

The total number of suspected M&CD cases increased by 78 to 7,228 this week - the smallest rise reported by Brazil to date. This should not be confused with comments in the latest World Health Organization's Zika virus (ZIKV) situation report which states...

"At this stage, based on the evidence available, WHO does not see an overall decline in the outbreak."

That statement refers to current data whereas Brazil's M&CD report #23 is describing events that may have occurred approximately 20 to 40 weeks ago.[3] I picked that range because foetal disorders with preceding ZIKV detection have been reported to occur very rapidly, between 17 and 20 weeks in one case study.[4]

The chart above reports the number of newly suspected M&CD diagnoses in Brazil up to 23-April-2016. The cumulative curve (yellow dots; left hand axis) is steady and growing, but slowly steadily. This was the lowest weekly rise (orange bars; right-hand axis) on record.

Confirmed and discarded M&CD diagnoses...

M&CD cases under investigation decreased by 31 to 3,710 this week - the fifth consecutive decrease.

In the graph above, we can see that 79 (blue bars; right hand axis) suspected M&CD diagnoses were discarded upon closer investigation.The rate of these resolved diagnoses (line with blue dots, left-hand axis) is slowing but still seems to be outpacing the rate of confirmed M&CD diagnoses (red dots, left-hand axis). The cumulative number of M&CD diagnoses does continue its climb this week (+30), but this is the smallest addition of new diagnoses on record (red bars; right-hand axis).

The number of these M&CD diagnoses to be confirmed with a ZIKV infection also grows (green dots; left-hand axis) but by just 2 new detections to 194 this week (green bars; right-hand axis). That's the smallest rise on record. Those confirmed ZIKV infections represent 16% of all confirmed diagnoses and 3% of all suspect M&CD cases - but these are not fair comparisons for a range of reasons I won't go on about here.

Why are M&CD diagnoses slowing...?

It's not precisely known why the numbers of M&CD diagnoses are slowing in Brazil. Whatever their cause(s), the trigger(s) for the anomalies occurred in the past - as far as 9 months or as close as perhaps 20 weeks. One suggestion which ties in with the timing of arbovirus epidemics in Brazil, is the weather and its impact on the mosquito breeding cycle. (Thanks Luis F. B. Correia) Mosquitoes are assumed to be the major vector for transmitting ZIKV, wherever in the world it may be. That's a safe bet as far as we know. Undoubtedly, reporting on mosquito detections is not a priority. Only Mexico has reported infected wild-caught mosquitoes to date.[5] There have been more monkeys identified as ZIKV-infected than mosquitoes![5,6] For now at least.

The rainy season begins in the north-east (where M&CD has mostly been diagnosed) in May. Infections are likely to pick up from then - if we crudely add 6-9 months to May 2015 we get to October-2015 - January-2016.

August saw a rise in microcephaly diagnoses in Pernambuco State in the north-east.[6]

November is when the Brazil ministry declared a link between M&CD and ZIKV.[7]

It all kinda fits.

None of these numbers are precise though because when and where ZIKV was becoming established in Brazil is not known. It is predicted to have been as early as May-December 2013 based on analysis of viral genome sequences to hand,[9] but local transmission was not detected (looked for?) until April/May 2015.[9,10] It may have been there earlier.

Solid data and answers continue to evade trapping. As do ZIKV positive mosquitoes apparently.

References...

Static pages

Tuesday, 5 July 2016

Sunday, 19 June 2016

Sunday, 12 June 2016

Saturday, 11 June 2016

Wednesday, 25 May 2016

Monday, 23 May 2016

Sunday, 15 May 2016

Wednesday, 11 May 2016

Sunday, 1 May 2016

Friday, 29 April 2016