Raffin

After a high total announced on the 27th yesterday the total back down to 1,169. Following a pattern lately. Actually 1,298 positives were found, so nearly 130 not reported for some reason. Positivity from the 26.2k tests was at 5.0%. Tests on the way at 27.7k.

Top locations:


National Reproduction number is now estimated at 1.0, NCR 0.93. (Jan 24).

Deaths at 71. No RDs reported again. Few have been lately.
Case fatality rate up at 2.03. Close to Sweden at 2.04, one of Europe's worst performers on deaths.
ABS-CBN data analytics have looked at the delays in reporting deaths. They also take a brief look at the RDs. Basically the delays have meant that the Philippine health system is only now seen for doing a very poor job, rather than just a poor job 6 months ago.

https://news.abs-cbn.com/news/01/28/...ugust-doh-data

Critical down to 1,036, down 66, severe at 769, down 8.

More detail on cases from Jan 27:


Bicol 20








NCR contribution at 18.7%, Region 4A at 10.3%. Both "old" epicenters at 29% of total cases.
NCR had 7 cities in the top 20.
CAR cities prominent at top of the urban table.
The rise in Cebu City and its province cases this month is greatly concerning the OCTA experts:


Though hospital facilities are coping for now the Reproduction number high at 1.6.

https://news.abs-cbn.com/news/01/28/...ays-octa-group

The DOH are careful to class the UK variant transmission in Bontoc as "local", rather than use the more stronger term "community". Whereas the OCTA group seem to be sure it is community spread there and are saying that the latest rises in Cebu could also be due to the presence of the UK variant. Genomic testing is slow here.

Some of the latest DOH charts (ignore the trend lines in all charts as they do not account for the significant data reporting delays)"

The national chart:




NCR....a slight rise.


Calabarzon..slight rise..mostly due to Cavite.


Davao del Sur..its rapid rise moderated a little lately.

Notable that the situation in Davao City and its province is not getting the attention of Cebu. While new cases have dropped recently whereas Cebu's have kept on rising through January, positivity there is greater at 10% to Cebu's 6%. The media seem reluctant to say much about covid in a region controlled by those close to the President.

Gazza-d

Just a note about the UK variant and pcr testing. Purely by luck, not design, the UK pcr test detects and distinguishes between the old variant and the UK variant. I know the US pcr test doesn't so do we assume the Philippines pcr test doesn't also.

Raffin

I think we do.
Dr John recently went through some very good data from the ONS which was about comparing symptoms for UK variant with those of the standard one. Basically many symptoms were stronger, eg cough, some were the same and it was only loss of smell/taste which was a lot less with the variant. So while not definitive more severe symptoms can be added to its more rapid spread to add to suspicion of the presence of UK variant when genomic tests are not available or slow to process.

Gazza-d

I don't think that will work as judging symptoms is subjective and even with the old variant the strength of symptoms varies from mild to full blown

Raffin

Doctors are generally good at judging symptoms and with some like fever there is a measurement that can be made. Where they can't they can ask the patient eg rate your pain..1 to 10. Or just ask can you taste you food? I would have thought that responses there are almost 100% reliable. Both the old virus and the new UK variant have the full range of symptoms, but the ONS researchers have found statistically significant differences between the two:





As can be seen cough, sore throat, fatigue, muscle ache. loss of smell, taste are significantly different between the two eg cough and loss of smell/taste showing the greatest differences. But also fatigue and muscle ache with significant differences.
Also: with the UK variant more symptoms were reported ie there were statistically less asymptomatic cases.
So there is a distinct difference between the two types of virus in terms of symptoms.

In a situation where genome testing is slow and/or expensive and some idea is needed on whether a new variant has been established in a region then a survey can be done. At the very least hospital docs can be telephoned and emailed or a proper survey can be easily worked up. .Maybe those hospitals collect symptom data anyway?. For a place like Cebu City where cases are rising quickly a week's cases are at least 1,000, a decent sample size. Then compare with the existing DOH symptom data or other countries for the old virus. Also with the UK new virus symptom data or data from the other European countries affected. The UK had a large amount of data for the recent survey with about 50% for each virus type. With a much smaller potential outbreak here eg Cebu, the sample size will be much lower and that would be taken into account statistically as to whether large scale genomic testing is justified.

At present fear from seeing the effect of the UK variant in the UK and some European countries without much evidence of the UK variant being established here is haunting government leaders and is already affecting their decisions..

Bealinehx

I saw the same presentation and the effects of the “new virus “ are similar to my experience last August/September so perhaps the latest and more contagious virus has been around and undetected for some time

Gazza-d

Looking at those charts the only symptom showing a significant difference is the cough, all the others are to close to call, the limits shown by the black bars

Raffin

Statisticians at the ONS reported by Dr John say that four other symptom areas are "more likely". That isn't "too close to call" as you put it. It's just not as strong as statistically significant, at the usual 95% level of confidence. They are ruling out about the same or less. The large sample sizes of both virus types in the research allows them to say that. Their research is read and used by medical professionals and academics...they're not going to say something is morel likely when it isn't.

Raffin

On Jan 29 another 1,849 cases. Eight labs closed. With over 200 now no idea if that is significant. Over 400 cases were from a backlog. Positives from 23k tests and positivity slightly higher than of late at 6.2%. Tests coming along at a much higher 36.7k.
The DOH are discontinuing the "top 5" locations, saying it confuses the public. They say they can look at the DOH covid tracker site. But it is updated later on the day and is not user friendly. I think the top 5 regions would be better anyway.

Deaths 48 with 2 RDs.
Critical 1,016 and Severe 771...down 20 and up 2 respectively.

More detail on Jan 28 cases:


Other Mindanao 53







NCR 24.6%, Region 4A 13.3%. The two together 37.9%., much higher than the previous day.
NCR had 9 cities in the top 20.
A nearly 7% increase in Active cases on the day.

The ridiculous travel ban on arrivals from over 30 countries "will not be extended after Jan 31"!!

The President has set the Quarantine levels starting Feb 1.

https://news.abs-cbn.com/news/01/29/...ovid-19-update

CAR goes from MGCQ to GCQ:

CAR..incl Baguio City..steep rise

NCR stays in GCQ...again. You can see the NCR chart on yesterday's post, showing a slight rise.

Batangas stays in GCQ:


Yes...its case numbers rising steeply..

It's difficult to see how Cebu stayed in MGCQ


Cebu City

Although only 2 of its hospitals are at even moderate levels of occupancy

Keeping the major economic area in GCQ when cases are only rising gradually following the holidays is justified by the President's spokesman when he asserts that "almost 75% of the economy is open in GCQ areas". Maybe..but business people will remain nervous of a future move back to ECQ. The President has the UK variant in mind, people know that and that he is capable of a panic reaction if it is ever just detected a few times in the NCR.

Last, Davao City stayed in GCQ, despite this:

https://www.msn.com/en-ph/news/natio...ce/ar-BB1dar6T

It didn't get a stricter quarantine. I wonder why?

I'm sure some of these decisions are not following evidence based expert recommendations,

Raffin

Yesterday 2,109 cases announced with 6 labs not reporting. Tested were 27k and of those positives 1,357, so a positivity of 5%. A backlog of results of 750 or so added. Tests in process at 32k.
No locational detail available until the DOH give data later today.
I am interested to see what the TV news does each evening with this lack of information. I don't think they are going to talk about the locations of yesterday's cases each evening.
You do wonder if the government is getting sensitive about the increased regional spread of the virus.

Deaths 71 with 5RDs. At last the number of RDs are going down.
Case fatality rate 2.04%..the same again as Sweden's.
Allowing for both deaths and recoveries the number of active cases rose by 5%, on the day before but Active Cases will fall tomorrow when weekly mass recoveries are announced.
Critical cases down 55 at 961, severe cases up 5 at 776.
Critical cases have fallen significantly lately from the levels of late last year....maybe better treatment, increased deaths plus a lagged effect from lower admissions late last year all factors. Needs investigating, but complicated by the delays in reporting deaths.

Case locations for Jan 29:


Plus Bicol 27







NCR 19.4%, Region 4A 12.1%...total of main regional epicenter 31.5%.
NCR with 8 cities in the top 20.

Cebu top province and second urban area.
Davao still showing high daily numbers but recent data indicates its cases falling from their recent peak:


Davao City

Passi City is a 4th class conurbation in IloIlo, pop about 80k.

https://news.abs-cbn.com/news/01/30/...vid-19-variant

Forty eight genome tests for variants have drawn a blank and they are short of the reagents

Raffin

Last day of January and a total over 2k, the second day in a row. And a higher 10 labs did not report. Over 400 backlog of results, which were at a higher positivity, 6.1%, than for the day before. Tests coming along 32.3k.
Location information again not given.....we must wait a day.
Deaths high again at 80, bringing the case fatality rate up again to 2.04%.

Mass recoveries added to the recovery of the Active total. They were up 4k on last Sunday at 11.7k. So the Active total is now at 27,318, over 400 less than the number announced last Sunday.
Severe condition patients now 765, down 11...critical at 902, down 59.

Detail on Jan 30 cases:


Plus Bicol 36.


Plus Las Pinas 19, Muntinlupa 18.






NCR 23.4%, 4A 10.3%...total 33.7%..10 NCR cities in the top 20...so a third of cases from the former main epicenters
Notable that QC had 27% of the NCR cases.

But provincially Davao, Cebu and IloIlo again with large numbers.


IloIlo province chart shows a big recent spike:

But the chart for the city shows much smaller recent increases:



For the final week of January average daily cases were down by 8.4% on the previous week at 1,692. But average daily deaths went up from 44 to 69.
However larger case numbers for the last two days indicate that the Xmas holiday effect is now being shown. A week or two later than many predicted. Perhaps the holiday period for many this year has been extended due to lower economic activity levels and there are more difficulties facing people wanting to be tested.

Testing stays in the 20 t0 30k range each day and that needs to be increased somewhat to pick up the increased regional spread of the virus. National positivity never went much below the WHO control standard of 5% in January and is now rising. At present the large regional numbers are coming from the capital cities but the recent figures from IloIlo and the showing of numbers from smaller towns in other provinces over recent days show the virus may be generally rising in smaller provincial conurbations.

Not a good picture when vaccines are coming late to the country and the vaccination programme will be more difficult and slower to implement with regional spread now firmly established.


A recent Dr John update with some interesting information on Wuhan and vaccine politics.

Can't report tomorrow but hope to catch up on Wednesday.

Gazza-d

The BBC are reporting that scientists are concerned that the UK variant has acquired a mutation similar to the South African and Brazilian variants. Not good news but shows viruses are constantly changing.

Philosophical 11

This is different to what I have read. It is called the UK variant because it was discovered in the UK because of our advanced testing methods but originally came from S. Africa. Yes, viruses are constantly changing which is one reason why we have not eliminated the common cold or influenza to name just but two.

spouse of scouse

Yes, I was reading that earlier. It's a very opportunistic virus as the acquisition of this mutation shows
https://www.newscientist.com/article...riant-spreads/

Gazza-d

It's now looking like two new mutations.