Infectious diseases and clinical pharmacology expert Dr. Benjamin Co has been thankfully breaking down coronavirus numbers in his personal blog since the outbreak started. The perspective he provides is informative, and comforting in those who are craving for a clear picture of how we are faring against the virus. Dr. Co will share daily updates and analysis of the Department of Health reported numbers with ANCX.
[Disclaimer: Whatever is written here is based on information released by the Department of Health (DoH) at the time of publication. Whatever changes DoH makes in their data later on…well that’s a different story in itself and as they say in their disclaimer: “the total cases reported may be subject to change as these numbers undergo constant cleaning and validation.”]
If yesterday was a shocker, it was to prepare us for worse days ahead. The Department of Health announces 4,063 confirmed cases from 81.3 percent submission reports today. This brings our total cases to 93,354.
While we remain number 26 in the world today, we are a few hundred cases away from Egypt. For yesterday’s cases, we were in the top 10 (no pride there) among countries contributing to the pool of COVID-19 cases.
Today, National Capital Region (NCR) contributed to 55.8 percent of the total number of cases with 2,267 cases. The other provinces that were among the top five included Cebu (654), Laguna (200), Rizal (123), and Cavite (117). These provinces/region alone accounted for 82.7 percent (3,361) of the total cases today.
The number of active cases is now up at 26,153 from a previous of around 22,000 because of only 165 recoveries (from the overly dramatic 38,000 recoveries yesterday). This brings the touted 73 percent recovery rate crashing to 69.8 percent.
There were 40 reported deaths, bringing the fatality rate to 2.17 percent.
Of the 40 deaths today, 13 were from NCR, 12 from Region VII, 7 from Region III, two each from Regions VI, XI and IV-A, and one apiece from Zamboanga Peninsula and Mimaropa.
Of these 40 deaths, 27 occurred in July, 2 in June, two in May, seven last April, and two last March.
Eighty-three cases were removed from the total case count.
Data for July 30, 2020 (reported on July 31) show there are 95 accredited testing sites (72 RT-PCR and 23 GeneXpert laboratories) in the country. How many are functional is a totally different question altogether as the number of testing facilities submitting reports on time is a work in progress.
The Philippines has tested close to approximately 1.26 percent of the total population as it registers 1,379,866 individual tests done. (How many are repeat tests from previous positive patients or new confirmed cases is not indicated.)
We will break down the more than 4,0000 cases tomorrow, and it will be interesting to see what the Data Drop will reveal. With this number of new confirmed cases, those unknowns will remain the bothersome bunch.
The data yesterday
Let’s start off dissecting the surprising news yesterday by looking at the data for samples tested.
On July 29, 2020, close to 30,000 samples were tested, with 28,437 individuals tested, yielding 3,743 positives for a 13.2 percent daily positivity rate and a cumulative positivity rate up now at 9.3 percent.
With more testing being done yet yielding higher daily positivity rate only means that there are more patients out there that are likely positive and we have not yet captured. Remember, the more positives you get with more testing means only one thing—this pandemic is not under control. You can tell that situation on the ground is improving only when with more testing, more negative patients are reported and the daily and cumulative positivity rate drop to five percent or less for two consecutive weeks. Please, don’t play with the numbers. We’re not there yet.
NCR is the most dense among all regions in the country with close to 15 million people living in less than 700 square kilometers of land area. It is home also to 17 cities that serve as the driver of the economy in a country with 7,641 islands. The table below shows how the three major epicenters contributed to the total cases on July 29. NCR, Region VII, and Region IVA alone brought in over 90 percent of the total cases.
Note that the data may not be complete because some of the testing facilities are not yet uploaded on the DoH Covid Tracker site.
So we had the most number of cases reported in a single day yesterday, 3,954. Of these, 479 (12.11 percent) had no known region. The story of the data of the Health Agency.
The top five regions in terms of total number of cases are NCR (48,389), Central Visayas (14,773), Calabarzon (8,113), Central Luzon (2,132), and Western Visayas (1,222).
The top five regions in terms of cases reported yesterday were NCR (1,703), Central Visayas (997), Calabarzon (428), Central Luzon (69), and Zamboanga Peninsula (52).
There were 32 cases from repatriates reported and all regions had at least one case.
Of the 873 cases (22 percent) classified as unknown (no tagged location or unidentified), 479 had no known region, 42 had no known province from Region IV-A while the remaining 352 had no identified municipality/city but had tagged provinces. NCR had the most number of unknowns—no surprise there.
Of the identified cases in NCR, the following cities saw triple digits in cases Quezon City (256), Manila (167), Navotas (121), Makati (115), and Taguig (114).
Cities with double digits but more than 50 were: Pasay (88), Caloocan (85), Parañaque (80), and Muntinlupa (67).
Other cities with double digit cases but less than 50 were Malabon (49), Marikina (48), Mandaluyong (42), Valenzuela (42), Pasig (37), Las Piñas (32), and San Juan (16).
Pateros reported only one case.
More than 20 percent (343) of the reported cases in NCR yesterday had no tagged locations.
Among the other top regions outside of NCR, the following provinces in those regions had the highest cases: Cebu with 958 in Region VII, Laguna with 177 in Region IV-A, Bulacan with 37 in Regional’s III, and Zamboanga del Sur with 51 in Region IX.
Of the 997 cases from Central Visayas, 406 were from Cebu City. Two other cities reported triple digits—Mandaue (157) and Lapu-Lapu (116).
Those with double digits included Talisay (50), Consolacion and Minglanilla (35 each), Liloan (28), Compostela (16), Cordova (14), Danao (13), San Fernando (12), and Argao, Naga and Toledo with 10 each.
There were 39 municipalities/cities that reported single digit cases.
Calabarzon had a total of 428 cases in 51 cities/municipalities in the region. Biñan leads with 45 cases. The other cities/municipalities in the region with double digits were Santa Rosa (43), Antipolo (39), San Pedro (29), Calamba (22), Bacoor (20), Cabuyao (19), Cainta (15), Dasmariñas (13), General Trias (11), and Imus (10).
The rest of the cities/municipalities had single digit cases.
There were 48 unidentified cases (no tagged location).
Region III came in fourth with 69 cases in 32 cities/municipalities. San Fernando, Pampanga led with 12 cases.
Rounding up the top five is Region IX, which saw 48 cases in Zamboanga alone.
As of yesterday, the seven-day average for cases and deaths in the Philippines is at 1,890 new cases/day and 16 deaths/day, respectively.
I’ve been harping at how slow the recoveries actually were. In general, for asymptomatic to mild infections, the recovery should be anywhere from 10 to 14 days from the onset of illness. The US Center for Disease Control, for example, uses the 10-days period as barometer for recovery. While we play a more conservative approach, this is fine because there’s really no definite duration when absolute recovery occurs.
Scientific evidence strongly supports what is called a time-based discharge. Singapore for example uses 21 days as their barometer while others refer to the consensus that based on clinical data, transmitting COVID-19 is unlikely after the 14th day of onset of illness. PCR may still pick up fragments of SARS-CoV-2 material on repeat swab after day 14 of illness, but these fragments are no longer transmissible and infective to others and that the virus is not a viable. Hence, after this period, patients are no longer infectious.
As of yesterday, this is what the Philippines data looked like. Clearly from the graph, one will see that as of July 15, 2020 (or 15 days before the declaration of more than 38,000 recoveries), the Philippines had 58,850 total cases and 1,614 total deaths. As of yesterday, we had 89,374 total cases and 1,983 deaths. This is an additional of 30,524 cases and 369 deaths in the last 15 days of July alone.
Assuming that all the cases had recovered from July 15 back, it would imply that only 30,155 cases are active (30,525 minus 369 deaths). Yet we have fewer active cases—22,327—as of yesterday using the time-based criteria in suddenly sweeping the recovery backlog. The difference of 8,000 cases using this methodology should be clarified.
What is equally troublesome are the patients who turn up positive but have no tagged location from a regional to a city/municipality level. There are even deaths reported that have unknown locations. Why do I bring this up and why have I always been critical of the “unknowns?” Because it’s not only the contact tracing, tracking and isolation of the positive cases; it includes being classified as eventual recoveries (or sadly, deaths). If we do not know where they are from the get go, how do we even know where to look for them to find out if they have recovered or died? Who follows up these patients? And that’s the problem using time-based dynamics when data is incomplete. There are too many assumptions made. The Health Agency assumes that if they have not gotten back to us, they have recovered. They forget that on the flip side, it is also possible that the patient may have died.
If the government plans to use the time-based recovery criteria, it should only be for patients that are identified or have tagged location details. As I have mentioned in the past, it is futile to do swabbing if you won’t be able to follow-up or locate these patients later on. Worse is that there is no more effort to locate these unidentified individuals on a later date. As the data shows, they just pile up under one classification: the unknown.
Pooled Testing, the pros and cons
There is talk of the Philippines studying the group testing method in order to minimize cost at the same time achieve efficiency.
What exactly is pooled testing?
The US Center for Disease Control issued an Interim Guidance for Use of Pooling Procedures in SARS-CoV-2. The link to the guidance for those interested in knowing more about this is provided here:
Sometimes referred to as pool testing, pooled testing, batch testing — means combining respiratory samples from several people and conducting one lab test on the combined pool of samples to detect SARS-CoV-2.
Why is pooling used?
It allows laboratories to test more samples with fewer testing materials and can be useful in scenarios like returning groups of workers to aa workplace.
The basic idea here is that we can test more people faster using fewer tests at lower cost. Instead of testing one person at a time, samples from several individuals are mixed together and tested by batches. If the batch returns negative then everyone in the “pool” is clear. If the batch returns positive or indeterminate, then everyone in the “pool” undergoes individual testing.
For example, for a batch of 25 people, we can divided them into five groups of five. Samples are taken from everyone but mixed with samples from people in the group they belong to. Each grouped sample is tested, meaning instead of testing for 25, we only do 5 tests. If one test will cost, say PHP 5,000, doing 25 individual tests will cost PHP 125,000 while doing five group tests will cost only 25,000p.
Let’s say that of the 25 people, one person truly has the virus, then only one group will likely test positive. That group will need to go through individual testing to identify who among them was the cause for the grouped sample turning up positive. It would still be cost efficient considering that you’d spend PHP 25,000 for the group tests, and then an additional PHP 25,000 for individual tests or a total of PHP 50,000 over having all 25 individuals tested independently.
But here’s where it gets tricky. This method is useful if the infection rate in the community or setting is low. But if the infection rate in the community is high, pooled testing should not be used because it becomes more costly in the end. Knowing the prevalence of the disease in the community should be a prime indicator on whether pooled sampling should and can be used there.
Of course this will depend also on how laboratories charge for group sampling and whether dilution of samples from pooling can reduce the accuracy of PCR that look for viral RNA in samples. Too large pools result in inaccurate results.
With more than 280,000 cases sustained overnight, the seven-day average is now at 256,265 cases/day. Total deaths are up at 6,340 today with a seven-day average of 5,752 deaths/day.
The global case fatality rate is lower at 3.87 percent and recoveries remain at 62.6 percent. [Recovery rates are not very reliable indicators because they are subjective based on the country’s definition of how and when they consider patients “recovered.” Case in point is the Philippines with the sudden time-based endpoint change. Death rates on the other hand, while more definitive of outcomes take a longer time to report and validate.]
Data from WorldOMeters.info.
The United States has more than 4.6 million total cases with 68,569 new cases reported yesterday. They also reported the most deaths in the world with 1,465 dying due to COVID-19.
The top three states with new cases yesterday were Florida (+9,956), Texas (+8,843), and California (+8,174).
Brazil is in second with 2,613,789 total cases. The country reported 1,189 deaths yesterday.
India had 54,966 cases overnight to bring their total to 1,639,350.
Top 10 countries that had the highest new cases overnight were:
- USA – 69,569
- Brazil – 58,271
- India – 54,966
- South Africa – 11,046
- Colombia – 9,965
- Peru – 6,809
- Argentina – 6,377
- Mexico – 5,752
- Russia – 5,509
- Philippines – 3,871
With the 4,063 cases today, the Philippines plays catch-up now to Egypt which is just 400 cases ahead of ours.
We are at the precipice of seeing casualties in the next four to eight weeks. Someone or some people should be made accountable for how this pandemic is being handled. At the end of the day, all lives matter.