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.
Refer to the link DOH.gov.ph or up-to-date data or to COVID19.gov.ph. (The latter is not a secure site.) The new site for the Department of Health is user friendly, provides more information where a COVID19 tracker is seen. Readers can check their official site where Data Drop for raw data can be found.
One useful site is COVID19stats, where one can see most of the DoH data in graph format.
It’s the backlog
We have had more cases the past three days compared to the declining trend last week. The DoH reported overnight 539 new confirmed cases, 92 new recoveries, and 17 new deaths. We were forewarned yesterday by the spokesperson of the agency to “expect an increase in numbers in the coming days”—and increase it did!
We recorded our highest numbers at 538 last March 31, 2020. Today, we set a new record to beat!
The question that begs an answer—is this due to backlogs alone or a combination of all possible events (i.e., increased/expanded testing, and more cases due to repatriates) that caused the large number of cases? Based on the numbers announced today by the Department of Health, there should be an answer to this new phenomenon.
In the past week, NCR was hovering between 120-170 cases a day. It is now up at 330 cases today.
For the 380 reported cases last night, 282 (74 percent) were from Luzon (NCR alone made up 254 of the Luzon cases), 0 in Visayas (which is highly unusual because they came from 70 cases last May 25), and 10 in Mindanao (with 6 coming from the Davao Region). In short, the fluctuations of cases is a national problem as it is seen in the reports down to the local governments.
Based on the timeline of the modified GCQ (which is barely 14 days), the slight laxity in the lockdown cannot be responsible for the significant rise in numbers the past three days. Considering the incubation period and duration of illness of SARS-CoV-2, it will take approximately two weeks before you will see if relaxing the tight quarantine controls is responsible for the sudden uptrend in cases the past three days.
The figure above shows that the highest number of cases was seen 15 days after the ECQ was put into effect (March 31, 2020). The rolling seven-day average after that date was 225 cases/day. As pointed out in my previous blog posts, the number of cases and the positive results from the agency have no significant correlation at all because the data is all over the place.
The figure below shows a summary of the testing capacity (number conducted, tested individuals, positive, and negative results) from May 20 to 26, 2020. Ironically, even with the daily tests being conducted, we’re swinging like a pendulum not in sync. There are days when more testing is reported, and there are days when it’s not even within the touted targeted number of the government. [Note: the data provided below is a cumulative summary. The ones in parenthesis indicate the increase in number of tests conducted, tested individuals, and those who tested positive or negative for the day.]
Test results are released anywhere from 12 hours (most of the private hospitals) to as long as 10 days (for government facilities). Even if we centered only at all the positive individuals for the whole week, none of the dates would come close to the 539 “new confirmed cases” reported by the health agency today. The closest is the 525 positive cases reported May 22, almost seven days ago.
Then there are the repatriates added to the daily statistics. Unless the number of repatriates who tested positive would exceed 300, then there is no way that the rise in numbers can be attributable to them alone.
Which clearly points to only one fact—the mixing of old and new data. Patients as far back as April 2020 are recently being included. Initially they came in aliquots. But as the pandemic dragged on and more cases were reported, the deluge in lumping them to “catch up” with recent data shows how bad data analytics is being handled by the agency.
They should be made to explain with clarity the discrepancies in the daily data reports and inconsistencies that is obvious. Data integrity is important in epidemiology.
Let’s ask the relevant questions:
- What is the reason for the more than two-fold rise today based on a rolling seven-day average of confirmed cases in the country?
- If there is (and I am sure there is) a backlog, how far back and how much is the backlog of data that needs to be validated and encoded?
- Why is the turnaround time for RT-PCR testing faster in private hospitals versus government facilities? And what is the degree of quality assurance in the results for RT-PCR so that we minimize getting false-positive results?
- If patients undergo retesting, and still test positive, how is that recorded by the government agency in the total positive cases reported for the day? Is it a new case (it should not be)? If it is not considered a new case, how many of the patients retested retested positive? Up to how many positive tests did patients have to undergo before the agency finally deemed that the patient had recovered, and that there was no more need to repeat the test (because it had been done 5x and has been over 45 days already and the patient has been well since day 14) and declare it as a genetic remnant of the virus?
- If patients get tested in one facility today and then retested 72 hours later in another facility, how is that kind of data treated? For example, there are patients who may be asymptomatic or have mild flu-like symptoms, get tested in a government facility, test positive, then decide to get retested in a different hospital—but test negative, twice! How is this kind of information handled and encoded by the health agency?
- Why is the reporting of recoveries and deaths so late? When I began tracking the local data several months ago, the latency of recoveries and deaths (before a public announcement is made) averaged five days. Now it averages 10 days (and even more, particularly for deaths). More than half are reported after 8 days or more.
The figure above shows the latency of report for recoveries and deaths. Only the data points with published actual dates of death or recovery were included. Of the 904 deaths (as of yesterday), 724 had actual dates of death recorded. Of the 724, 485 died before they were announced to have positive RT-PCR results. Because of this time frame, the latency in death reporting was based on the remaining 239 cases. On the average, it takes almost 12 days before a death from COVID-19 is publicly announced.
How we are doing compared to the rest of the world
Trajectory of several countries in days since the confirmed cases first reached 30 per day. (The Philippines is in pink.)
Daily new confirmed COVID-19 deaths. (The Philippines is in pink.)
Daily new confirmed COVID-19 tests. (The Philippines is in pink.)
The figures above show the rolling seven-day average for confirmed cases, deaths, and testing done in various countries. (The Philippines is in pink). The shift in decline of tests done over the past days compared to the past weeks is clearly visible and is unable to explain the rise in cases in the past three days. As we now approach the middle of the week, we have begun to bend the curve—upward!
And we keep going back to the culprit—the backlog.
What does the backlog tell us? That all previously publicly announced data were underreported. Were policy decisions being made based on what was evidently underreported data?
In spite of the varied daily reports that show an increase in the number of cases, the doubling time for cases and deaths remain long in the Philippines. Based on the figures below, our doubling time approximates every 10 days for cases and deaths, respectively (in spite the sudden upsurge in cases).
How rapidly are the cases increasing in the Philippines?
How rapidly are the deaths increasing in the Philippines?
With the increase in cases, the Philippines now contributes to 0.27 percent (from 0.25 percent) of the total confirmed cases in the world and 0.26 percent (from 0.25 percent) of the total deaths attributable to COVID-19.
Are we bending the curve?
Seven-day rolling average of confirmed cases (Philippines)
Seven-day rolling average of deaths (Philippines)
The figures above show that while we began a downward trajectory at the end of the last week, the first three days of the week had reversed our trend and bent the curve upward. According to the Department of Health press release, we expect to see more of the increase the next few days as there “are now more encoders and validations being made” in the backlog.
Good news. Bad news.
The announced new cases, recoveries and deaths are a tally of reported cases for the day.
Does the increase in new cases and deaths alarming?
In every disease, death is an unfortunate outcome. When reported and recorded accurately, they provide a true picture of the clinical course of a disease. When the cases increase but the deaths remain proportionately low, then the overall outcome is good.
Case fatality rate is lower at 5.9 percent (vs 6.16 percent global average, vs. 2.45 percent ASEAN average) and recovery rate is also lower at 23.1 percent (vs. 43.2 percent world average, vs. 48.1 percent ASEAN average) because of the increase in number of cases for the day. It is also the first time in several months that our CFR is below 6 percent.
To say that the pandemic is under control will require fulfillment of two parameters. The number of confirmed cases and the number of deaths must have the same trajectory. As long as there are active cases in the community, there will be ongoing transmission of the virus and the potential to cause disease. Hence, the need for real-time data.
What is the relevance of latent data in the continuing assessment of recommendations and policies on health and other aspects of governance? Bad data muddles decision making.
To get in touch with the Department of Health, the COVID hotline is (02)894-COVID loc 1555.
Disclaimers on the data:
(1) These three parameters (new confirmed cases, new recoveries, new deaths) are not real-time data. The data provided by the Department of Health is the date of public announcement. Even global data will vary in time of reporting, depending on the reporting capacity of that country. To date, the latency period of the Department of Health on reporting recoveries averages almost 10 days (with more than 50 percent reported after eight days and more) and deaths averaging almost 12 days (with more than 50 percent being reported after eight days or more).
(2) Depending on where testing is done, RT-PCR test results take an average of one to two days to process. Barring any delays, all tests done should ideally be released by at least 48 hours (the earlier the better). However, the test results released from government facilities range from three to 14 days, probably due to an overwhelming number of tests being conducted when compared to private hospitals where fewer number of tests are done.
TOTAL CONFIRMED CASES: 5,803,785
TOTAL DEATHS: 357,714 (case fatality rate: 6.16 percent)
TOTAL RECOVERED: 2,508,944 (case recovery rate: 43.2 percent)
Note that every reference has its own cut-off time for reporting. For the global data, WorldOMeters is used as its reference.
The total confirmed cases nears the six million mark. The average trend in the past week averages 120,000 new confirmed cases daily with more testing being done worldwide. At the current growth rate at least one million new confirmed cases are registered every eight to nine days. The six million mark is projected to be breached on or before May 30, 2020.
Daily confirmed cases since December 31, 2019. The last time we looked back at the lowest numbers was on February 24, 2020. It has been an upward trajectory since and has plateaued at >80,000 confirmed cases per day since April 5.
The United States of America continues to lead globally in the number of total confirmed cases at 1,745,803 with a case fatality rate (CFR) of 5.85 percent after surpassing the 100,000 mark with 102,107 total deaths recorded. The recovery rate for the US is up at 28.1 percent. Among the states, New York leads with 374,672 total confirmed cases and 29,553 total deaths, and remain steady with a 7.9 percent case fatality rate (CFR).
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Brazil remains on second with a CFR of 6.2 percent. Russia is in third with a CFR of 1.1 percent. India is in the 10th spot with 158,970 total confirmed cases with a lower CFR of 2.86 percent today.
As several countries ramp up testing in various degrees, more new confirmed cases are being reported. With more testing and aggressive contact tracing, we are able to identify patients who may be asymptomatic or pre-symptomatic and are potentially infective to the vulnerable population. This explains why with more testing, we see a better picture of the extent of the pandemic. With more testing, the death rates go down.
The median average of case fatality rates worldwide has further declined to 6.16 percent (from 6.18 percent yesterday). For the past two to three months, around 80 to 90 percent of patients are either asymptomatic or have mild disease and recover unremarkably.
Recoveries far outnumber the deaths with a ratio of approximately 7.01:1. (The ratio of recoveries continues to increase, and will reassuringly do so, over deaths because of increased testing and better minimum healthcare standards.)