Two days ago, main COVID testing laboratory Research Institute for Tropical Medicine did not submit a report. Photo from Wikimedia Commons
Culture Spotlight

We have a lot more COVID testing laboratories now—but are they sending reports?

For example, around 11 did not submit reports two days ago, including major testing laboratory the Research Institute for Tropical Medicine. This does not augur well for our country’s bravado in testing capacity, says our resident expert. BY BENJAMIN CO MD
ANCX | Jun 28 2020

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. 

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Data as of June 28, 2020, 8 P.M.

At the 4 o’clock habit of the health agency, there are 653 new confirmed cases: 485 fresh and 168 late (75:25 ratio).

National Capital Region (NCR) continues to haul in the highest number with 356 new confirmed cases, accounting for more than 54 percent. In second are the “others” with 137, Region VII is third with 131, and repatriates is fourth with 29. 

Of the eight reported deaths, 5 of them died in June. The death rate continues its downward trend at 3.5 percent while the recovery rate is at 27.3 percent (a very, very slow recovery rate considering that most of our cases are mild and asymptomatic, and the rest of the world averages more than 50 percent recovery rate).

According to data from the Department of Health (DoH), of the remaining 24,137 active cases, 99.4 percent of them are mild (23,090 or 95.7 percent) or asymptomatic (898 or 3.7 percent). There are two added severe cases today from 123 yesterday to 125 today while the critically ill remain at 24.

The graph on deaths by date of death had some data with proxy. Proxy in data analytics and machine learning may pose discrimination and bias in the outcome of the data. Choosing proxy variables is subjective. While the Health Agency does not explain what proxy variables it chose to arrive at this extrapolation, hopefully, they are weak variables.

 

The day before

Let’s dissect yesterday’s 730 cases and the bothersome 234 “others,” which accounted for 32 percent of the total cases yesterday. 

When broken down per region, there were 54 cases “for validation.” One death fell under this category. 

NCR continued to dominate the haul with 336 new confirmed cases and 10 deaths. Region VII followed with 207 cases and one death. 

The “others” who reported double digits were Region IVA (+40), Region VIII (+26), Region III (+22), and 10 each for Region XI and the repatriates. Only two regions did not report any cases: Region II and BARMM.

It was the same story again with NCR, where many (if not most) of the cases are “for validation” or “unknown.”

Of the 336 cases from NCR, 156 or 46 percent were under the category “unknown.” That’s worse than yesterday’s 42 percent. And of the 10 deaths in NCR, four of them fell under the category “unknown/for validation.” As to how these are later reconciled is a mystery altogether, because we don’t see the Health Agency altering or even correcting the data of the various LGUs, particularly in NCR. After all, this is a gargantuan task to undertake. Just this week alone, they will need to reconcile 1,113 cases under this category. 

The cities that took the haul? Quezon City had 40 cases, followed by Manila with 29, Caloocan with 16, Taguig with 15, Parañaque with 12, and Makati with 11 cases. 

The rest of the cities reported single digit numbers and Pateros was the only city that had no case yesterday. 

Ten deaths were reported in NCR. Of the 10, four had no location. The remaining 6 all came from one city – Malabon.

Region VII reported 207 cases with one death yesterday. It is rare that you will see a large number of “unknown” locations anywhere outside of NCR. Yesterday, the report from Region VII had 70 cases under this category. That’s 34 percent of the cases reported yesterday that had no tagged location. And that’s a first for reporting from Region VII.

Among those with tagged locations, Cebu City had 73, Cebu Province had 31 with one death, Mandaue with 19, Lapu-Lapu with nine, Bohol with four, and Negros Oriental with one.

Region IVA had the third highest number of cases with a total of 40. Cavite led the haul with 15 cases, followed by Rizal with 12, Laguna with seven, one apiece for Batangas, Lucena, and Quezon, and three under “unknown.”

Region VIII is back, as it reported 26 cases overnight. Ten of these cases were from Southern Leyte, nine from Leyte, five from Samar, one from Ormoc, and one “unknown.”

Region III had 22 cases. There were eight cases each from Bataan and Bulacan, four from Nueva Ecija, one from Pampanga, and one “unknown.”

The last region to contribute double digits was Region XI with 10 cases: six from Davao City, three from Compostela Valley, and one case from Davao Oriental. 

These regions? They were simply part of the “others” in yesterday’s report.

In terms of testing, we are now over 675,000 tests with lesser tests done overnight. Only a little less than 13,000 tests were performed in 12,279 individuals. As you can see, out of 63 testing labs only 52 submitted their reports on June 26. This includes the major testing laboratory, the Research Institute for Tropical Medicine that had no report on this day. 

The positivity rate for June 26, 2020 is higher at 7.8 percent compared to the previous day low of 7.53 percent. The cumulative average is now up at seven percent from a previous 6.9 percent. 

As of today, there are 50 licensed RT-PCR laboratories and 19 licensed Gene-Expert Labs accredited to do confirmatory testing in the Philippines, bringing the total of testing laboratories to 69. And while the government can boast of more laboratories being accredited, there are also more laboratories that are not testing or testing less or not submitting any data on time. This does not augur well for the bravado in the testing capacity.

The results vary according to the facility and below is the list of the facilities with > 10 percent positivity rate. Those highlighted in yellow show the highest cumulative positive rates. Of the 63 accredited testing centers in the country, only 52 submitted data last June 26. That’s 11 laboratories out of the 63 that have data submitted. This is observed in the summary of the testing facilities that have >10 percent positivity rates. Notice that on June 26, 2020, there are now three facilities that did not submit any test results, for whatever reason. 

The following testing facilities had a >10 percent cumulative average positivity rate. Those highlighted are the ones with increase positive rates overnight. However, one is cautioned in the interpretation of cumulative averages. It simply means these are the total positives since the start of operation of the facility and not the daily positive rate for the facility.

All data are cumulative average of positive tests.

Using the same list above on facilities with >10 percent cumulative positive rates, highlighted in red are those with increased daily positive rates compared to their cumulative average. Most of them are from Metro Manila. And the spike in daily positive rates are worrisome.

CA – cumulative average; DA – daily average

 

The week in review

The graphs below summarize our whole journey for the past three months. Somewhere along the way, while we did well, we faltered as well. On the one hand, we’re faring better than other countries. But that is no reason to let our guard down because this pandemic does more harm to a developing nation like ours than it does to more industrialized nations. 

This week alone, the Philippines had 5,417 total new confirmed cases (average of 773 case/day), with most of them fluctuating either in the NCR or Region VII. The number of cases in Region VII had gone down toward the end of the week, but it is not because of the sudden lockdown being imposed there. There are facilities that have run out of kits. If you look at other facilities that are still testing, the daily positive rate has increased exponentially, and is overwhelming the testing centers in the region.

Over the whole week, the Philippine reported a total of 86 deaths (average of 12 to 13 deaths/day) with most of them having died in June.

While the case fatality rate is at its lowest of 3.5 percent, the number of cases will continue to rise with increased testing. Unfortunately, while we announce that we now have 69 accredited testing facilities, of the 63 that submit reports (and are operational already), the number of facilities reporting are largely declining as well. On June 26, only 52 of these 63 facilities submitted. Even the reference laboratory the Research Institute of Tropical Medicine had no reports to submit. 

Then there’s the problem of data management. This week alone, 790 of the cases were “for validation,” which means that there had no tagged location or some important data was missing. That’s 14 percent of the total cases for the week alone. And when you dig deep into the individual regions, NCR leads with more than 40-60 percent being reported that are “unknown/for validation” or have no tagged residences—including patients that have died. 

Demographic data for the week shows that based on 34,074 data points, 7.5 percent of the cases are in the pediatric age group (<19 years old) while the senior citizen age bracket account for 16 percent of the other end of the spectrum. The majority of patients >75 percent belong to the 20-59 years old age group. 

In terms of fatality rates, those younger than 19 years old have a 2.6 percent death rate while senior citizens have a 54 percent fatality rate. Fatality rate is lowest in the 20-29 and 30-39 years old age groups and increase exponentially for every decade of life. 

The second quarter comes to a close in two days. And if we are to extrapolate the data and trend in data during the second quarter of the year—both locally and globally—the outlook for the third quarter doesn’t look optimistic. 

With the clinical trials on both treatment and vaccine in full swing, let’s hope that one of these bear fruit. Sooner than later.

[Disclaimer: All data are verified based on the Data Drop of the Department of Health. All information used in the analysis are from the Health Agency’s data drop site.]

 

The world

It’s official. June 28, 2020 marks the day when the world crossed the 10 million mark for positive cases of coronavirus and 500,000 deaths. The global case fatality rate stands at roughly 5 percent (4.97 percent) with a recovery rate of 54.12 percent.

Almost six million are closed cases with 92 percent recoveries and eight percent deaths. While the fatality may seem low, this is a staggering number because they are deaths due to one virus and half of the year isn’t even over yet.

The world takes a one day respite with a little more than 150,000 cases reported yesterday and a little more than 4,000 deaths. This is enough to push the world beyond the critical 10 million cases and half a million deaths.

The United States surged with the highest number of cases in the world overnight (+43,581) bringing their total count to almost 2.6 million. At the rate it is reporting confirmed cases, the US is set to breach a record high of three million cases in one week.

The top three states that contributed to the cases overnight were Florida (+9,585), Texas (+6,709) and California (+4,226). The death rate in the US stands at 4.93 percent, a little lower than the average global fatality rate.

Top 10 countries with most cases yesterday were: USA (+43,581), Brazil (+35,887), India (+20,131), South Africa (+7,200), Russia (+6,852), Mexico (+208,392), Chile (+4,406), Colombia (+4,149), Saudi Arabia (+3,927), and Peru (+3,625).

Over the past two weeks, the Americas alone have contributed to more than 50 percent the global cases of coronavirus.

North America leads with more than three million cases, mainly driven by the USA with almost 2.6 million cases, with Mexico a distant second with 212,802 cases and Canada in third with over 100,000 cases. The case fatality rate of these countries are: 4.93 percent for the US, 12.5 percent for Mexico, and 8.3 percent for Canada. The average case fatality rate for North America is 5.48 percent.

South America on the other hand has over 2.1 million cases as of yesterday. Brazil has over 1.3 million cases followed in second by Peru with 275,989 cases and Chile with 267,766 cases. The case fatality rate of these countries are: 4.3 percent for Brazil, 3.3 percent for Peru, and two percent for Chile. The average case fatality rate for South America is 3.86 percent.

Europe is seeing a considerable decline in its daily new confirmed cases. Only Russia is reporting more than 5,000 cases a day. The rest of the Europe including hard hit Italy, Spain, Belgium, the Netherlands and even the UK are reporting less cases than the Philippines. The average case fatality rate for Europe stands highest at 7.93 percent based on continent. 

There are fewer deaths and the death rate is much lower in South America than North America. The death rates and the number of cases are not correlated in terms of outcome. 

The top 10 countries in the world contribute to two-thirds with close to 6.7M reported cases.

Based on infection density (infection based on the population of the country), Qatar remains to have the highest infection density with 33,072 cases per million population.

With more cases reported in other parts of the world overnight than the Philippines, the Philippines stays in 109th position with 321 cases/million. 

For every death, there are approximately 11 recoveries.