A bulk of new COVID-19 cases continues to come from Cebu City 2
Cebu City is now fifth in the list of Philippine cities with the most number of COVID-19 cases. Photo by Reuters
Culture

A bulk of new COVID-19 cases continues to come from Cebu City

More cases come out of Central Visayas. On a more positive note, our doubling time is now almost a month. BY BENJAMIN CO MD
ANCX | Apr 25 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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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 but is still direly lacking in what the relevant information should be. I advise the readers to look through their official site. 

COVID19stats.ph is a new site which gives you a very good summary of the Philippines data. (summary of those that are unable to access this site is seen below)

A bulk of new COVID-19 cases continues to come from Cebu City 3

Overall situation. Of the total cases, 1,286 are considered resolved. There are 6,008 active cases based on the provided data.

A bulk of new COVID-19 cases continues to come from Cebu City 4

The figure below shows the daily new cases (blue), new deaths (red) and new recoveries (green) since the start of the first case reported in the country. Notice the increase in new cases after the initial Metro Manila quarantine followed a day later by the Luzon-wide ECQ (enhanced community quarantine). When mass testing had begun in some sectors, the number of new cases started to decline. The green line shows the slow and gradual increase in daily recoveries.

A bulk of new COVID-19 cases continues to come from Cebu City 5

Note that the recoveries in green have been higher than the deaths in red for the past 10 days.

A bulk of new COVID-19 cases continues to come from Cebu City 6

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Doubling time lets us know the number of days it takes for the confirmed cases (or death rates) to double and can be determined linearly or exponentially. The linear scale is used in this report which shows that the doubling time is almost a month based on the seven day average daily growth rate of 2.62 percent. (This is approximately 7.2 days on a logarithmic scale). The longer the doubling time the lower the growth rate. The lower the growth rate, the closer come to “flattening the curve.”

The Philippines has 1,286 closed cases. This means that of the 7,294 cases to date, 1286 have had outcomes—with 62 percent recoveries (792 cases) and 38 percent (494) resulting in death.

 

Are we testing enough?

The figure below shows the overall summary of SARS-CoV-2 testing in the country as of April 23, 2020. On the average, more than 86 percent of patients tested (with symptoms or asymptomatic or those who came in contact with positive patients) would test negative.

There were 211 new confirmed cases with close to 5,000 tests done in the last 24 hours.

A bulk of new COVID-19 cases continues to come from Cebu City 7

SARS-CoV-2 Testing in the Philippines

 

A bulk of new COVID-19 cases continues to come from Cebu City 8

Number of tests conducted and number of individuals tested

 

The figure above that shows the tests conducted, number of people tested. For now, at least 12 percent of patients tested turned out positive while the remaining 88 percent were negative.

Of the 4,336 tests conducted yesterday, 4,029 individuals had interpretable tests: 279 positive and 3,729 negative. This does not mean that there are 279 new confirmed cases. Patients who previously tested positive will need retesting and may remain positive in spite of being clinically better. Three hundred seven of the tests conducted most likely had non-definitive results (equivocal or invalid) and therefore are discarded.

 

Does the type of test matter?

It is important to remember that the confirmed cases depend on how much we actually test. Without testing there is no data. Without data on who is infected with the virus, there is no way of understanding the pandemic. There is also no way we can determine methodically whether various measures like the ECQ, social distancing, and other epidemiological parameters actually work in “flattening the curve.”

There are two kinds of tests for COVID-19:

  • Those that test for the presence of the virus (aimed to establish whether a person is currently infected)

  • Those that test for the presence of antibodies (aimed to establish whether a person has been infected at some point in the past)

RT-PCR (real time polymerase chain reaction) is the former test. The latter are called serological tests, basically because you will need blood samples to run these tests.

The table below summarizes the diagnostic accuracy between these two types of tests that are available. This is based on one of the earliest studies out of China from Zhao J et al. whose team looked at the diagnostic test sensitivity of various testing methods. From the onset, it is important to remember that no test is perfect. During the first week of illness (or approximately first 10 days), RT-PCR would be the ideal test as its sensitivity (ability of a test to correctly identify those with the disease [true positive rate]) is highest. Lateral flow immunoassays (for example, pregnancy kits) and ELISA (enzyme-linked immunosorbent assays) to detect antibodies elicited by the virus are available as well.

While the RT-PCR that we are currently using in the Philippines may be cumbersome and take time for results to come out, they are well correlated with the severity of the disease and viral load and remain the gold standard.

The other rapid diagnostic kits that will require blood samples in determining two specific immunoglobulins (IgM and IgG) can “rapidly” provide results. While IgM levels may be detected during the early stage of the infection, sensitivity and accuracy is sacrificed and can pose problems because we would be detecting false negatives (patients who are infected and yet test negative).

A bulk of new COVID-19 cases continues to come from Cebu City 9

At this point, many of these tests should still be conducted in the healthcare setting with qualified personnel conducting the tests and correlating them with the clinical presentation of the patient. All rapid testing modalities should also first be validated as many testing kits vary in sensitivity and accuracy. There are kits that may cross-react with other circulating RNA viruses and hence give a false-positive test result as well. Finally, the timing of the test is important in the interpretation of the result.

Perhaps in the near future, as we have more and better information regarding the performance of the rapid tests and better and more accurate generation rapid tests may be made available in the market which we can use as part of a mix method in tracking the coronavirus pandemic. At this point, it may give people a false sense of security over the results of the test.

As to whether there is a direct correlation between a positive IgG (past infection) and long-term immunity is still unknown. Germany for example, is currently undertaking a program where it is testing at random the population and will engage these same patients to undergo monthly testing to determine if there indeed is consistency in the immune response to the virus.

 

New cases per day

In order to see how a curve is being flattened, one needs to look at the individual cases per day. Today was a good day—102 new cases out of 4,336 tests conducted (>4000 individuals). This means that there were less new confirmed cases with the same testing capacity. However, we will need time to bring the number of daily cases down and sustain it at that low level before we can say we have truly “flattened the curve.”

A bulk of new COVID-19 cases continues to come from Cebu City 10

Are we flattening the curve?

 

A bulk of new COVID-19 cases continues to come from Cebu City 11

New cases based on region

 

The table above shows that of the 102 new cases announced by the DoH, 73 had residence information tagged (with 29 missing residence information). While the NCR has 34 additional cases, it is worrisome that Central Visayas contributed to 29 additional cases. Of the 29 additional cases in Central Visayas, 28 were from Cebu (Cebu City 19 new confirmed cases, Lapu-Lapu City 9 new confirmed cases).

 

By demographics

Majority of the cases are more than 25 years old. The pediatric age group (<18 years old) makes up only 2.5 percent of the total cases while the senior citizens make up almost 36.6 percent of the total. Notice now how the 25 to 54 year old age group have formed the bulk of COVID-19 cases.

Recovery rates are better in those less than 54 years old with a mortality rate of more than 51 percent for senior citizens.

A bulk of new COVID-19 cases continues to come from Cebu City 12
A bulk of new COVID-19 cases continues to come from Cebu City 13

 

By location: Most vs least COVID cases

Deciding which communities to extend, enhance or ease the ECQs will depend on data in each region. The total number of cases is not enough to say that most of the confirmed cases are found in that region. We need to remember that the density of the region and individual cities and municipalities are important parameters.

Two cities outside of NCR are now in the top 10 cities with most COVID-19 cases per million residents: Cebu City in number 5 (378.27/million) and Balanga, Bataan (301.89/million) in number 10.

The table below shows the cases by region. Among the regions with the most confirmed cases of COVID-10, region I has the highest CFR at 22 percent (11 deaths in 51 cases), followed by region XI at 15 percent (17 deaths in 117 confirmed cases). The NCR has a CFR of 7 percent (338 deaths in 4916 cases).

A bulk of new COVID-19 cases continues to come from Cebu City 14

Top 10 regions with confirmed COVID-19 cases in the Philippines

 

While Quezon City has the most number of cases by city (1110 confirmed cases), its CFR is only 8 percent. The table below shows that the highest CFR is in Pasig with 37 deaths (14 percent) in 261 confirmed cases.

 

A bulk of new COVID-19 cases continues to come from Cebu City 15

Top ten cities with COVID-19 cases in the Philippines

 

One city outside of the National Capital Region is in the top ten of confirmed cases of COVID-19. Cebu City is now in 5th spot with 349 confirmed cases and 5 deaths. Davao City remains in number 16 with 17 deaths of 98 cases, or a CFR of 17 percent, the highest among all the urban cities in the country.

 

The Department of Health hotline is (02)8-6517800 loc 1149-1150. People who present with fever and/or respiratory symptoms are encouraged to get in touch with the DoH.

 

Global statistics

Update as of 7pm 25 April 2020 (Saturday)

TOTAL CONFIRMED CASES: 2,834,697

TOTAL DEATHS: 197,421 (case fatality rate: 7 percent)

TOTAL RECOVERED: 808,024 (case recovery rate: 28.5 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 cases has exceeded the 2.8 million mark. The average trend in the past week has averaged ~75,000 confirmed cases daily. Overnight, there were more than 100,000 new cases reported. With more testing being conducted all over the world, this is expected.

The United States of America leads globally in the number of total cases at 905,333 with a case fatality rate (CFR) of 5.74 percent with around 52,000 total deaths recorded. The US had almost 40,000 new cases overnight, again attributable to more testing done. The recovery rate for the US is up at 11.93 percent. Among the states, New York leads with 277,445 cases with 21,291deaths with a CFR lower at 7.67 percent.

While the United States may have the highest number of cases and number of deaths in the world at 51,949, Belgium is back on top with the highest case fatality rate at 15.08 percent (6679 deaths in 44293 cases) and Bahamas in second at 15.07 percent (11 deaths in 77 cases). Eight countries with more than > 50 cases AND no fatalities reported from COVID-19 are: Vietnam, Cambodia, Maldives, Uganda, Rwanda, Madagascar, Mozambique and Guinea-Bissau.

Germany has the highest number of recoveries with 109,800 (70.8 percent) of 155,054 confirmed cases . Cambodia has the highest recovery rate at 95.9 percent (117 of 122 cases) and no deaths reported since their first case of COVID-19. Note that Cambodia has had no new case since April 13, 2020. with only 6 new cases and 0 deaths reported in the last 24 hours. The following countries have the lowest recovery rates: Netherlands (0.28 percent, 102 recovered from 37,729 cases), Norway (0.43 percent, 32 recovered from 7463 cases), and the United Kingdom (0.5 percent, 724 recovered from 144,640 cases).

 

Top Twenty Countries in the World with COVID-19 Cases  

A bulk of new COVID-19 cases continues to come from Cebu City 16

Total cases, recoveries, and deaths of top 20 countries with COVID-19.

The median average of case fatality rates is now at 7.01 percent and is predicted to climb to ~7.2 percent before the end of the month.