University of Santo Tomas (UST) researchers Rev. Fr. Nicanor Austriaco, O.P., Ph.D., and Dr. Bernhard Egwolf tackled their research on COVID-19 infection rate forecasts and strategies to flatten the curve during an online discussion held on July 6, 2020. The session, titled “Perspectives on the Pandemic: a UST College of Science Webcast,” was part of the Modified Enhanced Online Week of Science.
Egwolf explained that one aspect of mitigating the risk of the disease is trying to predict how fast the virus will spread, which necessitated the UST CoV-2 Model.
The UST CoV-2 Model
The research paper, initially released on May 24, 2020 at the UST official website, originally focused on the impact of Enhanced Community Quarantine (ECQ) and the spread of COVID-19 in the National Capital Region (NCR) of the Philippines. Called the “UST CoV-2 Model,” the researchers used real-time mobility data to modify the DELPHI Epidemiological Model, a machine-learning capable model developed by a team at the Massachusetts Institute of Technology, where Fr. Austriaco obtained his Doctor of Philosophy degree in Biology. Using this model, it was initially found that the implementation of the ECQ was able to save thousands of lives in the NCR.
Fr. Austriaco and Dr. Egwolf updated the study on June 17, this time focusing on impact of the more relaxed General Community Quarantine (GCQ) that has been implemented for the month of June. At the time of this study’s publication, the researchers calculated the positivity rate and found that from a high of 30% positivity rate in the beginning of April, the rate dropped to now around 5% in early June, bolstering their finding of low community spread within NCR.
The study was updated more recently on June 25 by the University of the Philippines OCTA Research team, to which Fr. Austriaco also belongs, to include forecasts in other COVID-19 hotspots such as Cebu.
Among the team’s updated findings is that “Based on the current number of cases in the Philippines (including uncategorized cases) and assuming the trends continue, this projects to more than 60,000 COVID-19 cases by July 31, with 1,500 deaths. In NCR, the projection is 27,000 cases by July 31, while in the province of Cebu, the projection is 15,000 cases by July 31, assuming a continued implementation of ECQ. We emphasize that the projected increase in cases and deaths can be prevented by rapidly identifying and breaking chains of viral transmission.”
As Fr. Austriaco explained during the webcast, “The model can be used to forecast any pandemic’s spread, bacterial or viral. It’s not dependent on the actual pathogen, but simply the mathematical data on the rate of spread. We are modelling the behavior of the pathogen as it spreads within the population.”
Improving Disease Response and Control
“Now that more people are out since the strict quarantine [has been lifted in favor of modified GCQ], it’s more important to do contact tracing more quickly. If there’s more mobility, then there’s also a chance that the virus can spread even faster. Tracking is one of the most important things to do now,” Dr. Egwolf urged upon being asked what he would advise the Inter-Agency Task Force on Emerging Infectious Diseases (IATF-EID)
Fr. Austriaco echoed Dr. Egwolf, saying that “The NCR is undergoing a surge now, so if you look at the last week, it’s clear that the number of cases is rising rapidly and it looks like the positivity rate and the hospitalization rate in the NCR is dramatically increasing over the last few days.”
Due to this rapid increase, the team is prepared to run the UST CoV 2 model again to update the necessary figures. However, Fr. Austriaco expressed some concerns with the incomplete data from the Department of Health. He explained that “… a problem is that the DOH predicts that the data for the last week is not complete. And we know that, in this time of pandemic, there’s going to be logjams of data and its validation. We understand that. However, [with incomplete data] it’s difficult for the model to make forecasts that are as accurate as they could be if we had all the data. So when I run the model today, I will stop the data from about five days ago. But when you’re in the middle of the surge, the last 5 days is crucial, since you need to know how steep the curve is, how fast the number of cases are increasing. With a five day lag, the model can only tell us what would’ve happened based on data five days ago and not from today’s situation.”
Aside from forecasting the spread of the disease, the researchers pointed out that there are also things that can be learned from the response of neighboring countries to the pandemic.
“One of the things we are learning from around the world, is that the challenge of controlling the pandemic is inherently dependent upon how many cases you had when you shut down the country the first time,” said Fr. Austriaco. He gave the example of countries such as Thailand and Taiwan which were quick to ban flights from affected areas, particularly Wuhan. Their swift response meant a comparatively easier time in containing the infection.
“There are estimates that every day that lockdown was delayed is at least a week longer that we have to worry about getting the numbers down. Second, we have highly concentrated cities in NCR. We have areas where social distancing is not practical because of urban poverty. That presents a struggle when you use quarantine to regulate a pandemic because distancing and proper isolation simply isn’t feasible. Targeted lockdown is a solution, but more contact tracing really has to be done within the areas in lockdown. One of the weak points [resulting in the current surge] is that tracing isn’t being done properly. Lockdown the affected barangay, identify the afflicted persons, do contact tracing, and isolate those people,” Fr. Austriaco emphasized.
The provincial return program being done without proper testing and the transportation issues that lead to people not being able to physically distance themselves were cited as other factors which may have contributed to the rapid rise of the disease’s spread.
Joining the webcast were Ms. Amalea Dulcene Nicolasora from the Research Institute for Tropical Medicine and Director Benedict Maralit, Ph.D., from the Philippine Genome Center. It was hosted by the College of Science faculty members Asst. Prof. Michael Bahrami-Hessari and Mr. Reuel M. Bennett. The session is available on the UST College of Science’s Facebook page through this link: https://www.facebook.com/193178557513642/videos/2711702989049035/?v=2711702989049035
Call for better reporting amid surge
On July 14, 2020, Fr. Austriaco and Dr. Egwolf once again echoed their earlier calls for testing and tracing in their updated report that covered the latter half of June 2020 until July 12. They disclosed that the aforementioned surge in NCR cases is happening in an “unknown city.”
“The number of COVID-19 positive persons is disproportionately increasing in this category relative to the other geographical regions in the NCR. Statistically, this cannot be explained by random clerical or encoding errors. Instead, it may suggest that LGUs may be withholding geographical information when they suspect that individuals in their barangays are positive for COVID-19. However, without proper geographical identification of positive cases, it will be difficult for public health authorities to properly understand the extent of the surge and to control the pandemic through contact tracing, tracking, and isolation,” the report underscores.
The data showed that in the earlier half of June, the positivity rate ranged between 6 to 8% of tests. In the period covered by the updated report, the positivity rate is now around 10 to 12 percent, more than double of the World Health Organization’s (WHO) threshold of 5%. To be below this threshold indicates that, by WHO standards, the pandemic is under control.
To determine the hot spots daily cases in June were separated to two-week intervals and were each assigned to one of the component cities of the NCR. It was revealed that the DOH category of “Unknown City” was the main source of the dramatic rise in positive cases.
With this concerning increase in cases, the hospitalization occupancy has also notably spiked. Eleven cities and municipalities of NCR, namely, Makati, Las Piñas, Quezon City, Valenzuela, Pateros, Manila, Mandaluyong, Malabon, Navotas, Taguig, and Muntinlupa have exceeded the 70% “Danger” hospitalization occupancy limit that the DOH set. However, the number of ventilators in use has not had the same increase, which may point to milder cases being experienced by a younger patient population, as reported in the news media.
The researchers strongly recommend: maintaining the General Community Quarantine of NCR until positivity rates are ideally below five percent and hospitalization occupancy rates are below 50%; “enforcing public health reporting policies that will lower the number of ‘unknown’ positive cases that lack a geographical identifier; applying timely and closely supervised targeted lockdowns ; and restricting the movement of people who wish to leave the NCR until the surge has been brought under control.
It was also pointed out that “If localized lockdowns are unable to slow the spread in the NCR, the government must be ready to return the component cities of the NCR to an MECQ or even an ECQ to protect our health care system and to minimize cases and deaths.”
Fr. Nicanor Pier Giorgio Austriaco, O.P., Ph.D., S.Th.D., a Research Fellow at the Center for Religious Studies and Ethics and a Visiting Professor of the College of Science in UST, also holds the posts of Professor of Biology and Theology at the Providence College in the United States, and Principal Investigator of Austriaco Lab. He has published over 50 peer-reviewed papers in biology, philosophy, and theology, and two books, including “Biomedicine and Beatitude: An Introduction to Catholic Bioethics,” which was recognized as a 2012 Choice Outstanding Academic Title by the Association of College and Research Libraries. He is a bioethics consultant for the Catholic Bishops Conferences of the United States and of the Philippines.
Assoc. Prof. Bernhard Egwolf, Dr. rer. nat, from the UST Department of Mathematics and Physics, holds a Doctor of Natural Sciences in Physics degree from the Ludwig Maximilian University of Munich, Germany. His studies have been published in reputable journals, like the Journal of Computational Chemistry, Journal of Biological Chemistry, and the Journal of Molecular Biology, among others. He took part in a two-year post-doctoral research fellowship in the University of Chicago in 2007 upon receiving a grant from the German Research Foundation. Currently, he is a researcher at the UST Research Center for Natural and Applied Sciences.
(From left, top row): Dr. Egwolf, Fr. Austriaco, Asst. Prof. Bahrami-Hessari, and (bottom row:) Mr. Bennett during the webcast.
1 – Fr. Austriaco and Dr. Egwolf’s data on the COVID-19 related ICU bed occupancy in NCR’s component cities show that seven cities have exceeded the 70% occupancy limit set by the DOH. [Figure obtained from http://www.ust.edu.ph/ust-cov2-model/]
2 – In contrast to the hospitalization occupancy data, the number of ventilators in use as of the publication date seem to be lower. [Figure obtained from http://www.ust.edu.ph/ust-cov2-model/]
3 – The surge in NCR cases are attributed to an “unknown city” by the DOH [Figure obtained from http://www.ust.edu.ph/ust-cov2-model/]