We’ll Beat You COVID-19!

Science Fields

Koç University Researchers Are at Work

It has been more than one and a half months since the first case of COVID-19 was reported in our country. Even though we are learning and experiencing new things about both the virus that causes the disease and the disease itself every day, this did not get in the way of scientists to roll up their sleeves and go into battle.

Right now, perhaps thousands of studies are being conducted at many universities and research institutions all over the world to find effective solutions for COVID-19. In Turkey, there are countless studies that are being carried out under the leadership of competent organizations, namely The Ministry of Health and TÜBİTAK (The Scientific and Technological Research Council of Turkey) and there is intense work within universities on matters such as disease diagnosis, treatment, determining how the disease spreads, management of the pandemic, development of patient tracking systems, vaccination, medication and equipment production, and organizing support systems.

Koç University is also one of the institutions that embraces the challenge and works on the issue vigorously with its departmental prowess. There are currently 39 multifaceted projects managed within the university most of which are interdisciplinary and could even be considered as supra-disciplinary. Some of these projects focus on diagnosis and treatment while others zero in on follow-up and even support; all projects are carried out with utmost scrutiny.

The first step in combating disease is diagnosis. If you have an accurate diagnostic system, the primary line of defence against an outbreak includes fast and effective detection of infected individuals and appropriate interventions. One of the projects that is managed at Koç University focuses on developing a novel diagnostic kit and measuring device based on SERS technique which will be able to detect whether COVID-19 is present in a patient’s nasal droplets with high sensitivity and fast response time.

Moreover, one of the most popular topics of the discussion revolves around whether or not the microdroplets in the air carry coronavirus and whether or not there is a risk of infection due to these droplets. Imaging studies which target microdroplets and aerosols in the air, as well as the development of a PCR system which collects samples from the air, are among the projects that are underway.

The next step is the treatment process. Medication is surely the most powerful instrument in this process. While everyone is waiting for the “magic pill” nowadays, scientists are at laboratories testing perhaps millions of molecules. Another study that is carried out at Koç University is based on observations of strong inflammatory response due to intense cytokine storms which can be triggered by various factors such as infection and medication use among patients who suffer more severe disease despite ventilation. There is also a project that is based on manufacturing anakinra and biosimilars since treating these patients with anti-inflammatory biologics like tocilizumab and anakinra has shown positive results. Yet in another drug research project, a study to identify drugs that block the spread of the virus in epithelial cells of the lungs was carried out. In the study, drugs that have the least side effects were identified among those that are currently used to treat other diseases and that have been approved by the FDA to inhibit the enzymes that are essential to the life cycle of SARS-CoV-2019; drugs that can block the spread were identified using a computer simulation.

Surely, manufacturing certain medical devices to help patients persevere through the process with ease is as vital as developing drugs that compensate for the devastating impact of the virus.

Again, in addition to the ventilators that are manufactured in laboratories at Koç University, a portable breathing support system, the ECMO machine, and a sensitive lung simulator are among the systems that are developed; robotic automation of PCR systems is also under development.

In addition, follow-ups are also as important as treatment. The goal is to develop a system for monitoring infected patients who are quarantined at home by health teams, optimizing the order, time, and route of team visits to facilitate systematic follow-up and response as well as developing cost-effective software/hardware based on Bluetooth and Wi-Fi signaling techniques, especially for high-risk older adults. Patient follow-ups, maintenance of social distancing, and application of telehealth are within the scope of the project.

It is also crucial to consider the big picture in terms of diseases like COVID-19 which impacts the whole world and does not discriminate; investigation of the discrepancy between death rates in other countries is the subject of a project which will give us important clues about fighting the disease. Also, projects focused on the examination of thorax CT images by using artificial intelligence or those that are about dynamic modelling of the spread of the virus offer important insights into the preventative steps that can be taken both in the present and in the future. In addition, there are projects underway to support clinicians who are treating patients in more complicated conditions; projects that investigate the psychological impact of the pandemic on radiotherapy patients or the role of Autism Spectrum Disorder (ASD) in understanding the COVID-19 infection and projects that investigate the challenges that are brought on by the virus in ASD patients’ continuation of treatment show that dealing with COVID-19 will require more effort than simply fighting off an infection. The goal of these projects is to come up with solutions to support patients and clinicians who are fighting diseases besides COVID-19.

These are just a handful of the studies that are carried out at Koç University, below, you can find the complete list of the projects that are undertaken by researchers who have mobilized together and put tireless effort into research during this process.

We are certain that all of these studies will be worth the effort and under the guidance of science, humanity will come out of this process stronger than ever.

Koç University COVID-19 R&D Activities

 Diagnosis / Detection

*Development and Clinical Validation of Diagnostic Kit for COVID-19 and Other Viral Infections

In this project, a new diagnostic kit and measurement device based on SERS technique with high speed, sensitivity and selectivity is developed and COVID-19 presence in patients’ nasal fluid will be tested in the laboratory and in clinical trials. High sensitivity, the fast response will be achieved and COVID-19-specific diagnosis will be provided. Large-scale test kit fabrication processes will be established for low cost and domestic production.

Prof. İhsan Solaroğlu, Prof. Önder Ergönül, Prof. Füsun Can, Asst. Prof. M. Cengiz Onbaşlı, Müslüm İlgi, Prof. Hakan Ürey, Dr. Arzu Baygül, Asst. Prof. Aykut Coşkun (School of Medicine, Electrical And Electronics Engineering)

*Distribution Profiles of Coronavirus by Schlieren Imaging Method

Schlieren imaging is a method that enables to visualize the density variations based on refractive index changes of the media. Warm air, transparent micro-droplets and nano-scale aerosol particles released through breathing, coughing and sneezing that are invisible to the naked human eye can be imaged in real-time at micron resolution spatially by this technique. We plan to set up a special Schlieren optical system to achieve microsecond temporal resolution with the help of addition of an ultrafast Photron AX100 camera.

Asst. Prof. Hasan Demirci (Molecular Biology & Genetics Department)

*Diagnostic Software Based on Artificial Intelligence Based Lung Tomography

In this study, 92% test accuracy has been achieved in diagnosis. After the completion of the research, the artificial intelligence model is expected to diagnose viral lung infections with over 95% test accuracy.

Asst. Prof. Mehmet Cengiz OnbaşlI (Electrical-Electronics Engineering), Radyoloji Ekibi (School of Medicine, Amerikan Hastanesi)

*Development of Air Sampling PCR for COVİD-19 

A PCR system is being developed by sampling air at room temperature. Synthetic RNA samples will be used as virus controls at BS1 level.

Asst. Prof. Aşkın Kocabaş (Department of Physics)

 Drug Development

*Producing a Drug to Treat Cytokine Storm Caused by COVID-19-Induced Pneumonia

In severe COVID-19 patients, the disease induces a cytokine storm, followed by the severe inflammatory response, even when the patients are placed on ventilators. When treated with anti-inflammatory drugs such as anakinra and tocilizumab, some of the severe COVID-19 patients responded well and were saved. The goal of our project consortium is to produce anakinra and its bioequivalent derivatives.

Asst. Prof. Cem Albayrak, Assoc. Prof. Seda Kızılel, Prof. Dr. Burak Erman (Chemical-Biological Engineering)

*Antiviral Drug Development for COVID-19

In this project drug repurposing approach was used to identify drugs (widely used and well-tolerated) among the FDA approved drug library by in-silico methods. After completion of the project, we wrote the manuscript titled as “In Silico Identification of Widely Used and Well Tolerated Drugs That May Inhibit SARSCov- 2 3C-like Protease and Viral RNA-Dependent RNA Polymerase Activities, and May Have Potential to Be Directly Used in Clinical Trials” and It was submitted to a scientific journal for publication.

Prof. Halil Kavaklı, Dr. İbrahim Barış (Chemistry and Biology Engineering, Molecular Biology and Genetics)

*SARS-CoV-2 Virus-Human Structural Interactome

The interactions between SARS-CoV-2 proteins and human proteins and their structural models are aimed to be found using the HMI-Pred prediction algorithm developed in our group. The interactome will be used in drug repositioning studies for COVID-19. Partners: Banu Ozkan ASU, USA, Ruth Nussinov, NCI, NIH, USA.

Prof. Attila Gürsoy, Prof. Özlem Keskin (Computer Engineering, Chemical-Biological Engineering)

*Investigation of the effectiveness of active ingredients in drugs against COVID-19

In this project, KU research group will perform X-ray crystallographic analysis of lead compounds against the treatment of COVID-19 identified by in-silico docking calculations of drugs (that are currently in clinical use) that are performed by Dr. Serdar Durdagi from Bahçeşehir University. It is a drug-repurposing effort led by Dr. Mehmet Altay Unal from Ankara University Stem Cell Center.

Asst. Prof. Hasan Demirci (College Of Sciences – Molecular Biology And Genetics)

Treatment / Tracking

*A New Multi-Functional Portable Respiratory Support System (In the stage of an agreement with a commercial company)

More details soon to follow

*In contact with Arcelik R&D for potential help in manufacturing of some parts of ICU Ventilators in KU Manufacturing Research Center in case needed.

More details soon to follow

*Robotic Automation of PCR System for Covid-19 Tests (a New Project)

More details soon to follow

*Development of a New Extracorporeal Membrane Oxygenation (ECMO) Device for Hospitals (New Project)

More details soon to follow

*A New Medical Support System for Expanded Therapy of Acute and Chronic Lung Failure (New Project)

More details soon to follow

Prof. Dr. İsmail Lazoğlu (Mechanical Engineering)

*EVSA (EVde SAğlık) Project

The project aims to plan the timing, ordering, and routing of the household visits within a planning horizon for health field teams as a part of home health care delivery services, by developing a decision support system using smart technology and innovative methodology.

Prof. Dr. Sibel Salman (Industrial Engineering), Prof. Dr. Önder Ergönül (Infectious Diseases And Pulmonology, School Of Medicine), Dr. İlker Kayı, Prof. Sibel Sakarya (Public Health, School Of Medicine)

*System Design for the Surveillance of COVID-19 Patients and Social Distancing Control

In this project, we aim to develop low-cost software/hardware solutions based on Bluetooth and Wireless Fidelity (Wi-Fi) signaling techniques particularly for elderly patients in the high-risk group. The applications that will be considered may include the surveillance of COVID-19 patients, social distancing control and telemedicine.

Assoc. Prof. Ertuğrul Başar (Electrical And Electronics Engineering)

*Prototype Design of The Pressure Measurement System of Tofas R&D Ventilator Which Went Into Mass Production

In cooperation with the Tofaş R&D team, we provided a prototype of the measuring system and pressure transducers, which is a critical component of this system that is now in mass production. This measurement system was previously developed for device projects at Koç University and have already been tested in the patients. For this reason, this measurement system, which is currently difficult to obtain, was provided quickly.

*Prototype Design and Production of Intensive Care Unit Systems That Allow Remote Patient Management And Improved Testing Chambers

With the help of our intensive care, anesthesiologist and cardiac surgeon colleagues, a biomedical engineering/clinician collaboration network has been established in order to identify the current needs of COVID-19 response. Current studies are carried out to develop robotic systems and patient care units for remote patient monitoring. We applied for funding from Istanbul Development Agency for project support.

*Development of Accurate In Vitro Lung Physiology Simulators at The Bench Top

Although there are various ventilator design and production campaigns ongoing worldwide, there is a shortage of accurate lung simulators, which can replicate both the disease and healthy physiological response. These systems enable validation and improve the safety of ventilators before they are used in COVID-19 patients. Through our previous experience with in vitro cardiovascular system simulators, we started developing physiological lung mock-up systems. To our knowledge, there are only two simulators in Istanbul which are now idle due to lack of trained personnel. These simulators are important for both testing devices during the prototype design phase and also training new doctors recruited for COVID-19 patents.

*Prototype Production of Extracorporeal Membrane Oxygenator Components That are Used in Most Severe COVID-19 Patients

Extracorporeal membrane oxygenator (ECMO), which is a critical device for the most severe COVID-19 patients at intensive care units. Compared to the artificial ventilators, ECMO is a much more complex blood-wetted device that requires technological expertise for its design and production. Since 2019 with the support of TÜBİTAK, we are working on to develop ECMO oxygenators and their cannulas.

Prof. Kerem Pekkan (Mechanical Engineering)

*Safe-Zone Mobile Tracking Application

This project aims to track individuals in space and time through Bluetooth and QR marker technologies for disease surveillance. Location and proximity data will be processed with the state of the art machine learning and AI techniques to build models of risk and contagion.

Assoc. Prof. Metin Sezgin (Computer Engineering) 

Evaluation / Support

*Identifying Possible Reasons for Observing Diverse COVID-19 Fatality Rates in Different Countries

Statistical analysis of economical, health-related, and population-related indicators of 36 countries to identify main factors for having diverse fatality rates.

Assoc. Prof. Mehmet Gönen, Prof. Önder Ergönül (Department of Industrial Engineering, School Of Medicine)

*Analysis of Chest CT Images Using Artificial Intelligence for COVID-19 Diagnosis and Prognosis

Developing artificial intelligence algorithms to diagnose COVID-19 and to predict the prognosis using chest CT images collected at KUH and American Hospital from COVID-19 patients, healthy subjects, and non-COVID-19 pneumonia patients.

Prof. Sergin Akpek, Prof. Çetin Atasoy, Dr. Terman Gümüş, Prof. Önder Ergönül, Assoc. Prof. Mehmet Gönen (School of Medicine, Department Of Industrial Engineering)

*Evaluating Prognostic Differences and Predicting Possible Cause of Deaths for COVID-19 Patients at KUH and American Hospital

Identifying the prognostic differences between COVID-19 patients treated with different therapy options at KUH an American Hospital using statistical analyses and developing predictive algorithms to choose the best therapy option for newly admitted COVID-19 patients.

Dr. Şiran Keske, Assoc. Prof. Süda Tekin, Dr. Mahir Kapmaz, Prof. Dr. Nahit Çakar, Prof. Levent Tabak, Assoc. Prof. Evren Şentürk, Prof. Önder Ergönül, Assoc. Prof. Mehmet Gönen (School of Medicine, Department Of Industrial Engineering)

*Dynamic Modelling of SARS-COV-2 Spread

The aim of this study is to analyze the spread of SARS-COV-2 in Turkey and İstanbul using the well-known SEIR (Susceptible-Exposed-Infected-Recovered) model in epidemic research. We plan to extend this model to represent factors such as test capacity and general policies for containing the spread. In this way, we will be able to evaluate the results of different policies (such as the peak time for the number of infected and deceased, the total number of infected and deceased).

Prof. Lerzan Örmeci, Prof. Zeynep Akşin, Assoc. Prof. Evrim Güneş, Asst. Prof. Özge Karanfil, Prof. Barış Tan ve Prof. Önder Ergönül (Industrial Engineering, School of Medicine)

*Public Health Information Platform

We have been working on a digital health literacy project regarding COVID-19. We have started with 16 medical students from 5th year and we have built collaborations with the Psychiatry Department, MAVA and Psychology Department from the University. The Project aims to develop an online platform for frequently asked questions for COVID-19 with innovative features enabling the users to dynamically ask and receive answers.

*COVID-19 Multi-Country Student Well-being Study

We have been participating as a partner to a multi-country study assessing the wellbeing of university students during the COVID-19 pandemic. Data collection will start after the IRB approval along with other partnering universities from Turkey.

Dr. İlker Kayı, Prof. Sibel Sakarya (Public Health, School Of Medicine)

*The Effect of Prone Position Application on COVID-19 Disease in Patients Treated in the Service 

It is anticipated that intermittent prone position application to patients treated in the clinic may decrease intubation frequency, intensive care transition and mortality.

Prof. Benan Çağlayan (Pulmonary Medicine, School Of Medicine)

*Operation Strategies in Patients Undergoing Lung Resection During the COVID-19 Outbreak  

It is envisaged that it will provide an important contribution to what strategy should be followed in patients who are planned to undergo a lung operation during a pandemic.

Assoc. Prof. Serhan Tanju (Thoracic Surgery, School Of Medicine)

*Psychological Effects of COVID-19 Pandemia on Radiation Oncologists  

Morbidity and mortality of COVID-19 infection might be high, and cancer patients are under a high risk group to face detrimental infection complications. Treating this high risk group, including possibly asymptomatic infected patients as well as patients with COVID-19 diagnosis at admission or during treatment, increases the risk to be infected in healthcare providers, especially the physicians in close contact with the patients. This study is aiming to reveal the details of this psychological burden in radiation oncologists to propose a related action plan.

*Effect of COVID-19 Pandemia on Clinical Practice in Radiation Oncology 

Morbidity and mortality of COVID-19 infection might be high, and cancer patients are under a high-risk group to face detrimental infection complications. The radiation oncologists have to decide which indications could require emergent radiotherapy, as well as cancelled or delayed/postponed radiotherapy approach, in addition to how to start or complete the ongoing treatments appropriately, in these pandemic environments without any level I evidence guideline to secure the decisions. This study is aiming to reveal the details of changes and modifications made in clinical practice including safety and treatment schemes in radiation oncology clinics to propose a related action plan.

Prof. Uğur Selek (Radiation Oncology, School Of Medicine)

*Psychological Effects of COVID-19 Pandemia on Patients Under Treatment in Radiation Oncology 

Morbidity and mortality of COVID-19 infection might be high in cancer patients. Therefore, patients under treatment for their cancer feel increased psychological pressure whether to continue their treatment or to give a break, despite giving all medical information. This study is aiming to reveal the details of this psychological burden to propose a related action plan.

Prof. Yasemin Bölükbaşı (Radiation Oncology, School Of Medicine)

*Could PSA be a Prognostic Marker in Men with COVID-19?

Evaluation of PSA in COVID-19 positive and symptomatic male patients of different age groups at different stages of the disease (service, intensive care, intubation, extubation and healing) with other inflammatory markers (CRP, D-dimer, Ferritin, IL-6).

Prof. Tarık Esen (Urology, School Of Medicine)

*The Role of Autism Spectrum Disorder (ASD) in Understanding COVID-19 Infection and the Problems Caused by COVID-19 Infection in the Treatment of Patients with ASD

When individuals diagnosed with ASD are isolated at home during the COVID-19 process, there will be a significant increase in almost all problematic behavior areas (such as excessive mobility, stereotypical behavior, self-harming behavior). It is anticipated that obsessive and repetitive behaviors will increase at the highest rate among problem behavior sub-fields. It is predicted that there will be a decline in some social communication areas that individuals diagnosed with ASD gain through special education. An increase in the sensory sensitivity of ASD children is expected in this period. Also, ASD children’s sleep problems are expected to increase in this period. There is a positive correlation between primary caregiver (mother) anxiety and the child’s behavioral problems.

Dr. Tuba Mutluer, Dr. Hale Yapıcı Eser, Prof. Prof. Vedat Şar (Psychiatry And Child Psychiatry, School of Medicine)

*Sarcopenia and Related Factors in COVID-19

To identify the severity of muscle wasting and loss of muscle mass and determine the associated factors in patients during SARS CoV2 infection.

*The Effectiveness of Physical Rehabilitation in Intensive Care Unit in Acute Respiratory Distress Syndrome Secondary to SARS-CoV2 Infection; a Controlled Study

The aim of this project is to evaluate the effectiveness of physical rehabilitation in an intensive care unit (ICU) on the duration of mechanical ventilation, length of stay in ICU and in hospital, range of motion of the joints, muscle strength, physical performance and quality of life in SARS-CoV2 patients.

Prof. Özden Özyemişçi Taşkıran (Physical Medicine and Rehabilitation, School of Medicine)

*Prognostic value of serum Galectin-3 in COVID-19 infected patients  

Myocarditis is related to poor outcome in COVID-19 infected patients. In this study, the predictive value of Galectin-3 for poor outcome of which shows myocardial inflammation.

Dr. Said İncir (Biochemistry, School Of Medicine)

*Investigation of the Effects of COVID-19 Infection on the Coagulation System

In this study, it was aimed to identify the main factors playing a role in vascular thrombosis and to develop treatments that prevent thrombus formation.

Prof. Meltem Akay (Internal Medicine, School Of Medicine)

*Effects of Antihypertensive Treatment Agents on the Development of COVID-19 Infection

The role of ACE-2 protein has been demonstrated in viremia. Therefore, it is a study that will shed light on determining whether antihypertensive drugs acting on ACE should be used during the pandemic.

Assoc. Prof. Timur Selçuk Akpınar (Internal Medicine, School Of Medicine)

*Effects of COVID-19 Infection on Odor

COVID-19 infection can impair the sense of smell. Therefore, it is planned to evaluate the sense of smell and the effects of deterioration on the outcome.

Dr. Ozan Gökler (Otorhinolaryngology, School Of Medicine)