Genetics and Artificial Intelligence Drive Qatar University’s Covid-19 Research

As the number of people infected with the new coronavirus continues to climb in Qatar and neighboring countries, the Biomedical Research Center of Qatar University is accelerating work to support efforts to better understand the virus.

The center recently started several research projects related to the new virus, whose official name is SARS-CoV-2, for severe acute respiratory syndrome coronavirus 2. The center’s projects include a detailed analysis of cases of infection with the virus inside and outside Qatar, a study of the body’s immune responses to the virus, and a study evaluating the response of the virus to some antiviral drugs and natural compounds.

“We use computer modeling and artificial intelligence for genetic sequencing of the virus and to look for inhibitors that can prevent the infection of the cell,” said Hadi Yassine, an associate professor of epidemiology and infectious diseases at Qatar University who is research projects manager at the Biomedical Research Center. “This type of research enables us to predict the response of the virus to some drugs.”

As of April 14, more than 3,400 cases of Covid-19, the disease caused by the new coronavirus, had been reported in Qatar, with seven deaths. The disease emerged both in Qataris returning from Europe and in migrant workers. Qatar has blocked most incoming flights, closed public areas, and locked down an industrial area where many migrant workers live and infections have been high.

Identifying Potential Covid-19 Treatments

Using simulation technologies allows researchers to study millions of compounds quickly to identify drug candidates for testing. In this type of study, the researchers make a three-dimensional structure of the virus and then choose a number of drugs that are known to have anti-viral activities and use artificial intelligence to simulate the drugs’ interaction with the virus. If researchers identify a drug that is not currently being used to treat infected people, they can first test its efficacy in the laboratory.

“We already found some promising results and expect to publish them within the next couple of weeks,” Fatiha Benslimane, a research associate at the center, said.

Benslimane is involved in another research project for the genomic sequencing of the virus with the aim of identifying any mutations. Although other research institutions have sequenced the genome, or complete genetic sequence, of the virus, a variety of researchers are now looking for mutations, or changes in the sequence.

All viruses undergo mutations during their life cycle. Some mutations have little or no effect on the virus, others can make it more deadly. By identifying such mutations, scientists can use artificial intelligence to integrate the mutation into a 3D structure of the virus, check if this specific mutation affects the virus’s interaction with the current treatment regime, and hence update current treatment protocols.

“We are using the Oxford Nanpore Technology, which is one of the newest state of the art genomic sequencing technologies,” Benslimane said. “It allows us to deliver the sequence in just eight hours.”

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The researchers at the center have already identified certain mutations and are in the process of disseminating the results to clinicians in Qatar.

Safety Challenges of Research on Covid-19

Studying a new virus like SARS-CoV-2 poses several challenges to researchers.

“There is a lot that we don’t know about this virus,” Yassine said. “This means we should be very careful when handling clinical samples. The safety level should be higher.”

Viruses of this type are studied in a Biosafety Level 3 laboratory. This is a special laboratory with a high degree of safety both in the equipment used and in the protocols that are followed. Such a laboratory is used to work on agents that may cause serious or potentially lethal diseases and may contaminate the environment.

Currently there is only one research laboratory of this level in Qatar.

“Not all institutions have the ability to build and run this kind of laboratory since building and maintaining it to function properly is very expensive,” Yassine said. “Also, bringing in samples requires consents and ethical approvals.  This can slow down research progress.”

While a significant portion of research in Qatar focuses on chronic diseases like diabetes, cancer and cardiovascular diseases, the Biomedical Research Center has focused its work on infectious diseases since its establishment in 2015.

Yassine believes that this allowed researchers to build their capabilities in this field and prepared them to quickly begin work on the SARS-CoV-2 virus.

“The accumulated experiences, from working with other similar viruses, like influenza and Middle East respiratory syndrome coronavirus, meant we were ready for virus outbreak scenarios,” he said.

“We already had laboratories that can accommodate such research. We had techniques in place for genomic sequencing. We have also developed the capabilities of students working in the laboratory to analyze the samples.”

Who Is Susceptible to the Disease?

The center also launched a study to identify genetic factors that increase the risk of the Covid-19 infection or of more serious complications from the infection among certain population.

“I am trying to look at the picture from the host side rather than the virus side,” Maria Smatti, a Ph.D. student and research assistant at the center, said. “We have the genomic data and the disease severity. We will try to correlate this information to see the common genes between people who have severe Covid-19 disease compared to those who have milder disease.”

This allows researchers to identify which population could have more severe symptoms due to genetic susceptibility. Clinicians and public health officials could then take special precautions to protect those who are particularly vulnerable to the disease.

Smatti said that previous studies had already found genes related to immune responses to viruses similar to the new coronavirus, but her work is broader as she is not only focusing on these known genes. Rather, she will check all mutations that correlate with the severity of Covid-19 infections.

The research is a collaboration between the center and Qatar genome program, in addition to being a collaboration with researchers and clinicians from Genomics England, which seeks to sequence 100,000 human genomes, and Imperial College London.

“We have access to more than 15,000 genomes of the Qatari population and to the data of 100,000 genomes from U.K. populations,” Smatti said. “We started looking into the data from Qatar Genome [which has the genomes of Qataris] and expect to finish this phase of the research by the year end.”

Yassine says that there is an established vision to develop scientific research in Qatar, but the Covid-19 disease has pushed the project forward.

“As we are faced with a real outbreak now, this is an opportunity to gain firsthand experience and build our capacity to combat any new virus or emerging disease that appears in the future,” he said.