Former Dubai-based Indian student at forefront of decoding COVID-19 genome in US

Dubai: In 1987, five pupils from Dubai were featured on the cover of Gulf News publication Junior News under the headline ‘High Flyers’. They were brilliant students with an eye on going to the US for higher studies.

One of them, Francis deSouza, then assistant headboy of St Mary’s Catholic High School, had just passed 10 ‘O’ level subjects with ‘A’ grades, had a passion for science and wanted to use it to help humanity.

Little did he realise then that the desire to help mankind would propel him to the position of President and CEO at Illumina, the company that makes the sequencing machines that decode the COVID-19 genome.

“In late 2019, our team in China started working with the local health authorities in Wuhan to help them identify the cause of the outbreak of pneumonia of unknown origin. Zhang Yongzhen at Fudan University in Shanghai, an experienced virologist, used an Illumina NovaSeq, a photocopier-size machine, to decode the COVID-19 genome and published the sequence online on January 10, 2020,” deSouza said in an exclusive interview with Gulf News.

DeSouza and Illumina then started working with vaccine manufacturers – companies like Moderna and Pfizer-BioNTech. They took the genome sequence that was published and immediately started working on their vaccines.

Today it costs $600 [to sequence a genome]. Our goal is to set the price for sequencing a genome to $100.

Francis deSouza, CEO, Illumina

“They never had a live virus on their site. They only worked with the genomic sequences coming out of Illumina machines – which is a profound responsibility – but it also enables this amazing class of genomic vaccines – mRNA vaccines,” deSouza said.

“Typically vaccines take 10 to 15 years. We have never had a coronavirus vaccine before. And yet we went in the course of the year, from identifying the pathogen to having vaccines being rolled out around the world.”

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“Then we started working with governments and health systems around the world to help track the spread of the virus. That was important because understanding how the virus spreads helps public policy decisions to be made.” Explaining this, deSouza said that if in a community, infections were coming from the outside, then travel restrictions could be imposed to protect the people.

“But if sequencing of the virus shows there is community spread, then travel restrictions will not help stop the virus. So tracking how it was spreading and how it was mutating became really important.”

Early years in Dubai

DeSouza thanks Dubai for his grounding in life. Growing up in the city from 1974 to 1987, he calls it a “special place, because it is such a wonderful mix of different cultures, different religions and people. It is a terrific place to grow up.”

Francis deSouza (standing, left) on the cover of Gulf News publication Junior News in 1987.
Image Credit: Gulf News archives

“The community was so supportive and cosmopolitan. Everybody respected each other.”

DeSouza’s father was working in Addis Ababa for a Japanese company before he was reassigned to Dubai. “As a child in Dubai you are in a terrific place. I have learnt from the values of the place – celebration of the diversity of the community and willingness to work hard.”

“I miss the shawarmas, thalis and sheesh kebabs, the picnics to Al Ain, Khor Fakkan and Umm Al Quwain.”

Education at MIT

After passing out of St Mary’s Catholic High School, deSouza pursued his passion for science and went to the Massachusetts Institute of Technology in 1987 at the age of 16.

Francis deSouza

“MIT was a fantastic experience. For somebody who loves science and the potential for what science can do, being in MIT was like a kid in a candy store – surrounded by people who were extraordinarily bright and passionate about what could be done,” deSouza said.

He studied Electrical Engineering and Computer Science for his undergraduate and graduate degrees, and then embarked on a career in its applications in technology.

After working in management consulting, deSouza launched a start-up instant messaging company in Boston that was acquired by Microsoft. After working in Microsoft for a few years, he started another company called IM Logic which did computer security. This was acquired by Symantec, where he worked for eight years and rose to be president of the company. DeSouza then came to Illumina and has been with the company for eight years.

Looking ahead

“I am drawn to working on the hard problems – the big problems we face, I want to make a difference in those problems,” deSouza says.

“I am now passionate about the potential for genomics to transform health across so many parts of our life – from helping us fight cancer, to helping agriculture, from diagnosing children with genetic diseases to helping us fight the pandemic. There is so much that genomics can do to improve our life.”

What is a genome?
■ A genome is an organism’s complete set of genetic instructions.
■ Each genome contains all the information needed to build that organism and allow it to grow and develop.
■ Our bodies are made up of millions of cells, each with their own complete set of instructions for making us.
■ The term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, Germany.
■ The term caught on after 1953, when Watson and Crick described the structure of DNA.
■ The Human Genome Project was launched in 1990 with multiple countries participating in sequencing the first human genome which took 15 years and cost about $3 billion.
■ Today it is possible to sequence the entire genome for less than $1,000 in less than a day.

“Our focus is on democratising access to genomics – bring the price of genomic sequencing down. Since we started bringing out sequencers in 2006-2007, we have brought the price down by over 99 per cent. When we first brought out the machine, it cost $150,000 to sequence a genome. Today it costs $600. We hope to take the price down by a further 80 per cent in future. Our goal is to set the price for sequencing a genome to $100. “

DeSouza says the power of genomics comes when everybody has access to it – whether it is to fight cancer, or the pandemic, to fight genetic diseases, more complex diseases like cardiovascular diseases or neurological conditions like Alzheimer’s or Parkinson’s.

Fight against COVID-19

Illumina now works with countries around the world, including those in the Middle East, to do genomic epidemiology – surveillance on how the virus is spreading and mutating.

What is genome sequencing?
■ Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome—the order of As, Cs, Gs, and Ts that make up an organism’s DNA.
■ The human genome is made up of over 3 billion of these genetic letters.
■ Biological samples – virus samples, blood or spit – are put into the sequencer machines which output the DNA and RNA sequences. These machines manufactured by companies like Illumina are sold in the commercial market – academic circles, hospitals, pharmaceutical development companies. Illumina partners and donates sequencers and consumables to 10 countries in Africa.
■ A new partnership of Illumina with Bill and Melinda Gates Foundation is seeking to expand donations into South Asia.

“We need the genomic epidemiology surveillance tools in every country, because if there is a country where the virus is rampant or mutating, ultimately it will affect all of us,” deSouza said.

Illumina is also working with the research community to try to understand why some people get mild symptoms or are asymptomatic, whereas the coronavirus can sometimes be fatal for others. The company is also working with scientists on host genomics to find the pathway of the disease.

Illumina’s plans in Dubai
■ By the end of 2021, Illumina plans to open a new office and “Solution Centre” in the Dubai World Trade Centre.
■ The centre will provide specialist genomics support and training for partners and customers from across the Middle East – from customers who are brand new to sequencing, to those who use advanced applications.
■ It will house the latest Illumina technology – a range of sequencers from low to high end, as well as micro-array and bioinformatics solutions.
■ In addition to other staff it will create specialist science jobs in genomics.
■ Illumina has more than 150 customers using sequencing instruments in a dozen Middle Eastern countries.

When can we find a solution to COVID-19?

“We have solutions on a number of fronts. The work to be done is to get the solutions into the hands of the people who need them. The vaccines are effective, but over time the virus will mutate and we will need booster shots. We may get to the place where we may need annual vaccines,” deSouza said.

NovaSeq 6000, Illumina’s most advanced and powerful sequencer. Eight countries in the Middle East are using Illumina technology for coronavirus sequencing.
Image Credit: Supplied

Is there a risk of pandemics in future?

DeSouza says that outbreaks are inevitable, “but our goal should be to make COVID-19 the last pandemic.” This is possible if we develop a faster, automated system to identify breaks when they happen and containing them. “It is possible to create a system for surveillance of waste water systems – doing genomic sequences of the pathogens in waste water systems, so that you can identify if there a new pathogen outbreak.”

Image Credit: Graphic News / Vijith Pulikkal – Gulf News

Liquid biopsies – help for cancer patients

The pandemic is accelerating research in a number of areas, deSouza said. “mRNA vaccines have been developed for COVID-19. But mRNA vaccines are also being developed to fight malaria, cancer.

“Another field that is developing is the field of liquid biopsies – helping cancer patients by understanding tumour DNA that is in the blood. These blood tests can tell you about the cancer in a patient’s body, helping match cancer patients with personalised therapies.”

Globally cancer kills 10 million people every year. Over 70 per cent of these deaths occur because of an absence of early screening. “So if there was a screen and cancer is caught early, the chances of survival are much higher. Imagine having a blood test every year, so cancer can be caught early. Detecting cancer early can save more lives than everything we have done earlier.”

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