Oxford trailblazer in SL to help set up more nanopore sequencing facilities
41 Omicron detections through revolutionary low-cost, easy technology
The latest report is out – 41 of 176 samples sequenced from December 14 to 23, were infected by the Omicron variant of concern and the balance by Delta. The samples sequenced by the laboratory of the Sri Jayewardenepura University’s Department of Immunology and Molecular Medicine under Prof. Neelika Malavige were from the community as well as from people arriving at and departing from the airport. (See graphic)
“We are able to carry out such sequencing to keep a pulse on what is happening in Sri Lanka due to a revolutionary technology,” says Prof. Malavige.
The technology she is referring to is – nanopore sequencing in which a trailblazer is Dr. Lakmal Jayasinghe, the Vice President of Research and Development (R&D) in Biological Sciences at Oxford Nanopore Technologies.
It is Dr. Jayasinghe’s team which has come up with the only portable real-time device – smilingly called by him as the ‘ pocket size sequencer’ – known as MinION for the sequencing of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
The manufacturing facility of his company which is based at the Oxford Science Park in the United Kingdom, also takes the shape of the sleek and small MinION, he says.
“The earlier sequencing technology in use in Sri Lanka is very expensive, while the ‘sample preparation time’ is longer and complicated,” explains Dr. Jayasinghe, when the Sunday Times meets him for an exclusive interview this week.
Mixing work and leisure, he is in Sri Lanka to help anyone who is interested in this easy technology, not only for the early detection of COVID-19 variants and other pathogens but also for a range of other uses.
He has already supported the establishment of this technology for COVID sequencing at six laboratories in the country: the Sri Jayewardenepura University in June last year (2021); the Colombo University; the Kandy National Hospital; the Karapitiya Teaching Hospital; and two labs at the Medical Research Institute (MRI), Colombo.
“We trained the lab personnel with our Singapore customer service and technical support team and soon the labs were up and running. The Sri Jayewardenepura University, in fact, compared the previous method versus nanopore sequencing in a paper published in a scientific journal which found that nanopore is cheaper and easier to use,” he said.
This time around, he is here to assist the Peradeniya Medical Faculty lab to start COVID sequencing and a few other labs interested in agri-based applications.
Before delving into technicalities, Dr. Jayasinghe says that Oxford Nanopore has been listed by the Massachusetts Institute of Technology (MIT) Review as one of the “smartest” companies in the world. Its R& D programme has grown
significantly over the years to become a $7.5 billion biotechnology company after a recent initial public offering (IPO). The company has satellite offices in Cambridge (UK); New York, Boston and San Francisco ( United States of America); Singapore; Shanghai and Beijing (China); and a commercial presence that includes Japan, Germany, France and India.
Oxford Nanopore has more than 1,400 patents and patent applications across 200 patent families, with hundreds generated by internal R&D.
Next, it is a close look at what we are made of, from Dr. Jayasinghe as he says that DNA is the building block of life, whether human, animal, plant, bacterium or virus. DNA is made of four different types of sub-blocks or bases – A (adenine), C (cytosine), G (guanine) and T (thymine).
“Hundreds and thousands of these bases are arranged in a specific order to make a DNA strand. A piece of DNA with a specific sequence that defines a
specific trait is called a gene,” he says, citing genes which are responsible for the colour of the eyes of a person; for breast cancer; or the spike protein of the coronavirus.
He explains: “The complete set of genes in an organism which provides all the information the organism requires to function is the ‘genome’. The human genome is made of 3.2 billion bases; the rice genome of 430 million bases; and the E.coli genome of 4.6 million bases.
“In the genome of a virus such as COVID-19, there are about 30,000 bases. The order in which these bases are arranged within the DNA strand is the ‘sequence’ of the DNA. By knowing the DNA sequence of a gene or the genome, scientists can tell many things about the organism – What is it? What’s in it? What specific species is it? Is it changing? Is it healthy or diseased?
“With regard to COVID- 19, the sequence of the DNA of the virus will tell scientists which variant is spreading in a specific country or region, whether it is dangerous or more transmissible than other variants and whether it is responding to vaccines.”
It is this information which allows policy-makers to make ‘informed’ decisions on how to respond, without groping in the dark, reiterates Dr. Jayasinghe.
Armed with this valuable knowledge, it would be easy to decide whether a local
lockdown is adequate or there should be a full scale- up to a country- wide lockdown. It is important knowledge on which areas to prioritise, when vaccine rollouts are taking place.
Looking into the past, he says that DNA sequencing is not new. Scientists have been using many different methods to sequence DNA over decades. It had taken 13 years and more than $3 billion for an international team of researchers to complete the sequencing and mapping of the first human genome. Since then,
due to advances in DNA sequencing technologies, both the cost of sequencing and the time it takes to sequence a genome have come down significantly.
The latest set of technologies developed for DNA sequencing is generally called ‘ next generation sequencing’ ( NGS) methods, he says, pointing out that nanopore sequencing is one of the latest NGS technologies developed by Oxford Nanopore Technologies.