pioneer in SL to help set up more nanopore sequencing facilities | Print edition

By Kumudini Hettiarachchi and Ruqyyaha Deane

41 Omicron detections thanks to revolutionary simple and economical technology

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MinION shaped Oxford manufacturing plant

The latest report is out – 41 of 176 samples sequenced December 14-23 were infected with the omicron variant of concern and the rest with Delta.

Samples sequenced by the laboratory of the Department of Immunology and Molecular Medicine at Sri Jayewardenepura University under the direction of Professor Neelika Malavige came from the community as well as people arriving and departing from the airport. (See graphic)

“We are able to do such sequencing to keep the pulse of what is happening in Sri Lanka thanks to revolutionary technology,” says Professor Malavige.

The technology she is referring to is nanopore sequencing in which a pioneer is Dr Lakmal Jayasinghe, vice president of research and development (R&D) in biological sciences at Oxford Nanopore Technologies.

It was Dr. Jayasinghe’s team that developed the only real-time portable device – which he smilingly calls the “pocket sequencer” – known as the MinION for sequencing DNA (acid deoxyribonucleic) and RNA (ribonucleic acid).

His company’s manufacturing plant, based at Oxford Science Park in the UK, also takes the form of the sleek and tiny MinION, he says.

“The first sequencing technology used in Sri Lanka is very expensive, while the ‘sample preparation time’ is longer and more complicated,” says Dr Jayasinghe, when the Sunday Times meet him for an exclusive interview this week.

Combining work and leisure, he is in Sri Lanka to help anyone interested in this simple technology, not only for the early detection of COVID-19 variants and other pathogens, but for a range of other uses as well.

NASA astronaut Kate Rubins first used nanopore sequencing technology in space in August 2016.

It has already supported the implementation of this technology for COVID sequencing in six laboratories in the country: Sri Jayewardenepura University in June of last year (2021); the University of Colombo; Kandy National Hospital; Karapitiya University Hospital; and two laboratories at the Institute for Medical Research (IRM), Colombo.

“We trained the lab staff with our customer service and technical support team in Singapore and the labs were up and running quickly. Sri Jayewardenepura University, in fact, compared the previous method to sequencing nanopores in an article published in a scientific journal which found that nanopores are cheaper and easier to use, ”he said.

This time around, he’s here to help the Peradeniya Faculty of Medicine lab start COVID sequencing and a few other labs interested in agricultural applications.

Before getting into the technical details, Dr Jayasinghe says that Oxford Nanopore has been ranked by the Massachusetts Institute of Technology (MIT) Review as one of the “smartest” companies in the world. Its R&D program has grown significantly over the years to become a $ 7.5 billion biotech 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 in 200 patent families, including hundreds generated by internal R&D.

Then it’s a close examination of what we’re made of, from Dr Jayasinghe who says DNA is the lifeblood of life, be it human, animal, plant, bacterial or viral. DNA is made up of four different types of subblocks or bases – A (adenine), C (cytosine), G (guanine), and T (thymine).

“Hundreds and thousands of these bases are arranged in a specific order to form a strand of DNA. A piece of DNA with a specific sequence that defines a specific trait is called a gene, ”he says, citing genes that are responsible for the color of a person’s eyes; for breast cancer; or the coronavirus spike protein.

He explains: “The complete set of genes in an organism that provides all the information the organism needs to function is the ‘genome’. The human genome is made up 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 like COVID-19, there are approximately 30,000 bases. The order in which these bases are arranged in the DNA strand is the “sequence” of the DNA. By knowing the DNA sequence of a gene or genome, scientists can tell a lot about the organism – what is it? What’s inside ? What specific species is it? Does this change? Is he healthy or sick?

“With regard to COVID-19, the
The DNA sequence 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 responds to vaccines.

It is this information that enables policy makers to make “informed” decisions about how to react, without fumbling in the dark, reiterates Dr Jayasinghe.

Armed with this valuable knowledge, it would be easy to decide whether a local lockdown is adequate or if there should be a full scale up to a countrywide lockdown. It is important to know which areas to prioritize when vaccine deployment takes place.

Looking back, he says DNA sequencing is nothing new. Scientists have used many different methods to sequence DNA for 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, thanks to advances in DNA sequencing technologies, the cost of sequencing and the time required to sequence a genome have dramatically decreased.

The latest set of technologies developed for DNA sequencing is commonly referred to as ‘next generation sequencing’ (NGS) methods, he says, noting that nanopore sequencing is one of the latest NGS technologies developed by Oxford Nanopore Technologies. .

(See PLUS coverage for
profile of Dr Lakmal Jayasinghe)

Spread of Omicron in SL

Here are the highlights from Friday’s press conference at the Office of Health Promotion (HPB): Director of DGPS Dr Ranjith Batuwanthudawe –

The latest sequencing carried out by Sri Jayewardenepura University this week indicates that around 23% of the total number of samples are infected with Omicron. This indicates a spread of Omicron in the country. Nowadays there are also several illnesses with symptoms resembling fever. It is important that people receive the reminder. There are questions on how to update the immunization card. Contact the office of the medical officer of health (MS) in your area. When you get the new vaccination certificate, discard the previous one to avoid confusion.

Consultant physician Dr. Upul Dissanayake of the Sri Lanka National Hospital (NHSL) –

There are more dengue patients than COVID patients. If someone has a fever, it could be either illness. We are seeing some side effects including headaches after the booster. If the muscle aches, fatigue, or headaches worsen, the person who took the booster may actually be suffering from dengue, as these are common symptoms of dengue. See a doctor to check if it is dengue fever, another disease, or a side effect of the booster. In the hope that there won’t be a resurgence of another wave of COVID-19 after the 31st night, the plea is for people to take advantage of the New Year’s Eve while maintaining social distancing.

The Head of the Disaster Preparedness and Response Division of the Ministry of Health, Dr Hemantha Herath –

Public gatherings could lead to the spread of COVID-19. It is therefore essential to maintain social distancing and to respect health instructions. We have lifted restrictions to continue socio-economic activities and urge the public to respect preventive measures. For questions about the advice that public and private sector offices should follow if they are hosting New Years celebrations – follow health guidelines, do not congregate in small rooms and when consuming food, at which time masks should be removed, do so in a ventilated and spacious environment.


From all over the world

Fatigue, joint pain, colds and headaches are four common signs of Omicron that are different from those caused by the Delta variant, a UK-based study (the ZOE COVID study) has found.

Loss of smell and taste, which were common signs of Delta, was barely seen in Omicron’s case.

In other reports, a South African study found that a single dose of the Johnson & Johnson COVID-19 vaccine supplemented with a booster reduced the risk of hospitalization by up to 85% when Omicron was dominant.

The study evaluated the effectiveness of a booster vaccine (Ad26.COV2-S) on more than 69,000 health workers six to nine months after the primary vaccination.

The results of the real-world study have yet to be peer-reviewed.

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