Wednesday, January 26, 2022

UK Virus Hunting Labs seeks to strengthen global variant network

LONDON – Air conditioners in the Wellcome Sanger Institute’s lab humming continuously, combating the heat thrown by rows of high-tech sequencing machines that work seven days a week analyzing the genetic material of COVID-19 cases from across the UK We do.

The laboratory is an example of how British scientists have industrialized the process of genomic sequencing during pandemics, cutting the time and cost required to generate a unique genetic fingerprint for each coronavirus case analyzed. This made the UK a world leader in COVID-19 sequencing, helping public health officials to track the spread of new variants, develop vaccines and decide whether to enforce lockdowns.

But now researchers from the Sanger Institute in Cambridge and laboratories around the UK have a new mission: to share what they have learned with other scientists as COVID-19 has no relation to national borders.

Evan Harrison, a senior research fellow at Sanger, said the Omicron variant is now fueling a new wave of infections around the world, showing the need for global collaboration. Omicron was first identified by scientists in southern Africa, who quickly published their findings, giving public health officials around the world time to prepare.

Since dangerous mutations of the virus can occur anywhere, scientists everywhere must monitor its development to protect everyone, Harrison said, paralleling the need to accelerate vaccination in the developing world.

“We need to be prepared globally,” he said. “We can’t just put a fence around any one country or parts of the world, because that’s not going to cut it.”

The UK prioritized sequencing in the pandemic after Professor Sharon Peacock of the University of Cambridge identified the key role it plays in combating the virus and received government funding for a national network of scientists, laboratories and testing centres, called COVID-19 Genomics UK. known as the Consortium. , This allowed the UK to mobilize academic and scientific expertise, as British researchers first identified the chemical structure of DNA in 1953.

The consortium is now supporting efforts to boost global sequencing efforts with a training program focused on researchers in developing countries. With funding from the UK government, the Consortium and the Wellcome Connecting Science plan to offer online courses in sampling, data sharing and working with public health agencies to help researchers build a national research programme.

“There is a disparity in access to sequencing around the world, and[the project]is committed to contributing to efforts to close this gap,” the group announced earlier this year, announcing plans to offer the first courses. “

By sequencing as many positive cases as possible, the researchers hope to identify forms of concern early on, then track their spread to provide early warnings for health officials.

The UK has supplied more COVID-19 sequences to global clearinghouses than any country other than the US and has sequenced a greater percentage of its cases than any other major country worldwide.

Researchers in the UK have submitted 1.68 million sequences, covering 11.7% of reported cases, according to data compiled by GISAID, which encourages rapid sharing of information about COVID-19 and the flu. promotes. The US supplied 2.22 million sequences, or 3.8% of its reported cases.

Most countries are doing some indexing but the quantity and speed varies greatly. While 205 jurisdictions have shared sequences with GSAID, more than half have sequences and share less than 1% of their total cases.

Over the past two years, laboratories around the UK have refined the process of collecting and analyzing COVID-19 samples until it is similar to manufacturing strategies over time. Specific protocols cover each step – from swabs to reporting – including systems to ensure that supplies are in the right place at the right time to keep work running.

According to Wellcome Sanger, this has helped reduce the cost of analysis of each genome by 50%, while reducing the turnaround time from sample to sequence to five days from three weeks.

According to Dr. Eric Topol, president of innovative medicine at Scripps Research in San Diego, California, increasing sequencing capacity is like building a pipeline. In addition to buying expensive sequencing machines, countries need staff trained to supply chemical reagents, work with and interpret sequences, and to ensure that data is shared quickly and transparently.

Topol said that putting all those pieces in place is a challenge for America, let alone developing countries.

Genomic sequencing is “essential as a surveillance tool around the world, as many of these low- and middle-income countries do not have sequencing capacity, especially with any reasonable turnaround time,” he said. “So the idea that there’s a helping hand out there from the Welcome Center is awesome. We need that.”

Welcome Sengar’s state-of-the-art lab receives samples continuously from across the country. Lab assistants carefully prepare genetic material and load it onto plates that are inserted into sequencing units that decipher each sample’s unique DNA code. Scientists then analyze the data and compare it with previously identified genomes to track mutations and see if new trends emerge.

With COVID-19 changing constantly, the priority is to investigate new and dangerous variants, including those that may be resistant to vaccines, Harrison said. The information is important to help researchers modify existing vaccines or develop new ones to combat the ever-changing virus.

Harrison praised South Africa for its work on the highly permeable Omicron variant and quickly shared its research with international authorities. Unfortunately, many countries then restricted travel to South Africa, hurting its economy.

Harrison said developing countries should be encouraged to publish data on the new variants without fear of economic repercussions because penalizing countries such as South Africa would only hinder sharing of information that could affect the spread of COVID-19 and future risks. necessary to deal with epidemics.

“The main thing, obviously, is this constant regular monitoring,” he said. “And I think the most important step now is moving on a global scale.”

For now, it also means a lot of work, every day, to supervise. But this kind of vigilance has its benefits, said lab manager Tristram Bellerby.

“It’s nice to see that our work in finding these new forms has been valuable,” he said. “I hope that at some point it can help us get out of the situation in which we find ourselves.

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