Saturday, January 23, 2021

Corona Daily 204: The Discovery of the UK Variant


Those of you who have tested for Covid know that a person wearing PPE inserts a swab into your nostril, rotates it causing an uneasy ticklish sensation. If your travel, or job or playing sport depends on the result, you spend one or two days on tenterhooks. This is one test where a negative result is welcome.

Do you know what happens to that sample of your nasal secretions? Once the sample is analysed, in most countries, it is destroyed. Not so in Britain.

All the labs in Britain, after testing swabs for the virus, dispatch the leftover material in refrigerated vans to the Wellcome Sanger Institute, a genomics central lab. That lab stores them in spacious freezers. The robots then take over, separate the positive samples and deposit them in tiny, muffin-sized plates. Machines then map their genomes, producing 30,000 letter-long genetic codes that get uploaded to an internet library.

British biologists then decide where to place the different virus mutations on the evolutionary tree. This tree is a bit like a family tree with pictures posted against each name. Siblings may have lots of similarities to each other and to their parents. Cousins may also share certain features like the colour of eyes or hair.

Britain has generated more than 165,000 sequences, meaning analyzed and placed on the evolution tree that many mutations of the coronavirus. To give a perspective, the USA with five times larger population has sequenced 74,000, Germany 3,400.

The sequencing campaign began very early, on 4 March, when the number of infections in Britain was less than 100. A Cambridge microbiologist, Sharon Peacock, sent emails to all British genomicists, asking each one to call him back. Setting aside rivalries and egos, they formed a consortium which managed to raise £20 million ($27 million) of government funds in two weeks. The importance of this effort would be understood many months later.

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One of the several covid patients admitted to a hospital in Cambridge in May 2020 was a man in his seventies, with lymphoma. Strong anti-cancer drugs had reduced his immunity. In an isolation room, he struggled to breathe. He was given all available treatments, including plasma with antibodies from recovered patients. Every test continued to be positive, the virus refused to leave him.

He fought on for 101 days in the hospital. Britain’s sequencing efforts meant each of his swabs was analysed and sequenced. In total, the virus particles coursing through the man’s lungs were sequenced 23 times, a real scientific treasure.

The patient died in August. Because he was isolated, it was assumed he hadn’t infected anyone. His weak immune system and the prolonged infection had given the virus a playground to perform several mutations. Dr Steven Kemp, an infectious disease expert, called the patient the gold standard patient.

One of the patient’s mutations, named 69-70del, changes the shape of the spike protein. Another N501Y, can help the protein bind more tightly to human cells.

Dr Kemp searched for those changes every day in the global database. There seemed little to worry about.

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On another continent, doctors and nurses at a South African hospital group noticed a strange spike in the number of covid patients in their wards in late October. The lockdown restrictions had been relaxed; spring had started for this southern hemisphere nation. But the numbers were now growing too quickly.

“Is this a different strain?” One hospital official asked in a group email in early November. Was this the same coronavirus or a new dangerous mutation?

Professor Tulio de Oliveira, a geneticist at the Nelson Mandela School of Medicine in Durban began analyzing swabs, couriered in dry ice packages. On 1 December, he emailed Andrew Rambaut, a British scientist, and asked him to review some of his findings: a series of strange mutations on the virus’s outer surface.

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Continued tomorrow.

Ravi 


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