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.
*****
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.
*****
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.
*****
Continued tomorrow.
Ravi
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