The coronavirus variants causing panic around the world may be starting in people with weak immune systems who spend weeks or months battling the virus, scientists have warned.
Doctors in the US revealed a Covid strain living in an immunosuppressed patient for 150 days changed so much that they could find 50 differences in its genetic code.
These changes, which happen randomly as the virus reproduces in order to spread, are what can drive changes in its shape which can affect the way the virus functions.
Fifty per cent of the alterations in the US patient occurred on the virus’s spike protein, which it uses to bind to human cells, despite the spike accounting for just two per cent of the virus’ genetic code.
The reasons researchers are concerned about this is because the spike protein is what the immune system targets when it tries to destroy the virus, so any major changes to it could make the current crop of vaccines less effective.
The US patient, a 45-year-old man from Boston, was also on a cocktail of antiviral and antibody therapies which may have put ‘evolutionary pressure’ on the virus to evolve to evade the immune response, according to Professor Ian Jones, a virologist at the University of Reading.
The study provides clues about how the three variants causing international alarm in the UK, Brazil and South Africa, may have originated. All three also have key changes on their spike proteins which make them either more transmissible, deadly or immune-resistant.
Coronavirus constantly mutates as it spreads between people and reproduces inside hosts but the majority of the changes make no difference to the way the virus looks or behaves.
Most people who catch the disease are able to recover within a fortnight, and remain infectious for an even shorter time, which gives the virus a tiny window to evolve and jump to other people.
But in people who struggle to shake off infection for months, such as cancer and transplant patients, coronavirus is given ample opportunity to genetically shape-shift and spread back into the population, Professor Jones told MailOnline.

People who are sick with Covid-19 for an exceptionally long time may be breeding grounds for new variants of the coronavirus to emerge, scientists say, because their continuous infection gives it opportunities to evolve (Stock image of staff at a hospital in London, England)
The patient in Boston was treated at Brigham and Women’s Hospital after being admitted in spring last year, the Los Angeles Times reports.
He was diagnosed with a rare disorder called antiphospholipid syndrome in his twenties, which caused his immune system to attack his own organs and create deadly blood clots.
He had been prescribed immunosuppressive drugs which kept his immune system in check and prevented fatal overreactions – but the medicine meant his body was less able to fight off the coronavirus.
During his 154-day Covid battle he was admitted to hospital six times, including stints in ICU, before passing away from the disease last summer.
He was eventually put on three courses of the antiviral medication remdesivir, and one dose of Regeneron’s experimental cocktail of monoclonal antibodies, blood cells which help the body fight off the pathogen.
Swabs taken from his nose and throat revealed that, compared with a sample taken during his first hospitalisation, the virus had changed in 20 places.
The genetic code, a sequence of 30,000 molecules, had changed in 11 places and nine parts of it had disappeared completely.
And following tests after he had been admitted to hospital multiple times kept finding dozens more of these changes every time his illness worsened.
Doctors weren’t sure whether he kept getting sicker because his weak immune system couldn’t destroy the virus or because it kept mutating so much that the white blood cells and antibodies couldn’t recognise it as the same virus.
One doctor at the hospital that treated the man, Dr Jonathan Li, said this series of changes in the virus was basically a condensed, sped-up version of what happens as the virus spreads between people around the world.
And Boston immunologist Dr Bruce Walker told the LA Times that infection in a patient with a weak immune system that can’t clear the infection on its own is ‘the worst possible scenario for developing mutations’.
Doctors are also more likely to be put those patients with chronic Covid on a long course of drugs or therapies, which puts ‘evolutionary pressure’ on the virus, he added.
Professor Jones told MailOnline: ‘Couple those two together, then you could give the virus much longer to select for changes that then evade therapies or immune responses.’
He added: ‘Covid is normally an acute infection and most people clear it in about two weeks.
‘Mutations are a ticking time clock, and in normal patients the virus has five days worth of throwing out mutants to see if they give an advantage.
‘But in immuno-compromised patients that might be more than a month, which gives the virus much longer to accumulate mutations.
‘It doesn’t necessarily means these mutations will make virus any worse, but it increases the risk of one of them being able to [change the way it behaves].
‘The added-on factor is that because immunosuppressed people may not be able to mount a natural immune response, it’s possible they will then be treated with therapies.
‘They are treated with antivirals like remdesivir, which seeks to inhibit virus replication directly, and the second one is therapeutic antibodies, which is given as an injection, giving immune compromised people the immunity they cannot gen themselves.
‘Couple these two together then you could select for viruses that then evade either of those therapies — evading an antibody response or therapeutic response.
‘The virus will then select mutations that would be an advantage in those environments.’
Once the virus accumulates a mutation that gives it an evolutionary edge over other strains inside an immunocompromised person, it still needs to spread back into the population to become widespread.
This means the host has to be ‘well enough to cough or sneeze’, according to Professor Jones, which makes makes the emergence of such variants even more unlikely.
The virologist said this highlights the need for stringent personal protective equipment (PPE) in hospitals, where most chronically-ill Covid patients end up during their battle with the disease, to halt the spread of dangerous variants in their tracks.
He added: ‘If these patients are in hospitals and covered in PPE they are not going to transmit anything’.
This post was first published on DailyMail.