Every time the coronavirus passes from person to person it picks up tiny changes to its genetic code, but scientists are starting to notice patterns in how the virus is mutating.

 In recent months while treating severe cases with convalescent plasma scientists and virologists investigated various virus’s genetic material in the samples and they noticed something astonishing – Covid-19 was evolving before their eyes.

 "We saw some remarkable changes in the virus over that time," says a consultant at the hospital and a clinical microbiologist at the University of Cambridge who analysed the samples.

 "We saw mutations that seemed to suggest the virus was showing signs of adaptation to avoid the antibodies in the convalescent plasma treatment. It was the first time we had seen something like this happening in a person in real time."

Over a year after the global Covid-19 pandemic started, the issue of mutations looms large. New variants capable of spreading faster are emerging and leading to inevitable questions about whether they will make the newly approved vaccines less effective. To date, there is little evidence they are, but scientists are already starting to explore how the Covid-19 virus will mutate in the future and whether they might be able to head it off. In the first of a two part series looking at Covid-19 mutations, we look at what they have learned so far.

 Among the mutations identified was a deletion of two amino acids – known as H69 and V70 – in the spike protein sitting on the outside of the Covid-19 virus. This protein plays a key role in the ability of the coronavirus to infect cells.

 The oily capsule that surrounds most of the virus is studded with these spikes sticking outwards, making it look like a crown when viewed through an electron microscope. It is this appearance that gives the coronavirus family its name – corona is Latin for crown. The spikes are also the main way Covid-19 recognises the cells it can infect and helps the virus penetrate them.

 When doctors looked closer at the spike protein deletion they had spotted, it produced worrying results. "We wanted to see what was happening worldwide and we stumbled upon this big expanding group of [H69/V70 deletion] sequences in the UK," says Gupta. "When we looked more closely, we found that there was a new variant causing a big outbreak."

 Even as they made this discovery at the end of last last year, infectious disease experts elsewhere in UK were struggling to understand rapidly rising case numbers in London and the south-east of England despite a national lockdown. They started to notice something strange in the results of Covid-19 tests being carried out on samples.

 The researchers behind the study say 20C-US has been spreading rapidly through the US since June, and predict it could soon become the dominant variant of Covid-19 in the US.

 In early 2021, another closely related new variant appeared in California, called CAL.20C. There were more than 1,000 cases of this variant reported at the start of February and in Los Angeles accounts for a quarter to one third of all Covid-19 cases.

 Recently, scientists in Canada, also identified two emerging variants that have been spreading around the world and are associated with "high fatality rates" compared to the earlier virus. One features a mutation called V1176F in the spike protein, which occurs alongside another mutation called D614G.

 The D614G mutation alone appeared relatively early on in the pandemic in Europe and caused a dramatic increase in how much virus was shed by patients it infected, helping it to spread more quickly. The addition of the V1176F mutation may alter this behaviour further, the Canadian researchers say, and it has appeared in several countries independently, suggesting it gives the virus an advantage.

 The other variant they identified appeared rapidly in Australia and carries a S477N mutation, which seems to have increased the virus's ability to bind to human cells.

 The researchers warn that these two new mutations "may pose significant public health concerns in the future" if they continue to spread and provide the virus with an advantage. They add that Covid-19 appears to be "evolving non-randomly and human hosts shape emergent variants with positive fitness that can easily spread into the population".

 Another variant of concern found to be circulating in New York in February 2021 has also worried scientists. This variant, designated B1.526, has been increasing in numbers and by mid-February accounted for 12.3% of the viruses analysed. It contains two key mutations – E484K and N501Y – that were also seen in the variants of concern from Brazil and South Africa.

 These signs of adaptation by the virus are not entirely surprising to scientists. In most viruses and disease-causing bacteria, the use of treatments and vaccines causes them to evolve ways of escaping them so they can continue to spread. Those that develop resistance to a treatment or can hide from the immune system will survive for longer to replicate and so spread their genetic material.

  One group of Chinese scientists used artificial viruses to test for mutations in the spike protein that could lead the virus to become resistant to antibodies taken from patients who had recovered from Covid-19. They found five mutations that did this, but one in particular – N234Q – dramatically increased the level of resistance to antibodies. Although this has yet to be seen in any of the variants of concern circulating around the world.

 Their study, however, also offers some hope as identifying these changes could be useful in the development of future vaccines.

 But as scientists watch the virus continue to change over the coming months, they will also be acutely aware of the many personal tragedies that lie behind the databases of virus genomes and graphs showing their spread. Almost three million people have lost their lives to Covid-19 so far as the mutations grow in numbers.

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