None of the SARS-CoV-2 virus mutations that have been documented so far increase transmissibility in humans, a new study has shown.
The research, led by UCL, UK, and published in the latest edition of Nature Communications, analysed virus genomes that were collected from 46,723 people with COVID-19 from 99 countries up until July 2020.
The study team, which also comprised scientists from Cirad and the Université de la Réunion, and the University of Oxford, identified 12,706 mutations in SARS-CoV-2.
Of these, 398 showed strong evidence they had occurred repeatedly and independently, and the researchers focused specifically on 185 that have occurred at least three times independently during the pandemic.
To test if the mutations increase transmission of the virus, the researchers modelled the virus’s evolutionary tree, to establish if a particular mutation was becoming increasingly common within a given branch of the evolutionary tree.
They found no evidence that any of the common mutations are increasing the virus’s transmissibility but discovered that the most common mutations are neutral for the virus.
This included the D614G mutation in the virus spike protein, which had been mooted as a common mutation that may make the virus more transmissible, but this study found it is not associated with significantly increasing transmission.
The researchers found that most of the common mutations appear to have been induced by the human immune system, rather than the virus adapting to its novel human host. This is different from another analysis by the same team of what happened when SARS-CoV-2 later jumped from humans into farmed minks.
First and corresponding author Dr Lucy van Dorp, of UCL Genetics Institute, said: “When we analysed virus genomes sourced from mink, we were amazed to see the same mutation appearing over and again in different mink farms, despite those same mutations having rarely been observed in humans before.”
Lead author Professor Francois Balloux, also of UCL Genetics Institute, added: “We may well have missed this period of early adaptation of the virus in humans. We previously estimated SARS-CoV-2 jumped into humans in October or November 2019, but the first genomes we have date to the very end of December. By that time, viral mutations crucial for the transmissibility in humans may have emerged and become fixed, precluding us from studying them.”
The researchers say the introduction of vaccines is likely to exert new selective pressures on the virus to escape recognition by the human immune system, which could lead to the emergence of vaccine-escape mutants.
However, they add that the computational framework they developed should be able to identify possible vaccine-escape mutations in a timely way.
“The news on the vaccine front looks great. The virus may well acquire vaccine-escape mutations in the future, but we’re confident we’ll be able to flag them up promptly, which would allow updating the vaccines in time if required,” added Prof Balloux.
van Dorp L, Richard D, Tan CSC et al. No evidence for increased transmissibility from recurrent mutations in the SARS-CoV-2 genome. Nature Communications 25 November 2020; doi: 10.1038/s41467-020-19818-2
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