Mutations map holds the key to bringing coronavirus under control
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Scientists studying mutations in the coronavirus have decoded more than 10,000 different genomes of the deadly pathogen, creating a comprehensive map that will be crucial in controlling the pandemic and developing drugs to treat it.
Since the first viral sample was analyzed in the Chinese city of Wuhan in December, international research teams have used phylogenetics to create a large family tree of the Sars-CoV-2 virus responsible for Covid-19, which reveals how it has spread since the epidemic. center to all over the world.
“Genomic epidemiology will be a vital tool in humanity’s efforts to beat Covid-19 and bring the world back to normal,” said Emma Hodcroft, evolutionary geneticist at the University of Basel in Switzerland who is part of the Nextstrain mapping project. “For starters, this will be essential in helping to distinguish between local and imported transmissions as we exit lockout.”
The mutation map will be used to understand any subsequent wave of viruses if and when the current epidemic can be brought under control, as well as the development of drugs and vaccines that will allow this to happen. When these are finally introduced, genome technology will be used to detect any signs of development of resistance. Around 80 vaccines and 150 drugs for Covid-19 are being developed worldwide.
All viruses mutate, and none of the changes in Sars-CoV-2 have changed their behavior or made it more dangerous – or not so far. The mutations could be as small as one of the approximately 30,000 biochemical letters that make up the virus. The biggest difference between genomes is currently 40 letters.
“People have talked about different strains evolving as the virus spreads and mutates, but we think it’s dangerous to use this term because it suggests that mutations make the virus more or less transmissible or virulent,” a said Dr. Hodcroft, whose collaboration has produced a series of spectacular graphics illustrating how the virus has spread. Scientists also share the results of their work through open databases such as Gisaid.
Like many viruses, Sars-CoV-2 stores its genes as RNA, the sister molecule of DNA. Because the viral genome evolves at a constant rate as it replicates, on average about 2.5 mutations per month, scientists can use it as a molecular clock. The genetic difference between the Sars-CoV-2 samples gives an accurate estimate of when the lines separated from each other.
This technique allowed researchers to determine when the virus started to circulate in China. “At the end of November, this is where our footage hits – maybe mid-November but not before,” said Dr. Hodcroft.
This cancels the idea that the virus reached certain western countries last year and circulated in secret before the epidemic was brought to the attention of the public.
“There is a lot of chatter on Twitter surrounding a rumor that the circulation of Covid-19 in California in the fall of 2019 resulted in collective immunity,” said Trevor Bedford, associate member of the Fred Hutchinson Cancer Research Center in Seattle, who heads the Nextstrain project. “This is empirically not the case.” Genome analysis confirms that Europe and North America had no cases before mid-January.
Examples of the geographic diversity of Covid-19 introductions can be best seen in Iceland, which has performed more genomic testing and analysis of Sars-CoV-2 than any other country per capita.
Kari Stefansson, CEO of deCode Genetics, an Icelandic genomics company, said it revealed how the virus entered the country from travelers from a number of countries, including those returning from ski holidays in the Alps end of February.
“We have found mutation patterns characteristic of epidemics all over the world,” he said. “We have representatives from the Iranian epidemic, the West Coast of the United States and all of Europe, including many from the United Kingdom.”
One aspect of Sars-CoV-2 is how it has evolved more slowly than some other viruses such as HIV or influenza. So far, only 40 differences have evolved between the most distant samples.
Although surveillance has not shown mutations that could affect its transmissibility or virulence, scientists are watching closely if they appear.
“As the epidemic progresses, some lines will proliferate and others will disappear,” said Nick Loman, professor of microbial genomics at the University of Birmingham.
“We could certainly have mutations that change the character of the virus,” he added, “although we have not yet seen this happen.”