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Biochemistry ChemVsCOVID

#ChemVsCOVID: How variant tracking and sequence sharing help the fight against the virus

ChemVsCOVID infographic marking 18 Dec 2020, the date on which the Alpha variant was designated as a variant of concern. The first column discusses tracking variants. Coronavirus variants arise from mutations in the virus RNA, its genetic code. These mutations occur over time as the virus copies itself. The mutations can be used to identify variants and track their spread. As of December 2021, over 6,000,000 SARS-CoV-2 genome sequences have been submitted to the shared GISAID database, from most of the countries in the world. 

The second column discusses variant consequences. Most mutations in the virus genome have little or no effect on the characteristics of the virus. But some mutations in the code cause more meaningful changes, such as those affecting the spike protein. The spike protein helps the virus enter cells. It’s the main target of vaccines and our body’s immune response. Changes to the spike protein’s structure may increase the virus’s infectivity and ability to evade immune responses.
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On this day a year ago, the Alpha variant of the SARS-CoV-2 virus was designated a variant of concern. The final graphic in the #ChemVsCOVID series with the Royal Society of Chemistry looks at how variants are tracked and what causes the differences between them.

It’s an unfortunate coincidence to find myself writing about the first coronavirus variant as the world grapples with another. The Alpha variant was the first variant of concern to be identified; since then, the Beta, Gamma, Delta, and now Omicron variants have all been similarly designated. As this graphic from Information is Beautiful shows, each of these variants differs in their transmissibility, and more crucially in how effective the current vaccines we have are in preventing infection.

It’s because of worldwide scientific collaboration that the world has been so quick to identify emerging variants of the virus. In particular, the GISAID database, an initiative originally set up to track genome data for influenza viruses, has amassed more than 6 million SARS-CoV-2 genome sequences since the beginning of the pandemic. These genomes are sequenced from positive PCR tests across the world, allowing scientists to see how the virus is changing as it spreads.

Coronavirus variants arise from mutations in the virus genetic code. These mutations are random, errors that occur over time as the virus copies itself again and again. If you had to copy out a page of text millions of times over, chances are you’d make the occasional mistake here or there, and the virus is no different.

Most of these mutations make little or no difference to how the virus behaves. But every now and then, a mutation can trigger a more meaningful change. Mutations in some areas of the virus’s genetic code are more likely to cause this; in particular, researchers are often more concerned about mutations on the virus spike protein. The spike protein helps the virus enter cells, and is also the main target of vaccines and our bodies’ immune response. Changes to its structure caused by mutations can lead to the virus entering cells more effectively, or even evading our natural or vaccine-induced immunity.

As the pandemic continues, scientists are learning more and more about which mutations are benign and which are concerning. This makes it easier to spot when an emerging variant might be problematic. For example, some of the mutations seen in the Omicron variant had previously been seen in other variants of concern, making it clear that Omicron could become similarly problematic.

Understanding the mutations present can also help control outbreaks. The Omicron variant has a mutation that causes an amino acid deletion in the virus’s S gene, significant because it is one of the genes commonly targeted by PCR tests. This has made it quicker and easier to identify Omicron cases, in theory giving an advantage to preventing transmission – though, in practice, the increased transmissibility of the Omicron variant seems to have diminished this advantage.

There are still issues with the genome sequencing approach. To date, only 17 countries have shared more than 50,000 sequences on the GISAID database, with many countries in the developing world sequencing and sharing only a low proportion of their total cases. This is an issue because it can increase the time before we know of an emerging variant, and as we’ve seen with Omicron, such a variant has the potential to drastically change the landscape of our fight against the virus.

Omicron will not be the last SARS-CoV-2 variant to trouble the world, but it is to be hoped that, with the continued genome sequencing surveillance, we can be as forewarned as possible against further variants which arise.

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