On May 1, I reported that the virus had mutated to spread faster. The key mutation was a change from the amino acid aspartate (abbreviated “D”) to the amino acid glycine (G) at position 614 of the spike protein sequence, a change known as D614G. The mutation didn't seem to make the disease worse, though there was a possibility it slightly increased the risk of winding up in the ICU.
Yesterday, researchers from India released a preprint* identifying a possible major mechanism for why it has spread so fast, and showing that the mutated form has spread mainly in North America and Europe, and not in East Asia. The authors argue that this can be explained by variations in human genes.
Up to this point, we have known the following about how the virus infects cells:
- First it binds to ACE2 on the surface of a cell using its spike protein.
- Then a human enzyme on the cell surface known as TMPRSS2 cleaves the spike protein in half.
- Cleavage of the spike protein allows the virus to fuse with the cell membrane.
- Fusion with the cell membrane allows the virus to travel into the cell.
A Possible Mechanism: How the Mutation Enables Increased Infection
According to computer modeling conducted by the researchers who wrote the new paper, the D614G mutation has altered the spike protein so that it can now get cleaved in a second spot by a different enzyme known as elastase.
If correct, this offers several big opportunities for the virus to spread faster:
- Now it has two ways to get cleaved. If there isn't enough TMPRSS2 in any given instance, it will have elastase as a second option.
- While TMPRSS2 is bound to the cell membrane, elastase is freely circulating in the extracellular fluid. There may be instances where TMPRSS2 and ACE2 are both available, but not located closely enough to initiate a fusion event. Under those circumstances the free-floating elastase should have better access to cleave the spike protein and initiate fusion.
- The spike protein may get cleaved in two spots instead of one. It is possible that a larger number of smaller pieces of the spike protein could have a “decoy” effect by distracting the immune system to focus on the broken pieces of the spike protein rather than the part of the spike protein busy infecting the human cells.
It is important to note that this was shown with computer modeling, and has not been verified using actual cells, viruses, and enzymes.
The Mutated Virus Spread Mainly in North America and Europe
The researchers analyzed 6,181 viral genomes submitted for international collection over the last three months to assess how it evolved in different regions. 91% of the samples were submitted from East Asia, Europe, and North America, making any conclusions strongest for these three regions.
There were 3,789 mutations, but only 11 were found at substantial prevalence in any population and only 8 affected the sequence of a protein made by the virus. Only 4 of those 11 mutations reached greater than 5% prevalence in any population.
The D614G mutation appears to have arose in China in mid-January, and was first found outside of Asia in Germany on January 28. By the close of January, the G mutation made up 1.7% of East Asian samples and a whopping 10% of European samples, but still had not reached North America.
By the end of February, the G mutation was 56.25% of European samples and 9.7% of North American samples. By contrast, it fell to less than 1% of Chinese samples, and only a single sample out of 206 (<0.5%) was found in other East Asian countries.
In March, sequence submission from East Asia dropped precipitously, possibly because of tight control of COVID-19. Meanwhile, the G mutation increased to 69% of European samples, and increased massively from 10% to 61% of North American samples.
Variations in Human Genes Explain the Spread of the Viral G Mutation
The researchers then looked for variations in the genes relevant to the viral infection process to explain why the mutation swept Europe and North America while leaving East Asia behind.
The genetic code is made of sequences of four nucleotides, A, T, C, and G. Single changes in these nucleotides are known as single nucleotide polymorphisms (SNPs) and are identified by rs numbers.
A single deletion of C identified by the rs number 35074065 exists in the part of the genome that regulates the expression of TMPRSS2 and another gene known as MX1. MX1 is responsible for promoting the production of inflammatory cytokines and for recruiting neutrophils to the lungs. Neutrophils produce large amounts of elastase, the enzyme that can help the mutated virus fuse to the cell membrane but can't help the ancestral virus.
The C deletion increases the expression of both TMPRSS2 and MX1. This may be because two proteins that mediate the response to type 1 interferon bind to this region, an activator and a suppressor. The C deletion eliminates the binding sequence for the suppressor, but doesn't do anything to affect the binding of the activator. This suggests that the C deletion allows a greater stimulation of these two genes by type 1 interferon.
The frequency of the C deletion is only 1.24% for East Asians, but is 26% in North America and 40% in Europe. This could explain why the mutation has spread so fast and so far in North America and Europe. In fact, the the prevalence of the human C deletion accounted for 91% of the variation in the prevalence of the viral G mutation within populations across the globe.
Perhaps the fact that the C deletion is still a minority allele even in Europe and North America also explains why the viral G mutation seems to have saturated in the two populations at about 60% (an observation that could be altered if its population substantially changes in future reports).
In addition to the C deletion in the regulatory region that controls TMPRSS2 and MX1, they identified a second SNP that might contribute to the differential spread of the G mutation. A transition of C to T at rs12329760 of the TMPRSS2 gene might affect its ability to cleave the spike protein with the G mutation. The T variant is homozygous at a rate of 4% of North Americans, 7% of Europeans and 19% of East Asians, and variation it its prevalence can explain 40% of the variation in the prevalence of the viral G mutation. However, they only speculated that the T allele is less able to cleave the G-mutated spike protein, and didn't even support that with computer modeling, let alone actual enzymes and viruses.
Stronger and Weaker Points in This Paper
While the relative spread of the G mutation across different populations is clearly supported by the frequency of the G mutation among internationally submitted viral genomes, the mechanisms discussed in this paper are based on inferences made from computer modeling and how we expect changes in the sequences to alter the binding of proteins involved in the interferon response and the enzyme elastase. These will need to be confirmed in vitro (in a lab dish) using actual cells, enzymes, and viruses.
My Thoughts on This Paper
This paper suggests three things to me:
- Studies and arguments about whether one country was hit harder or recovered faster because of its policies need to take into account the different genetics of their populations and how it has impacted the spread of the G mutation.
- If the suggested mechanisms are confirmed in vitro, would larger samples than the small study I reported on May 1 show the G mutation leads to a more severe disease? This would seem almost necessary, if the G mutation makes the virus better able to infect cells (hence, greater viral load) and makes interferon more harmful (greater TMPRSS2 and MX1).
- If the suggested mechanisms are confirmed in vitro, this may offer an additional explanation for why smoking and chronic obstructive pulmonary disease (COPD) are associated with worse COVID-19 outcomes. Smoking drives COPD and emphysema by oxidizing alpha-1 antitrypsin, an inhibitor of elastase. Alpha-1 antitrypsin can be administered therapeutically by injection or inhalation and could be useful in G-form COVID-19 if elastase turns out to be relevant.
- If the suggested mechanisms are confirmed in vitro, this would add to my list for being cautious around interferon-boosting supplements, as I've outlined in The Food and Supplement Guide for the Coronavirus. Interferon would be more harmful in the context of the viral G mutation, since the human C deletion that appears to enable it works by increasing the TMPRSS2 and MX1 response to type 1 interferon.
At the moment I do not believe this paper has actionable implications for us as individuals, but it adds to the story of how the virus is evolving and it can help add critical context to why some countries are getting hit harder than others. It is more complicated than each country having different policies, and we can be more level-headed in our analysis of these outcomes when we appreciate the nuanced context.
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* The term “preprint” is often used in these updates. Preprints are studies destined for peer-reviewed journals that have yet to be peer-reviewed. Because COVID-19 is such a rapidly evolving disease and peer-review takes so long, most of the information circulating about the disease comes from preprints.