University Of Maryland Study Finds That Mutations In SARS-CoV-2 Accessory Proteins Play Key Roles In Pathogenesis, Clinical Manifestations And Disease Severity!

A new study by researchers from University of Maryland School of Medicine-USA and the J. Craig Venter Institute-USA has found that aside from the spike proteins, the various SARS-CoV-2 accessory proteins also play key roles in pathogenesis and in COVID-19 disease severity with mutations in them contributing to different clinical presentations.


 
The continued COVID-19 surges with the emergence of various new Omicron sub-lineages is a major global health threat.
 
Even with the development and deployment of various vaccines against the SARS-CoV-2 virus, the outbreaks and surges still persist and in fact even the new bivalent boosters are already being obsolete with the emergence of various more immune evasive Omicron sub-lineages.
 
The ever-continuous surges are largely driven by the emergence of viral variants, which can evade the current vaccines through mutations in the spike protein.
 
Though these differences in spike are important in terms of transmission and vaccine responses, these variants possess mutations in the other parts of their genome that also affect pathogenesis.
 
The mutations present in the accessory genes of particular interest to the study team as they have been shown to contribute to pathogenesis in the host through interference with innate immune signaling, among other effects on host machinery.
 
In order to study the effects of accessory protein mutations and other non-spike mutations on SARS-CoV-2 pathogenesis, the study team synthesized both viruses possessing deletions in the accessory genes as well as viruses where the WA-1 spike is replaced by each variant spike gene in a SARS-CoV-2/WA-1 infectious clone.
 
The study team then characterized the in vitro and in vivo replication of these viruses and compared them to both WA-1 and the full variant viruses.
 
The study findings revealed that the accessory proteins contribute to SARS-CoV-2 pathogenesis and the non-spike mutations in variants can contribute to replication of SARS-CoV-2 and pathogenesis in the host.
 
The study findings suggests that while spike mutations may enhance receptor binding and entry into cells, mutations in accessory proteins may alter clinical disease presentation.
 
The study findings were published in the peer reviewed journal: PNAS (Proceedings of the National Academy of Sciences.)
https://www.pnas.org/doi/full/10.1073/pnas.2204717119
 
The study team identified how multiple genes of SARS-CoV-2 affect disease severity, which could lead to new ways in how researchers can develop future vaccines or develop newer treatments.
 
The genes control the immune system of the host, contributing to how fiercely the body responds to a COVID-19 infection.
 
Though most individuals typically assume that the spike protein that forms the structural "crown" is the driving factor behind each new variant of COVID-19, numerous past studies also show that mutations in these other "accessory" genes also play a role in how the disease progresses.
 
As a result of this, the study team believe these accessory proteins warrant further study as their mutations increasingly may become more significant as newer variants ari se.
 
At present, the BA.4 variant of omicron, which circulated earlier this year, was overtaken by the latest BA.5 variant and its various early sub-lineages that are now predominant in circulation.
 
It is already known that both of these variants seem to evade the immune system due to mutations in the spike protein.
 
As a result of these spike mutations, the study team say the previous vaccines are not as effective in preventing disease.
 
Dr Matthew Frieman, Ph.D., Alicia and Yaya Foundation Professor of Viral Pathogen Research in The Department of Microbiology & Immunology at University of Maryland School of Medicine told Thailand Medical News, "What is interesting is that both BA.4 and BA.5 variants have the same genetic sequence for the spike protein. This means it's the other genes, the non-spike protein genes, that seem to affect the way the virus copies itself and causes disease. So, mutations in these other accessory genes are what has allowed variants like BA.5 to outcompete the earlier versions of the virus."
 
It should be noted that the SARS-CoV-2 virus has three kinds of genes ie those involved in making more copies of the virus, those that make the virus structure, and accessory genes that have other functions.
 
In this new research, the SARS-CoV-2 Research team wanted to find out the function of the accessory genes. In order to do this, the study team recreated viruses missing each of four accessory proteins and then infected mice with these new viruses or the original virus. Next, the team observed how each virus affected the mice.
 
Interestingly, the study team found that virus missing the ORF3a/b gene led to more mild infections than the original SARS-CoV-2 virus.
 
It was found that the mice with this virus strain lost less weight and had less virus in their lungs than mice infected with the original virus.
 
These study findings indicated that the ORF3a/b gene likely plays a role in either making more copies of the virus through viral replication or blocking the immune response to the infection. Other experiments suggested ORF3a/b has an extra job in the virus by seeming to activate the body's innate immune system, the first line of defense launched by the immune system, signaling that a foreign invader needs to be vanquished.
 
Surprisingly, the study team also found that mice infected with virus missing the ORF8 gene were sicker than mice with the original strain of SARS-CoV-2. These mice had increased inflammation in their lungs when compared with the original SARS-CoV-2 virus. The study team said that ORF8 seems to control the immune response in the lungs.
 
Dr Freiman commented, "By inhibiting the immune response, ORF8 helps the virus to replicate more in the lungs which worsens infection. When removed, it allowed the immune system to fight back harder.”
 
The study team next looked at how important the spike protein was for disease severity in each of the different variants of SARS-CoV-2. The researchers took the original virus and swapped out the spike gene with the spike gene of either the alpha, beta, gamma, or delta variant. Then they infected cells and mice and observed how each of these viruses replicated and entered healthy cells.
 
It was found that the virus uses the spike protein to hitchhike on the host's ACE2 receptors found on the outside of cells lining the lungs as a way to get inside and infect cells.
 
Interestingly, the study team found that the spike protein determines the severity of some of the variants, but not for others. The gamma variant was weaker than the other variants in its ability to replicate and infect.
 
The study team thinks that the mutations in genes outside of the "spike," particularly in the ORF8 gene, seem to play a role in making this version weaker than the others. Although the gamma variant circulated in Brazil, it did not spread further around the globe as it was overtaken by stronger variants.
 
The study team commented, "While the spike mutations are important for enhancing receptor binding and entry into cells, the study findings also showed that the mutations in the accessory proteins can alter clinical disease presentation."
 
They further added, "We need to learn more about the role of accessory protein mutations in COVID-19 infection, especially as new variants and subvariants keep emerging where these other proteins may play more of a starring role."
 
The study team plans to focus on dissecting more of ORF8's function in future studies.
 
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