Scientists demonstrate how glue points and sequence alignment information can flag residue SARS-CoV-2 variants

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The coronavirus disease 2019 (COVID-19) pandemic has ravaged the globe for more than a year, with an increasing emergence of new variants of concern that stand to undermine current measures aimed at controlling its spread. Many countries’ healthcare systems struggle to cope with surging cases caused by new variants with observed heightened transmissibility of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19.

Monitoring variants in SARS-CoV-2 represents a substantial challenge in the current global health crisis, as well as potential future viral outbreaks. Specifically, mutations and deletions in SARS-CoV-2’s spike protein have a significant impact on vaccines and drugs that take aim at this key structural viral protein to stem the pandemic.

Study: Transformations, Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B.1.1.7. Image Credit: Juan Gaertner / Shutterstock

Now, researchers in the U.S. — at the Virginia Commonwealth University, the University of Minnesota, and the NASA Ames Research Center — have demonstrated how dominant energetic landscape mappings or glue points, along with sequence alignment information can potentially identify key residue mutations and spike protein deletions tied with emerging variants.

SARS-CoV-2 mutations

Since SARS-CoV-2 first emerged in Wuhan City, Hubei Province, China, in December 2019, it exhibited high transmission rates across the globe. To date, the virus has spread to 192 countries and regions, causing over 107.48 million cases and 2.35 million deaths.

One of the present concerns about the pandemic is that the virus continues to mutate. Variants that have emerged show increased transmissibility and infection rates, hence, poses challenges to current and developing vaccines. SARS-CoV-2’s mutation rate has been estimated to be ∼ 10−3 substitutions per site per year.

In the past, the most popular mutation of SARS-CoV-2 is the spike protein mutation D614G, which has been linked to higher upper respiratory tract viral loads. The mutation is considered omnipresent in recent genomic sequences worldwide.  Further, another variant called the U.K. variant or VOC 202012/01 or B.1.1.7 has been identified over the past months. The variant is more contagious, and it has both deletions and mutations in the spike protein (including D1614G).

It is essential to determine how current and future variants drive altered transmission rates, viral loading differences, antibody and vaccine escape, and resistance to developed drugs for SARS-CoV-2.

The study

In the study, which appeared on the pre-print medRxiv* server, the team focused on analyzing mutations of the spike protein, as a partial guide to the potential effects of its mutations on viral function, structure, and possible behavioral changes.

The team also found excellent homology of stabilizing residue glue points in coronavirus spike proteins, which were called sequence homologous glue points. Overall, these flagged residue mutations or deletions were assessed using all-atom biocomputational molecular dynamics over about one microsecond to make sure structural and energetic changes in the spike protein linked variants.

Also, the team specifically studied both the SARS-CoV-2 theoretically-based triple mutant and the U.K. or B.1.1.7 variant. They computationally analyze structure and dynamic driven key mutations tied t the Down versus Up protomer states of the virus, which is the triple mutant that can weaken neighboring receptor-binding domain- N-terminal domain (RBD-NTD) interactions.

Further, the researchers comprehensively examined the U.K. variant and the D614G mutation to determine key differences in protomer configurations, which could affect the efficacy of vaccines and drugs to combat the pandemic.

Using the same method, the team also analyzed the U.K variant to determine key mutations or deletions in its spike protein, which could be responsible for the variant being more transmissible.

The team’s findings led to two key mutations, the D614G and the N501Y. Biophysical computations validated changes tied to the D614G that make it to a more angiotensin-converting enzyme 2 (ACE2) accessible state. Meanwhile, the N501Y has a potential human ACE2 glue point partner 41Y, which may lead to a strong residue pair interaction. This may explain why there is a higher infection rate of the U.K. B.1.1.7 and the South African B.1.351 variants.

The team concluded that these two key mutations may boost transmission and infection rates in two different ways. However, the team emphasized that further studies are needed to quantify this characteristic and its consequences.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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