Russian Scientists Investigate the Immune Response to COVID Variants (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa and Lambda)

HSE University researchers assessed the effectiveness of the T cell immune response to 11 variants of SARS-CoV-2. The researchers used their results to develop the T-cell COVID-19 Atlas portal (T-CoV).

The continued emergence of new SARS-CoV-2 mutations allows the virus to spread more effectively and evade antibodies. However, it is unclear whether new strains are able to evade T-cell immunity — one of the body’s main lines of defense against COVID-19.

The development of a T cell immune response is largely determined by genetic factors, including variations in the genes of the major histocompatibility complex (also known as HLA). Each HLA gene variant has a corresponding molecule that identifies a specific set of peptides (protein) of a virus. There are a large number of such gene variations, and each person has a unique set of them.

The effectiveness of developing T-cell immunity against strains of COVID-19 varies from person to person. Depending on the set of HLA molecules, some people’s immune systems will identify and destroy a mutated virus with the same efficacy as the basic form of the virus. In others, the response is less effective.

The research was conducted by a group of scientists from the Faculty of Biology and Biotechnology of HSE University and the Institute of Bioorganic Chemistry of the Russian Academy of Sciences, including Stepan Nersisyan, Anton Zhiyanov, Maxim Shkurnikov and Alexander Tonevitsky. They assessed the genetic features of the development of T-cell immunity against 11 major SARS-CoV-2 variants by analyzing the most common HLA gene variants. The researchers used their results to develop the T-cell COVID-19 Atlas portal (T-CoV, https://t-cov.hse.ru).

The researchers used bioinformatics to determine the binding affinities of hundreds of HLA molecule variations and tens of thousands of virus peptides of the major SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa and Lambda). . The team identified the HLA alleles that displayed the most significantly altered set of virus peptides identified. According to the scientists, mutated variants may pose a higher risk for people with these alleles.

‘T-cell immunity works in such a way that the variation in HLA molecules and T-cell receptors prevents viruses from evading the immune response. Our study did not find any variant of the HLA genotype that is significantly negatively affected by viral mutations. This means that even in conditions of reduced antibody effectiveness, T-cell immunity continues to work effectively,” said Aleksander Tonevitsky, Dean of the Faculty of Biology and Biotechnology at HSE University.

Reference: “T-CoV: A Comprehensive Portal of HLA-Peptide Interactions Affected by SARS-CoV-2 Mutations” by Stepan Nersisyan, Anton Zhiyanov, Maxim Shkurnikov, and Alexander Tonevitsky, Aug. 16, 2021, Nucleic Acids Research.
DOI: 10.1093/nar/gkab701