• Energy Research

Upsurge in infections by SARS-COV-2 variant from India, B.1.617.2 has become quite alarming. The molecular basis of the increase Infectivity and Transmissibility of B.1.617.2 is not well understood. Analysis of the primary structure of SPp of B.1.617.2 shows that T478K is a mutated phosphorylation site that is usually phosphorylated by GSK-3 and Cdk1 which are normally involved in the control of the cell cycle, cell proliferation and cell death. Through Structure Model Analysis and Thermodynamic Calculations, it is shown that phosphorylation of T478 of SPp of SARS-COV-2 serves to significantly decrease the stability and binding efficiency of SPp to ACE2. Mutation of T478 to T478K reverses the effect of phosphorylation of T478 and is accompanied by enhanced stability and binding efficiency of SPp to ACE2. It is proposed that phosphorylation of T478 of SPp of SARS-COV-2 is a cellular response mechanism to attenuate the binding of SPp to ACE2 and that mutation of T478 to T478K is exploited by SARS-COV-2 to counter the phosphorylation dependent inhibition of the binding of SPp to ACE2. Currently, it is not known whether neutralizing antibodies induced by currently available vaccines can interact with phospho-T478-SPp of SARS-COV-2. B.1.617.2 may become dominant if neutralizing antibodies induced by currently available vaccines are targeting dephospho- and phospho-T478-SPp of SARS-COV-2, and not T478K-SPp of SARS-COV-2. Also, currently available vaccines may be selecting for more infectious and virulent SARS-COV-2 strain.

SARS-COV-2, the etiologic agent of COVID-19 is able to infect cells through its Spike protein (SPp) which must first bind to its receptor ACE2. Most currently developed vaccines target the SARS-COV-2 encoded Spike protein. Many SARS-COV-2 variants have been identified that exhibit several mutations in their Spike protein. SARS-COV-2 variant, B.1.526 was identified in New York, U.S.A. [Annavajhala, M.K. (2021) medRxiv, DOI: 10.1101/2020.02.23.21) and shown to contain the mutations, L5F, T95I, D253G, E484K, S477N, D614G and A701V. T95 and S477 of SPp are phosphorylation sites for a number of Protein kinases, including Cdk1 and GSK-3. Here, through Computerized Structure Model Analysis and Thermodynamic Calculations, it is shown that phosphorylations of T95 and S477 increases the stabilities of SARS-COV-2 encoded SPp-ACE2 and SPp-DC-SIGN complexes with very marginal effects on the binding efficiencies between the components of the complexes, and mutations T95I and S477N antagonize the effects of the phosphorylations of T95 and S477. Thus, it appears that SARS-COV-2 variant, B.1.526 has adapted to exploit the protein phosphorylation apparatus of its host cells to its advantage, and the effects of phosphorylation of of T95 and S477 are blunted through random mutation. Whether Neutralizing Antibodies that target SPp can recognize the phosphorylated forms of SPp is currently unknown.

The origin of SARS-COV-2 has generated much controversy and debate. Several so-called experts and pundits have claimed that the Bat relative of SARS-COV-2, Yunnan_RaTG13 has undergone laboratory manipulation to generate SARS-COV-2. Examination of the sequence of the Spike protein (SPp) of Bat Yunnan_RaTG13 shows that the phosphorylation site T478 and surrounding amino acids that are present in SPp of SARS-COV-2 are missing in SPp of Yunnan_RaTG13. Here, through structure model analysis and thermodynamic calculation, it is shown that the binding efficiency of SPp of Yunnan_RaTG13-ACE2 complex is significantly distinct from SPp of SARS-COV-2-ACE2 complex. It is shown that phospho-T478 reduces the stability of SPp of SARS-COV-2-ACE2 complex and the binding efficiency of SPp of SARS-COV-2 to ACE2. Engineering T478 and surrounding amino acids into SARS-COV-2 would be futile as phosphorylation of T478 resulted in a SPp of SARS-COV-2 that binds ACE2 with lower binding efficiency and a SPp of SARS-COV-2-ACE2 complex that is significantly less stable. The above results clearly debunk the ides that SARS-COV-2 is derived from Bat Yunnan_RaTG13 through laboratory manipulation at the Wuhan Institute of Virology. The suggestion that SARS-COV-2 originated as a result of laboratory experimental manipulation of Bat Yunnan_RaTG13 at the Wuhan Institute of Virology is debunked because prior to the current work, no-one noticed that the phosphorylation site T478 and surrounding amino acids are missing in Bat Yunnan_RaTG13 and the function of phospho-T478 and surrounding amino acids was unknown. One does not engineer a virus that would make it less stable and less efficient at infecting its host cells. The present work shows that phosphorylation of T478 of SPp of SARS-COV-2 by cellular protein kinase such as GSK-3 and Cdk1 will be accompanied by lower and not higher rate of infection. The present work also shows that Pangolin Guangdong MP 789 is most probably an ancestor of SARS-COV-2 and Pangolin is most probably an intermediate carrier of SARS-COV-2 because the phosphorylation sites S477 and T478 and surrounding amino acids that are present within the ACE2 receptor binding domain of the SPp of SARS-COV-2 is also present in Pangolin Guangdong MP 789. It is not clear why research work on Pangolin coronaviruses and Pangolin as intermediate animal carrier of SARS-COV-2 has not received the attention that it deserves.