Understanding this issue can provide important information for the development of effective antiviral agents and universal vaccines, as well as for the design of accurate diagnostic assays, thus representing a crucial aspect to consider in ongoing public health measures to contain infection worldwide

Understanding this issue can provide important information for the development of effective antiviral agents and universal vaccines, as well as for the design of accurate diagnostic assays, thus representing a crucial aspect to consider in ongoing public health measures to contain infection worldwide. In this light, by analysing one of the largest sets of SARS-CoV-2 sequences, this study aimed to define key genetic elements, single or in clusters, underlying the evolutionary diversification of SARS-CoV-2 across continents, and their impact on protein structural stability by molecular dynamics simulations, on binding affinity of drug candidates by docking analysis and on epitope recognition by prediction models. Methods SARS-CoV-2 sequences A total of 12?150 high-quality and nearly complete SARS-CoV-2 genomic sequences were retrieved from https://www.gisaid.org/ (see Supplementary Information available as Supplementary data at Online). mutations were identified (prevalence: 0.5%), residing in different viral proteins. Sixteen out of 35 formed tight clusters involving multiple SARS-CoV-2 proteins, highlighting intergenic co-evolution. Some clusters (including D614GSpike + P323LRdRp + R203KN + G204RN) occurred in all continents, while others showed a geographically restricted circulation (T1198KPL-Pr + P13LN + A97VRdRp in Asia, L84SORF-8 + S197LN in Europe, Y541CHel + H504CHel + L84SORF-8 in America and Oceania). SBVS identified 20 best RdRp inhibitors and 21 best 3CL-Pr inhibitors belonging to different drug classes. Notably, mutations in RdRp or 3CL-Pr modulate, positively or negatively, the binding affinity of these drugs. Among them, P323LRdRp (prevalence: 61.9%) reduced the binding affinity of specific compounds including remdesivir while it increased the binding affinity of the purine Tripelennamine hydrochloride analogues penciclovir and tenofovir, suggesting potential hypersusceptibility. Finally, specific mutations (including Y541CHel + H504CHel) strongly hampered recognition of Class I/II Mdk epitopes, while D614GSpike profoundly altered the structural stability of a recently identified B cell epitope target of neutralizing antibodies (amino acids 592C620). Conclusions Key genetic elements reflect geographically dependent SARS-CoV-2 genetic adaptation, and may play a potential role in modulating drug susceptibility and hampering viral antigenicity. Thus, a close monitoring of SARS-CoV-2 mutational patterns is crucial to ensure the effectiveness of treatments and vaccines worldwide. Introduction The new coronavirus, termed SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), emerged in China at the end of 2019.1,2 Afterwards, SARS-CoV-2 was declared a pandemic and has been responsible for over 16 million cases with 650?000 deaths (https://www.gisaid.org/, updated 29 July 2020), causing a global health emergency of inconceivable magnitude.2,3 SARS-CoV-2 is an enveloped positive-sense RNA virus characterized by a genome encoding four structural proteins, 16 non-structural proteins (NSPs) and other regulatory proteins. The four Tripelennamine hydrochloride structural proteins are: the envelope (E), spike (S), membrane (M) and nucleocapsid (N) protein. The 16 NSPs include the 3-chymotrypsin-like protease (3CL-Pr), the papain-like protease (PL-Pr), the replication complex comprising the RNA-dependent RNA polymerase (RdRp), the helicase (Hel), the 3,5-exonuclease (NSP-14) and other NSPs involved in the different steps of viral replication.4 So far, 3CL-Pr and RdRp have been explored as the main drug targets for therapeutic approaches against SARS-CoV-2 infection.5 Preliminary studies suggest that SARS-CoV-2 is evolving during its spread worldwide and its genome is accumulating some new variations with respect to the SARS-CoV-2 strains that originated in China.6,7 Nevertheless, an in-depth definition of mutational profiles underlying SARS-CoV-2 genetic diversification across geographical areas and their functional characterization has not been extensively addressed. Furthermore, given the urgency of the SARS-CoV-2 outbreak, there has been considerable interest in repurposing existing drugs approved for treating other infections or for other medical indications.8 Nevertheless, no information is available on the role of SARS-CoV-2 mutations in affecting, positively or negatively, the binding affinity of these drug candidates. Understanding this issue can provide important information for the development of effective antiviral agents and universal vaccines, as well as for the design of accurate diagnostic assays, thus representing a crucial aspect to consider in ongoing public health measures to contain infection worldwide. In this light, by analysing one of the largest sets of SARS-CoV-2 sequences, this study aimed to define key genetic elements, single or in clusters, underlying the evolutionary diversification of SARS-CoV-2 across continents, and their impact on protein structural stability by molecular dynamics simulations, on binding affinity of drug candidates by docking analysis and on epitope recognition by prediction models. Methods SARS-CoV-2 sequences A total of 12?150 high-quality and nearly complete Tripelennamine hydrochloride SARS-CoV-2 genomic sequences were retrieved from https://www.gisaid.org/ (see Supplementary Information available as Supplementary data at Online). Sequences were obtained from samples collected between 24 December 2019 and 20 April 2020, and cover 69 countries with the following geographic distribution: Europe (through the Immune Epitope Database and Analysis Resource Tripelennamine hydrochloride (IEDB), by following the approach recently used in Grifoni (%)(%)(%)valueprediction, 12/16 mutations reduced the binding affinity for specific human leukocyte antigens (HLAs) compared with the WT epitope (Table?3). Importantly, a drastic drop in the binding affinity was observed for P1263LSpike (score for HLA-B*07:02 of the WT versus the mutated epitope: 0.649 versus 0.001), P504LHel (score for HLA-B*07:02 of the WT versus the mutated epitope: 0.725 versus 0.001) and Y541CHel (score for HLA-A*01:01 of the WT versus the mutated epitope: 0.976 versus 0.008) (Table?3). This suggests a process of antigenic drift favouring SARS-CoV-2 escape from T cell-mediated immune responses..