Differential binding of SARS-CoV-2 Spike protein variants to its cognate receptor hACE2 using molecular modeling based binding analysis

In silico analysis reveals hypoxia-induced miR-210-3p specifically targets SARS-CoV-2 RNA

Human coronaviruses (HCoVs) until the emergence of SARS in 2003 were associated with mild cold and upper respiratory tract infections. The ongoing pandemic caused by SARS-CoV-2 has enhanced the potential for infection and transmission as compared to other known members of this family. MicroRNAs (miRNA) are 21-25 nucleotides long non-coding RNA that bind to 3' UTR of genes and regulate almost every aspect of cellular function. Several human miRNAs have been known to target viral genomes, mostly to downregulate their expression and sometimes to upregulate also. In some cases, host miRNAs could be sequestered by the viral genome to create a condition for favourable virus existence. The ongoing SARS CoV-2 pandemic is unique based on its transmissibility and severity and we hypothesised that there could be a unique mechanism for its pathogenesis. In this study, we exploited in silico approach to identify human respiratory system-specific miRNAs targeting the viral genome of three highly pathogenic HCoVs (SARS-CoV-2 Wuhan strain, SARS-CoV, and MERS-CoV) and three low pathogenic HCoVs (OC43, NL63, and HKU1). We identified ten common microRNAs that target all HCoVs studied here. In addition, we identified unique miRNAs which targeted specifically one particular HCoV. miR-210-3p was the single unique lung-specific miRNA, which was found to target the NSP3, NSP4, and NSP13 genes of SARS-CoV-2. Further miR-210-NSP3, miR-210-NSP4, and miR-210-NSP13 SARS-CoV-2 duplexes were docked with the hAGO2 protein (PDB ID 4F3T) which showed Z-score values of -1.9, -1.7, and -1.6, respectively. The role of miR-210-3p as master hypoxia regulator and inflammation regulation may be important for SARS-CoV-2 pathogenesis. Overall, this analysis advocates that miR-210-3p be investigated experimentally in SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.

Vestibular disorders in patients after COVID-19 infection

Introduction

The COVID-19 clinical symptoms are primarily related to the respiratory system but may also be involved in many others, including the nervous system. Recently, vertigo or dizziness has been described as one of the clinical manifestations and possible complications of COVID-19.

Materials and methods

This clinical study was designed to describe the otorhinolaryngological evaluation and videonystagmographic (VNG) findings in patients with an antecedent of COVID-19 infection in the last 6 months. In this study, we sought to investigate the presence of persistent vestibular damage in healed COVID-19 patients and to determine the origin of vertigo by conducting a comprehensive vestibular examination. To evaluate the association precisely, an otoneurological assessement was conducted on all participants. The study group included 58 patients aged 23–75 years with vertigo, who were diagnosed with COVID-19 infection 6 months before the examination. Each participant was submitted to an evaluation consisting of anamnesis, otorhinolaryngological evaluation, and VNG.

Results

Spontaneous nystagmus with closed eyes was reported in 8 patients (13.8%). Positional nystagmus was observed in 15 patients (24.1%). Asymmetrical optokinetic nystagmus was observed in 18 patients (31%). A distorted record in the tracking pendulum test was present in 23 patients (39.7%). Square waves were observed in 34 COVID-19 patients (58.6%). Unilateral weakness (UW) was observed in 23 subjects (39.7%); among those with UW, 22 patients (95.7%) also demonstrated directional preponderance contralateral to the UW. Another 16 patients (27.6%) presented only directional advantage. The post-caloric recruitment was present in 38% patients.

Conclusion

Patients who had been diagnosed with COVID-19 seem to be more likely to suffer from vertigo/dizziness and to compensate more slowly. COVID-19 infection may cause inner ear damage and lead to vestibular dysfunction. The role of the central nervous system in the onset of equilibrium disorders should be considered. The presence of vertigo of central origin may indicate the neurotropic effect of SARS-CoV-2 following COVID-19. Imbalance may be the only symptom of COVID-19 and may also be a late complication of the disease due to post-infectious inflammation of the nervous tissue. Comprehensive studies are needed to investigate whether COVID-19 can cause long-term vestibular deficits.

Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins

The interaction between the Spike (S) protein of SARS-CoV-2 and the human angiotensin converting enzyme 2 (hACE2) is essential for infection, and is a target for neutralizing antibodies. Consequently, selection of mutations in the S protein is expected to be driven by the impact on the interaction with hACE2 and antibody escape. Here, for the first time, we systematically characterized the collective effects of mutations in each of the Omicron sub-lineages (BA.1, BA.2, BA.3 and BA.4) on both the viral S protein receptor binding domain (RBD) and the hACE2 protein using post molecular dynamics studies and dynamic residue network (DRN) analysis. Our analysis suggested that Omicron sub-lineage mutations result in altered physicochemical properties that change conformational flexibility compared to the reference structure, and may contribute to antibody escape. We also observed changes in the hACE2 substrate binding groove in some sub-lineages. Notably, we identified unique allosteric communication paths in the reference protein complex formed by the DRN metrics betweenness centrality and eigencentrality hubs, originating from the RBD core traversing the receptor binding motif of the S protein and the N-terminal domain of the hACE2 to the active site. We showed allosteric changes in residue network paths in both the RBD and hACE2 proteins due to Omicron sub-lineage mutations. Taken together, these data suggest progressive evolution of the Omicron S protein RBD in sub-lineages towards a more efficient interaction with the hACE2 receptor which may account for the increased transmissibility of Omicron variants.