Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure

Is BF.7 more infectious than other Omicron subtypes: Insights from structural and simulation studies of BF.7 spike RBD variant

Fear of a fresh infection wave and a global health issue in the ongoing COVID-19 pandemic have been rekindled by the appearance of two new novel variants BF.7 and BA.4/5 of Omicron lineages. Predictions of increased antibody evasion capabilities and transmissibility have been recognised in addition to the existing lineages (BA.1.1, BA.2, BA.2.12.1 and BA.3) as cause for worry. In comparison to Omicron, BA.4 and BF.7 share nine mutations in the spike protein, Leu371Phe, Thr376Ala, Asp405Asn, Arg408Ser, Ser446Gly, Leu452Arg, Phe486Val, Arg493Gln, Ser496Gly, whereas BF.7 contains an additional mutation, Arg346Thr, in the receptor binding domain (RBD) region. Due to the critical need for analysis and data on the BA.4 and BF.7 variants, we have computationally analyzed the interaction pattern between the Omicron, BA.4 and BF.7 RBD and angiotensin-converting enzyme 2 (ACE2) to determine the influence of these unique mutations on the structures, functions, and binding affinity of RBD towards ACE2. These analyses also allow to compare molecular models to previously reported data to evaluate the robustness of our methods for quick prediction of emerging future variants. The docking results reveal that BA.4 and BF.7 have particularly strong interactions with ACE2 when compared to Omicron, as shown by several parameters such as salt bridge, hydrogen bond, and non-bonded interactions. In addition, the estimations of binding free energy corroborated the findings further. BA.4 and BF.7 were found to bind to ACE2 with similar affinities (-72.14 and - 71.54 kcal/mol, respectively) and slightly stronger than Omicron (-70.04 kcal/mol). The differences in the binding pattern between the Omicron, BA.4 and BF.7 variant complexes indicated that the BA.4 and BF.7 RBD substitutions Asp405Asn, Ser446Gly, Leu452Arg, Phe486Val and Arg493Gln caused additional interactions with ACE2. In addition, normal mode analyses also indicate more stable conformations of BA.4 and BF.7 RBDs against human ACE2. Based on these structural and simulation analyses, we hypothesized that these changes may affect the binding affinity of BA.4 and BF.7 with ACE2.

Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month

The SARS-CoV-2 pandemic has seriously affected the population in Turkey. Since the beginning, phylogenetic analysis has been necessary to monitor public health measures against COVID-19 disease. In any case, the analysis of spike (S) and nucleocapsid (N) gene mutations was crucial in determining their potential impact on viral spread. We screened S and N regions to detect usual and unusual substitutions, whilst also investigating the clusters among a patient cohort resident in Kahramanmaraş city, in a restricted time span. Sequences were obtained by Sanger methods and genotyped by the PANGO Lineage tool. Amino acid substitutions were annotated comparing newly generated sequences to the NC_045512.2 reference sequence. Clusters were defined using phylogenetic analysis with a 70% cut-off. All sequences were classified as Delta. Eight isolates carried unusual mutations on the S protein, some of them located in the S2 key domain. One isolate displayed the unusual L139S on the N protein, while few isolates carried the T24I and A359S N substitutions able to destabilize the protein. Phylogeny identified nine monophyletic clusters. This study provided additional information about SARS-CoV-2 epidemiology in Turkey, suggesting local transmission of infection in the city by several transmission routes, and highlighting the necessity to improve the power of sequencing worldwide.

Common Biomarkers Associated with Delirium in Hospitalized Patients with COVID-19 at the Epicentre of Turkish Coronavirus Outbreak: A Case-Control Study

Introduction

To investigate the differences in biochemical characteristics between Coronavirus Disease 2019 (COVID-19) patients with and without delirium in non-intensive care (IC) COVID-19 units was aimed.

Methods

This study was designed as an observational, single-centered, and case-control study consisting of 43 delirious patients and matched 45 non-delirious patients admitted to non-IC COVID-19 units. Delirium was diagnosed by a consultant psychiatrist according to the DSM-5 delirium diagnostic criteria. Independent variables such as laboratory tests at the time of admission, clinical features, and patient characteristics were obtained from electronic medical records by researchers. In the primary analyses, binomial logistic regression models were used to investigate the factors associated with delirium, which was identified as the outcome variable. Multivariate logistic models were then adjusted for potential confounding factors, including age, gender, history of neurocognitive disorders and Charlson Comorbidity Index (CCI).

Results

We observed higher levels of urea, d-dimer, troponin-T, proB-type natriuretic peptide, and CCI in patients with delirium compared to patients without delirium. We also observed lower levels of estimated glomerular filtration rate (eGFR), serum albumin, and O₂ saturation and a decrease in the length of stay at the hospital. After adjusting for confounding factors such as gender, age, and comorbidity, we found that urea (adjusted estimate=0.015; 95% Confidence Interval [CI]=0.058-0.032, P=0.039), urea/creatinine ratio (adjusted estimate=0.008; 95% CI=0.002-0.013, P=0.011), and troponin-T (adjusted estimate=0.066; 95% CI=0.014-0.118, P=0.014) were independent biomarkers associated with delirium.

Conclusion

Delirium is associated with higher urea levels and urea/creatinine ratios in COVID-19 patients. In addition, the relationship between troponin-T and delirium may help understand the potential link between the brain and the heart in COVID-19. Additional multi-centred studies with larger sample sizes are needed to generalise these results.

Complete Genomic Characterisation and Mutation Patterns of Iraqi SARS-CoV-2 Isolates

This study was performed for molecular characterisation of the SARS-CoV-2 strains in Iraq and reveal their variants, lineages, clades, and mutation patterns. A total of 912 Iraqi sequences were retrieved from GISAID, which had been submitted from the beginning of the SARS-CoV-2 pandemic to 26 September 2022, along with 12 samples that were collected during the third and fifth waves of the SARS-CoV-2 pandemic. Next-generation sequencing was performed using an Illumina MiSeq system, and phylogenetic analysis was performed for all the Iraqi sequences retrieved from GISAID. Three established global platforms GISAID, Nextstrain, and PANGO were used for the classification of isolates into distinct clades, variants, and lineages. Analysis of the isolates of this study showed that all the sequences from the third wave were clustered in the GK clades and the 21J (Delta) clade according to the GISAID and Nextclade systems, while the PANGO system revealed that six sequences were B.1.617.2 and four sequences were of the AY.33 lineage. Furthermore, the latest e wave in the summer of 2022 was due to thpredominance of the BA.5.2 lineage of the 22B (Omicron) clade in Iraq. Our study revealed patterns of circulation and dominance of SARS-CoV-2 clades and their lineages in the subsequent pandemic waves in the country.