Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation

Significant association between asthma and a lower risk of mortality among COVID-19 patients in Spain: A meta-analysis

Background

Various prevalences of asthma in coronavirus disease 2019 (COVID-19) have been reported in different regions, and the association between asthma and COVID-19 subsequent mortality has been in debate. Thus, this study aimed to investigate whether there was a significant association between asthma and COVID-19 mortality in Spain through a meta-analysis.

Methods

The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines were strictly complied with conducting this study. The pooled odds ratio (OR) with a corresponding 95% confidence interval (CI) was calculated by a random-effects model. The I 2 statistics for heterogeneity, sensitivity analysis for robustness, Begg's test, and Egger's test for publication bias, along with subgroup analyses for confounding bias, were also performed to support the foundation of this study.

Results

The meta-analysis revealed that asthma was significantly associated with a lower risk of mortality among COVID-19 patients in Spain with a random-effects model (pooled OR = 0.78, 95% CI = 0.69-0.88, I 2 = 35%). Further subgroup analyses by male proportion and sample size also indicated that a statistically significant negative correlation did exist between asthma and COVID-19 mortality. Robustness and no publication on-bias were evidenced by sensitivity analysis, Egger's test, and Begg's test, respectively.

Conclusion

In conclusion, patients with asthma were found to have a lower risk of mortality from COVID-19 in Spain, especially among elderly patients. In addition, asthmatic patients infected with COVID-19 may be at risk of death compared to non-asthmatic patients, which is not a cause for undue concern, thereby reducing the burden of medication.

Revealing Molecular Patterns of Alzheimer's Disease Risk Gene Expression Signatures in COVID-19 Brains

Background

Various virus infections are known to predispose to Alzheimer's disease (AD), and a linkage between COVID-19 and AD has been established. COVID-19 infection modulates the gene expression of the genes implicated in progression of AD.

Objective

Determination of molecular patterns and codon usage and context analysis for the genes that are modulated during COVID-19 infection and are implicated in AD was the target of the study.

Methods

Our study employed a comprehensive array of research methods, including relative synonymous codon usage, Codon adaptation index analysis, Neutrality and parity analysis, Rare codon analyses, and codon context analysis. This meticulous approach was crucial in determining the molecular patterns present in genes up or downregulated during COVID-19 infection.

Results

G/C ending codons were preferred in upregulated genes while not in downregulated genes, and in both gene sets, longer genes have high expressivity. Similarly, T over A nucleotide was preferred, and selection was the major evolutionary force in shaping codon usage in both gene sets. Apart from stops codons, codons CGU - Arg, AUA - Ile, UUA - Leu, UCG - Ser, GUA - Val, and CGA - Arg in upregulated genes, while CUA - Leu, UCG - Ser, and UUA - Leu in downregulated genes were present below the 0.5%. Glutamine-initiated codon pairs have high residual values in upregulated genes. Identical codon pairs GAG-GAG and GUG-GUG were preferred in both gene sets.

Conclusions

The shared and unique molecular features in the up- and downregulated gene sets provide insights into the complex interplay between COVID-19 infection and AD. Further studies are required to elucidate the relationship of these molecular patterns with AD pathology.

Codon Pattern and Context Analysis in Genes Triggering Alzheimer's Disease and Latent Tau Protein Aggregation Post-Anesthesia Exhibited Unique Molecular Patterns Associated with Functional Aspects

Background

Previous reports have demonstrated post-operative dementia and Alzheimer's disease (AD), and increased amyloid-β levels and tau hyperphosphorylation have been observed in animal models post-anesthesia.

Objective

After surgical interventions, loss in memory has been observed that has been found linked with genes modulated after anesthesia. Present study aimed to study molecular pattern present in genes modulated post anesthesia and involved in characters progressing towards AD.

Methods

In the present study, 17 transcript variants belonging to eight genes, which have been found to modulate post-anesthesia and contribute to AD progression, were envisaged for their compositional features, molecular patterns, and codon and codon context-associated studies.

Results

The sequences' composition was G/C rich, influencing dinucleotide preference, codon preference, codon usage, and codon context. The G/C nucleotides being highly occurring nucleotides, CpGdinucleotides were also preferred; however, CpG was highly disfavored at p3-1 at the codon junction. The nucleotide composition of Cytosine exhibited a unique feature, and unlike other nucleotides, it did not correlate with codon bias. Contrarily, it correlated with the sequence lengths. The sequences were leucine-rich, and multiple leucine repeats were present, exhibiting the functional role of neuroprotection from neuroinflammation post-anesthesia.

Conclusions

The analysis pave the way to elucidate unique molecular patterns in genes modulated during anesthetic treatment and might help ameliorate the ill effects of anesthetics in the future.

Molecular Dissection of Herpes Simplex Virus Type 1 to Elucidate Molecular Mechanisms Behind Latency and Comparison of Its Codon Usage Patterns with Genes Modulated During Alzheimer's Disease as a Part of Host-Pathogen Interaction

BACKGROUND

Herpes simplex virus type 1 (HSV-1) is associated with Alzheimer's disease, which goes into a cycle of latency and reactivation. The present study was envisaged to understand the reasons for latency and specific molecular patterns present in the HSV-1.

OBJECTIVE

The objective is the molecular dissection of Herpes simplex virus type 1 to elucidate molecular mechanisms behind latency and compare its codon usage patterns with genes modulated during Alzheimer's disease as a part of host-pathogen interaction.

METHODS

In the present study, we tried to investigate the potential reasons for the latency of HSV-1 virus bioinformatically by determining the CpG patterns. Also, we investigated the codon usage pattern, the presence of rare codons, codon context, and protein properties.

RESULTS

The top 222 codon pairs graded based on their frequency in the HSV-1 genome revealed that with only one exception (CUG-UUU), all other codon pairs have codons ending with G/C. Considering it an extension of host-pathogen interaction, we compared HSV-1 codon usage with that of codon usage of genes modulated during Alzheimer's disease, and we found that CGT and TTT are only two codons that exhibited similar codon usage patterns and other codons showed statistically highly significant different codon preferences. Dinucleotide CpG tends to mutate to TpG, suggesting the presence of mutational forces and the imperative role of CpG methylation in HSV-1 latency.

CONCLUSIONS

Upon comparison of codon usage between HSV-1 and Alzheimer's disease genes, no similarities in codon usage were found as a part of host-pathogen interaction. CpG methylation plays an imperative role in latency HSV-1.

Impact of Toll-Like Receptor 2 and 9 Gene Polymorphisms on COVID-19: Susceptibility, Severity, and Thrombosis

Background

Toll-like receptors (TLRs) play an important role in activation of innate and adaptive immune responses.

Aim

We aimed to detect the association between TLR2 rs5743708 G>A and TLR9 rs5743836 C>T variants and COVID-19 disease susceptibility, severity, and thrombosis by using neutrophil extracellular traps (NETs).

Subjects and Methods

We included 100 adult COVID-19 patients as well as 100 age- and gender-matched normal controls. Participants were genotyped for TLR2 rs5743708 and TLR9 rs5743836. Citrullinated Histone (H3) was detected as an indicator of NETs.

Results

The mutant (G/A and C/C) genotypes and (A and C) alleles of TLR2 rs5743708 and TLR9 rs5743836, respectively, have been significantly related to a higher risk of COVID-19 infection, representing a significant risk factor for the severity of COVID-19. There was no significant association between the two variants and citrullinated histone (H3).

Conclusion

TLR2 rs5743708 and TLR9 rs5743836 variants have been significantly related to a higher risk and severity of COVID-19 infection but had no effect on thrombus formation.

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.