SARS-CoV-2 and Influenza Viruses: Strategies to Cope with Co-infection and Bioinformatics Perspective

Study on the correlation between DPP9 rs2109069 and IFNAR2 rs2236757 polymorphisms with COVID-19 mortality

Understanding the complex mechanisms of the immune system in dealing with the COVID-19 infection, which is probably related to the polymorphism in cytokine and chemokine genes, can explain the pro-inflammatory condition of patients. Therefore, in this study, the relationship between the frequency of single nucleotide polymorphisms in the two pro-inflammatory genes dipeptidylpeptidase 9 (DPP9) and interferon alpha and beta receptor subunit 2 (IFNAR2) and the severity of COVID-19 was assessed. This study involved 954 COVID-19 patients, including 528 recovered and 426 deceased patients. To investigate the polymorphisms of IFNAR2 rs2236757 and DPP9 rs2109069, we used the polymerase chain reaction with the restriction fragment length polymorphism assay. The results showed that IFNAR2 rs2236757 A allele is related to the reduced severity of the disease, whereas the incidence of DPP9 rs2109069 A allele was higher among the deceased than recovered individuals. On the other hand, in people carrying the G allele in the DPP9 gene polymorphism and the allele A in the IFNR2 gene polymorphism, the improvement of the disease was significantly higher. In conclusion, the results showed that IFNAR2 rs2236757 A allele is related to the decrease in the severity of the disease, while the frequency of DPP9 rs2109069 A allele was higher in deceased people than in recovered people. This shows the important role of genes related to inflammatory responses as well as the role of genetic variants of these genes in the severity of COVID-19.

An RNA-hydrolyzing recombinant minibody prevents both influenza A virus and coronavirus in co-infection models

With the lifting of COVID-19 non-pharmaceutical interventions, the resurgence of common viral respiratory infections was recorded in several countries worldwide. It facilitates viral co-infection, further burdens the already over-stretched healthcare systems. Racing to find co-infection-associated efficacy therapeutic agents need to be rapidly established. However, it has encountered numerous challenges that necessitate careful investigation. Here, we introduce a potential recombinant minibody-associated treatment, 3D8 single chain variable fragment (scFv), which has been developed as a broad-spectrum antiviral drug that acts via its nucleic acid catalytic and cell penetration abilities. In this research, we demonstrated that 3D8 scFv exerted antiviral activity simultaneously against both influenza A viruses (IAVs) and coronaviruses in three established co-infection models comprising two types of coronaviruses [beta coronavirus-human coronavirus OC43 (hCoV-OC43) and alpha coronavirus-porcine epidemic diarrhea virus (PEDV)] in Vero E6 cells, two IAVs [A/Puerto Rico/8/1934 H1N1 (H1N1/PR8) and A/X-31 (H3N2/X-31)] in MDCK cells, and a combination of coronavirus and IAV (hCoV-OC43 and adapted-H1N1) in Vero E6 cells by a statistically significant reduction in viral gene expression, proteins level, and approximately around 85%, 65%, and 80% of the progeny of 'hCoV-OC43-PEDV', 'H1N1/PR8-H3N2/X-31', and 'hCoV-OC43-adapted-H1N1', respectively, were decimated in the presence of 3D8 scFv. Taken together, we propose that 3D8 scFv is a promising broad-spectrum drug for treatment against RNA viruses in co-infection.

Global dynamics of IAV/SARS-CoV-2 coinfection model with eclipse phase and antibody immunity

Coronavirus disease 2019 (COVID-19) and influenza are two respiratory infectious diseases of high importance widely studied around the world. COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), while influenza is caused by one of the influenza viruses, A, B, C, and D. Influenza A virus (IAV) can infect a wide range of species. Studies have reported several cases of respiratory virus coinfection in hospitalized patients. IAV mimics the SARS-CoV-2 with respect to the seasonal occurrence, transmission routes, clinical manifestations and related immune responses. The present paper aimed to develop and investigate a mathematical model to study the within-host dynamics of IAV/SARS-CoV-2 coinfection with the eclipse (or latent) phase. The eclipse phase is the period of time that elapses between the viral entry into the target cell and the release of virions produced by that newly infected cell. The role of the immune system in controlling and clearing the coinfection is modeled. The model simulates the interaction between nine compartments, uninfected epithelial cells, latent/active SARS-CoV-2-infected cells, latent/active IAV-infected cells, free SARS-CoV-2 particles, free IAV particles, SARS-CoV-2-specific antibodies and IAV-specific antibodies. The regrowth and death of the uninfected epithelial cells are considered. We study the basic qualitative properties of the model, calculate all equilibria, and prove the global stability of all equilibria. The global stability of equilibria is established using the Lyapunov method. The theoretical findings are demonstrated via numerical simulations. The importance of considering the antibody immunity in the coinfection dynamics model is discussed. It is found that without modeling the antibody immunity, the case of IAV and SARS-CoV-2 coexistence will not occur. Further, we discuss the effect of IAV infection on the dynamics of SARS-CoV-2 single infection and vice versa.

Influenza and COVID-19 Co-infection

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Short-term celecoxib (celebrex) adjuvant therapy: a clinical trial study on COVID-19 patients

Background

It is known that severe acute respiratory coronavirus 2 (SARS-CoV-2) is the viral strain responsible for the recent coronavirus disease 2019 (COVID-19) pandemic. Current documents have demonstrated that the virus causes a PGE2 storm in a substantial proportion of patients via upregulating cyclooxygenase-2 (COX-2) and downregulating prostaglandin E2 (PGE2)-degrading enzymes within the host cell.

Aim

Herein, we aimed to study how short-term treatment with celecoxib (Celebrex), a selective COX-2 inhibitor, affects demographic features, early symptoms, O₂ saturation, and hematological indices of cases with COVID-19.

Methods

A total of 67 confirmed COVID-19 cases with a mild or moderate disease, who had been referred to an institutional hospital in south-eastern Iran from October 2020 to September 2021, were enrolled. Demographic characteristics, symptoms, and hematological indices of the patients were recorded within different time periods. One-way ANOVA or Kruskal–Wallis tests were used to determine differences between data sets based on normal data distribution.

Results

O₂ saturation was statistically different between the control group and patients receiving celecoxib (p = 0.039). There was no marked difference between the groups in terms of the symptoms they experienced (p > 0.05). On the first days following Celebrex therapy, analysis of complete blood counts showed that white blood cell (WBC) counts were markedly lower in patients treated with a high dose of celecoxib (0.4 g/day) than in controls (p = 0.026). However, mean lymphocyte levels in patients receiving a high dose of celecoxib (0.4 g/day) were markedly higher than in patients receiving celecoxib with half of the dose (0.2 g/day) for one week or the untreated subjects (p = 0.004). Changes in platelet count also followed the WBC alteration pattern.

Conclusion

Celecoxib is a relatively safe, inexpensive, and widely available drug with non-steroidal anti-inflammatory properties. The therapeutic efficacy of celecoxib depends on the administrated dose. Celecoxib might improve disease-free survival in patients with COVID-19.

Single nucleotide polymorphisms located in TNFA, IL1RN, IL6R, and IL6 genes are associated with COVID-19 risk and severity in an Iranian population

Cytokines play pivotal functions in coronavirus disease 2019 (COVID-19) pathogenesis. However, little is known about the rationale and importance of genetic variations associated with immune system responses, so-called "immunogenetic profiling." We studied whether polymorphisms of IL6, IL6R, TNFA, and IL1RN affect the disorder severity and outcome in patients infected with COVID19. We recruited 317 hospitalized patients with laboratory-confirmed COVID-19 from Bu-Ali hospital and 317 high-risk participants who had high exposure to COVID-19 patients but with a negative real-time-polymerase chain reaction (PCR) test. Multiple regression analyses were applied. We indicated that participants carrying the A allele in TNFA-rs361525, G>A (p < .004), the C allele in IL1RN-rs419598 T>C (p < .004), the A allele in IL6R-rs2228145, A>C (p = .047) are more susceptible to develop COVID-19. In contrast, those who carry the G allele of IL6-rs2069827, G>T (p = .01), are more protected from COVID-19. Also, we compared the various genotypes regarding the disorder severity and poor prognosis; we found that the AA genotype in TNFA is related to more aggressive illness and bad prognostic in contrast to the other inflammatory cytokines' genotypes. In addition, a high level of inflammatory indications, such as neutrophil-to-lymphocyte ratio and systemic immune-inflammation index, was observed in deceased patients compared with the survived subjects (p < .0001). We advised considering inflammatory cytokines polymorphisms as the main item to realize the therapeutic response against the acute respiratory distress syndrome induced by the SARS-CoV-2 virus.

Is Omicron the end of pandemic or start of a new innings?

In the middle of November 2021, Omicron (B.1.1.529), a novel variant of SARS-CoV-2 was identified in South Africa. Owing to continuous increasing cases with rapid transmissibility and immune evasion, the World Health Organization (WHO) has categorized this strain as a variant of concern (VOC). In total, over 60 mutations have been identified in Omicron (BA.1) and latterly, its three sub-lineages (BA.1.1, BA.2, and BA.3) have also been found with additional mutations and pathogenicity. The highly contagious Omicron causes less severe sickness than Delta, but it is still dangerous for those who have not been vaccinated. Following the unique identification of the Omicron variant, a fresh debate has erupted regarding the natural vaccines. A number of experts believe that Omicron can work as a natural vaccine, because it is similar to live attenuated vaccines in certain ways. Additionally, it was highlighted that the high rate of antibody generation in individuals cured of Omicron provide suggestive evidence in favor of those researchers who claimed Omicron acts as natural vaccine. Some disagreements also noted, as it also has tremendous health effects and high infection rate, as similar to the prior variants. This review summarizes the contradictory scenario among the scientists about Omicron variant.