COVID-19 pandemic: the delta variant, T-cell responses, and the efficacy of developing vaccines

Advancement in the development of mRNA-based vaccines for respiratory viruses

Acute respiratory infections are the leading cause of death and illness in children under 5 years old and represent a significant burden in older adults. Primarily caused by viruses infecting the lower respiratory tract, symptoms include cough, congestion, and low-grade fever, potentially leading to bronchiolitis and pneumonia. Messenger ribonucleic acid (mRNA)-based vaccines are biopharmaceutical formulations that employ mRNA molecules to induce specific immune responses, facilitating the expression of viral or bacterial antigens and promoting immunization against infectious diseases. Notably, this technology had significant relevance during the COVID-19 pandemic, as these formulations helped to limit SARS-CoV-2 virus infections, hospitalizations, and deaths. Importantly, mRNA vaccines promise to be implemented as new alternatives for fighting other respiratory viruses, such as influenza, human respiratory syncytial virus, and human metapneumovirus. This review article analyzes mRNA-based vaccines' main contributions, perspectives, challenges, and implications against respiratory viruses.

Real-time infectious disease endurance indicator system for scientific decisions using machine learning and rapid data processing

The SARS-CoV-2 virus, which induces an acute respiratory illness commonly referred to as COVID-19, had been designated as a pandemic by the World Health Organization due to its highly infectious nature and the associated public health risks it poses globally. Identifying the critical factors for predicting mortality is essential for improving patient therapy. Unlike other data types, such as computed tomography scans, x-radiation, and ultrasounds, basic blood test results are widely accessible and can aid in predicting mortality. The present research advocates the utilization of machine learning (ML) methodologies for predicting the likelihood of infectious disease like COVID-19 mortality by leveraging blood test data. Age, LDH (lactate dehydrogenase), lymphocytes, neutrophils, and hs-CRP (high-sensitivity C-reactive protein) are five extremely potent characteristics that, when combined, can accurately predict mortality in 96% of cases. By combining XGBoost feature importance with neural network classification, the optimal approach can predict mortality with exceptional accuracy from infectious disease, along with achieving a precision rate of 90% up to 16 days before the event. The studies suggested model's excellent predictive performance and practicality were confirmed through testing with three instances that depended on the days to the outcome. By carefully analyzing and identifying patterns in these significant biomarkers insightful information has been obtained for simple application. This study offers potential remedies that could accelerate decision-making for targeted medical treatments within healthcare systems, utilizing a timely, accurate, and reliable method.

RNA editing in host lncRNAs as potential modulator in SARS-CoV-2 variants-host immune response dynamics

Both host and viral RNA editing plays a crucial role in host's response to infection, yet our understanding of host RNA editing remains limited. In this study of in-house generated RNA sequencing (RNA-seq) data of 211 hospitalized COVID-19 patients with PreVOC, Delta, and Omicron variants, we observed a significant differential editing frequency and patterns in long non-coding RNAs (lncRNAs), with Delta group displaying lower RNA editing compared to PreVOC/Omicron patients. Notably, multiple transcripts of UGDH-AS1 and NEAT1 exhibited high editing frequencies. Expression of ADAR1/APOBEC3A/APOBEC3G and differential abundance of repeats were possible modulators of differential editing across patient groups. We observed a shift in crucial infection-related pathways wherein the pathways were downregulated in Delta compared to PreVOC and Omicron. Our genomics-based evidence suggests that lncRNA editing influences stability, miRNA binding, and expression of both lncRNA and target genes. Overall, the study highlights the role of lncRNAs and how editing within host lncRNAs modulates the disease severity.

SARS-CoV-2 virus-like particle variants alpha and delta mimic the native viruses in their differential inflammasome activating potential

The emerging SARS-CoV-2 variants are evolving to evade human immunity and differ in their pathogenicity. While evasion of the variants from adaptive immunity is widely investigated, there is a paucity of knowledge about their interactions with innate immunity. Inflammasome assembly is one of the most potent mechanisms of the early innate response to viruses, but when it is inappropriate, it can perpetuate tissue damage. In this study, we focused on the capacity of SARS-CoV-2 Alpha and Delta variants to activate the NLRP3 inflammasome. We compared the macrophage activation, particularly the inflammasome formation, using Alpha- and Delta-spike virus-like particles (VLPs). We found that VLPs of both variants activated the inflammasome even without a priming step. Delta-spike VLPs had a significantly stronger effect on triggering pyroptosis and inflammasome assembly in THP-1 macrophages than did Alfa-spike VLPs. Cells treated with Delta VLPs showed greater cleavage of caspase-1 and IL-1β release. Furthermore, Delta VLPs induced stronger cytokine secretion from macrophages and caused essential impairment of mitochondrial respiration in comparison to Alpha VLPs. Additionally, infection of primary human monocyte-derived macrophages with the SARS-CoV-2 variants confirmed the observations in VLPs. Collectively, we revealed that SARS-CoV-2 Delta had a greater impact on the inflammasome activation, cell death and mitochondrial respiration in macrophages than did the Alpha variant. Importantly, the differential response to the SARS-CoV-2 variants can influence the efficacy of therapies targeting the host's innate immunity.

Unraveling Acute and Post-COVID Cytokine Patterns to Anticipate Future Challenges

The aims of this study were to analyze cytokine profiles in patients with COVID-19, gain insights into the immune response during acute infection, identify cytokines associated with disease severity and post-COVID complications, and explore potential biomarkers for prognosis and therapeutic targets. Using a multiplex analysis, we studied the cytokine pattern in 294 acute COVID-19 and post-COVID patients with varying severities of infection. Our findings revealed that disease severity was associated with elevated levels of IL-15, IL-8, and fractalkine. Severe/extremely severe forms in comparison with mild/moderate disease were associated with MCP-1, IFNa2, IL-7, IL-15, EGF, IP-10, IL-8, Eotaxin, FGF-2, GROa, sCD40L, and IL-10. The key cytokines of post-COVID are FGF-2, VEGF-A, EGF, IL-12(p70), IL-13, and IL-6. By the sixth month after recovering from a coronavirus infection, regardless of disease severity, some patients may develop complications such as arterial hypertension, type 2 diabetes mellitus, glucose intolerance, thyrotoxicosis, atherosclerosis, and rapid progression of previously diagnosed conditions. Each complication is characterized by distinct cytokine profiles. Importantly, these complications can also be predicted during the acute phase of the coronavirus infection. Understanding cytokine patterns can aid in predicting disease progression, identifying high-risk patients, and developing targeted interventions to improve the outcomes of COVID-19.

Trends in the Epidemiology of Pneumocystis Pneumonia in Immunocompromised Patients without HIV Infection

The increasing morbidity and mortality of life-threatening Pneumocystis pneumonia (PCP) in immunocompromised people poses a global concern, prompting the World Health Organization to list it as one of the 19 priority invasive fungal diseases, calling for increased research and public health action. In response to this initiative, we provide this review on the epidemiology of PCP in non-HIV patients with various immunodeficient conditions, including the use of immunosuppressive agents, cancer therapies, solid organ and stem cell transplantation, autoimmune and inflammatory diseases, inherited or primary immunodeficiencies, and COVID-19. Special attention is given to the molecular epidemiology of PCP outbreaks in solid organ transplant recipients; the risk of PCP associated with the increasing use of immunodepleting monoclonal antibodies and a wide range of genetic defects causing primary immunodeficiency; the trend of concurrent infection of PCP in COVID-19; the prevalence of colonization; and the rising evidence supporting de novo infection rather than reactivation of latent infection in the pathogenesis of PCP. Additionally, we provide a concise discussion of the varying effects of different immunodeficient conditions on distinct components of the immune system. The objective of this review is to increase awareness and knowledge of PCP in non-HIV patients, thereby improving the early identification and treatment of patients susceptible to PCP.

IL-10/IL-6 ratio from nasal & oral swab samples, acts as an inflammatory indicator for COVID-19 patients infected with the delta variant

Background

Hyper-inflammatory immune response of SARS-CoV-2 is often characterized by the release of multiple pro-inflammatory cytokines with an impact on the expression of numerous other interleukins (ILs). However, from oral and nasal swab samples the specific quantitative association of the different IL-markers with the disease progression and its relationship with the status of vaccination remains unclear.

Materials and methods

Patients' combined oral and nasal swab samples were collected from both non-vaccinated and double-vaccinated individuals with high (Ct value < 25) and low (Ct value > 30) viral loads, along with uninfected donors. None of the patients were critically ill, or needed ICU support. The expression of different cytokines (IL6, IL10, IL1B, IFNG) and mucin (MUC5AC, MUC1) markers were assessed between different groups by qRT-PCR. The important cytokine markers differentiating between vaccinated and non-vaccinated patients were identified by PCA.

Conclusion

IL6 expression was higher in non-vaccinated COVID-19 patients infected with delta-variant irrespective of their viral-load compared to uninfected individuals. However, in double-vaccinated patients, only in high viral-load patients (Ct value < 25), IL6 expression increased. In high viral-load patients, irrespective to their vaccination status, IL10 expression was lower compared to the uninfected control group. Surprisingly, IL10 expression was lower in double-vaccinated patients with Ct value > 30. IL1B, and IFNG expression remained unaltered in uninfected and infected individuals. However, MUC5AC expression was lower in non-vaccinated patients with Ct value < 25 compared to control group. Our study unveiled that IL10/IL6 ratio can be used as a biomarker for COVID-19 patients upon proper establishment of it in a clinical setting.

Organic-Inorganic Hybrid Nanocomposites for Nanotheranostics: Special Focus on Preventing Emerging Variants of SARS-COV-2

The worldwide emerging cases of various respiratory viral diseases and the current escalation of novel coronavirus disease (COVID-19) make people considerably attentive to controlling these viruses through innovative methods. Most re-emerging respiratory diseases envelop RNA viruses that employ attachment between the virus and host cell to get an entry form using the host cell machinery. Emerging variants of COVD-19 also bring about a constant threat to public health as it has wide infectivity and can quickly spread to infect humans. This review focuses on insights into the current investigations to prevent the progression of incipient variants of Severe Acute Respiratory Syndrome Coronavirus (SARS-COV-2) along with similar enveloped RNA viruses that cause respiratory illness in humans and animals. Nanotheranostics is a trailblazing arena of nanomedicine that simultaneously helps prevent or treat diseases and diagnoses. Nanoparticle coating and nanofibers were extensively explored, preventing viral contaminations. Several studies have proven the virucidal activities of metal nanoparticles like copper, silver, and titanium against respiratory viral pathogens. Worldwide many researchers have shown surfaces coated with ionic nanoparticles like zinc or titanium act as potent antiviral agents against RNA viruses. Carbon nanotubes, quantum dots, silica nanoparticles (NPs), polymeric and metallic nanoparticles have also been explored in the field of nanotheranostics in viral detection. In this review, we have comprehensively discussed different types of metallic, ionic, organic nanoparticles and their hybrids showing substantial antiviral properties to stop the progression of the novel coronavirus disease focused on three key classes: prevention, diagnostics, and treatment.

COVID-19 vaccine hesitancy among health workers in rural Uganda: A mixed methods study

Background

COVID-19 vaccination is the latest preventive intervention strategy in an attempt to control the global pandemic. Its efficacy has come under scrutiny because of break through infections among the vaccinated and need for booster doses. Besides, although health workers were prioritized for COVID-19 vaccine in most countries, anecdotal evidence points to high levels of reluctance to take the vaccine among health workers. We assessed COVID-19 vaccine hesitancy among health workers in Dokolo district, northern Uganda.

Methods

This was a mixed-method, cross-sectional descriptive study. A customised self-administered data collection tool was used to collect quantitative data on characteristics, vaccination status and factors for or rejection of vaccine uptake. We conducted multivariable logistic regression to assess the association between selected exposures and vaccine hesitancy using Stata version 15. Conversely, qualitative data were collected using key informant interviews (KIIs) among 15 participants that were purposively selected. Data were analysed using thematic content analysis with the help of NVivo 12.0.

Results

Of the 346 health workers enrolled, (13.3% [46/346]) were vaccine hesitant. Factors associated with vaccine hesitancy included fear of side effects (Adjusted Odds Ratio [AOR]: 2.55; 95% Confidence Interval [95%CI]: 1.00, 6.49) and health workers' lack of trust in the information provided by health authorities (AOR: 6.74; 95% CI: 2.43, 18.72). Similar factors were associated with vaccine hesitancy when we used the vaccine hesitancy score. Fear of side effects, distrust in vaccine stakeholders, and lack of trust in the vaccine were barriers to COVID-19 vaccination among health workers.

Conclusion

A small proportion of health workers were found to be hesitant to take the COVID-19 vaccine in this study. The paucity of COVID-19 vaccine safety information, which eroded the health workers' trust in the information they received on the vaccine, was responsible for health workers hesitancy to take up the vaccine in Uganda.

mRNA vaccines against SARS-CoV-2 induce comparably low long-term IgG Fc galactosylation and sialylation levels but increasing long-term IgG4 responses compared to an adenovirus-based vaccine

Background

The new types of mRNA-containing lipid nanoparticle vaccines BNT162b2 and mRNA-1273 and the adenovirus-based vaccine AZD1222 were developed against SARS-CoV-2 and code for its spike (S) protein. Several studies have investigated short-term antibody (Ab) responses after vaccination.

Objective

However, the impact of these new vaccine formats with unclear effects on the long-term Ab response - including isotype, subclass, and their type of Fc glycosylation - is less explored.

Methods

Here, we analyzed anti-S Ab responses in blood serum and the saliva of SARS-CoV-2 naïve and non-hospitalized pre-infected subjects upon two vaccinations with different mRNA- and adenovirus-based vaccine combinations up to day 270.

Results

We show that the initially high mRNA vaccine-induced blood and salivary anti-S IgG levels, particularly IgG1, markedly decrease over time and approach the lower levels induced with the adenovirus-based vaccine. All three vaccines induced, contrary to the short-term anti-S IgG1 response with high sialylation and galactosylation levels, a long-term anti-S IgG1 response that was characterized by low sialylation and galactosylation with the latter being even below the corresponding total IgG1 galactosylation level. Instead, the mRNA, but not the adenovirus-based vaccines induced long-term IgG4 responses - the IgG subclass with inhibitory effector functions. Furthermore, salivary anti-S IgA levels were lower and decreased faster in naïve as compared to pre-infected vaccinees. Predictively, age correlated with lower long-term anti-S IgG titers for the mRNA vaccines. Furthermore, higher total IgG1 galactosylation, sialylation, and bisection levels correlated with higher long-term anti-S IgG1 sialylation, galactosylation, and bisection levels, respectively, for all vaccine combinations.

Conclusion

In summary, the study suggests a comparable "adjuvant" potential of the newly developed vaccines on the anti-S IgG Fc glycosylation, as reflected in relatively low long-term anti-S IgG1 galactosylation levels generated by the long-lived plasma cell pool, whose induction might be driven by a recently described T_H1-driven B cell response for all three vaccines. Instead, repeated immunization of naïve individuals with the mRNA vaccines increased the proportion of the IgG4 subclass over time which might influence the long-term Ab effector functions. Taken together, these data shed light on these novel vaccine formats and might have potential implications for their long-term efficacy.

HIV and SARS-CoV-2 Co-Infection: From Population Study Evidence to In Vitro Studies

Human immunodeficiency virus type 1 (HIV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have caused two major viral outbreaks during the last century. Two major aspects of HIV-1 and SARS-CoV-2 co-infection have been extensively investigated and deserve attention. First, the impact of the co-infection on the progression of disease caused by HIV-1 or SARS-CoV-2. Second, the impact of the HIV-1 anti-retroviral treatment on SARS-CoV-2 infection. In this review, we aim to summarize and discuss the works produced since the beginning of the SARS-CoV-2 pandemic ranging from clinical studies to in vitro experiments in the context of co-infection and drug development.

Delta variant (B.1.617.2) of SARS-CoV-2: Mutations, impact, challenges and possible solutions

Since commencement of COVID-19 pandemic, several SARS-CoV-2 variants have emerged amid containment efforts via vaccination. The Delta variant (B.1.617.2), discovered in October 2020, was designated as a VOC by the WHO on May 11, 2021. The enhanced transmissibility of Delta variant has been associated with critical mutations such as D614G, L452R, P681R, and T478K in the S-protein. The increased affinity of the S-protein and ACE2 has been postulated as a key reason for decreased vaccine efficacy. As per evidence, the Delta variant possesses increased transmissibility and decreased vaccine efficacy compared to other VOCs like Alpha and Beta. This has led to concerns regarding the acquisition of novel mutations in the Delta variant and outbreaks in vulnerable communities, including vaccinated people. In this mini-review of Delta variant, we have explained its evolution and characteristics, the impact of spike mutations on infectivity and immune evasion, and measures to combat future outbreaks.

Survival analysis of patients with COVID-19 admitted at six hospitals in Uganda in 2021: a cohort study

Background

Assessing factors associated with mortality among COVID-19 patients could guide in developing context relevant interventions to mitigate the risk. The study aimed to describe mortality and associated factors among COVID-19 patients admitted at six health facilities in Uganda.

Methods

We reviewed medical records of patients admitted with COVID-19 between January 1st 2021 and December 31st 2021 in six hospitals in Uganda. Using Stata version 17.0, Kaplan Meier and Cox regression analyses were performed to describe the time to death and estimate associations between various exposures and time to death. Finally, accelerated failure time (AFT) models with a lognormal distribution were used to estimate corresponding survival time ratios.

Results

Out of the 1040 study participants, 234 (22.5%: 95%CI 12.9 to 36.2%) died. The mortality rate was 30.7 deaths per 1000 person days, 95% CI (26.9 to 35.0). The median survival time was 33 days, IQR (9–82). Factors associated with time to COVID-19 death included; age ≥ 60 years [adjusted hazard ratio (aHR) = 2.4, 95% CI: [1.7, 3.4]], having malaria test at admission [aHR = 2.0, 95% CI:[1.0, 3.9]], a COVID-19 severity score of severe/critical [aHR = 6.7, 95% CI:[1.5, 29.1]] and admission to a public hospital [aHR = 0.4, 95% CI:[0.3, 0.6]]. The survival time of patients aged 60 years or more is estimated to be 63% shorter than that of patients aged less than 60 years [adjusted time ratio (aTR) 0.37, 95% CI 0.24, 0.56]. The survival time of patients admitted in public hospitals was 2.5 times that of patients admitted in private hospitals [aTR 2.5 to 95%CI 1.6, 3.9]. Finally, patients with a severe or critical COVID-19 severity score had 87% shorter survival time than those with a mild score [aTR 0.13, 95% CI 0.03, 0.56].

Conclusion

In-hospital mortality among COVID-19 patients was high. Factors associated with shorter survival; age ≥ 60 years, a COVID-19 severity score of severe or critical, and having malaria at admission. We therefore recommend close monitoring of COVID-19 patients that are elderly and also screening for malaria in COVID-19 admitted patients.

Effectiveness of Covid-19 vaccines (CovishieldTM and Covaxin ®) in healthcare workers in Mumbai, India: A retrospective cohort analysis

BACKGROUND

India started its vaccination programme for Coronavirus-19 infection (COVID-19) on 16 January 2021 with CovishieldTM (Oxford/Astra Zeneca vaccine manufactured by Serum Institute of India) and Covaxin ® (Bharat Biotech, India). We designed the present study to study the effectiveness of vaccines for COVID-19 in prevention of breakthrough infections and severe symptomatic cases among health care workers in a real-life scenario in Mumbai, India. Furthermore, we also wanted to study the factors associated with this effectiveness.

METHODS

This is cohort analysis of secondary data of 2762 individuals working in a tertiary health care setting in Mumbai, India (16 January 2021 to 16 October 2021). Vaccination records of all groups of health care staff (including the date of vaccination, type of vaccine taken, and date of positivity for COVID-19) were maintained at the hospital. The staff were tested for COVID-19 at least once a week and when symptomatic. The observation time for everyone was divided into unvaccinated, partially vaccinated (14 days after the first dose); and fully vaccinated (14 days after the second dose). If the individual was found to be positive, the day of positivity was considered the 'day of the event' for that individual. We combined unvaccinated/partially vaccinated into one group and completely vaccinated in the other group. We estimated hazard ratios (HR) and their 95% confidence intervals. The vaccine effectiveness (VE) was assessed as (1-HR)*100.

RESULTS

The mean age (SD) of the study participants was 32.3 (8.3) years; majority of these individuals had taken Covishield TM (99.0%) and only 0.9% (n = 27) had taken Covaxin ®. The incidence rate in the overall population was 0.067/100 person-days (PD). The incidence rate was significantly higher in the unvaccinated/partially vaccinated group compared with the fully vaccinated group (0.0989 / 100 PD vs 0.0403/100 PD; p < 0.001). The adjusted HR (aHR) in the fully vaccinated group compared with the unvaccinated/partially vaccinated group in the complete cohort was 0.30 (95% CI: 0.23, 0.39). Thus, the vaccine effectiveness (VE) for full vaccination was 70% (95% CI: 61%, 77%). It remained the same in the Covishield TM only cohort. The VE in completely vaccinated and with a history of previous infection was 88% (95% CI: 80%, 93%). Only 11 health care workers required hospitalization over the entire observation period; the incidence rate in our cohort was 0.0016 / 100 PD. None of the HCWs reported any severe adverse events after vaccination.

CONCLUSIONS

In this real-world scenario, we did find that complete vaccination reduced the rate of infection, particularly severe infection in health care personnel even during the severe delta wave in the country. Even among those infected, the hospitalisation rates were very low, and none died. We did not record any major side effects of vaccination in these personnel. Previous infection with COVID-19 and complete vaccination had a significantly higher effectiveness in prevention of infection.