[COVID-19: epidemiology and mutations : An update]

Transcriptomic analysis of differential expression between surviving and nonsurviving patients infected by the SARS-CoV-2 Delta variant

For a more precise understanding of the course of the pathological process in patients with severe COVID-19, it is necessary to continue the search for factors that affect the course of the pathological process and the possibility of a favorable outcome in critically ill patients. Comparative RNA-seq analysis of the transcriptome of peripheral blood mononuclear cell (PBMCs) in patients with a severe clinical course of COVID-19 caused by the SARS-CoV-2 Delta strain revealed a number of differentially expressed genes that distinguish patients with different clinical outcomes (survivors vs. nonsurvivors) in the period of 30 days after admission to the hospital. Most of them are associated with the "negative regulation of viral process" and "negative regulation of immune response" clusters. Moreover, in surviving patients, there is increased expression of the key genes C1QB, C1QA, ISG15, SERPING1, VSIG4, KLRD1, TRPM4, and HFE incorporated in these clusters. Among these key genes, the ISG15 gene, which links several clusters of gene ontology enrichments and encodes an interferon-induced ubiquitin-like protein, deserves special attention. Its product, ISG15, is known to be a primary substrate for SARS-CoV-2 protease PLpro, which plays a role in counteracting hosts' antiviral mechanisms.

Detection of SARS-CoV-2 binding receptors and miscellaneous targets as well as mucosal surface area of the human lacrimal drainage system

PURPOSE

Our aim was to evaluate a potential role for the lacrimal drainage system (LDS) as a portal of entry and conduit for SARS-CoV-2 in human infection. We also investigate the mucosal surface area. The relatively long tear contact time in a closed system raises the possibility that this pathway may contribute to the initiation of systemic infection. We looked for expression of ACE2, the main receptor for SARS-CoV-2, as well as cofactors such as TMPRSS2 and other enzymes such as cathepsinB, CD147, elastase1, furin, neuropilin1, neuropilin2, TMPRSS11D and trypsin which also play a role in SARS-CoV-2 infection, in this system.

METHODS

Human tissue samples of the draining tear ducts from body donors were analyzed by RT-PCR, Western blot and immunohistochemistry. It is not known whether the respective body donors were Sars-Cov-2 positive at any time; they were negative when they entered the institute. Besides, the draining LDS of body donors were measured to determine the mucosal surface in the lacrimal system.

RESULTS

The expression of the main receptor studied, ACE2, cofactors such as TMPRSS2 and other enzymes such as cathepsinB, CD147, elastase1, furin, neuropilin1, neuropilin2, TMPRSS11D and trypsin were all detected at the gene and protein level. The average mucosal surface area of the lacrimal sac and nasolacrimal duct was calculated to be 110 mm2.

CONCLUSION

The results show the presence of all analyzed receptors in the efferent LDS. With an average tear passage time of 3 min and a relatively large mucosal surface area, the LDS could therefore be considered as a portal of entry and conduit for SARS-CoV-2. In addition, it represents a surface that should be taken into consideration in the administration of topically applied medication to the ocular surface.

Transmissibility of the variant of concern for SARS-CoV-2 in six regions

Introduction

Differences in transmissibility of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in different districts are hard to assess. To address this, our study focused on calculating the Real-time reproduction number (R t ) for these variants in different regions.

Methods

According to the criteria defined by the World Health Organization (WHO), the global landscape was categorized into six distinct regions. In each region, the predominant SARS-CoV-2 variant was first identified based on the proportion of variant sequencing analysis results. Then, using serial interval (SI) parameters, we calculated R t for the relevant Variant of Concern (VOC) in each region. This approach enabled us to compare the R t values of the same variant across different regions and analyze the transmissibility of each region's variant in relation to the overall situation in that region.

Results

The progression of VOC for SARS-CoV-2 shows regional variations. However, a common sequence of evolution is observed: Wild-type → Alpha → Beta → Delta → Omicron. Moreover, an increasing trend is discerned within diverse regions where the shift in R t of distinct VOC corresponds with the overarching R t route of SARS-CoV-2 in specific regions.

Conclusion

As the COVID-19 pandemic advances, regional epidemiological trends are aligning, likely due to similar virus mutations and shared public health strategies, suggesting opportunities for standardized global responses.

Extracellular and intracellular antiviral effects of ultraviolet A against severe acute respiratory syndrome coronavirus-2 are variant-independent

Under controlled settings, narrow-band ultraviolet A (UVA) exposure exerts antiviral effects both in vivo and in vitro. The effect is thought to be mediated via direct effect on viral particles and indirectly, by modulation of metabolic pathways of host cells. We aimed to explore the extracellular and intracellular antiviral effects of UVA exposure against Alpha, Beta, and Delta variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

Vero E6 kidney normal epithelial cells and human tracheal epithelial cells were infected with Alpha, Beta, and Delta variants in a BSL-3 laboratory. To assess extracellular effects, SARS-CoV-2 variants were directly exposed to a single dose of UVA prior to infection of the host cells (Vero E6 kidney normal epithelial cells and human tracheal epithelial cells) The intracellular effects of UVA were assessed by first infecting the cells with SARS-CoV-2 variants followed by UVA treatment of infected cell monolayers. Efficacy was quantified by both plaque reduction assay and quantitative real-time polymerase chain reaction. Additionally, transcriptomic analysis was performed on exposed Vero E6 cells to assess differentially expressed genes and canonical pathways as compared to controls.

RESULTS

SARS-CoV-2 Alpha, Beta and Delta variants are susceptible to UVA exposure prior to infection of Vero E6 cells. Importantly, the UVA-driven reduction in Delta variant load could be reproduced in human primary tracheal cells. Beta and Delta variants load also significantly decreased during Vero E6 cells intracellular experiments. UVA-driven reductions in viral loads ameliorate several host metabolic pathways, including canonical pathways related to viral infection and interferon signaling.

CONCLUSION

Narrow-band UVA exhibits both extracellular effects on SARS-CoV-2 viral particles and intracellular effects on infected cells with SARS-CoV-2. Efficacy appears to be variant independent.

Association of hypernatremia with mortality in patients with COVID-19: A systematic review and meta-analysis

BACKGROUND

The COVID-19 pandemic worldwide has caused varying degrees of severity of lung damage in patients, with acute respiratory distress and death in severe cases. However, this is not directly caused by the virus itself, but by the production of inflammasome by monocytes in the body, leading to a systemic inflammatory response, which results in a very poor clinical prognosis for patients with COVID-19.

OBJECTIVE

The purpose of this meta-analysis was to look at the relationship between hypernatremia and mortality in COVID-19 patients.

METHODS

We searched the PubMed, Web of Science, Embase, and Cochrane databases for articles published from the inception of the database until August 27, 2022. Three researchers reviewed the literature, retrieved data, and assessed the quality of the literature, respectively. A meta-analysis was performed using State 17 software to assess the value of the effect of hypernatremia on mortality in patients with new coronavirus pneumonia.

RESULTS

A total of nine publications was finally included in this study, including a total of 11,801 patients with COVID-19, including 1278 in the hypernatremia group and 10,523 in the normonatremia group. Meta-analysis showed that hypernatremia was associated with mortality in patients with COVID-19 [OR = 4.15, 95% CI (2.95-5.84), p = .002, I² = 66.7%] with a sensitivity of 0.36 [0.26, 0.48] and a specificity of 0.88 [0.83, 0.91]. The posterior probability of mortality was 42% in patients with COVID-19 hypernatremia and 15% in patients who did not have COVID-19 hypernatremia.

CONCLUSION

According to available data, hypernatremia is associated with death in patients with COVID-19.

Effectiveness of Rapid Antigen Testing in Forensic Cases of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, Including Delta Variant

ABSTRACT

The polymerase chain reaction is indispensable for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in forensic cases. However, studies regarding the effectiveness of rapid antigen testing (RAT) in forensic cases remain limited. Therefore, we investigated the efficacy of RAT compared with reverse-transcription quantitative polymerase chain reaction (RT-qPCR) for confirming SARS-CoV-2 infection (including the delta variant). Before the external examination or autopsy, we collected samples from the nasopharyngeal mucosa, which were then assessed via RAT (QuickNavi COVID-19 Ag kit, QuickNavi-Flu+COVID-19 Ag kit) and RT-qPCR. Reverse-transcription quantitative polymerase chain reaction results were positive in 73 of 1255 cases, and 21 cases were identified as those of delta variants. Low RT-qPCR threshold cycle value cases and delta variant infections were more likely to result in coronavirus disease-related deaths. The sensitivity of the QuickNavi COVID-19 Ag kit was 76.32%, and that of the QuickNavi-Flu+COVID-19 Ag kit was 77.14%. The specificity of both RATs was 100%. In QuickNavi COVID-19 Ag kit cases, delta variant cases showed lower sensitivity than non-delta variant cases, even for a similar viral load. Thus, RAT in forensic cases is sufficiently useful as a screening test for SARS-CoV-2 infection. However, RAT carries a risk of false negatives, especially for delta variant cases.

An Executed Plan to Combat COVID-19 in the United States

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019. To date, this coronavirus is responsible for greater than 90 million cases in the United States and more than 1 million confirmed deaths. When this virus came to the United States, testing was unorganized, no effective treatments were known, and no vaccines had been discovered. A plan to correct these deficiencies through cooperative science and efficient clinical trials was implemented to combat this novel virus. This plan developed efficient and inexpensive tests, highly effective medicines to treat and prevent disease progression, and vaccines to immunize the population.

Knowledge, perception, and acceptance toward the booster dose of COVID-19 vaccine among patients visiting dental clinics in Aseer region of KSA

Scientists have emerged with innovative research on non-human primates showing that the booster dose of the COVID-19 vaccine increases neutralizing antibody levels against all variants. The current cross-sectional survey was designed to evaluate the knowledge, perception, and acceptance of the booster dose of the COVID-19 vaccine among the patients visiting the various dental clinics in Aseer region, Kingdom of Saudi Arabia. A total of 609 dental patients were selected from various dental clinics by a simple random probability sampling method. The questionnaire was designed in multiple languages and categorized as demographic information, knowledge, perception, and acceptance of participants to a booster dose. An anonymous, self-administered, closed-ended online, and paper-based questionnaire was used to assess the above parameters. In the current survey, the majority of the participants were Saudis (80.8%) with an age mean of 37.7 ± 8.7 years. About 68.6% (418 out of 609) of participants had poor knowledge about the booster dose. Significant differences in the levels of knowledge were found in relation to gender, area of residency, education, nationality, and occupation. The distribution of level of perception of booster dose differs significantly among participants of different marital statuses and nationalities. Hesitation to booster was reported more in the rural than in the urban population. Despite a low level of knowledge, a higher level of good perception and acceptance of booster doses were reported among the studied population.

Aspects of Antiviral Strategies Based on Different Phototherapy Approaches: Hit by the Light

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused the COVID-19 pandemic spreading around the world from late 2019, served as a ruthless reminder of the threat viruses pose to global public health. The synthesis of new antiviral drugs, as well as repurposing existing products, is a long-term ongoing process which has challenged the scientific community. One solution could be an effective, accessible, and rapidly available antiviral treatment based on phototherapy (PT). PT has been used to treat several diseases, and relies on the absorption of light by endogenous molecules or exogenous photosensitizers (PS). PT has often been used in cancer treatment and prophylaxis, and as a complement to established chemotherapy and immunotherapy in combined therapeutic strategy. Besides significant applications in anticancer treatment, studies have demonstrated the beneficial impact of PT on respiratory, systemic, emerging, and oncogenic viral infections. The aim of this review was to highlight the potential of PT to combat viral infections by summarizing current progress in photodynamic, photothermal, and photoacoustic approaches. Attention is drawn to the virucidal effect of PT on systemic viruses such as the human immunodeficiency virus and human herpes viruses, including the causative agent of Kaposi sarcoma, human herpes virus (HHV8). PT has good potential for disinfection in anti-norovirus research and against pandemic viruses like SARS-CoV-2.

Clinical-Epidemiology Aspect of Inpatients With Moderate or Severe COVID-19 in a Brazilian Macroregion: Disease and Countermeasures

COVID-19, also known as coronavirus disease 2019, is an infectious viral disease caused by SARS-CoV-2, a novel coronavirus. Since its emergence, its epidemiology has been explored; however, for some regions of the world, COVID-19's behavior, incidence, and impact remain unclear. In continental nations like Brazil, this lack of knowledge results in nonuniform control, prevention, and treatment measures, which can be controversial in some locations. This study aimed to describe the epidemiological profile of patients with COVID-19 in the macroregion of Triângulo Sul in the state of Minas Gerais (MG), Brazil. Between March 25 and October 21, 2020, data were collected and statistically analyzed from 395 hospitalized patients in the city of Uberaba, MG, suspected to have moderate or severe forms of the disease. Of the 395 suspected cases, 82% were confirmed to be positive for COVID-19. The mean age of positive patients was 58.4 years, and 60.76% were male. Following these patients throughout their hospitalization, a mortality rate of 31.3% was observed. In the population positive for COVID-19, the risk of death increased by 4% for each year of the patient's age. Likewise, the older the patient, the longer their hospitalization and the higher the risk of developing acute respiratory failure. Among the treatments tested in patients, heparin was associated with protection against mortality, and the absence of anticoagulant use was linked to a more than six times greater risk of death. Finally, comorbidities in patients with COVID-19 were positively correlated with increased hospitalization time. In summary, this study revealed that age, presence of comorbidities, length of hospitalization, and drug treatment considerably altered COVID-19's lethality. To understand infection rates and the factors involved in COVID-19's lethality, knowledge of the local epidemiology is necessary.

Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19

As the new year of 2020 approaches, an acute respiratory disease quietly caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease 2019 (COVID-19) was reported in Wuhan, China. Subsequently, COVID-19 broke out on a global scale and formed a global public health emergency. To date, the destruction that has lasted for more than two years has not stopped and has caused the virus to continuously evolve new mutant strains. SARS-CoV-2 infection has been shown to cause multiple complications and lead to severe disability and death, which has dealt a heavy blow to global development, not only in the medical field but also in social security, economic development, global cooperation and communication. To date, studies on the epidemiology, pathogenic mechanism and pathological characteristics of SARS-CoV-2-induced COVID-19, as well as target confirmation, drug screening, and clinical intervention have achieved remarkable effects. With the continuous efforts of the WHO, governments of various countries, and scientific research and medical personnel, the public's awareness of COVID-19 is gradually deepening, a variety of prevention methods and detection methods have been implemented, and multiple vaccines and drugs have been developed and urgently marketed. However, these do not appear to have completely stopped the pandemic and ravages of this virus. Meanwhile, research on SARS-CoV-2-induced COVID-19 has also seen some twists and controversies, such as potential drugs and the role of vaccines. In view of the fact that research on SARS-CoV-2 and COVID-19 has been extensive and in depth, this review will systematically update the current understanding of the epidemiology, transmission mechanism, pathological features, potential targets, promising drugs and ongoing clinical trials, which will provide important references and new directions for SARS-CoV-2 and COVID-19 research.

Complete AV Block in Vaccinated COVID-19 Patient

Background. Coronavirus 2019 (COVID-19) was initially identified approximately in December 2019 at Wuhan, China, as patients presented with vague prodromal and respiratory symptoms. With the developing investigation of its clinical manifestation, cardiac symptoms have been widely reported including acute coronary syndromes, myocarditis, arrhythmias, heart failure, and cardiac arrest. Case Summary. An 84 year-old male with history of coronary artery disease, hypertension, and hyperlipidemia presented to an outside urgent care with prodromal symptoms. The patient had received the second Pfizer vaccine three months prior. This presentation, he was found to be COVID-19 positive as well as bradycardic with a complete AV block. He was transferred to a tertiary center for further evaluation and management. However, after transfer, the patient refused further invasive cardiac interventions and after medical therapy was discharged home in complete AV block. Discussion. We report a novel case of a Pfizer-vaccinated patient whose initial presenting symptoms of COVID-19 included a complete AV block as well as the challenges and difficulties in approaching such patients. Although this patient’s etiology of his complete AV block may result from multiple factors, given the acuity in setting of concurrent COVID-19 infections, top differentials include viral myocarditis, COVID-19-induced Takotsubo cardiomyopathy complicated by a complete AV-block, or a direct conduction pathway infection. Management of patients should focus on a multidisciplinary approach, and prevention is critical via vaccination.

Emergence of Two Distinct SARS-CoV-2 Gamma Variants and the Rapid Spread of P.1-like-II SARS-CoV-2 during the Second Wave of COVID-19 in Santa Catarina, Southern Brazil

The western mesoregion of the state of Santa Catarina (SC), Southern Brazil, was heavily affected as a whole by the COVID-19 pandemic in early 2021. This study aimed to evaluate the dynamics of the SARS-CoV-2 virus spreading patterns in the SC state from March 2020 to April 2021 using genomic surveillance. During this period, there were 23 distinct variants, including Beta and Gamma, among which the Gamma and related lineages were predominant in the second pandemic wave within SC. A regionalization of P.1-like-II in the Western SC region was observed, concomitant to the increase in cases, mortality, and the case fatality rate (CFR) index. This is the first evidence of the regionalization of the SARS-CoV-2 transmission in SC and it highlights the importance of tracking the variants, dispersion, and impact of SARS-CoV-2 on the public health systems.

Covid-19 vaccines work but other factors play a relevant role: a data analysis on spread and mortality in 24 countries

BACKGROUND

The aim was to outline a methodology to monitor the impact of vaccinations in different countries comparing at two different times within countries and between countries the frequency of new cases and Covid-19 related deaths and the percentage of vaccinations conducted.

DESIGN AND METHODS

The 25 countries with the largest increase in SARS-CoV-2 cases on 8 August 2021 were evaluated. In each nation was calculated the proportion of Covid-19 deaths divided per new cases x 100 and the proportion of new cases per 1.000 inhabitants on 10 January 2021 (before vaccinations' distribution) and 8 August 2021 (when large percentage of the population had been vaccinated in many countries).

RESULTS

The study shows that in the countries with the highest number of cases as of 8 August 2021, the proportion of vaccinations carried out in the population correlates negatively with both the proportion between Covid-19 dead people x100 infected people and with the rate of new cases. However, the proportion of vaccinations does not correlate with the differences in the two same indicators considered in the weeks observed, thus additional factors seem to play an important role.

CONCLUSIONS

This work indicates that mass vaccination is associated with a lower spread of the pandemic and, to greater extent, with a lowering of mortality in infected people.

Multivalent Vaccine Strategies in Battling the Emergence of COVID-19 Variants

The emergence of new SARS-CoV-2 variants has led to increased transmission and more severe cases of COVID-19, with some having the ability to escape the existing vaccines. This review discusses the importance of developing new vaccine strategies to keep pace with these variants to more effectively manage the pandemic. Many of the new vaccine approaches include multivalent display of the most highly mutated regions in the SARS-CoV-2 spike protein such that they resemble a virus particle and can stimulate an effective neutralization response. It is hoped that such approaches help to manage the existing pandemic and provide a robust infrastructure toward fast tracking responses across the world in case of future pandemics.