Influenza virus and SARS-CoV-2: pathogenesis and host responses in the respiratory tract

Antiviral Activities of Ethyl Pheophorbides a and b Isolated from Aster pseudoglehnii against Influenza Viruses

Screening of the antiviral and virucidal activities of ethanol extracts from plants endemic to the Republic of Korea revealed the inhibitory activity of a 70% ethanol extract of the whole plant of A. pseudoglehnii (APE) against influenza virus infection. Two chlorophyll derivatives, ethyl pheophorbides a and b, isolated as active components of APE, exerted virucidal effects with no evident cytotoxicity. These compounds were effective only under conditions of direct incubation with the virus, and exerted no effects on the influenza A virus (IAV) surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). Interestingly, virucidal activities of ethyl pheophorbides a and b were observed against enveloped but not non-enveloped viruses, suggesting that these compounds act by affecting the integrity of the viral membrane and reducing infectivity.

Polymeric Materials as Indispensable Tools to Fight RNA Viruses: SARS-CoV-2 and Influenza A

Towards the end of 2019 in Wuhan, suspicions of a new dangerous virus circulating in the air began to arise. It was the start of the world pandemic coronavirus disease 2019 (COVID-19). Since then, considerable research data and review papers about this virus have been published. Hundreds of researchers have shared their work in order to achieve a better comprehension of this disease, all with the common goal of overcoming this pandemic. The coronavirus is structurally similar to influenza A. Both are RNA viruses and normally associated with comparable infection symptoms. In this review, different case studies targeting polymeric materials were appraised to highlight them as an indispensable tool to fight these RNA viruses. In particular, the main focus was how polymeric materials, and their versatile features could be applied in different stages of viral disease, i.e., in protection, detection and treatment.

Effect of Vaccination against SARS-CoV-2 on Long COVID-19: A Narrative Review

Vaccines against SARS-CoV-2 have saved millions of lives and played an important role in containing the COVID-19 pandemic. Vaccination against SARS-CoV-2 is also associated with reduced disease severity and, perhaps, with COVID-19 symptom burden. In this narrative review, we present, in a clinically relevant question-and-answer manner, the evidence regarding the association between vaccination against SARS-CoV-2 and long COVID-19. We discuss how the mechanism of action of vaccines could interplay with the pathophysiology of post-COVID-19 condition. Furthermore, we describe how specific factors, such as the number of vaccine doses and the type of SARS-CoV-2 variants, may affect post-COVID-19 condition. We also discuss the role of timing for vaccination in relation to the onset of long COVID-19 symptoms, as it seems to affect the frequency and severity of the condition. Additionally, we describe the potential modifying effect of age, as well as the association of type and level of immune response with long COVID-19. We also describe how system-specific long COVID-19 sequelae, namely neurocognitive-psychologic symptoms and cardiovascular pathology, could be altered by vaccination. Last, we address the question of whether seasonal influenza vaccination has a meaningful impact on the frequency of long COVID-19.

Mild SARS-CoV-2 infection results in long-lasting microbiota instability

Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology.

IMPORTANCE

Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.

Nucleoside analogs for management of respiratory virus infections: mechanism of action and clinical efficacy

The COVID-19 pandemic has accelerated the development of nucleoside analogs to treat respiratory virus infections, with remdesivir being the first compound to receive worldwide authorization and three other nucleoside analogs (i.e. favipiravir, molnupiravir, and bemnifosbuvir) in the pipeline. Here, we summarize the current knowledge concerning their clinical efficacy in suppressing the virus and reducing the need for hospitalization or respiratory support. We also mention trials of favipiravir and lumicitabine, for influenza and respiratory syncytial virus, respectively. Besides, we outline how nucleoside analogs interact with the polymerases of respiratory viruses, to cause lethal virus mutagenesis or disturbance of viral RNA synthesis. In this way, we aim to convey the key findings on this rapidly evolving class of respiratory virus medication.

Recent trends and advancements in electrochemiluminescence biosensors for human virus detection

Researchers are constantly looking to find new techniques of virus detection that are sensitive, cost-effective, and accurate. Additionally, they can be used as a point-of-care (POC) tool due to the fact that the populace is growing at a quick tempo, and epidemics are materializing greater often than ever. Electrochemiluminescence-based (ECL) biosensors for the detection of viruses have become one of the most quickly developing sensors in this field. Thus, we here focus on recent trends and developments of these sensors with regard to virus detection. Also, quantitative analysis of various viruses (e.g., Influenza virus, SARS-CoV-2, HIV, HPV, Hepatitis virus, and Zika virus) with a specific interest in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was introduced from the perspective of the biomarker and the biological receptor immobilized on the ECL-based sensors, such as nucleic acids-based, immunosensors, and other affinity ECL biosensors.

Molecular and cellular similarities in the brain of SARS-CoV-2 and Alzheimer's disease individuals

Infection with the etiological agent of COVID-19, SARS-CoV-2, appears capable of impacting cognition, which some patients with Post-acute Sequelae of SARS-CoV-2 (PASC). To evaluate neuro-pathophysiological consequences of SARS-CoV-2 infection, we examine transcriptional and cellular signatures in the Broadman area 9 (BA9) of the frontal cortex and the hippocampal formation (HF) in SARS-CoV-2, Alzheimer's disease (AD) and SARS-CoV-2 infected AD individuals, compared to age- and gender-matched neurological cases. Here we show similar alterations of neuroinflammation and blood-brain barrier integrity in SARS-CoV-2, AD, and SARS-CoV-2 infected AD individuals. Distribution of microglial changes reflected by the increase of Iba-1 reveal nodular morphological alterations in SARS-CoV-2 infected AD individuals. Similarly, HIF-1α is significantly upregulated in the context of SARS-CoV-2 infection in the same brain regions regardless of AD status. The finding may help to inform decision-making regarding therapeutic treatments in patients with neuro-PASC, especially those at increased risk of developing AD.

TEASER

SARS-CoV-2 and Alzheimer's disease share similar neuroinflammatory processes, which may help explain neuro-PASC.

Characteristics and Outcomes of Cryptococcosis among Patients with and without COVID-19

The effect of COVID-19 on the risk and prognosis of cryptococcosis is unclear. We compared the characteristics and outcomes of cryptococcosis in patients with and without COVID-19. Patients 18 years and older with cryptococcosis were identified from TriNetX and separated into two cohorts based on a diagnosis of COVID-19 within 3 months of the index diagnosis of cryptococcosis. Differences examined between groups included comorbidities, immunosuppressive medications, ED visits, hospitalizations, ICU admissions, mechanical ventilation, and deaths. The propensity score matching was performed based on demographics and comorbidities. Of the 6998 patients with cryptococcosis included, 4.4% (n = 306) had COVID-19 prior to cryptococcosis. Mortality was higher in patients with COVID-19 compared to those without COVID-19 (14% vs. 11%, p = 0.032). Additionally, those with COVID-19 were older (55.2 ± 14.4 vs. 51.9 ± 15.2 years, p < 0.001) with higher rates of transplant (29% vs. 13%, p < 0.001), neoplastic disease (37% vs. 21%, p < 0.001), chronic kidney disease (42% vs. 18%, p < 0.001), or diabetes (35% vs. 19%, p < 0.001) but not HIV (30% vs. 31%, p = 0.618). Glucocorticoid use was more common in those with COVID-19 (52% vs. 27%, p < 0.001). More patients with COVID-19 required ED visits (29% vs. 23%, p = 0.025) and ICU admission (18% vs. 11%, p < 0.001). After propensity score matching, patients with COVID-19 had higher rates of neoplastic disease, heart failure, chronic kidney disease, and glucocorticoid use but did not experience worse outcomes compared to those without COVID-19. Patients with COVID-19 who developed cryptococcosis had independently higher rates of comorbidities and glucocorticoid use but similar outcomes, including death, versus those without COVID-19.

Analysis of Expression Pattern of snoRNAs in Human Cells A549 Infected by Influenza A Virus

Small nucleolar RNAs (snoRNAs) are a highly expressed class of non-coding RNAs known for their role in guiding post-transcriptional modifications of ribosomal RNAs and small nuclear RNAs. Emerging studies suggest that snoRNAs are also implicated in regulating other vital cellular processes, such as pre-mRNA splicing and 3'-processing of mRNAs, and in the development of cancer and viral infections. There is an emerging body of evidence for specific snoRNA's involvement in the optimal replication of RNA viruses. In order to investigate the expression pattern of snoRNAs during influenza A viral infection, we performed RNA sequencing analysis of the A549 human cell line infected by influenza virus A/Puerto Rico/8/1934 (H1N1). We identified 66 that were upregulated and 55 that were downregulated in response to influenza A virus infection. The increased expression of most C/D-box snoRNAs was associated with elevated levels of 5'- and 3'-short RNAs derived from this snoRNA. Analysis of the poly(A)+ RNA sequencing data indicated that most of the differentially expressed snoRNAs synthesis was not correlated with the corresponding host genes expression. Furthermore, influenza A viral infection led to an imbalance in the expression of genes responsible for C/D small nucleolar ribonucleoprotein particles' biogenesis. In summary, our results indicate that the expression pattern of snoRNAs in A549 cells is significantly altered during influenza A viral infection.

Respiratory illness virus infections with special emphasis on COVID-19

Viruses that emerge pose challenges for treatment options as their uniqueness would not know completely. Hence, many viruses are causing high morbidity and mortality for a long time. Despite large diversity, viruses share common characteristics for infection. At least 12 different respiratory-borne viruses are reported belonging to various virus taxonomic families. Many of these viruses multiply and cause damage to the upper and lower respiratory tracts. The description of these viruses in comparison with each other concerning their epidemiology, molecular characteristics, disease manifestations, diagnosis and treatment is lacking. Such information helps diagnose, differentiate, and formulate the control measures faster. The leading cause of acute illness worldwide is acute respiratory infections (ARIs) and are responsible for nearly 4 million deaths every year, mostly in young children and infants. Lower respiratory tract infections are the fourth most common cause of death globally, after non-infectious chronic conditions. This review aims to present the characteristics of different viruses causing respiratory infections, highlighting the uniqueness of SARS-CoV-2. We expect this review to help understand the similarities and differences among the closely related viruses causing respiratory infections and formulate specific preventive or control measures.

Therapeutic and palliative role of a Unani herbal decoction in COVID-19 and similar respiratory viral illnesses: Phytochemical & pharmacological perspective

ETHNOPHARMACOLOGICAL RELEVANCE

Outbreaks of respiratory viral infections like Severe Acute Respiratory Syndrome, Middle-East Respiratory Syndrome, and Coronavirus Disease-2019 have been a regular occurrence in the past 100 years. A significant proportion of the morbidity and mortality in influenza is attributed to the co-morbidities and complications induced by the disease, involving the vital organs and physiological functions. In this context, traditional medicines offer effective protective, palliative, and therapeutic benefits, as observed in several studies on various types of influenza, including COVID-19. The Unani herbal decoction comprising of 'Unnāb (Ziziphus jujuba Mill. fruit), Sapistān (Cordia dichotoma G. Forst. fruit), and Behīdāna (Cydonia oblonga Mill. seed) was originally prescribed by Hakim Ajmal Khan (1868-1927 AD) for various respiratory ailments as a bronchodilator, anti-inflammatory, and for clearing the respiratory tract. During COVID-19, the decoction was prescribed by the Ministry of Ayurveda, Yoga, Unani, Siddha, and Homeopathy (AYUSH), Government of India, for mild patients in home isolation, and also as a self-care drink for healthy people. Preliminary studies are of the view that the decoction could reduce COVID-19 incidence and prevent severe disease in the population where it was administered.

AIMS OF THE STUDY

We intend to review the pharmacological activity of the Unani decoction ingredients, i.e., Z. jujuba, C. dichotoma, and C. oblonga, in context with respiratory viral infections and their co-morbidities, to develop an understanding of its action mechanism.

METHODOLOGY

We reviewed Unani classical textbooks for information on the therapeutic activity of the decoction ingredients. Scientific studies published in English from the year 2000 onwards on leading scientific websites (PubMed, MEDLINE, Scopus, and Springer) were searched for information regarding the efficacy of the drugs in influenza and its common complications. Non-English language articles, or those published prior to 2000, and those which included plant parts other than those traditionally included in the decoction were excluded.

OBSERVATIONS

A wide range of therapeutic and palliative effects have been observed in the three herbs included in the Unani decoction, including anti-viral, anti-bacterial, immuno-modulatory, anti-inflammatory, hepato-, and nephroprotective, anti-atherosclerotic, anti-tussive, broncho-dilatory, and regulation of gut microbiota. Together, these effects can help to mitigate and prevent most of the complications caused as a result of respiratory viral infections.

CONCLUSION

The combined effects of ingredients in this Unani herbal decoction can potentially help to mitigate most of the pathological changes and complications caused by influenza viruses. With further clinical research, the decoction may be potentially utilized as a prophylactic and therapeutic against viral influenza.

Deficiency of C-reactive protein or human C-reactive protein transgenic treatment aggravates influenza A infection in mice

C-reactive protein (CRP) has been shown to be a potential candidate target in the immunotherapy of severe influenza A infection. However, it is unclear on the pathogenesis associated with CRP in influenza infections. Here, we used influenza A H1N1 CA04 to infect human CRP transgenic mice (KI), CRP knockout mice (KO), and wild-type mice (WT), respectively, and compared the viral pathogenicity and associated immune response in those mice. The results showed that CA04 infection resulted in 100%, 80%, and 60% death in KO, KI, and WT mice, respectively. Compared to WT mice, CA04 infection resulted in higher TCID50 in lungs on day 3 after infection but lowered HI antibody titers in sera of survivors on day 21 after infection in KI mice. ELISA assay showed that IFN-γ concentration was significantly increased in sera of WT, KI, or KO mice on day 7 after infection, and IL-17 was remarkably increased in sera of WT mice but decreased in sera of KI mice while no significant change in sera of KO mice on day 3 or 7 after infection. Quantitative RT-PCR showed that the relative expression levels of immune checkpoint CTLA-4, LAIR-1, GITR, BTLA, TIM-3, or PD-1 mRNA in the lung presented decreased levels on day 3 or 7 after infection in KI or KO mice. The correlation analysis showed that mRNA expression levels of the 6 molecules positively correlated with viral TICD50 in WT mice but negatively correlated with viral TCID50 in KI or KO mice. However, only LAIR-1 presented a significant correlation in each lung tissue of WT, KI, or KO mice with CA07 infection statistically. IHC results showed that LAIR-1 positive cells could be found in WT, KO, or KI mice lung tissues with CA04 infection, and the positive cells were mainly distributed in an inflammatory dense area. Our results suggested that deficiency of CRP or human CRP transgenic treatment aggravates influenza A virus infection in mice. CRP is a double sword in immune regulation of influenza infection in which IL-17 and immune checkpoint may be involved.

Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS2) affected the geriatric population. Among research models, Golden Syrian hamsters (GSH) are one of the most representative to study SARS2 pathogenesis and host responses. However, animal studies that recapitulate the effects of SARS2 in the human geriatric population are lacking. To address this gap, we inoculated 14 months old GSH with a prototypic ancestral strain of SARS2 and studied the effects on virus pathogenesis, virus shedding, and respiratory and gastrointestinal microbiome changes. SARS2 infection led to high vRNA loads in the nasal turbinates (NT), lungs, and trachea as well as higher pulmonary lesions scores later in infection. Dysbiosis throughout SARS2 disease progression was observed in the pulmonary microbial dynamics with the enrichment of opportunistic pathogens (Haemophilus, Fusobacterium, Streptococcus, Campylobacter, and Johnsonella) and microbes associated with inflammation (Prevotella). Changes in the gut microbial community also reflected an increase in multiple genera previously associated with intestinal inflammation and disease (Helicobacter, Mucispirillum, Streptococcus, unclassified Erysipelotrichaceae, and Spirochaetaceae). Influenza A virus (FLUAV) pre-exposure resulted in slightly more pronounced pathology in the NT and lungs early on (3 dpc), and more notable changes in lungs compared to the gut microbiome dynamics. Similarities among aged GSH and the microbiome in critically ill COVID-19 patients, particularly in the lower respiratory tract, suggest that GSHs are a representative model to investigate microbial changes during SARS2 infection. The relationship between the residential microbiome and other confounding factors, such as SARS2 infection, in a widely used animal model, contributes to a better understanding of the complexities associated with the host responses during viral infections.

Insights into pandemic respiratory viruses: manipulation of the antiviral interferon response by SARS-CoV-2 and influenza A virus

The outbreak of the COVID-19 pandemic one year after the centennial of the 1918 influenza pandemic reaffirms the catastrophic impact respiratory viruses can have on global health and economy. A key feature of SARS-CoV-2 and influenza A viruses (IAV) is their remarkable ability to suppress or dysregulate human immune responses. Here, we summarize the growing knowledge about the interplay of SARS-CoV-2 and antiviral innate immunity, with an emphasis on the regulation of type-I or -III interferon responses that are critically implicated in COVID-19 pathogenesis. Furthermore, we draw parallels to IAV infection and discuss shared innate immune sensing mechanisms and the respective viral countermeasures.

Development of a multi-recombinase polymerase amplification assay for rapid identification of COVID-19, influenza A and B

The coronavirus disease 2019 (COVID-19) pandemic caused extensive loss of life worldwide. Further, the COVID-19 and influenza mix-infection had caused great distress to the diagnosis of the disease. To control illness progression and limit viral spread within the population, a real-time reverse-transcription PCR (RT-PCR) assay for early diagnosis of COVID-19 was developed, but detection was time-consuming (4-6 h). To improve the diagnosis of COVID-19 and influenza, we herein developed a recombinase polymerase amplification (RPA) method for simple and rapid amplification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 and Influenza A (H1N1, H3N2) and B (influenza B). Genes encoding the matrix protein (M) for H1N1, and the hemagglutinin (HA) for H3N2, and the polymerase A (PA) for Influenza B, and the nucleocapsid protein (N), the RNA-dependent-RNA polymerase (RdRP) in the open reading frame 1ab (ORF1ab) region, and the envelope protein (E) for SARS-CoV-2 were selected, and specific primers were designed. We validated our method using SARS-CoV-2, H1N1, H3N2 and influenza B plasmid standards and RNA samples extracted from COVID-19 and Influenza A/B (RT-PCR-verified) positive patients. The method could detect SARS-CoV-2 plasmid standard DNA quantitatively between 10² and 10⁵ copies/ml with a log linearity of 0.99 in 22 min. And this method also be very effective in simultaneous detection of H1N1, H3N2 and influenza B. Clinical validation of 100 cases revealed a sensitivity of 100% for differentiating COVID-19 patients from healthy controls when the specificity was set at 90%. These results demonstrate that this nucleic acid testing method is advantageous compared with traditional PCR and other isothermal nucleic acid amplification methods in terms of time and portability. This method could potentially be used for detection of SARS-CoV-2, H1N1, H3N2 and influenza B, and adapted for point-of-care (POC) detection of a broad range of infectious pathogens in resource-limited settings.

Influenza A virus NS1 protein represses antiviral immune response by hijacking NF-κB to mediate transcription of type III IFN

Background

Non-structural protein 1 (NS1), one of the viral proteins of influenza A viruses (IAVs), plays a crucial role in evading host antiviral immune response. It is known that the IAV NS1 protein regulates the antiviral genes response mainly through several different molecular mechanisms in cytoplasm. Current evidence suggests that NS1 represses the transcription of IFNB1 gene by inhibiting the recruitment of Pol II to its exons and promoters in infected cells. However, IAV NS1 whether can utilize a common mechanism to antagonize antiviral response by interacting with cellular DNA and immune-related transcription factors in the nucleus, is not yet clear.

Methods

Chromatin immunoprecipitation and sequencing (ChIP-seq) was used to determine genome-wide transcriptional DNA-binding sites for NS1 and NF-κB in viral infection. Next, we used ChIP-reChIP, luciferase reporter assay and secreted embryonic alkaline phosphatase (SEAP) assay to provide information on the dynamic binding of NS1 and NF-κB to chromatin. RNA sequencing (RNA-seq) transcriptomic analyses were used to explore the critical role of NS1 and NF-κB in IAV infection as well as the detailed processes governing host antiviral response.

Results

Herein, NS1 was found to co-localize with NF-κB using ChIP-seq. ChIP-reChIP and luciferase reporter assay confirmed the co-localization of NS1 and NF-κB at type III IFN genes, such as IFNL1, IFNL2, and IFNL3. We discovered that NS1 disturbed binding manners of NF-κB to inhibit IFNL1 expression. NS1 hijacked NF-κB from a typical IFNL1 promoter to the exon-intron region of IFNL1 and decreased the enrichment of RNA polymerase II and H3K27ac, a chromatin accessibility marker, in the promoter region of IFNL1 during IAV infection, consequently reducing IFNL1 gene expression. NS1 deletion enhanced the enrichment of RNA polymerase II at the IFNL1 promoter and promoted its expression.

Conclusion

Overall, NS1 hijacked NF-κB to prevent its interaction with the IFNL1 promoter and restricted the open chromatin architecture of the promoter, thereby abating antiviral gene expression.

Electrospun-Based Membranes as a Key Tool to Prevent Respiratory Infections

The use of electrospun meshes has been proposed as highly efficient protective equipment to prevent respiratory infections. Those infections can result from the activity of micro-organisms and other small dust particles, such as those resulting from air pollution, that impair the respiratory tract, induce cellular damage and compromise breathing capacity. Therefore, electrospun meshes can contribute to promoting air-breathing quality and controlling the spread of such epidemic-disrupting agents due to their intrinsic characteristics, namely, low pore size, and high porosity and surface area. In this review, the mechanisms behind the pathogenesis of several stressors of the respiratory system are covered as well as the strategies adopted to inhibit their action. The main goal is to discuss the performance of antimicrobial electrospun nanofibers by comparing the results already reported in the literature. Further, the main aspects of the certification of filtering systems are highlighted, and the expected technology developments in the industry are also discussed.

COVID-19 and Saudi medical students: A cross-sectional study on knowledge, preventive behaviors, and risk perception

Background

The knowledge, preventive behaviors, and risk perception of the COVID-19 pandemic among health care workers can affect virus transmission and control. As the primary individuals in contact with infected patients, health care workers risk infection. There are a few studies on the knowledge and self-practice prevention for COVID-19 among medical students.

Objectives

This study evaluated the COVID-19-related knowledge, preventive behaviors, and risk perceptions among medical students and interns.

Methods

This study used a quantitative cross-sectional evaluation of the Saudi Arabian medical students utilizing a previously published online survey in 2020.

Results

The study questionnaire was completed by 474 respondents. The average knowledge and preventive behavior score was significantly lower in males. The reported source of information showed a statistically significant association with knowledge and was higher in the respondents who reported world health organization (WHO)/centers for disease control and prevention (CDC)/UpToDate as their main source of information. The National Guidelines of the Ministry of Health was the second source to be reported for seeking information. A statistically significant positive correlation was observed between the knowledge and preventive measures scores. The respondents who did not follow any information regarding COVID-19 had significantly lower knowledge and preventive behavior scores than those obtaining knowledge from sources. The preventive behavior score was not significantly different between clinical and pre-clinical students.

Conclusion

This study assessed the knowledge, perceptions, and practices of COVID-19 following the onset of the pandemic in Saudi Arabia, indicating an acceptable level of undergraduate students' knowledge regarding the epidemic and its control measures.

The role of RHIM in necroptosis

The RIP homotypic interaction motif (RHIM) is a conserved protein domain that is approximately 18–22 amino acids in length. In humans, four proteins carrying RHIM domains have been identified: receptor-interacting serine/threonine protein kinase (RIPK) 1, RIPK3, Z-DNA-binding protein 1 (ZBP1), and TIR domain-containing adapter-inducing IFN-β (TRIF), which are all major players in necroptosis, a distinct form of regulated cell death. Necroptosis is mostly presumed to be a fail-safe form of cell death, occurring in cells in which apoptosis is compromised. Upon activation, RIPK1, ZBP1, and TRIF each hetero-oligomerize with RIPK3 and induce the assembly of an amyloid-like structure of RIPK3 homo-oligomers. These act as docking stations for the recruitment of the pseudokinase mixed-lineage kinase domain like (MLKL), the pore-forming executioner of necroptosis. As RHIM domain interactions are a vital component of the signaling cascade and can also be involved in apoptosis and pyroptosis activation, it is unsurprising that viral and bacterial pathogens have developed means of disrupting RHIM-mediated signaling to ensure survival. Moreover, as these mechanisms play an essential part of regulated cell death signaling, they have received much attention in recent years. Herein, we present the latest insights into the supramolecular structure of interacting RHIM proteins and their distinct signaling cascades in inflammation and infection. Their uncovering will ultimately contribute to the development of new therapeutic strategies in the regulation of lytic cell death.

Host Predictors of Broadly Cross-Reactive Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern Differ Between Infection and Vaccination

BACKGROUND

Following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or vaccination there is significant variability between individuals in protective antibody levels against SARS-CoV-2, and within individuals against different virus variants. However, host demographic or clinical characteristics that predict variability in cross-reactive antibody levels are not well-described. These data could inform clinicians, researchers, and policymakers on the populations most likely to require vaccine booster shots.

METHODS

In an institutional review board-approved prospective observational cohort study of staff at St. Jude Children's Research Hospital, we identified participants with plasma samples collected after SARS-CoV-2 infection, after mRNA vaccination, and after vaccination following infection, and quantitated immunoglobulin G (IgG) levels by enzyme-linked immunosorbent assay to the spike receptor binding domain (RBD) from 5 important SARS-CoV-2 variants (Wuhan Hu-1, B.1.1.7, B.1.351, P.1, and B.1.617.2). We used regression models to identify factors that contributed to cross-reactive IgG against 1 or multiple viral variants.

RESULTS

Following infection, a minority of the cohort generated cross-reactive antibodies, IgG antibodies that bound all tested variants. Those who did had increased disease severity, poor metabolic health, and were of a particular ancestry. Vaccination increased the levels of cross-reactive IgG levels in all populations, including immunocompromised, elderly, and persons with poor metabolic health. Younger people with a healthy weight mounted the highest responses.

CONCLUSIONS

Our findings provide important new information on individual antibody responses to infection/vaccination that could inform clinicians on populations that may require follow-on immunization.

MAGI1 inhibits interferon signaling to promote influenza A infection

We have shown that membrane-associated guanylate kinase with inverted domain structure-1 (MAGI1), a scaffold protein with six PSD95/DiscLarge/ZO-1 (PDZ) domains, is involved in the regulation of endothelial cell (EC) activation and atherogenesis in mice. In addition to causing acute respiratory disease, influenza A virus (IAV) infection plays an important role in atherogenesis and triggers acute coronary syndromes and fatal myocardial infarction. Therefore, the aim of this study is to investigate the function and regulation of MAGI1 in IAV-induced EC activation. Whereas, EC infection by IAV increases MAGI1 expression, MAGI1 depletion suppresses IAV infection, suggesting that the induction of MAGI1 may promote IAV infection. Treatment of ECs with oxidized low-density lipoprotein (OxLDL) increases MAGI1 expression and IAV infection, suggesting that MAGI1 is part of the mechanistic link between serum lipid levels and patient prognosis following IAV infection. Our microarray studies suggest that MAGI1-depleted ECs increase protein expression and signaling networks involve in interferon (IFN) production. Specifically, infection of MAGI1-null ECs with IAV upregulates expression of signal transducer and activator of transcription 1 (STAT1), interferon b1 (IFNb1), myxovirus resistance protein 1 (MX1) and 2'-5'-oligoadenylate synthetase 2 (OAS2), and activate STAT5. By contrast, MAGI1 overexpression inhibits Ifnb1 mRNA and MX1 expression, again supporting the pro-viral response mediated by MAGI1. MAGI1 depletion induces the expression of MX1 and virus suppression. The data suggests that IAV suppression by MAGI1 depletion may, in part, be due to MX1 induction. Lastly, interferon regulatory factor 3 (IRF3) translocates to the nucleus in the absence of IRF3 phosphorylation, and IRF3 SUMOylation is abolished in MAGI1-depleted ECs. The data suggests that MAGI1 inhibits IRF3 activation by maintaining IRF3 SUMOylation. In summary, IAV infection occurs in ECs in a MAGI1 expression-dependent manner by inhibiting anti-viral responses including STATs and IRF3 activation and subsequent MX1 induction, and MAGI1 plays a role in EC activation, and in upregulating a pro-viral response. Therefore, the inhibition of MAGI1 is a potential therapeutic target for IAV-induced cardiovascular disease.

Effect of vibration associated with cryotherapy on vaccine-related pain and anxiety levels in adults: study protocol for a randomized clinical trial

Background

Vaccination is one of the most effective strategies for prevention and eradication of immunopreventable diseases, but community acceptance of vaccination can be influenced by different factors, such as pain and anxiety. The use of high-frequency vibration associated with cryotherapy has been used to manage pain and anxiety during the vaccination process in children, but studies with adults are still scarce. This study aims to evaluate the effect of high-frequency vibration associated with cryotherapy on the levels of self-reported pain and anxiety related to administration of the Influenza vaccine intramuscularly in adults.

Methods

A two-arm, parallel, randomized clinical trial conducted in a Brazilian Primary Health Care Unit is proposed. A sample of 350 adults will be randomly assigned to participate in the control group, receiving the vaccine intramuscularly according to the standard protocol of the service, or in the intervention group, receiving the vaccine by the same route and using a portable device of high frequency vibration associated with cryotherapy for 30 s before and during administration. The primary endpoints will be self-reported levels of pain, assessed before and after vaccine administration. Secondary endpoints will be levels of anxiety, satisfaction with vaccine administration, and discomfort caused by high frequency vibration and temperature of the frozen bag in contact with the skin. Self-reported levels of pain and anxiety will be compared before and after vaccination as well as between the control and intervention groups.

Discussion

By evaluating the effect of high-frequency vibration associated with cryotherapy on pain and anxiety levels, we expect to find evidence that will support nursing practice, in order to promote greater comfort and safety in the vaccination process and, consequently, greater compliance by the population, by minimizing its undesirable effects.

Trial registration

Human Research Ethics Committee Opinion Number: 5.138.564. Approved on December 2, 2021. Brazilian Registry of Clinical Trials (REBEC): Registration number RBR-5zgy25w. Registered on December 09, 2021.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13063-022-06564-7.

Easy Fabrication of a Polymeric Transparent Sheet to Combat Microbial Infection

Surges in infectious diseases and their transmission in households and commercial and healthcare settings have increased the use of polymeric materials as protective covers. Despite ongoing efforts, conventional polymeric materials still pose the threat of surface-associated transmission of pathogens due to the fact that they lack antimicrobial properties. Here, we have developed an easy-to-fabricate polymeric sheet [quaternary polymeric transparent sheet (QPTS)] that shows an excellent antimicrobial property and is also transparent in nature, increasing its practical applications in a wide range of surfaces. The sheet was fabricated by combining cationic amphiphilic water-soluble polyethylenimine derivative (QPEINH-C₆) and poly(vinyl alcohol) (PVA). The optimum composition (QPTS-3) exhibited a complete reduction of bacterial and fungal infection (∼3-4 log reduction) within 15 min. QPTS-3 also exhibited activity against antibiotic-insusceptible metabolically inactive bacterial cells. The sheet prevented the growth of MRSA biofilm even after 72 h of incubation, which was confirmed through electron microscopy on the QPTS sheet. Most importantly, ∼99.9% of the influenza viral load was reduced completely within 30 min of exposure of the sheet. Apart from the antimicrobial property, the sheet successfully retained its transparency (∼88%) and maintained a significant mechanical strength (∼15 N), highlighting its potential applications in commercial and healthcare settings.

Reactive oxygen species associated immunoregulation post influenza virus infection

An appropriate level of reactive oxygen species (ROS) is necessary for cell proliferation, signaling transduction, and apoptosis due to their highly reactive character. ROS are generated through multiple metabolic pathways under a fine-tuned control between oxidant and antioxidant signaling. A growing number of evidence has proved their highly relevant role in modulating inflammation during influenza virus infection. As a network of biological process for protecting organism from invasion of pathogens, immune system can react and fight back through either innate immune system or adaptive immune system, or both. Herein, we provide a review about the mechanisms of ROS generation when encounter influenza virus infection, and how the imbalanced level of ROS influences the replication of virus. We also summarize the pathways used by both the innate and adaptive immune system to sense and attack the invaded virus and abnormal levels of ROS. We further review the limitation of current strategies and discuss the direction of future work.

Virus Infection and Systemic Inflammation: Lessons Learnt from COVID-19 and Beyond

Respiratory infections with newly emerging zoonotic viruses such as SARS-CoV-2, the etiological agent of COVID-19, often lead to the perturbation of the human innate and adaptive immune responses causing severe disease with high mortality. The responsible mechanisms are commonly virus-specific and often include either over-activated or delayed local interferon responses, which facilitate efficient viral replication in the primary target organ, systemic viral spread, and rapid onset of organ-specific and harmful inflammatory responses. Despite the distinct replication strategies, human infections with SARS-CoV-2 and highly pathogenic avian influenza viruses demonstrate remarkable similarities and differences regarding the mechanisms of immune induction, disease dynamics, as well as the long-term sequelae, which will be discussed in this review. In addition, we will highlight some important lessons about the effectiveness of antiviral and immunomodulatory therapeutic strategies that this pandemic has taught us.

Immune determinants of chronic sequelae after respiratory viral infection

The acute effects of various respiratory viral infections have been well studied, with extensive characterization of the clinical presentation as well as viral pathogenesis and host responses. However, over the course of the recent COVID-19 pandemic, the incidence and prevalence of chronic sequelae after acute viral infections have become increasingly appreciated as a serious health concern. Post-acute sequelae of COVID-19, alternatively described as “long COVID-19,” are characterized by symptoms that persist for longer than 28 days after recovery from acute illness. Although there exists substantial heterogeneity in the nature of the observed sequelae, this phenomenon has also been observed in the context of other respiratory viral infections including influenza virus, respiratory syncytial virus, rhinovirus, severe acute respiratory syndrome coronavirus, and Middle Eastern respiratory syndrome coronavirus. In this Review, we discuss the various sequelae observed following important human respiratory viral pathogens and our current understanding of the immunological mechanisms underlying the failure of restoration of homeostasis in the lung.

Tetracycline-induced mitohormesis mediates disease tolerance against influenza

Mitohormesis defines the increase in fitness mediated by adaptive responses to mild mitochondrial stress. Tetracyclines inhibit not only bacterial but also mitochondrial translation, thus imposing a low level of mitochondrial stress on eukaryotic cells. We demonstrate in cell and germ-free mouse models that tetracyclines induce a mild adaptive mitochondrial stress response (MSR), involving both the ATF4-mediated integrative stress response and type I interferon (IFN) signaling. To overcome the interferences of tetracyclines with the host microbiome, we identify tetracycline derivatives that have minimal antimicrobial activity, yet retain full capacity to induce the MSR, such as the lead compound, 9-tert-butyl doxycycline (9-TB). The MSR induced by doxycycline (Dox) and 9-TB improves survival and disease tolerance against lethal influenza virus (IFV) infection when given preventively. 9-TB, unlike Dox, did not affect the gut microbiome and also showed encouraging results against IFV when given in a therapeutic setting. Tolerance to IFV infection is associated with the induction of genes involved in lung epithelial cell and cilia function, and with downregulation of inflammatory and immune gene sets in lungs, liver, and kidneys. Mitohormesis induced by non-antimicrobial tetracyclines and the ensuing IFN response may dampen excessive inflammation and tissue damage during viral infections, opening innovative therapeutic avenues.

The Pre-Existing Human Antibody Repertoire to Computationally Optimized Influenza H1 Hemagglutinin Vaccines

Computationally optimized broadly reactive Ag (COBRA) hemagglutinin (HA) immunogens have previously been generated for several influenza subtypes to improve vaccine-elicited Ab breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA Ags. Cross-reactivity between wild-type HA and H1 COBRA HA proteins P1, X6, and Y2 were observed for isolated mAbs. The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 HA head and stem domains, and most mAbs had hemagglutination inhibition and neutralizing activity against 2009 pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had hemagglutination inhibition and neutralizing activity against a prepandemic H1 strain. One mAb, P1-05, targeted the stem region of H1 HA, but did not compete with a known stem-targeting H1 mAb. We determined that mAb P1-05 recognizes a recently discovered HA epitope, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by mAb P1-05, suggesting the importance of protein design for vaccine formulations. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA-reactive B cells that target head, central stalk, and anchor epitopes, and they demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes.

Competition of SARS-CoV-2 Variants in Cell Culture and Tissue: Wins the Fastest Viral Autowave

Replication of viruses in living tissues and cell cultures is a “number game” involving complex biological processes (cell infection, virus replication inside infected cell, cell death, viral degradation) as well as transport processes limiting virus spatial propagation. In epithelial tissues and immovable cell cultures, viral particles are basically transported via Brownian diffusion. Highly non-linear kinetics of viral replication combined with diffusion limitation lead to spatial propagation of infection as a moving front switching from zero to high local viral concentration, the behavior typical of spatially distributed excitable media. We propose a mathematical model of viral infection propagation in cell cultures and tissues under the diffusion limitation. The model is based on the reaction–diffusion equations describing the concentration of uninfected cells, exposed cells (infected but still not shedding the virus), virus-shedding cells, and free virus. We obtain the expressions for the viral replication number, which determines the condition for spatial infection progression, and for the final concentration of uninfected cells. We determine analytically the speed of spatial infection propagation and validate it numerically. We calibrate the model to recent experimental data on SARS-CoV-2 Delta and Omicron variant replication in human nasal epithelial cells. In the case of competition of two virus variants in the same cell culture, the variant with larger individual spreading speed wins the competition and eliminates another one. These results give new insights concerning the emergence of new variants and their spread in the population.

Integrins are double-edged swords in pulmonary infectious diseases

Integrins are an important family of adhesion molecules that are widely distributed on immune cells in the lungs. Of note, accumulating evidences have shown that integrins are double-edged swords in pulmonary infectious diseases. On one hand, integrins promote the migration of immune cells to remove the invaded pathogens in the infected lungs. However, on the other hand, integrins also act as the targets for pathogens to escape from host immune system, which is a potential factor leading to further tissue damage. Thus, the innovative therapeutic strategies based on integrins has inspired well-founded hopes to treat pulmonary infectious diseases. In this review, we illustrate the involvement of integrins in pulmonary infectious diseases, and further discuss the innovative therapeutic targets based on integrins.

Influenza Vaccination and COVID-19 Outcomes in People Older than 50 Years: Data from the Observational Longitudinal SHARE Study

Existing literature on the association between influenza vaccination and COVID-19 infection/outcomes is conflicting. Therefore, we aimed to investigate the association between influenza vaccination and COVID-19 outcomes in a large cohort of adults who participated in the SHARE (Survey of Health, Ageing, and Retirement in Europe). Information regarding influenza vaccination in the previous year, and medical and demographic characteristics, were self-reported. Positivity for COVID-19, symptomatology, and hospitalization were also ascertained using self-reported information. An adjusted logistic regression analysis (including 15 baseline factors or propensity score) was used to assess the association between influenza vaccination and COVID-19 outcomes. A total of 48,408 participants (mean age 67 years; 54.1% females) were included. The prevalence of influenza vaccination was 38.3%. After adjusting for 15 potential confounders, influenza vaccination was significantly associated with a lower risk of positivity for COVID-19 (OR = 0.95; p < 0.0001), symptomatic forms (OR = 0.87; p < 0.0001), and hospitalization for COVID-19 (OR = 0.95; p < 0.0001). The results were similar when using a propensity score approach. In conclusion, influenza vaccination may be beneficial for the prevention of COVID-19, as the present study found that influenza vaccination was associated with a small/moderate lower risk of COVID-19 infection and adverse outcomes.

Emerging Role of ZBP1 in Z-RNA Sensing, Influenza Virus-Induced Cell Death, and Pulmonary Inflammation

Influenza viruses cause respiratory tract infections, which lead to human disease outbreaks and pandemics. Influenza A virus (IAV) circulates in diverse animal species, predominantly aquatic birds. This often results in the emergence of novel viral strains causing severe human disease upon zoonotic transmission. Innate immune sensing of the IAV infection promotes host cell death and inflammatory responses to confer antiviral host defense. Dysregulated respiratory epithelial cell death and excessive proinflammatory responses drive immunopathology in highly pathogenic influenza infections. Here, we discuss the critical mechanisms regulating IAV-induced cell death and proinflammatory responses. We further describe the essential role of the Z-form nucleic acid sensor ZBP1/DAI and RIPK3 in triggering apoptosis, necroptosis, and pyroptosis during IAV infection and their impact on host defense and pathogenicity in vivo. We also discuss the functional importance of ZBP1-RIPK3 signaling in recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viral infections. Understanding these mechanisms of RNA virus-induced cytopathic and pathogenic inflammatory responses is crucial for targeting pathogenic lung infections and human respiratory illness.

Time-Dependent Increase in Susceptibility and Severity of Secondary Bacterial Infections During SARS-CoV-2

Secondary bacterial infections can exacerbate SARS-CoV-2 infection, but their prevalence and impact remain poorly understood. Here, we established that a mild to moderate infection with the SARS-CoV-2 USA-WA1/2020 strain increased the risk of pneumococcal (type 2 strain D39) coinfection in a time-dependent, but sex-independent, manner in the transgenic K18-hACE2 mouse model of COVID-19. Bacterial coinfection increased lethality when the bacteria was initiated at 5 or 7 d post-virus infection (pvi) but not at 3 d pvi. Bacterial outgrowth was accompanied by neutrophilia in the groups coinfected at 7 d pvi and reductions in B cells, T cells, IL-6, IL-15, IL-18, and LIF were present in groups coinfected at 5 d pvi. However, viral burden, lung pathology, cytokines, chemokines, and immune cell activation were largely unchanged after bacterial coinfection. Examining surviving animals more than a week after infection resolution suggested that immune cell activation remained high and was exacerbated in the lungs of coinfected animals compared with SARS-CoV-2 infection alone. These data suggest that SARS-CoV-2 increases susceptibility and pathogenicity to bacterial coinfection, and further studies are needed to understand and combat disease associated with bacterial pneumonia in COVID-19 patients.

Mucosal immune responses to infection and vaccination in the respiratory tract

The lungs are constantly exposed to inhaled debris, allergens, pollutants, commensal or pathogenic microorganisms, and respiratory viruses. As a result, innate and adaptive immune responses in the respiratory tract are tightly regulated and are in continual flux between states of enhanced pathogen clearance, immune-modulation, and tissue repair. New single-cell-sequencing techniques are expanding our knowledge of airway cellular complexity and the nuanced connections between structural and immune cell compartments. Understanding these varied interactions is critical in treatment of human pulmonary disease and infections and in next-generation vaccine design. Here, we review the innate and adaptive immune responses in the lung and airways following infection and vaccination, with particular focus on influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The ongoing SARS-CoV-2 pandemic has put pulmonary research firmly into the global spotlight, challenging previously held notions of respiratory immunity and helping identify new populations at high risk for respiratory distress.

CNBP restricts SARS-CoV2 by regulating IFN and disrupting RNA-protein condensates

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades antiviral immunity through the expression of viral proteins that block detection, signaling, interferon (IFN) induction, and IFN-stimulated gene (ISG) expression1, 2. Weak induction of type I IFNs is associated with a hyperinflammatory response in patients that develop severe COVID-193, 4, 5. Here we uncover a role for cellular nucleic acid-binding protein (CNBP) in restricting SARS-CoV-2. Typically, CNBP resides in the cytosol and, in response to RNA sensing pathways, undergoes phosphorylation, nuclear translocation, and IFNβ enhancer DNA binding to turn on IFNβ gene transcription. In SARS-CoV-2-infected cells CNBP coordinates IFNβ gene transcription. In addition, CNBP binds SARS-CoV-2 viral RNA directly. CNBP competes with the nucleocapsid (N) protein and prevents viral RNA and nucleocapsid protein from undergoing liquid-liquid phase separation (LLPS) forming condensates critical for viral replication. Consequently, cells and animals lacking CNBP have higher viral loads and CNBP-deficient mice succumb rapidly to infection. Altogether, these findings identify CNBP as a key antiviral factor for SARS-CoV-2, functioning both as a regulator of antiviral IFN gene expression and a cell intrinsic restriction factor that disrupts LLPS to limit viral replication and spread.

'All In One' SARS-CoV-2 variant recognition platform: Machine learning-enabled point of care diagnostics

Point of care (PoC) devices are highly demanding to control current pandemic, originated from severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Though nucleic acid-based methods such as RT-PCR are widely available, they require sample preparation and long processing time. PoC diagnostic devices provide relatively faster and stable results. However they require further investigation to provide high accuracy and be adaptable for the new variants. In this study, laser-scribed graphene (LSG) sensors are coupled with gold nanoparticles (AuNPs) as stable promising biosensing platforms. Angiotensin Converting Enzyme 2 (ACE2), an enzymatic receptor, is chosen to be the biorecognition unit due to its high binding affinity towards spike proteins as a key-lock model. The sensor was integrated to a homemade and portable potentistat device, wirelessly connected to a smartphone having a customized application for easy operation. LODs of 5.14 and 2.09 ng/mL was achieved for S1 and S2 protein in the linear range of 1.0-200 ng/mL, respectively. Clinical study has been conducted with nasopharyngeal swabs from 63 patients having alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2) variants, patients without mutation and negative patients. A machine learning model was developed with accuracy of 99.37% for the identification of the SARS-Cov-2 variants under 1 min. With the increasing need for rapid and improved disease diagnosis and monitoring, the PoC platform proved its potential for real time monitoring by providing accurate and fast variant identification without any expertise and pre sample preparation, which is exactly what societies need in this time of pandemic.

Untapping host-targeting cross-protective efficacy of anticoagulants against SARS-CoV-2

Responding quickly to emerging respiratory viruses, such as SARS-CoV-2 the causative agent of coronavirus disease 2019 (COVID-19) pandemic, is essential to stop uncontrolled spread of these pathogens and mitigate their socio-economic impact globally. This can be achieved through drug repurposing, which tackles inherent time- and resource-consuming processes associated with conventional drug discovery and development. In this review, we examine key preclinical and clinical therapeutic and prophylactic approaches that have been applied for treatment of SARS-CoV-2 infection. We break these strategies down into virus- versus host-targeting and discuss their reported efficacy, advantages, and disadvantages. Importantly, we highlight emerging evidence on application of host serine protease-inhibiting anticoagulants, such as nafamostat mesylate, as a potentially powerful therapy to inhibit virus activation and offer cross-protection against multiple strains of coronavirus, lower inflammatory response independent of its antiviral effect, and modulate clotting problems seen in COVID-19 pneumonia.

Alterations in microbiota of patients with COVID-19: potential mechanisms and therapeutic interventions

The global coronavirus disease 2019 (COVID-19) pandemic is currently ongoing. It is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A high proportion of COVID-19 patients exhibit gastrointestinal manifestations such as diarrhea, nausea, or vomiting. Moreover, the respiratory and gastrointestinal tracts are the primary habitats of human microbiota and targets for SARS-CoV-2 infection as they express angiotensin-converting enzyme-2 (ACE2) and transmembrane protease serine 2 (TMPRSS2) at high levels. There is accumulating evidence that the microbiota are significantly altered in patients with COVID-19 and post-acute COVID-19 syndrome (PACS). Microbiota are powerful immunomodulatory factors in various human diseases, such as diabetes, obesity, cancers, ulcerative colitis, Crohn’s disease, and certain viral infections. In the present review, we explore the associations between host microbiota and COVID-19 in terms of their clinical relevance. Microbiota-derived metabolites or components are the main mediators of microbiota-host interactions that influence host immunity. Hence, we discuss the potential mechanisms by which microbiota-derived metabolites or components modulate the host immune responses to SARS-CoV-2 infection. Finally, we review and discuss a variety of possible microbiota-based prophylaxes and therapies for COVID-19 and PACS, including fecal microbiota transplantation (FMT), probiotics, prebiotics, microbiota-derived metabolites, and engineered symbiotic bacteria. This treatment strategy could modulate host microbiota and mitigate virus-induced inflammation.

The Continued Threat of Influenza A Viruses

Influenza A virus (IAV) is a major cause of respiratory infections worldwide, with the most severe cases occurring in the very young and in elderly individuals [...]

An easy-to-use antimicrobial hydrogel effectively kills bacteria, fungi, and influenza virus

Various drug resistant pathogens such as bacteria, fungi and viruses enter a host through different routes, which can lead to health-related problems and even fatalities. Propagation of these infectious microbes majorly occurs through the mucosal openings or upon topical contact. To curb their transmission or to cure infections associated with these pathogens, herein we describe the development of an antimicrobial hydrogel, based on a water soluble quaternary lipophilic polyethyleneimine derivative (QPEINH-C₆). The cationic polymer QPEINH-C₆ exhibited antibacterial activity against drug-resistant Gram-positive bacteria (MIC = 10-62 μg mL^-1) and Gram-negative bacteria (MIC = 117-123 μg mL^-1). The derivative showed killing of human pathogenic fungi (MIC = 58-67 μg mL^-1), including their clinical isolates. The rapid bactericidal and fungicidal nature were confirmed from the fast inactivation kinetics of bacterial cells (methicillin resistant S. aureus and vancomycin resistant S. aureus) within 3-6 hours and C. albicans within 1 h with ∼5-6 log reduction in the microbial burden. This antibacterial and antifungal cationic polymer was then used to construct an antimicrobial shear-thinning hydrogel (Bacfuvir), through non-covalent crosslinking with biocompatible gellan and polyvinyl alcohol (PVA). This hydrogel displayed ∼5-7 log reduction of numerous multidrug-resistant bacteria and their stationary phase cells which are insusceptible to conventional antibiotics. In addition, >99.9 % viable bacterial burden was reduced from preformed biofilm matrices of drug-resistant bacteria. Alongside, fluconazole-resistant C. albicans strains were killed completely within 15-60 min upon exposure to Bacfuvir gel. Most importantly, MRSA and C. albicans cells were reduced (3-4 log) in polymicrobial biofilms after hydrogel treatment. The hydrogel exhibited 99.9 % reduction of influenza viruses in a rapid manner. Due to the biocompatibility of Bacfuvir gel on topical application in a murine model and easy administration owing to its shear-thinning behaviour, this hydrogel can markedly contribute to mitigating drug-resistant bacterial, fungal and viral infections in healthcare settings.

Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q

The Receptor Binding Domain (RBD) of SARS-CoV-2, located on the S1 subunit, plays a vital role in the virus binding and its entry into the host cell through angiotensin-converting enzyme 2 (ACE2) receptor. Therefore, understanding the dynamic effects of mutants on the SARS-CoV-2 RBD is essential for discovering drugs to inhibit the virus binding and disrupt its entry into the host cells. A recent study reported a double mutant of SARS-CoV-2, L452R-E484Q, located in the RBD region. Thus, this study employed various computational algorithms and methods to understand the structural impact of both individual variants L452R, E484Q, and the double mutant L452R-E484Q on the native RBD of spike glycoprotein. The effects of the mutations on native RBD structure were predicted by in silico algorithms, which predicted changes in the protein structure and function upon the mutations. Subsequently, molecular dynamics (MD) simulations were employed to understand the conformational stability and functional changes on the RBD upon the mutations. The comparative results of MD simulation parameters displayed that the double mutant induces significant conformational changes in the spike glycoprotein RBD, which may alter its biological functions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03151-0.

Complications of Critical COVID-19: Diagnostic and Therapeutic Considerations for the Mechanically Ventilated Patient

Patients admitted to the ICU with critical COVID-19 often require prolonged periods of mechanical ventilation. Difficulty weaning, lack of progress, and clinical deterioration are commonly encountered. These conditions should prompt a thorough evaluation for persistent or untreated manifestations of COVID-19, as well as complications from COVID-19 and its various treatments. Inflammation may persist and lead to fibroproliferative changes in the lungs. Infectious complications may arise including bacterial superinfection in the earlier stages of disease. Use of immunosuppressants may lead to the dissemination of latent infections, and to opportunistic infections. Venous thromboembolic disease is common, as are certain neurologic manifestations of COVID-19 including delirium and stroke. High levels of ventilatory support may lead to ventilator-induced injury to the lungs and diaphragm. We present diagnostic and therapeutic considerations for the mechanically ventilated patient with COVID-19 who shows persistent or worsening signs of critical illness, and we offer an approach to treating this complex but common scenario.

Dysregulation in erythrocyte dynamics caused by SARS-CoV-2 infection: possible role in shuffling the homeostatic puzzle during COVID-19

Introduction

The evolving COVID-19 pandemic became a hallmark in human history, not only by changing lifestyles, but also by enriching scientific knowledge on viral infection and its consequences.

Objective

Although the management of cardiorespiratory changes is pivotal to a favorable prognosis during severe clinical findings, dysregulation of other systems caused by SARS-CoV-2 infection may imbalance erythrocyte dynamics, such as a bidirectional positive feedback loop pathophysiology.

Method and Results

Recent evidence shows that SARS-CoV-2 is capable of affecting the genetics and dynamics of erythrocytes and this coexists with a non-homeostatic function of cardiovascular, respiratory and renal systems during COVID-19. In hypothesis, SARS-CoV-2-induced systematical alterations of erythrocytes dynamics would constitute a setpoint for COVID-19-related multiple organ failure syndrome and death.

Conclusion

The present review covers the most frequent erythrocyte-related non-homeostatic findings during COVID-19 capable of providing mechanistic clues of SARS-CoV-2-induced infection and inspiring therapeutic-oriented scientific evidence.

Impact of Therapeutics on Unified Immunity During Allergic Asthma and Respiratory Infections

Asthma is a common chronic respiratory disease that affects millions of people worldwide. Patients with allergic asthma, the most prevalent asthma endotype, are widely considered to possess a defective immune response against some respiratory infectious agents, including viruses, bacteria and fungi. Furthermore, respiratory pathogens are associated with asthma development and exacerbations. However, growing data suggest that the immune milieu in allergic asthma may be beneficial during certain respiratory infections. Immunomodulatory asthma treatments, although beneficial, should then be carefully prescribed to avoid misuse and overuse as they can also alter the host microbiome. In this review, we summarize and discuss recent evidence of the correlations between allergic asthma and the most significant respiratory infectious agents that have a role in asthma pathogenesis. We also discuss the implications of current asthma therapeutics beyond symptom prevention.

Longitudinal SARS-CoV-2 Testing among the Unvaccinated Is Punctuated by Intermittent Positivity and Variable Rates of Increasing Cycle Threshold Values

The coronavirus disease 2019 (COVID-19) pandemic is complicated by cases of vaccine breakthrough and reinfection and widespread transmission of variants of concern (VOCs). Consequently, the need to interpret longitudinal positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests is crucial in guiding clinical decisions regarding infection control precautions and treatment. Although diagnostic real-time reverse transcription (RT)-PCR tests yield C_T values that are inversely correlated with RNA quantity, these tests are only approved for qualitative interpretation. In this study, we performed a retrospective review of 72,217 SARS-CoV-2 positive tests and identified 264 patients with longitudinal positivity prior to vaccination and VOC circulation. Patients with longitudinal positivity fell into two categories: short-term (207, 78%) or prolonged (57, 22%) positivity, defined as ≤28 (range, 1 to 28; median, 16) days and >28 (range, 29 to 152; median, 41) days, respectively. In general, C_T values increased over time in both groups; however, 11 short-term-positive patients had greater amounts of RNA detected at their terminal test than at the first positive test, and 6 patients had RNA detected at C_T values of <35 at least 40 days after initial infection. Oscillating positive and negative results occurred in both groups, although oscillation was seen three times more frequently in prolonged-positive patients. Patients with prolonged positivity had diverse clinical characteristics but were often critically ill and were discharged to high-level care or deceased (22%). Overall, this study demonstrates that caution must be emphasized when interpreting C_T values as a proxy for infectivity, a predictor of severity, or a guide for patient care decisions in the absence of additional clinical context, particularly among the unvaccinated population. IMPORTANCE We describe the duration of positivity and the COVID-19 treatment and outcome characteristics of an unvaccinated population of patients with prolonged SARS-CoV-2 positivity. This investigation serves to highlight challenges in using C_T values to guide clinical decisions among unvaccinated individuals.

An overview of the biological and multifunctional roles of IL-38 in different infectious diseases and COVID-19

Undoubtfully, the normal immune system can make a potential response to variable pathogens and neutralize or kill them depending on the type of infection through innate and acquired immunity. Cytokines have poly-peptide nature and are considered as signaling molecules that could amplify or alleviate immune responses besides their other biological functions. Interleukin 38 (IL-38) is a member of the IL-1 family cytokine that, however, its anti-inflammatory role has been observed in different autoimmune diseases like systemic lupus erythematosus (SLE), psoriasis, and Sjogren’s syndrome; there is a controversy about the cytokine pro-inflammatory function. In the current review, we skimmed IL-38 structure, signaling mechanism, and its immunological functions, IL-38-producing immune cells. Also, we argued about the role of this cytokine in viral infections including hepatitis B (HBV), hepatitis C (HCV), influenza (Flu), and COVID-19. Also, it illustrated the IL-38 protective effects on sepsis. Moreover, we explained the modulatory role of IL-38 in the COVID-19 cytokine storm.

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19.

Time-Dependent Increase in Susceptibility and Severity of Secondary Bacterial Infection during SARS-CoV-2 Infection.. [PMID: 35262077 PMCID: PMC8902874 DOI: 10.1101/2022.02.28.482305]

Secondary bacterial infections can exacerbate SARS-CoV-2 infection, but their prevalence and impact remain poorly understood. Here, we established that a mild to moderate SARS-CoV-2 infection increased the risk of pneumococcal coinfection in a time-dependent, but sex-independent, manner in the transgenic K18-hACE mouse model of COVID-19. Bacterial coinfection was not established at 3 d post-virus, but increased lethality was observed when the bacteria was initiated at 5 or 7 d post-virus infection (pvi). Bacterial outgrowth was accompanied by neutrophilia in the groups coinfected at 7 d pvi and reductions in B cells, T cells, IL-6, IL-15, IL-18, and LIF were present in groups coinfected at 5 d pvi. However, viral burden, lung pathology, cytokines, chemokines, and immune cell activation were largely unchanged after bacterial coinfection. Examining surviving animals more than a week after infection resolution suggested that immune cell activation remained high and was exacerbated in the lungs of coinfected animals compared with SARS-CoV-2 infection alone. These data suggest that SARS-CoV-2 increases susceptibility and pathogenicity to bacterial coinfection, and further studies are needed to understand and combat disease associated with bacterial pneumonia in COVID-19 patients.

Engineered Nanoparticulate Vaccines to Combat Recurring and Pandemic Influenza Threats

Reoccurring seasonal flu epidemics and occasional pandemics are among the most severe threats to public health. Current seasonal influenza vaccines provide limited protection against drifted circulating strains and no protection against influenza pandemics. Next-generation influenza vaccines, designated as universal influenza vaccines, should be safe, affordable, and elicit long-lasting cross-protective influenza immunity. Nanotechnology plays a critical role in the development of such novel vaccines. Engineered nanoparticles can incorporate multiple advantageous properties into the same nanoparticulate platforms to improve vaccine potency and breadth. These immunological properties include virus-like biomimicry, high antigen-load, controlled antigen release, targeted delivery, and induction of innate signaling pathways. Many nanoparticle influenza vaccines have shown promising results in generating potent and broadly protective immune responses. This review will summarize the necessity and characteristics of next-generation influenza vaccines and the immunological correlates of broad influenza immunity and focus on how cutting-edge nanoparticle technology contributes to such vaccine development. The review will give new insights into the rational design of nanoparticle universal vaccines to combat influenza epidemics and pandemics.