Comparative review of respiratory diseases caused by coronaviruses and influenza A viruses during epidemic season

Spectrum of COVID-19 cases in Arkhangelsk, Northwest Russia: Findings from a population-based study linking serosurvey, registry data, and self-reports of symptoms

INTRODUCTION

The spectrum of COVID-19 manifestations makes it challenging to estimate the exact proportion of people who had the infection in a population, with the proportion of asymptomatic cases likely being underestimated. We aimed to assess and describe the spectrum of COVID-19 cases in a sample of adult population aged 40-74 years in Arkhangelsk, Northwest Russia, a year after the start of the pandemic.

MATERIALS AND METHODS

A population-based survey conducted between February 24, 2021 and June 30, 2021 with an unvaccinated sample aged 40-74 years (N = 1089) combined a serological survey data, national COVID-19 case registry, and self-reported data on COVID-19 experience and symptoms. Based on the agreement between these sources, we classified the study participants as non-infected and previously infected (asymptomatic, non-hospitalized and hospitalized symptomatic) cases, and compared these groups regarding demographics, lifestyle and health characteristics.

RESULTS

After a year of the pandemic in Arkhangelsk, 59.7% 95% confidence intervals (CI) (56.7; 62.6) of the surveyed population had had COVID-19. Among those who had been infected, symptomatic cases comprised 47.1% 95% CI (43.2; 51.0), with 8.6% 95% CI (6.6; 11.1) of them having been hospitalized. Of the asymptomatic cases, 96.2% were not captured by the healthcare system. Older age was positively associated, while smoking showed a negative association with symptomatic COVID-19. Individuals older than 65 years, and those with poor self-rated health were more likely to be hospitalized.

CONCLUSION

More than half of the infected individuals were not captured by the healthcare-based registry, mainly those with asymptomatic infections. COVID-19 severity was positively associated with older age and poor self-rated health, and inversely associated with smoking. Combining different sources of surveillance data could reduce the number of unidentified asymptomatic cases and enhance surveillance for emerging infections.

Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro

SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health and economic burdens. Although vaccines against SARS-CoV-2 have been developed, their long-term efficacy and specificity have not been determined, and antiviral drugs remain necessary. Flavonoids, which are commonly found in plants, fruits, and vegetables and are part of the human diet, have attracted considerable attention as potential therapeutic agents due to their antiviral and antimicrobial activities and effects on other biological activities, such as inflammation. The present study uses a combination of biochemical, cellular, molecular dynamics, and molecular docking experiments to provide compelling evidence that the flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) has antiviral activity against SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) that is synergistically enhanced by magnesium, zinc, and vitamin C. The IC50 of luteolin against 2 µM 3CLpro is 78 µM and decreases 10-fold to 7.6 µM in the presence of zinc, magnesium, and vitamin C. Thermodynamic stability analyses revealed that luteolin has minimal effects on the structure of 3CLpro, whereas metal ions and vitamin C significantly alter the thermodynamic stability of the protease. Interactome analysis uncovered potential host-virus interactions and functional clusters associated with luteolin activity, supporting the relevance of this flavone for combating SARS-CoV-2 infection. This comprehensive investigation sheds light on luteolin's therapeutic potential and provides insights into its mechanisms of action against SARS-CoV-2. The novel formulation of luteolin, magnesium, zinc, and vitamin C may be an effective avenue for treating COVID-19 patients.

COVID-19 Frequency in Hospitalized Psychiatric Patients: A Systematic Review

OBJECTIVE

The COVID-19 pandemic affected individuals in different contexts (e.g. long-term care facilities, schools, communities), including psychiatric hospitals. Thus, the objective of this systematic review, duly registered and approved on PROSPERO (CRD42023427835), is to assess the frequency of positive COVID-19 cases among patients hospitalized in psychiatric hospitals.

METHODS

A total of 4,922 articles were identified in the database searches, and 17 studies conducted in psychiatric hospitals from different regions of the world were selected.

RESULTS

The frequency of positive COVID-19 cases among patients hospitalized in psychiatric hospitals ranged from 1.8% to 98.8%. Out of a total of 19,573 patients hospitalized in psychiatric hospitals, the pooled mean frequency of positive COVID-19 cases was 11.9%. The majority of patients presented COVID-19 symptoms (e.g. cough, fever and others). The COVID-19 diagnosis was primarily conducted through RT-PCR testing in 88.9% of the studies.

CONCLUSION

In conclusion, there is discrepancy in the methodology of the studies assessing the frequency of positive COVID-19 cases in psychiatric hospitals. However, this review allowed us to understand how the COVID-19 pandemic has impacted the population hospitalized in psychiatric hospitals.

Molecular screening of phytocompounds targeting the interface between influenza A NS1 and TRIM25 to enhance host immune responses

BACKGROUND

Influenza A virus causes severe respiratory illnesses, especially in developing nations where most child deaths under 5 occur due to lower respiratory tract infections. The RIG-I protein acts as a sensor for viral dsRNA, triggering interferon production through K63-linked poly-ubiquitin chains synthesized by TRIM25. However, the influenza A virus's NS1 protein hinders this process by binding to TRIM25, disrupting its association with RIG-I and preventing downstream interferon signalling, contributing to the virus's evasion of the immune response.

METHODS

In our study we used structural-based drug designing, molecular simulation, and binding free energy approaches to identify the potent phytocompounds from various natural product databases (>100,000 compounds) able to inhibit the binding of NS1 with the TRIM25.

RESULTS

The molecular screening identified EA-8411902 and EA-19951545 from East African Natural Products Database, NA-390261 and NA-71 from North African Natural Products Database, SA-65230 and SA- 4477104 from South African Natural Compounds Database, NEA- 361 and NEA- 4524784 from North-East African Natural Products Database, TCM-4444713 and TCM-6056 from Traditional Chinese Medicines Database as top hits. The molecular docking and binding free energies results revealed that these compounds have high affinity with the specific active site residues (Leu95, Ser99, and Tyr89) involved in the interaction with TRIM25. Additionally, analysis of structural dynamics, binding free energy, and dissociation constants demonstrates a notably stronger binding affinity of these compounds with the NS1 protein. Moreover, all selected compounds exhibit exceptional ADMET properties, including high water solubility, gastrointestinal absorption, and an absence of hepatotoxicity, while adhering to Lipinski's rule.

CONCLUSION

Our molecular simulation findings highlight that the identified compounds demonstrate high affinity for specific active site residues involved in the NS1-TRIM25 interaction, exhibit exceptional ADMET properties, and adhere to drug-likeness criteria, thus presenting promising candidates for further development as antiviral agents against influenza A virus infections.

Research on the impact mechanism of changes in the production of medical solid waste in China before and after COVID-19

The changes of medical solid waste (MSW) output in recent years have had a significant impact on the spread of the virus. There is a high-risk transmission of MSW in various stages such as storage, transportation, and treatment during the COVID-19. To cope with the risks brought by the epidemic, normalized prevention consumes a large amount of protective clothing, medical masks, goggles, packaging bags, and other related medical supplies. There is a significant uncertainty in the amount of MSW output that poses a risk of COVID-19 infection in the event of an emergency, which increases the difficulty of collecting and handling epidemic prevention MSW. The analysis of MSW data from 2000 to 2022 found a stable growth trend before 2019. However, the MSW data was a sudden increase trend from 2020 to 2022, and the COVID-19 in China was characterized by an initial stage, an outbreak stage, and a stable growth stage. The range of MSW output during the epidemic was (1.19-1.75) × 106 t a-1. The amount of MSW was approximately 1.19 × 106 t a-1 during the normalized epidemic period, and its treatment cost was as high as 3.57 × 109 yuan (RMB)·a-1. The distribution of MSW output was uneven due to factors such as climate conditions, population data, and local economy. This study has important reference value for epidemic medical material reserves and MSW treatment.

Vaccination against influenza viruses reduces infection, not hospitalization or death, from respiratory COVID-19: A systematic review and meta-analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 and has brought a huge burden in terms of human lives. Strict social distance and influenza vaccination have been recommended to avoid co-infections between influenza viruses and SARS-CoV-2. Scattered reports suggested a protective effect of influenza vaccine on COVID-19 development and severity. We analyzed 51 studies on the capacity of influenza vaccination to affect infection with SARS-CoV-2, hospitalization, admission to Intensive Care Units (ICU), and mortality. All subjects taken into consideration did not receive any anti-SARS-CoV-2 vaccine, although their status with respect to previous infections with SARS-CoV-2 is not known. Comparison between vaccinated and not-vaccinated subjects for each of the four endpoints was expressed as odds ratio (OR), with 95% confidence intervals (CIs); all analyses were performed by DerSimonian and Laird model, and Hartung-Knapp model when studies were less than 10. In a total of 61 029 936 subjects from 33 studies, influenza vaccination reduced frequency of SARS-CoV-2 infection [OR plus 95% CI = 0.70 (0.65-0.77)]. The effect was significant in all studies together, in health care workers and in the general population; distance from influenza vaccination and the type of vaccine were also of importance. In 98 174 subjects from 11 studies, frequency of ICU admission was reduced with influenza vaccination [OR (95% CI) = 0.71 (0.54-0.94)]; the effect was significant in all studies together, in pregnant women and in hospitalized subjects. In contrast, in 4 737 328 subjects from 14 studies hospitalization was not modified [OR (95% CI) = 1.05 (0.82-1.35)], and in 4 139 660 subjects from 19 studies, mortality was not modified [OR (95% CI) = 0.76 (0.26-2.20)]. Our study emphasizes the importance of influenza vaccination in the protection against SARS-CoV-2 infection.

Point-of-Care Devices for Viral Detection: COVID-19 Pandemic and Beyond

The pandemic of COVID-19 and its widespread transmission have made us realize the importance of early, quick diagnostic tests for facilitating effective cure and management. The primary obstacles encountered were accurately distinguishing COVID-19 from other illnesses including the flu, common cold, etc. While the polymerase chain reaction technique is a robust technique for the determination of SARS-CoV-2 in patients of COVID-19, there arises a high demand for affordable, quick, user-friendly, and precise point-of-care (POC) diagnostic in therapeutic settings. The necessity for available tests with rapid outcomes spurred the advancement of POC tests that are characterized by speed, automation, and high precision and accuracy. Paper-based POC devices have gained increasing interest in recent years because of rapid, low-cost detection without requiring external instruments. At present, microfluidic paper-based analysis devices have garnered public attention and accelerated the development of such POCT for efficient multistep assays. In the current review, our focus will be on the fabrication of detection modules for SARS-CoV-2. Here, we have included a discussion on various strategies for the detection of viral moieties. The compilation of these strategies would offer comprehensive insight into the detection of the causative agent preparedness for future pandemics. We also provide a descriptive outline for paper-based diagnostic platforms, involving the determination mechanisms, as well as a commercial kit for COVID-19 as well as their outlook.

Symptom profiles of community cases infected by influenza, RSV, rhinovirus, seasonal coronavirus, and SARS-CoV-2 variants of concern

Respiratory viruses that were suppressed through previous lockdowns during the COVID-19 pandemic have recently started to co-circulate with SARS-CoV-2. Understanding the clinical characteristics and symptomatology of different respiratory viral infections can help address the challenges related to the identification of cases and the understanding of SARS-CoV-2 variants' evolutionary patterns. Flu Watch (2006-2011) and Virus Watch (2020-2022) are household community cohort studies monitoring the epidemiology of influenza, respiratory syncytial virus, rhinovirus, seasonal coronavirus, and SARS-CoV-2, in England and Wales. This study describes and compares the proportion of symptoms reported during illnesses infected by common respiratory viruses. The SARS-CoV-2 symptom profile increasingly resembles that of other respiratory viruses as new strains emerge. Increased cough, sore throat, runny nose, and sneezing are associated with the emergence of the Omicron strains. As SARS-CoV-2 becomes endemic, monitoring the evolution of its symptomatology associated with new variants will be critical for clinical surveillance.

Potential cross-species transmission of highly pathogenic avian influenza H5 subtype (HPAI H5) viruses to humans calls for the development of H5-specific and universal influenza vaccines

In recent years, highly pathogenic avian influenza H5 subtype (HPAI H5) viruses have been prevalent around the world in both avian and mammalian species, causing serious economic losses to farmers. HPAI H5 infections of zoonotic origin also pose a threat to human health. Upon evaluating the global distribution of HPAI H5 viruses from 2019 to 2022, we found that the dominant strain of HPAI H5 rapidly changed from H5N8 to H5N1. A comparison of HA sequences from human- and avian-derived HPAI H5 viruses indicated high homology within the same subtype of viruses. Moreover, amino acid residues 137A, 192I, and 193R in the receptor-binding domain of HA1 were the key mutation sites for human infection in the current HPAI H5 subtype viruses. The recent rapid transmission of H5N1 HPAI in minks may result in the further evolution of the virus in mammals, thereby causing cross-species transmission to humans in the near future. This potential cross-species transmission calls for the development of an H5-specific influenza vaccine, as well as a universal influenza vaccine able to provide protection against a broad range of influenza strains.

Quinones as Promising Compounds against Respiratory Viruses: A Review

Respiratory viruses represent a world public health problem, giving rise to annual seasonal epidemics and several pandemics caused by some of these viruses, including the COVID-19 pandemic caused by the novel SARS-CoV-2, which continues to date. Some antiviral drugs have been licensed for the treatment of influenza, but they cause side effects and lead to resistant viral strains. Likewise, aerosolized ribavirin is the only drug approved for the therapy of infections by the respiratory syncytial virus, but it possesses various limitations. On the other hand, no specific drugs are licensed to treat other viral respiratory diseases. In this sense, natural products and their derivatives have appeared as promising alternatives in searching for new compounds with antiviral activity. Besides their chemical properties, quinones have demonstrated interesting biological activities, including activity against respiratory viruses. This review summarizes the activity against respiratory viruses and their molecular targets by the different types of quinones (both natural and synthetic). Thus, the present work offers a general overview of the importance of quinones as an option for the future pharmacological treatment of viral respiratory infections, subject to additional studies that support their effectiveness and safety.

Influenza and Pneumococcal Vaccination and the Risk of COVID-19: A Systematic Review and Meta-Analysis

A number of studies have investigated the potential on-specific effects of some routinely administered vaccines (e.g., influenza, pneumococcal) on COVID-19 related outcomes, with contrasting results. In order to elucidate this discrepancy, we conducted a systematic review and meta-analysis to assess the association between seasonal influenza vaccination and pneumococcal vaccination with SARS-CoV-2 infection and its clinical outcomes. PubMed and medRxiv databases were searched up to April 2022. A random effects model was used in the meta-analysis to pool odds ratio (OR) and adjusted estimates with 95% confidence intervals (CIs). Heterogeneity was quantitatively assessed using the Cochran's Q and the I2 index. Subgroup analysis, sensitivity analysis and assessment of publication bias were performed for all outcomes. In total, 38 observational studies were included in the meta-analysis and there was substantial heterogeneity. Influenza and pneumococcal vaccination were associated with lower risk of SARS-CoV-2 infection (OR: 0.80, 95% CI: 0.75-0.86 and OR: 0.70, 95% CI: 0.57-0.88, respectively). Regarding influenza vaccination, it seems that the majority of studies did not properly adjust for all potential confounders, so when the analysis was limited to studies that adjusted for age, gender, comorbidities and socioeconomic indices, the association diminished. This is not the case regarding pneumococcal vaccination, for which even after adjustment for such factors the association persisted. Regarding harder endpoints such as ICU admission and death, current data do not support the association. Possible explanations are discussed, including trained immunity, inadequate matching for socioeconomic indices and possible coinfection.

Nutraceutical prospects of Houttuynia cordata against the infectious viruses

The novel enveloped β-coronavirus SARS-CoV-2 (COVID-19) has offered a surprising health challenge all over the world. It develops severe pneumonia leading to acute respiratory distress syndrome (ARDS). Like SARS-COV-2, other encapsulated viruses like HIV, HSV, and influenza have also offered a similar challenge in the past. In this regard, many antiviral drugs are being explored with varying degrees of success to combat the associated pathological conditions. Therefore, upon scientific validation & development, these antiviral phytochemicals can attain a futuristic nutraceutical prospect in managing different encapsulated viruses. Houttuynia cordata (HC) is widely reported for activities such as antioxidant, anti-inflammatory, and antiviral properties. The major antiviral bioactive components of HC include essential oils (methyl n-nonyl ketone, lauryl aldehyde, capryl aldehyde), flavonoids (quercetin, rutin, hyperin, quercitrin, isoquercitrin), and alkaloids (norcepharadione B) & polysaccharides. HC can further be explored as a potential nutraceutical agent in the therapy of encapsulated viruses like HIV, HSV, and influenza. The review listed various conventional and green technologies that are being employed to extract potent phytochemicals with diverse activities from the HC. It was indicated that HC also inhibited molecular targets like 3C-like protease (3CLPRO) and RNA-dependent RNA polymerase (RdRp) of COVID-19 by blocking viral RNA synthesis and replication. Antioxidant and hepatoprotective effects of HC have been evident in impeding complications from marketed drugs during antiviral therapies. The use of HC as a nutraceutical is localized within some parts of Southeast Asia. Further technological advances can establish it as a nutraceutical-based functional food against pathogenic enveloped viruses like COVID 19.

Comparing the Cytokine Storms of COVID-19 and Pandemic Influenza

Emerging respiratory viruses are major health threats due to their potential to cause massive outbreaks. Over the past 2 years, the coronavirus disease 2019 (COVID-19) pandemic has caused millions of cases of severe infection and deaths worldwide. Although natural and vaccine-induced protective immune mechanisms against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been increasingly identified, the factors that determine morbimortality are less clear. Comparing the immune signatures of COVID-19 and other severe respiratory infections such as the pandemic influenza might help dissipate current controversies about the origin of their severe manifestations. As such, identifying homologies in the immunopathology of both diseases could provide targets for immunotherapy directed to block shared pathogenic mechanisms. Meanwhile, finding unique characteristics that differentiate each infection could shed light on specific immune alterations exploitable for diagnostic and individualized therapeutics for each case. In this study, we summarize immunopathological aspects of COVID-19 and pandemic influenza from the perspective of cytokine storms as the driving force underlying morbidity. Thereby, we analyze similarities and differences in the cytokine profiles of both infections, aiming to bring forward those molecules more attractive for translational medicine and drug development.

Microfluidics-Based POCT for SARS-CoV-2 Diagnostics

A microfluidic chip is a tiny reactor that can confine and flow a specific amount of fluid into channels of tens to thousands of microns as needed and can precisely control fluid flow, pressure, temperature, etc. Point-of-care testing (POCT) requires small equipment, has short testing cycles, and controls the process, allowing single or multiple laboratory facilities to simultaneously analyze biological samples and diagnose infectious diseases. In general, rapid detection and stage assessment of viral epidemics are essential to overcome pandemic situations and diagnose promptly. Therefore, combining microfluidic devices with POCT improves detection efficiency and convenience for viral disease SARS-CoV-2. At the same time, the POCT of microfluidic chips increases user accessibility, improves accuracy and sensitivity, shortens detection time, etc., which are beneficial in detecting SARS-CoV-2. This review shares recent advances in POCT-based testing for COVID-19 and how it is better suited to help diagnose in response to the ongoing pandemic.

Assessing the added value of linking electronic health records to improve the prediction of self-reported COVID-19 testing and diagnosis

Since the beginning of the Coronavirus Disease 2019 (COVID-19) pandemic, a focus of research has been to identify risk factors associated with COVID-19-related outcomes, such as testing and diagnosis, and use them to build prediction models. Existing studies have used data from digital surveys or electronic health records (EHRs), but very few have linked the two sources to build joint predictive models. In this study, we used survey data on 7,054 patients from the Michigan Genomics Initiative biorepository to evaluate how well self-reported data could be integrated with electronic records for the purpose of modeling COVID-19-related outcomes. We observed that among survey respondents, self-reported COVID-19 diagnosis captured a larger number of cases than the corresponding EHRs, suggesting that self-reported outcomes may be better than EHRs for distinguishing COVID-19 cases from controls. In the modeling context, we compared the utility of survey- and EHR-derived predictor variables in models of survey-reported COVID-19 testing and diagnosis. We found that survey-derived predictors produced uniformly stronger models than EHR-derived predictors-likely due to their specificity, temporal proximity, and breadth-and that combining predictors from both sources offered no consistent improvement compared to using survey-based predictors alone. Our results suggest that, even though general EHRs are useful in predictive models of COVID-19 outcomes, they may not be essential in those models when rich survey data are already available. The two data sources together may offer better prediction for COVID severity, but we did not have enough severe cases in the survey respondents to assess that hypothesis in in our study.

Low prevalence of community-acquired influenza coinfections among COVID-19 patients in Al-Madinah, Saudi Arabia: A retrospective cohort study

Background

Coinfections with respiratory viruses among SARS CoV-2 patients have been reported by several studies during the current COVID-19 pandemic. Most of these studies designated these coinfections as being hospital-acquired infections; however, there is inadequate knowledge about community-acquired respiratory coinfections among SARS CoV-2 patients.

Methods

In this retrospective cohort study, we investigated the seroprevalence of influenza A, influenza B, and parainfluenza-2 among newly hospitalized patients with confirmed COVID-19 infections (n = 163). The study was conducted during the early phase of the COVID-19 pandemic in Saudi Arabia (from April to October 2020). The patients’ serum samples were subjected to commercial immunoglobulin M (IgM) antibody tests against the three aforementioned viruses.

Results

Seropositivity for influenza A and B and parainfluenza-2 occurred only in 4.2% (7/163) of COVID-19 patients, indicating simultaneous acute infections of these three viruses with SARS CoV-2 infection. All coinfection cases were mild and misdiagnosed during the care period in the hospital.

Conclusion

This study highlights the low prevalence of community-acquired respiratory infections among COVID-19 patients in the current pandemic and we discussed the possible factors for this finding. During newly emerging epidemics or pandemics, considering other respiratory viruses circulating in the community is essential to avoid their misdiagnosis and account for their possible negative effects on pandemic disease management and prognosis.

Discovering trends and hotspots of biosafety and biosecurity research via machine learning

Coronavirus disease 2019 (COVID-19) has infected hundreds of millions of people and killed millions of them. As an RNA virus, COVID-19 is more susceptible to variation than other viruses. Many problems involved in this epidemic have made biosafety and biosecurity (hereafter collectively referred to as ‘biosafety’) a popular and timely topic globally. Biosafety research covers a broad and diverse range of topics, and it is important to quickly identify hotspots and trends in biosafety research through big data analysis. However, the data-driven literature on biosafety research discovery is quite scant. We developed a novel topic model based on latent Dirichlet allocation, affinity propagation clustering and the PageRank algorithm (LDAPR) to extract knowledge from biosafety research publications from 2011 to 2020. Then, we conducted hotspot and trend analysis with LDAPR and carried out further studies, including annual hot topic extraction, a 10-year keyword evolution trend analysis, topic map construction, hot region discovery and fine-grained correlation analysis of interdisciplinary research topic trends. These analyses revealed valuable information that can guide epidemic prevention work: (1) the research enthusiasm over a certain infectious disease not only is related to its epidemic characteristics but also is affected by the progress of research on other diseases, and (2) infectious diseases are not only strongly related to their corresponding microorganisms but also potentially related to other specific microorganisms. The detailed experimental results and our code are available at https://github.com/KEAML-JLU/Biosafety-analysis.

Staphylococcus epidermidis Controls Opportunistic Pathogens in the Nose, Could It Help to Regulate SARS-CoV-2 (COVID-19) Infection?

Staphylococcus epidermidis is more abundant in the anterior nares than internal parts of the nose, but its relative abundance changes along with age; it is more abundant in adolescents than in children and adults. Various studies have shown that S. epidermidis is the guardian of the nasal cavity because it prevents the colonization and infection of respiratory pathogens (bacteria and viruses) through the secretion of antimicrobial molecules and inhibitors of biofilm formation, occupying the space of the membrane mucosa and through the stimulation of the host's innate and adaptive immunity. There is a strong relationship between the low number of S. epidermidis in the nasal cavity and the increased risk of serious respiratory infections. The direct application of S. epidermidis into the nasal cavity could be an effective therapeutic strategy to prevent respiratory infections and to restore nasal cavity homeostasis. This review shows the mechanisms that S. epidermidis uses to eliminate respiratory pathogens from the nasal cavity, also S. epidermidis is proposed to be used as a probiotic to prevent the development of COVID-19 because S. epidermidis induces the production of interferon type I and III and decreases the expression of the entry receptors of SARS-CoV-2 (ACE2 and TMPRSS2) in the nasal epithelial cells.

Evaluation of the Alinity m Resp-4-Plex Assay for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2, Influenza A Virus, Influenza B Virus, and Respiratory Syncytial Virus

The rapid emergence of the coronavirus disease 2019 (COVID-19) pandemic has introduced a new challenge in diagnosing and differentiating respiratory infections. Accurate diagnosis of respiratory infections, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is complicated by overlapping symptomology, and stepwise approaches to testing for each infection would lead to increased reagent usage and cost, as well as delays in clinical interventions. To avoid these issues, multiplex molecular assays have been developed to differentiate between respiratory viruses in a single test to meet clinical diagnostic needs. To evaluate the analytical performance of the FDA emergency use authorization (EUA)-approved Abbott Alinity m resp-4-plex assay (Alinity m) in testing for SARS-CoV-2, influenza A virus, influenza B virus, and respiratory syncytial virus (RSV), we compared its performance to those of both the EUA-approved Cepheid Xpert Xpress SARS-CoV-2, influenza A/B virus, and RSV assay (Xpert Xpress) and the EUA-approved Roche Cobas SARS-CoV-2 and influenza A/B virus assay (Cobas) in a single-center retrospective analysis. High concordance was observed among all three assays, with kappa statistics showing an almost perfect agreement (>0.90). The limit of detection (LOD) results for SARS-CoV-2 showed the Alinity m exhibiting the lowest LOD at 26 copies/mL, followed by the Cobas at 58 copies/mL and the Xpert Xpress at 83 copies/mL, with LOD results for the influenza A virus, influenza B virus, and RSV viral targets also showing equivalent or better performance on the Alinity m compared to the other two platforms. The Alinity m can be used as a high-volume testing platform for SARS-CoV-2, influenza A virus, influenza B virus, and RSV and exhibits analytical performance comparable to those of both the Xpert Xpress and Cobas assays. IMPORTANCE The rapid emergence of SARS-CoV-2 has introduced a new challenge in diagnosing and differentiating respiratory infections, especially considering the overlapping symptomology of many of these infections and differences in clinical interventions depending on the pathogen identified. To avoid these issues, multiplex molecular assays like the one described in this article need to be developed to differentiate between the most common respiratory pathogens in a single test and most effectively meet clinical diagnostic needs.

Comparison of patient characteristics and in-hospital mortality between patients with COVID-19 in 2020 and those with influenza in 2017-2020: a multicenter, retrospective cohort study in Japan

Background

COVID-19 has worse mortality than influenza in American and European studies, but evidence from the Western Pacific region is scarce.

Methods

Using a large-scale multicenter inpatient claims data in Japan, we identified individuals hospitalised with COVID-19 in 2020 or influenza in 2017–2020. We compared patient characteristics, supportive care, and in-hospital mortality, with multivariable logistic regression analyses for in-hospital mortality overall, by age group, and among patients with mechanical ventilation.

Findings

We identified 16,790 COVID-19 patients and 27,870 influenza patients, with the different age distribution (peak at 70–89 years in COVID-19 vs. bimodal peaks at 0–9 and 80–89 years in influenza). On admission, the use of mechanical ventilation was similar in both groups (1·4% vs. 1·4%) but higher in the COVID-19 group (3·3% vs. 2·5%; p<0·0001) during the entire hospitalisation. The crude in-hospital mortality was 5·1% (856/16,790) for COVID-19 and 2·8% (791/27,870) for influenza. Adjusted for potential confounders, the in-hospital mortality was higher for COVID-19 than for influenza (adjusted odds ratio [aOR] 1·83, 95% confidence interval [CI] 1·64–2·04). In age-stratified analyses, the aOR (95%CI) were 0·78 (0·56–1·08) and 2·05 (1·83–2·30) in patients aged 20–69 years and ≥70 years, respectively (p-for-interaction<0·0001). Among patients with mechanical ventilation, the aOR was 0·79 (0·59–1·05).

Interpretation

Patients hospitalised with COVID-19 in Japan were more likely to die than those with influenza. However, this was mainly driven by findings in older people, and there was no difference once mechanical ventilation was started.

Funding

Ministry of Health, Labour and Welfare of Japan (21AA2007).

Viral coinfections in COVID-19

The most consequential challenge raised by coinfection is perhaps the inappropriate generation of recombinant viruses through the exchange of genetic material among different strains. These genetically similar viruses can interfere with the replication process of each other and even compete for the metabolites required for the maintenance of the replication cycle. Due to the similarity in clinical symptoms of most viral respiratory tract infections, and their coincidence with COVID-19, caused by SARS-CoV-2, it is recommended to develop a comprehensive diagnostic panel for detection of respiratory and nonrespiratory viruses through the evaluation of patient samples. Given the resulting changes in blood markers, such as coagulation factors and white blood cell count following virus infection, these markers can be of diagnostic value in the detection of mixed infection in individuals already diagnosed with a certain viral illness. In this review, we seek to investigate the coinfection of SARS-CoV-2 with other respiratory and nonrespiratory viruses to provide novel insights into the development of highly sensitive diagnostics and effective treatment modalities.

Willingness to Receive the COVID-19 and Seasonal Influenza Vaccines among the Saudi Population and Vaccine Uptake during the Initial Stage of the National Vaccination Campaign: A Cross-Sectional Survey

This study aimed to assess the willingness to receive the coronavirus disease 2019 (COVID-19) and seasonal influenza vaccines and vaccine uptake during the early stage of the national vaccination campaign in Saudi Arabia. A cross-sectional online survey was conducted among adult Saudis between 20 January and 20 March 2021. The questionnaire addressed vaccine hesitancy, perceived risk, willingness, and vaccine uptake. Approximately 39% of the participants expressed vaccine hesitancy, and 29.8% and 24% felt highly vulnerable to contracting COVID-19 and seasonal influenza, respectively. The majority (59.5%) were willing to receive the COVID-19 vaccine, although only 31.7% were willing to receive the flu vaccine. Adjusted analysis showed that vaccine hesitancy (OR 0.34, 95% CI 0.27-0.43) and the perception of being at high risk (OR 2.78, 95% CI 1.68-4.60) independently affected the intention to be vaccinated. Vaccine hesitancy was similar among those who were willing to be vaccinated (29.8%) and those who had already been vaccinated (33.1%). The perceived risk was significantly higher among those who had been vaccinated (48.1%) than among those who were willing to be vaccinated but had not yet been vaccinated (29.1%). In conclusion, the acceptance of the COVID-19 vaccine in Saudi Arabia is high. Saudis who received the vaccine had a similar level of vaccine hesitancy and a higher level of perceived risk.

Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot

Respiratory viral infections are the leading cause of morbidity and mortality in the world; however, there are several groups of viruses that are insufficiently routinely sought for, and can thus be considered neglected from a diagnostic and clinical standpoint. Timely detection of seasonality of certain respiratory viruses (e.g., enveloped viruses such as seasonal coronaviruses) in the local context can aid substantially in targeted and cost-effective utilization of viral diagnostic approaches. For the other, non-enveloped and year-round viruses (i.e., rhinovirus, adenovirus, and bocavirus), a continuous virological diagnosis needs to be implemented in clinical laboratories to more effectively address the aetiology of respiratory infections, and assess the overall impact of these viruses on disease burden. While the coronavirus disease 2019 (COVID-19) pandemic is still actively unfolding, we aimed to emphasize the persistent role of seasonal coronaviruses, rhinoviruses, adenoviruses and bocaviruses in the aetiology of respiratory infections. Consequently, this paper concentrates on the burden and epidemiological trends of aforementioned viral groups on a global level, but also provides a snapshot of their prevalence patterns in Croatia in order to underscore the potential implications of viral seasonality. An overall global prevalence in respiratory tract infections was found to be between 0.5 and 18.4% for seasonal coronaviruses, between 13 and 59% for rhinoviruses, between 1 and 36% for human adenoviruses, and between 1 and 56.8% for human bocaviruses. A Croatian dataset on patients with respiratory tract infection and younger than 18 years of age has revealed a fairly high prevalence of rhinoviruses (33.4%), with much lower prevalence of adenoviruses (15.6%), seasonal coronaviruses (7.1%), and bocaviruses (5.3%). These insights represent a relevant discussion point in the context of the COVID-19 pandemic where the testing of non-SARS-CoV-2 viruses has been limited in many settings, making the monitoring of disease burden associated with other respiratory viruses rather difficult.

Expression of Surfactant Protein D Distinguishes Severe Pandemic Influenza A(H1N1) from Coronavirus Disease 2019

The differentiation between influenza and coronavirus disease 2019 (COVID-19) could constitute a diagnostic challenge during the ongoing winter owing to their clinical similitude. Thus, novel biomarkers are required to enable making this distinction. Here, we evaluated whether the surfactant protein D (SP-D), a collectin produced at the alveolar epithelium with known immune properties, was useful to differentiate pandemic influenza A(H1N1) from COVID-19 in critically ill patients. Our results revealed high serum SP-D levels in patients with severe pandemic influenza but not those with COVID-19. This finding was validated in a separate cohort of mechanically ventilated patients with COVID-19 who also showed low plasma SP-D levels. However, plasma SP-D levels did not distinguish seasonal influenza from COVID-19 in mild-to-moderate disease. Finally, we found that high serum SP-D levels were associated with death and renal failure among severe pandemic influenza cases. Thus, our studies have identified SP-D as a unique biomarker expressed during severe pandemic influenza but not COVID-19.

COVID-19: Myths and Reality

COVID-19, a new human respiratory disease that has killed nearly 3 million people in a year since the start of the pandemic, is a global public health challenge. Its infectious agent, SARS-CoV-2, differs from other coronaviruses in a number of structural features that make this virus more pathogenic and transmissible. In this review, we discuss some important characteristics of the main SARS-CoV-2 surface antigen, the spike (S) protein, such as (i) ability of the receptor-binding domain (RBD) to switch between the "standing-up" position (open pre-fusion conformation) for receptor binding and the "lying-down" position (closed pre-fusion conformation) for immune system evasion; (ii) advantage of a high binding affinity of the RBD open conformation to the human angiotensin-converting enzyme 2 (ACE2) receptor for efficient cell entry; and (iii) S protein preliminary activation by the intracellular furin-like proteases for facilitation of the virus spreading across different cell types. We describe interactions between the S protein and cellular receptors, co-receptors, and antagonists, as well as a hypothetical mechanism of the homotrimeric spike structure destabilization that triggers the fusion of the viral envelope with the cell membrane at physiological pH and mediates the viral nucleocapsid entry into the cytoplasm. The transition of the S protein pre-fusion conformation to the post-fusion one on the surface of virions after their treatment with some reagents, such as β-propiolactone, is essential, especially in relation to the vaccine production. We also compare the COVID-19 pathogenesis with that of severe outbreaks of "avian" influenza caused by the A/H5 and A/H7 highly pathogenic viruses and discuss the structural similarities between the SARS-CoV-2 S protein and hemagglutinins of those highly pathogenic strains. Finally, we touch on the prospective and currently used COVID-19 antiviral and anti-pathogenetic therapeutics, as well as recently approved conventional and innovative COVID-19 vaccines and their molecular and immunological features.

Coinfection With SARS-CoV-2 and Influenza A(H1N1) in a Patient Seen at an Influenza-like Illness Surveillance Site in Egypt: Case Report

Background

Sentinel surveillance of influenza-like illness (ILI) in Egypt started in 2000 at 8 sentinel sites geographically distributed all over the country. In response to the COVID-19 pandemic, SARS-CoV-2 was added to the panel of viral testing by polymerase chain reaction for the first 2 patients with ILI seen at one of the sentinel sites. We report the first SARS-CoV-2 and influenza A(H1N1) virus co-infection with mild symptoms detected through routine ILI surveillance in Egypt.

Objective

This report aims to describe how the case was identified and the demographic and clinical characteristics and outcomes of the patient.

Methods

The case was identified by Central Public Health Laboratory staff, who contacted the ILI sentinel surveillance officer at the Ministry of Health. The case patient was contacted through a telephone call. Detailed information about the patient’s clinical picture, course of disease, and outcome was obtained. The contacts of the patient were investigated for acute respiratory symptoms, disease confirmation, and outcomes.

Results

Among 510 specimens collected from patients with ILI symptoms from October 2019 to August 2020, 61 (12.0%) were COVID-19–positive and 29 (5.7%) tested positive for influenza, including 15 (51.7%) A(H1N1), 11 (38.0%) A(H3N2), and 3 (10.3%) influenza B specimens. A 21-year-old woman was confirmed to have SARS-CoV-2 and influenza A(H1N1) virus coinfection. She had a high fever of 40.2 °C and mild respiratory symptoms that resolved within 2 days with symptomatic treatment. All five of her family contacts had mild respiratory symptoms 2-3 days after exposure to the confirmed case, and their symptoms resolved without treatment or investigation.

Conclusions

This case highlights the possible occurrence of SARS-CoV-2/influenza A(H1N1) coinfection in younger and healthy people, who may resolve the infection rapidly. We emphasize the usefulness of the surveillance system for detection of viral causative agents of ILI and recommend broadening of the testing panel, especially if it can guide case management.

Clinical and Immunological Factors That Distinguish COVID-19 From Pandemic Influenza A(H1N1)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is a global health threat with the potential to cause severe disease manifestations in the lungs. Although COVID-19 has been extensively characterized clinically, the factors distinguishing SARS-CoV-2 from other respiratory viruses are unknown. Here, we compared the clinical, histopathological, and immunological characteristics of patients with COVID-19 and pandemic influenza A(H1N1). We observed a higher frequency of respiratory symptoms, increased tissue injury markers, and a histological pattern of alveolar pneumonia in pandemic influenza A(H1N1) patients. Conversely, dry cough, gastrointestinal symptoms and interstitial lung pathology were observed in COVID-19 cases. Pandemic influenza A(H1N1) was characterized by higher levels of IL-1RA, TNF-α, CCL3, G-CSF, APRIL, sTNF-R1, sTNF-R2, sCD30, and sCD163. Meanwhile, COVID-19 displayed an immune profile distinguished by increased Th1 (IL-12, IFN-γ) and Th2 (IL-4, IL-5, IL-10, IL-13) cytokine levels, along with IL-1β, IL-6, CCL11, VEGF, TWEAK, TSLP, MMP-1, and MMP-3. Our data suggest that SARS-CoV-2 induces a dysbalanced polyfunctional inflammatory response that is different from the immune response against pandemic influenza A(H1N1). Furthermore, we demonstrated the diagnostic potential of some clinical and immune factors to differentiate both diseases. These findings might be relevant for the ongoing and future influenza seasons in the Northern Hemisphere, which are historically unique due to their convergence with the COVID-19 pandemic.

COVID-19's Impact on Willingness to Be Vaccinated against Influenza and COVID-19 during the 2020/2021 Season: Results from an Online Survey of Canadian Adults 50 Years and Older

There is considerable overlap in age-related risk factors for influenza and COVID-19. We explored the impact of the pandemic on anticipated influenza and COVID-19 vaccination behaviour in the 2020/2021 season. In May 2020, we conducted online surveys of Canadian adults 50 years and older via a market research panel platform, as part of a series of annual surveys to understand experiences with influenza. Given the current pandemic, respondents were also asked about COVID-19’s impact on their vaccination decision-making for the 2020/2021 season. Of 1001 respondents aged 50–64 years, 470 (47.0%) originally intended on receiving the influenza vaccine and still planned to do so, while 200 (20%) respondents who had planned to abstain now reported willingness to receive the vaccine due to COVID-19. In the 65+ age group, 2525 (72.1%) reported that they had planned to be vaccinated and that COVID-19 had not changed their mind, while 285 individuals (8.1%) reported that they had initially planned to forgo the vaccine but now intended to receive it. Reasons for this change included COVID-19’s demonstration of the devastating potential of viruses; and to protect against influenza, and decrease vulnerability to COVID-19. If the COVID-19 vaccine was available, 69.1% of 50–64 year olds and 79.5% of those 65 years and older reported they would opt to receive it. The COVID-19 pandemic has been a sobering demonstration of the dangers of infectious disease, and the value of vaccines, with implications for influenza and COVID-19 immunization programs.

SARS-CoV-2 Causes a Different Cytokine Response Compared to Other Cytokine Storm-Causing Respiratory Viruses in Severely Ill Patients

Hyper-induction of pro-inflammatory cytokines, also known as a cytokine storm or cytokine release syndrome (CRS), is one of the key aspects of the currently ongoing SARS-CoV-2 pandemic. This process occurs when a large number of innate and adaptive immune cells activate and start producing pro-inflammatory cytokines, establishing an exacerbated feedback loop of inflammation. It is one of the factors contributing to the mortality observed with coronavirus 2019 (COVID-19) for a subgroup of patients. CRS is not unique to the SARS-CoV-2 infection; it was prevalent in most of the major human coronavirus and influenza A subtype outbreaks of the past two decades (H5N1, SARS-CoV, MERS-CoV, and H7N9). With a comprehensive literature search, we collected changing the cytokine levels from patients upon infection with the viral pathogens mentioned above. We analyzed published patient data to highlight the conserved and unique cytokine responses caused by these viruses. Our curation indicates that the cytokine response induced by SARS-CoV-2 is different compared to other CRS-causing respiratory viruses, as SARS-CoV-2 does not always induce specific cytokines like other coronaviruses or influenza do, such as IL-2, IL-10, IL-4, or IL-5. Comparing the collated cytokine responses caused by the analyzed viruses highlights a SARS-CoV-2-specific dysregulation of the type-I interferon (IFN) response and its downstream cytokine signatures. The map of responses gathered in this study could help specialists identify interventions that alleviate CRS in different diseases and evaluate whether they could be used in the COVID-19 cases.

A Review on SERS-Based Detection of Human Virus Infections: Influenza and Coronavirus

The diagnosis of respiratory viruses of zoonotic origin (RVsZO) such as influenza and coronaviruses in humans is crucial, because their spread and pandemic threat are the highest. Surface-enhanced Raman spectroscopy (SERS) is an analytical technique with promising impact for the point-of-care diagnosis of viruses. It has been applied to a variety of influenza A virus subtypes, such as the H1N1 and the novel coronavirus SARS-CoV-2. In this work, a review of the strategies used for the detection of RVsZO by SERS is presented. In addition, relevant information about the SERS technique, anthropozoonosis, and RVsZO is provided for a better understanding of the theme. The direct identification is based on trapping the viruses within the interstices of plasmonic nanoparticles and recording the SERS signal from gene fragments or membrane proteins. Quantitative mono- and multiplexed assays have been achieved following an indirect format through a SERS-based sandwich immunoassay. Based on this review, the development of multiplex assays that incorporate the detection of RVsZO together with their specific biomarkers and/or secondary disease biomarkers resulting from the infection progress would be desirable. These configurations could be used as a double confirmation or to evaluate the health condition of the patient.

CXCL17 Is a Specific Diagnostic Biomarker for Severe Pandemic Influenza A(H1N1) That Predicts Poor Clinical Outcome

The C-X-C motif chemokine ligand 17 (CXCL17) is chemotactic for myeloid cells, exhibits bactericidal activity, and exerts anti-viral functions. This chemokine is constitutively expressed in the respiratory tract, suggesting a role in lung defenses. However, little is known about the participation of CXCL17 against relevant respiratory pathogens in humans. Here, we evaluated the serum levels and lung tissue expression pattern of CXCL17 in a cohort of patients with severe pandemic influenza A(H1N1) from Mexico City. Peripheral blood samples obtained on admission and seven days after hospitalization were processed for determinations of serum CXCL17 levels by enzyme-linked immunosorbent assay (ELISA). The expression of CXCL17 was assessed by immunohistochemistry (IHQ) in lung autopsy specimens from patients that succumbed to the disease. Serum CXCL17 levels were also analyzed in two additional comparative cohorts of coronavirus disease 2019 (COVID-19) and pulmonary tuberculosis (TB) patients. Additionally, the expression of CXCL17 was tested in lung autopsy specimens from COVID-19 patients. A total of 122 patients were enrolled in the study, from which 68 had pandemic influenza A(H1N1), 24 had COVID-19, and 30 with PTB. CXCL17 was detected in post-mortem lung specimens from patients that died of pandemic influenza A(H1N1) and COVID-19. Interestingly, serum levels of CXCL17 were increased only in patients with pandemic influenza A(H1N1), but not COVID-19 and PTB. CXCL17 not only differentiated pandemic influenza A(H1N1) from other respiratory infections but showed prognostic value for influenza-associated mortality and renal failure in machine-learning algorithms and regression analyses. Using cell culture assays, we also identified that human alveolar A549 cells and peripheral blood monocyte-derived macrophages increase their CXCL17 production capacity after influenza A(H1N1) pdm09 virus infection. Our results for the first time demonstrate an induction of CXCL17 specifically during pandemic influenza A(H1N1), but not COVID-19 and PTB in humans. These findings could be of great utility to differentiate influenza and COVID-19 and to predict poor prognosis specially at settings of high incidence of pandemic A(H1N1). Future studies on the role of CXCL17 not only in severe pandemic influenza, but also in seasonal influenza, COVID-19, and PTB are required to validate our results.

Prevalence and risk indicators of first-wave COVID-19 among oral health-care workers: A French epidemiological survey

BACKGROUND

Previous studies have highlighted the increased risk of contracting the COVID-19 for health-care workers and suggest that oral health-care workers may carry the greatest risk. Considering the transmission route of the SARS-CoV-2 infection, a similar increased risk can be hypothesized for other respiratory infections. However, no study has specifically assessed the risk of contracting COVID-19 within the dental profession.

METHODS

An online survey was conducted within a population of French dental professionals between April 1 and April 29, 2020. Univariable and multivariable logistic regression analyses were performed to explore risk indicators associated with laboratory-confirmed COVID-19 and COVID-19-related clinical phenotypes (i.e. phenotypes present in 15% or more of SARS-CoV-2-positive cases).

RESULTS

4172 dentists and 1868 dental assistants responded to the survey, representing approximately 10% of French oral health-care workers. The prevalence of laboratory-confirmed COVID-19 was 1.9% for dentists and 0.8% for dental assistants. Higher prevalence was found for COVID-19-related clinical phenotypes both in dentists (15.0%) and dental assistants (11.8%). Chronic kidney disease and obesity were associated with increased odds of laboratory-confirmed COVID-19, whereas working in a practice limited to endodontics was associated with decreased odds. Chronic obstructive pulmonary disease, use of public transportation and having a practice limited to periodontology were associated with increased odds of presenting a COVID-19-related clinical phenotype. Moreover, changes in work rhythm or clinical practice were associated with decreased odds of both outcomes.

CONCLUSIONS

Although oral health-care professionals were surprisingly not at higher risk of COVID-19 than the general population, specific risk indicators could exist, notably among high aerosol-generating dental subspecialties such as periodontology. Considering the similarities between COVID-19-related clinical phenotypes other viral respiratory infections, lessons can be learned from the COVID-19 pandemic regarding the usefulness of equipping and protecting oral health-care workers, notably during seasonal viral outbreaks, to limit infection spread.

IMPACT

Results from this study may provide important insights for relevant health authorities regarding the overall infection status of oral health-care workers in the current pandemic and draw attention to particular at-risk groups, as illustrated in the present study. Protecting oral health-care workers could be an interesting public health strategy to prevent the resurgence of COVID-19 and/or the emergence of new pandemics.

Conversion of L-arabinose to L-ribose by genetically engineered Candida tropicalis

l-Ribose, a starting material for the synthesis of l-nucleoside, has attracted lots of attention since l-nucleoside is responsible for the antiviral activities of the racemic mixtures of nucleoside enantiomers. In this study, the l-ribulose-producing Candida tropicalis strain was engineered for the conversion of l-arabinose to l-ribose. For the construction of a uracil auxotroph, the URA3 gene was excised by homologous recombination. The expression cassette of codon-optimized l-ribose isomerase gene from Acinetobacter calcoaceticus DL-28 under the control of the GAPDH promoter was integrated to the uracil auxotroph. The resulting strain, K1 CoSTP2 LsaAraA AcLRI, was cultivated with the glucose/l-arabinose mixture. At 45.5 h of fermentation, 6.0 g/L of l-ribose and 3.2 g/L of l-ribulose were produced from 30 g/L of l-arabinose. The proportion between l-ribose and l-ribulose was approximately 2:1 and the conversion yield of l-arabinose to l-ribose was about 20% (w/w). The l-ribose-producing yeast strain was successfully constructed for the first time and could convert l-arabinose to l-ribose in one-pot fermentation using the mixture of glucose and l-arabinose.

The Hierarchical Classifier for COVID-19 Resistance Evaluation

Finding dependencies in the data requires the analysis of relations between dozens of parameters of the studied process and hundreds of possible sources of influence on this process. Dependencies are nondeterministic and therefore modeling requires the use of statistical methods for analyzing random processes. Part of the information is often hidden from observation or not monitored. That is why many difficulties have arisen in the process of analyzing the collected information. The paper aims to find frequent patterns and parameters affected by COVID-19. The novelty of the paper is hierarchical architecture comprises supervised and unsupervised methods. It allows the development of an ensemble of the methods based on k-means clustering and classification. The best classifiers from the ensemble are random forest with 500 trees and XGBoost. Classification for separated clusters gives us higher accuracy on 4% in comparison with dataset analysis. The proposed approach can be used also for personalized medicine decision support in other domains. The features selection allows us to analyze the following features with the highest impact on COVID-19: age, sex, blood group, had influenza.

Necessary problems in re-emergence of COVID-19

The ongoing pandemic of coronavirus disease 2019 poses a great threat to human beings. Although numerous patients have recovered, re-positive cases have been reported in several countries. Till now, we still know very little about the disease and its pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, more attention should be paid to the following aspects, such as post-discharge surveillance, asymptomatic infection, re-evaluation of influenza-like symptoms, and dynamic monitoring of genomic mutation of SARS-CoV-2.

Difference in levels of SARS-CoV-2 S1 and S2 subunits- and nucleocapsid protein-reactive SIgM/IgM, IgG and SIgA/IgA antibodies in human milk

OBJECTIVE

This study evaluated the presence and the levels of antibodies reactive to SARS-CoV-2 S1 and S2 subunits (S1 + S2), and nucleocapsid protein.

STUDY DESIGN

The levels of SARS-CoV-2 S1 + S2- and nucleocapsid-reactive SIgM/IgM, IgG and SIgA/IgA were measured in human milk samples from 41 women during the COVID-19 pandemic (2020-HM) and from 16 women 2 years prior to the outbreak (2018-HM).

RESULTS

SARS-CoV-2 S1 + S2-reactive SIgA/IgA, SIgM/IgM and IgG were detected in 97.6%, 68.3% and 58.5% in human milk whereas nucleocapsid-reactive antibodies were detected in 56.4%, 87.2% and 46.2%, respectively. S1 + S2-reactive IgG was higher in milk from women that had symptoms of viral respiratory infection(s) during the last year than in milk from women without symptom. S1 + S2- and nucleocapsid-reactive IgG were higher in the 2020-HM group compared to the 2018-HM group.

CONCLUSIONS

The presence of SARS-CoV-2-reactive antibodies in human milk could provide passive immunity to breastfed infants and protect them against COVID-19 diseases.

Influenza and Influenza Vaccine: A Review

Influenza is a highly contagious, deadly virus, killing nearly half a million people yearly worldwide. The classic symptoms of influenza are fever, fatigue, cough, and body aches. In the outpatient setting, diagnosis can be made by clinical presentation with optional confirmatory diagnostic testing. Antiviral medications should be initiated as soon as possible, preferably within 24 hours of initiation of symptoms. The primary preventive measure against influenza is vaccination, which is recommended for all people 6 months of age or older, including pregnant and postpartum women, unless the individual has a contraindication. Vaccination should occur at the beginning of flu season, which typically begins in October. It takes approximately 14 days after vaccination for a healthy adult to reach peak antibody protection. There are challenges associated with vaccine composition and vaccine uptake. It takes approximately 6 to 8 months to identify and predict which influenza strains to include in the upcoming season's vaccine. During this time, the influenza virus may undergo antigenic drift, that is, mutating to avoid a host immune response. Antigenic drift makes the vaccine less effective in some seasons. The influenza virus occasionally undergoes antigenic shift, in which it changes to a novel virus, creating potential for a pandemic. There are also barriers to vaccine uptake, including lack of or limited access to care and misconceptions about receiving the vaccine. Interventions that improve access to and uptake of the influenza vaccine must be initiated, targeting multiple levels, including health care policy, patients, health care systems, and the health care team. This article reviews information about influenza identification, management, and prevention.

COVID-19 Pandemic: The Influence of Culture and Lessons for Collaborative Activities

The rapid epidemiological shift from an epidemic/outbreak in Wuhan, China, to a global pandemic of COVID-19 in less than 3 months came with lessons the world's health system should learn to prepare for the future outbreaks. Since February 20, 2020, the total number of confirmed cases of COVID-19 has been increased very slowly in the countries of East Asia, including Japan, South Korea, and China, when compared with those in the Western countries. This chapter begins with an overview of the impact of COVID-19 on healthcare workers and public health facilities, followed by immediate global actions and research in response to the newly emerged pandemic. It includes an evaluation of the potential influence of culture on the implementation of different protective measures to combat the COVID-19 pandemic while at the same time offering suggestions that will make it easier for all populations to adapt protective steps against COVID-19 and other respiratory infectious diseases. Finally, the chapter provides a detailed discussion of lessons we have learned from the pandemic, leading to the conclusion that the transition from individualism to collaborative efforts is the treatment of universal pandemics.

COVID-19 or non-COVID viral pneumonia: How to differentiate based on the radiologic findings?

Influenza viruses were responsible for most adult viral pneumonia. Presently, coronavirus disease 2019 (COVID-19) has evolved into serious global pandemic. COVID-19 outbreak is expected to persist in months to come that will be synchronous with the influenza season. The management, prognosis, and protection for these two viral pneumonias differ considerably and differentiating between them has a high impact on the patient outcome. Reverse transcriptase polymerase chain reaction is highly specific but has suboptimal sensitivity. Chest computed tomography (CT) has a high sensitivity for detection of pulmonary disease manifestations and can play a key-role in diagnosing COVID-19. We reviewed 47 studies and delineated CT findings of COVID-19 and influenza pneumonia. The differences observed in the chest CT scan can be helpful in differentiation. For instance, ground glass opacities (GGOs), as the most frequent imaging finding in both diseases, can differ in the pattern of distribution. Peripheral and posterior distribution, multilobular distribution, pure or clear margin GGOs were more commonly reported in COVID-19, whereas central or peri-bronchovascular GGOs and pure consolidations were more seen in influenza A (H1N1). In review of other imaging findings, further differences were noticed. Subpleural curvilinear lines, sugar melted sign, intra-lesional vascular enlargement, reverse halo sign, and fibrotic bands were more reported in COVID-19 than H1N1, while air space nodule, tree-in-bud, bronchiectasia, pleural effusion, and cavitation were more seen in H1N1. This delineation, when combined with clinical manifestations and laboratory results may help to differentiate these two viral infections.

Risks of ventilator-associated pneumonia and invasive pulmonary aspergillosis in patients with viral acute respiratory distress syndrome related or not to Coronavirus 19 disease

Background

Data on incidence of ventilator-associated pneumonia (VAP) and invasive pulmonary aspergillosis in patients with severe SARS-CoV-2 infection are limited.

Methods

We conducted a monocenter retrospective study comparing the incidence of VAP and invasive aspergillosis between patients with COVID-19-related acute respiratory distress syndrome (C-ARDS) and those with non-SARS-CoV-2 viral ARDS (NC-ARDS).

Results

We assessed 90 C-ARDS and 82 NC-ARDS patients, who were mechanically ventilated for more than 48 h. At ICU admission, there were significantly fewer bacterial coinfections documented in C-ARDS than in NC-ARDS: 14 (16%) vs 38 (48%), p < 0.01. Conversely, significantly more patients developed at least one VAP episode in C-ARDS as compared with NC-ARDS: 58 (64%) vs. 36 (44%), p = 0.007. The probability of VAP was significantly higher in C-ARDS after adjusting on death and ventilator weaning [sub-hazard ratio = 1.72 (1.14–2.52), p < 0.01]. The incidence of multi-drug-resistant bacteria (MDR)-related VAP was significantly higher in C-ARDS than in NC-ARDS: 21 (23%) vs. 9 (11%), p = 0.03. Carbapenem was more used in C-ARDS than in NC-ARDS: 48 (53%), vs 21 (26%), p < 0.01. According to AspICU algorithm, there were fewer cases of putative aspergillosis in C-ARDS than in NC-ARDS [2 (2%) vs. 12 (15%), p = 0.003], but there was no difference in Aspergillus colonization.

Conclusions

In our experience, we evidenced a higher incidence of VAP and MDR-VAP in C-ARDS than in NC-ARDS and a lower risk for invasive aspergillosis in the former group.

Bioengineered in Vitro Tissue Models to Study SARS-CoV-2 Pathogenesis and Therapeutic Validation

Given the various viral outbreaks in the 21st century, specifically the present pandemic situation arising from SARS-CoV-2 or the coronavirus, of unknown magnitude, there is an unmet clinical need to develop effective therapeutic and diagnostic strategies to combat this infectious disease worldwide. To develop precise anticoronavirus drugs and prophylactics, tissue engineering and biomaterial research strategies can serve as a suitable alternative to the conventional treatment options. Therefore, in this Review, we have highlighted various tissue engineering-based diagnostic systems for SARS-CoV-2 and suggested how these strategies involving organ-on-a-chip, organoids, 3D bioprinting, and advanced bioreactor models can be employed to develop in vitro human tissue models, for more efficient diagnosis, drug/vaccine development, and focusing on the need for patient-specific therapy. We believe that combining the basics of virology with tissue engineering techniques can help the researchers to understand the molecular mechanism underlying viral infection, which is critical for effective drug design. In addition, it can also serve to be a suitable platform for drug testing and delivery of small molecules that can lead to therapeutic tools in this dreaded pandemic situation. Additionally, we have also discussed the essential biomaterial properties which polarize the immune system, including dendritic cells and macrophages, toward their inflammatory phenotype, which can thus serve as a reference for exhibiting the role of biomaterial in influencing the adaptive immune response involving B and T lymphocytes to foster a regenerative tissue microenvironment. The situation arising from SARS-CoV-2 poses a challenge to scientists from almost all disciplines, and we feel that tissue engineers can thus provide new translational opportunities in this dreadful pandemic situation.

Using the Past to Maximize the Success Probability of Future Anti-Viral Vaccines

Rapid obtaining of safe, effective, anti-viral vaccines has recently risen to the top of the international agenda. To maximize the success probability of future anti-viral vaccines, the anti-viral vaccines successful in the past are summarized here by virus type and vaccine type. The primary focus is on viruses with both single-stranded RNA genomes and a membrane envelope, given the pandemic past of influenza viruses and coronaviruses. The following conclusion is reached, assuming that success of future strategies is positively correlated with strategies successful in the past. The primary strategy, especially for emerging pandemic viruses, should be development of vaccine antigens that are live-attenuated viruses; the secondary strategy should be development of vaccine antigens that are inactivated virus particles. Support for this conclusion comes from the complexity of immune systems. These conclusions imply the need for a revision in current strategic planning.

Structural features of coronavirus SARS-CoV-2 spike protein: Targets for vaccination

Various human pathogenic viruses employ envelope glycoproteins for host cell receptor recognition and binding, membrane fusion and viral entry. The spike (S) glycoprotein of betacoronavirus SARS-CoV-2 is a homotrimeric class I fusion protein that exists in a metastable conformation for cleavage by host cell proteases furin and TMPRSS2, thereby undergoing substantial structural rearrangement for ACE2 host cell receptor binding and subsequent viral entry by membrane fusion. The S protein is densely decorated with N-linked glycans protruding from the trimer surface that affect S protein folding, processing by host cell proteases and the elicitation of humoral immune response. Deep insight into the sophisticated structure of SARS-CoV-2 S protein may provide a blueprint for vaccination strategies, as reviewed herein.

Why is temperature sensitivity important for the success of common respiratory viruses?

This review explores the idea that temperature sensitivity is an important factor in determining the success of respiratory viruses as human parasites. The review discusses several questions. What is viral temperature sensitivity? At what range of temperatures are common respiratory viruses sensitive? What is the mechanism for their temperature sensitivity? What is the range of temperature along the human airway? What is it that makes respiratory viruses such successful parasites of the human airway? What is the role of temperature sensitivity in respiratory zoonoses? A definition of temperature sensitivity is proposed, as “the property of a virus to replicate poorly or not at all, at the normal body temperature of the host (restrictive temperature), but to replicate well at the lower temperatures found in the upper airway of the host (permissive temperature).” Temperature sensitivity may influence the success of a respiratory virus in several ways. Firstly; by restricting the infection to the upper airways and reducing the chance of systemic infection that may reduce host mobility and increase mortality, and thus limit the spread of the virus. Secondly; by causing a mild upper airway illness with a limited immune response compared to systemic infection, which means that persistent herd immunity does not develop to the same extent as with systemic infections, and re‐infection may occur later. Thirdly; infection of the upper airway triggers local reflex rhinorrhea, coughing and sneezing which aid the exit of the virus from the host and the spread of infection in the community.

Influenza and COVID-19 coinfection: Report of six cases and review of the literature

Coronavirus disease 2019 (COVID-19) pandemic caused infection in a season when influenza is still prevalent. Both viruses have similar transmission characteristics and common clinical manifestations. Influenza has been described to cause respiratory infection with some other respiratory pathogens. However, the information of COVID-19 and influenza coinfection is limited. In this study, we reported our coinfected cases and reviewed the literature. We included all COVID-19 diagnosed patients. All patients with a presumed diagnosis of COVID-19 were routinely screened for influenza. Their thorax radiology was reviewed for COVID-19-influenza differentiation. During the study period, 1103 patients have been diagnosed with COVID-19. Among them, six patients (0.54%) were diagnosed coinfected with influenza. There have been 28 more coinfected patients reported. Laboratory-based screening studies reported more patients. Thorax radiology findings were compatible with COVID-19 in five and with influenza in one of our patients. Our cases were mild to moderate in severity. The reported cases in the literature included patients died (n = 2) and those living ventilator dependent or under mechanical ventilation. COVID-19 and influenza coinfection is rare. Screening studies report more cases, suggesting that unless screening patients with COVID-19, the coinfection remains undiagnosed and underestimated. Increasing experience in thoracic radiology may contribute to diagnose the responsible virus(es) from the clinical illness. Influenza vaccine for larger population groups can be recommended to simplify clinicians' work.