SARS: the first pandemic of the 21st century

Lessons learnt from broad-spectrum coronavirus antiviral drug discovery

INTRODUCTION

Highly pathogenic coronaviruses (CoVs), such as severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and the most recent SARS-CoV-2 responsible for the COVID-19 pandemic, pose significant threats to human populations over the past two decades. These CoVs have caused a broad spectrum of clinical manifestations ranging from asymptomatic to severe distress syndromes (ARDS), resulting in high morbidity and mortality.

AREAS COVERED

The accelerated advancements in antiviral drug discovery, spurred by the COVID-19 pandemic, have shed new light on the imperative to develop treatments effective against a broad spectrum of CoVs. This perspective discusses strategies and lessons learnt in targeting viral non-structural proteins, structural proteins, drug repurposing, and combinational approaches for the development of antivirals against CoVs.

EXPERT OPINION

Drawing lessons from the pandemic, it becomes evident that the absence of efficient broad-spectrum antiviral drugs increases the vulnerability of public health systems to the potential onslaught by highly pathogenic CoVs. The rapid and sustained spread of novel CoVs can have devastating consequences without effective and specifically targeted treatments. Prioritizing the effective development of broad-spectrum antivirals is imperative for bolstering the resilience of public health systems and mitigating the potential impact of future highly pathogenic CoVs.

Prospective follow-up of overactive bladder symptoms in patients with prior SARS-CoV-2 infection

PURPOSE

SARS-CoV-2 infection can result in genitourinary symptoms, such as frequency, urgency, nocturia, and pain/pressure. In this study, we followed the progression of overactive bladder (OAB) symptoms in patients that reported new or worsening OAB symptoms after coronavirus disease-19 (COVID-19) diagnosis.

MATERIALS AND METHODS

Individuals from a COVID-19 serology study were invited to participate in a follow-up study. Respondents were divided into three groups based on prior COVID-19 testing. Patients scored symptoms retrospectively before the pandemic, at study onset, and prospectively during 12-month follow-up. Genitourinary symptoms were assessed using international consultation on incontinence questionaire for OAB (ICIQ-OAB). Change in ICIQ-OAB scores from baseline were calculated. The minimal important difference of one on ICIQ-OAB is considered a significant change.

RESULTS

26.0% of participants previously had positive COVID polymerase chain reaction (PCR) test (PCR+), 5.6% a positive serology test only (Ser+), and 65.5% were COVID naïve (COVID-). 23.8% of participants reported a significant increase in ICIQ-OAB score at study onset compared to prepandemic. ICIQ-OAB scores were similar at prepandemic but significantly higher at study start (p < 0.001) in PCR+ group. During follow-up, change in ICIQ-OAB scores from baseline remained unchanged for COVID- group, but gradually reduced for PCR+, reaching similar levels as COVID- group by 12 months. By 12 months, 71.4% of PCR+, 42.9% of Ser+, and 68.8% of COVID- participants still reported significant increase in ICIQ-OAB scores.

CONCLUSIONS

Most COVID-19 patients experienced return of symptoms to baseline, indicative of the potential resolution of COVID-associated cystitis. A subset of cases did not, raising questions about the underlying factors contributing to this outcome. Additional research is needed to assess long COVID on urological health.

Whole genome analysis reveals unique traits of SARS-CoV-2 in pediatric patients

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to challenge the global healthcare with emerging variants and higher infectivity as well as morbidities. This study investigated potential age-related variations through genomic characterization of the virus under common clinical settings. A cohort comprising 71 SARS-CoV-2 strains from both infected infants and accompanying adults, diagnosed via RT-PCR at a tertiary pediatric hospital and research center, underwent Illumina paired-end sequencing. The subsequent analysis involved standard genomic screening, phylogeny construction, and mutational analyses. The analyzed SARSCoV- 2 strains were compared with globally circulating variants. The overall distribution revealed 67.61 % Delta, 25.7 % Omicron, and 1 % either Kappa or Alpha variants. In 2021, Delta predominated at ∼ 94 %, with Alpha/Kappa accounting for around 5 %. However, in 2022, over 94 % of the samples were Omicron variants, signifying a substantial shift from Delta dominance. Delta variants constituted 69.5 % of infections in adults and 78.5 % in infants, while Omicron variants were responsible for 31 % of cases in infants and 18 % in adults. The Spike region harbored the majority of mutations, with T19R being the most prevalent mutation in the Delta lineage. Notably, the frequencies of this mutation varied between infants and adults. In Omicron samples, G142D emerged as the most prevalent mutation. Our dataset predominantly featured clade 21A and lineage B.1.617.2. This study underscores the differential clinical presentations and genomic characteristics of SARS-CoV-2 in pediatric patients and accompanying adults. Understanding the dynamic evolution of the SARS- CoV-2 in both pediatric and adults can help in strengthening prophylactic measures.

SARS-CoV-2 Infection-Dependent Modulation in Vital Components of the Serum Profile of Severely SARS-CoV-2 Infected Patients

Background

COVID-19 modulates many serological biomarkers during the progress of disease severity. The study aimed to determine COVID-19 severity-associated perturbance in the serum profile.

Methods

A retrospective study including COVID-19-positive individuals (n = 405) was accomplished. The serum profile of COVID-19 participants was mined from laboratory records. Severity-associated alteration in the serum profile was evaluated using Pearson correlation, regression, VCramer, Bayesian posterior VCramer, and bias factor using R-base-RStudio-version-3.3.0 with a significant cut-off of p < 0.05.

Results

Significantly different mean ± standard deviation (SD) (highly versus moderately severe) of C-reactive protein (CRP), ferritin, neutrophil-lymphocyte ratio (NLR), D-dimer, platelets, prothrombin time (PT), partial prothrombin time (PTT), troponin 1, lactate dehydrogenase (LDH), aspartate-aminotransferase (AST), alanine aminotransferase (ALT), and AST/ALT ratio was observed (p < 0.001). Highly severe COVID-19 associated with CRP, ferritin, NLR, in D-dimer, PT, PTT, troponin 1, AST/ALT ratio, AST and ALT (adjusted odds ratio (AOR): 1.346, 1.05, 1.46, 1.33, 1.42, 1.23, 4.07, 3.9, 1.24, 1.45, p < 0.001). CRP with ferritin (r = 0.743), NLR (r = 0.77), white blood cells (WBC) (r = 0.8), troponin1 with LDH (r = 0.757), and D-dimer with platelets (r = -0.81) were highly correlated. X2pearson (p < 0.001), VCramer (0.71), Bayesian-VCramer (0.7), and bias-factor (-125) for troponin 1 indicate the strong association of troponin 1 level and with COVID-19 severity. X2pearson (p < 0.001), VCramer (1), Bayesian-VCramer (0.98), and bias-factor (-266.3) for NLR exhibited a very strong association of pathologic conditions with the high severity of the disease.

Conclusion

These biomarkers of inflammation (CRP, Ferritin, NLR), coagulation disorders (D-dimer, PT, and PTT) cardiac abnormality (troponin 1), and liver injury (AST/ALT) could be crucial in low-medical resource settings as potential prognosticator/predictors of the COVID-19 severity and clinical outcomes. Moreover, the outcome of this study could be leveraged for the early prediction of disease severity during SARS-CoV or Middle East Respiratory Coronavirus (MERS-CoV) infection.

Finally neutralizing the threat? A novel SARS-CoV-2 vaccine platform that elicits enhanced neutralizing antibody responses

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak took the world by storm due to its rapid global spread and unpredictable disease outcomes. The extraordinary ascension of SARS-CoV-2 to pandemic status motivated a world-wide effort to rapidly develop vaccines that could effectively suppress virus spread and mitigate severe disease. These efforts culminated in the development and deployment of several highly effective vaccines that were heralded as the beginning-of-the-end of the pandemic. However, these successes were short lived due to the unexpected and continuous emergence of more transmissible and immune-evasive SARS-CoV-2 variants. Thus, attention has shifted toward developing novel vaccine platforms that elicit more robust and sustained neutralizing antibody responses. Recent findings by Muñoz-Alía and colleagues address this by combining a live recombinant measles vaccine platform with novel biochemical approaches to generate vaccine candidates that bolster the potency of neutralizing antibody responses against diverse SARS-CoV-2 spike proteins (M. Á. Muñoz-Alía, R. A. Nace, B. Balakrishnan, L. Zhang, et al., mBio 9:e02928-23, 2024, https://doi.org/10.1128/mbio.02928-23).

A Mechanistic Understanding of the Modes of Ca2+ Ion Binding to the SARS-CoV-1 Fusion Peptide and Their Role in the Dynamics of Host Membrane Penetration

The SARS-CoV-1 spike glycoprotein contains a fusion peptide (FP) segment that mediates the fusion of the viral and host cell membranes. Calcium ions are thought to position the FP optimally for membrane insertion by interacting with negatively charged residues in this segment (E801, D802, D812, E821, D825, and D830); however, which residues bind to calcium and in what combinations supportive of membrane insertion are unknown. Using biological assays and molecular dynamics studies, we have determined the functional configurations of FP-Ca2+ binding that likely promote membrane insertion. We first individually mutated the negatively charged residues in the SARS CoV-1 FP to assay their roles in cell entry and syncytia formation, finding that charge loss in the D802A or D830A mutants greatly reduced syncytia formation and pseudoparticle transduction of VeroE6 cells. Interestingly, one mutation (D812A) led to a modest increase in cell transduction, further indicating that FP function likely depends on calcium binding at specific residues and in specific combinations. To interpret these results mechanistically and identify specific modes of FP-Ca2+ binding that modulate membrane insertion, we performed molecular dynamics simulations of the SARS-CoV-1 FP and Ca2+ions. The preferred residue pairs for Ca2+ binding we identified (E801/D802, E801/D830, and D812/E821) include the two residues found to be essential for S function in our biological studies (D802 and D830). The three preferred Ca2+ binding pairs were also predicted to promote FP membrane insertion. We also identified a Ca2+ binding pair (E821/D825) predicted to inhibit FP membrane insertion. We then carried out simulations in the presence of membranes and found that binding of Ca2+ to SARS-CoV-1 FP residue pairs E801/D802 and D812/E821 facilitates membrane insertion by enabling the peptide to adopt conformations that shield the negative charges of the FP to reduce repulsion by the membrane phospholipid headgroups. This calcium binding mode also optimally positions the hydrophobic LLF region of the FP for membrane penetration. Conversely, Ca2+ binding to the FP E801/D802 and D821/D825 pairs eliminates the negative charge screening and instead creates a repulsive negative charge that hinders membrane penetration of the LLF motif. These computational results, taken together with our biological studies, provide an improved and nuanced mechanistic understanding of the dymanics of SARS-CoV-1 calcium binding and their potential effects on host cell entry.

Cryo-electron microscopy in the fight against COVID-19-mechanism of virus entry

Cryogenic electron microscopy (cryo-EM) and electron tomography (cryo-ET) have become a critical tool for studying viral particles. Cryo-EM has enhanced our understanding of viral assembly and replication processes at a molecular resolution. Meanwhile, in situ cryo-ET has been used to investigate how viruses attach to and invade host cells. These advances have significantly contributed to our knowledge of viral biology. Particularly, prompt elucidations of structures of the SARS-CoV-2 spike protein and its variants have directly impacted the development of vaccines and therapeutic measures. This review discusses the progress made by cryo-EM based technologies in comprehending the severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2), the virus responsible for the devastating global COVID-19 pandemic in 2020 with focus on the SARS-CoV-2 spike protein and the mechanisms of the virus entry and replication.

In silico screening of SARS-CoV2 helicase using African natural products: Docking and molecular dynamics approaches

In the current medical era, there is an urgent necessity to identify new effective drugs to enrich the COVID-19's therapeutic arsenal. The SARS-COV-2 NSP13/helicase enzyme has been identified as a potential target for developing novel COVID-19 inhibitors. In this work, we aimed at endorsing effective natural products with potential inhibitory action towards the NSP13 through the virtual screening of 1012 natural products of botanical and marine origin from the South African Natural Compounds Database (SANCDB). The molecules were docked into the NTPase active site, and the best twelve compounds were chosen for further analysis. Thereafter, a combination of molecular dynamics simulations and MM-GBSA free energy calculations were carried out for a subset of best hits complexed with NSP13 helicase. We believe that the findings of this work will pave the way for additional research and experimental validation of some natural products as viable NSP13 helicase inhibitors.

Impact of adapting paediatric intensive care units for adult care during the COVID-19 pandemic: a scoping review

OBJECTIVES

The objectives were to categorise the evidence, map out the existing studies and explore what was known about the organisation of paediatric intensive care units (PICUs) during the first 18 months of the COVID-19 pandemic. Additionally, this review set out to identify any knowledge gaps in the literature and recommend areas for future research.

DESIGN

Scoping review.

METHODS

This study used Arksey and O'Malley's six-stage scoping review framework. A comprehensive search was conducted using the following databases, CINAHL Complete; MEDLINE; PsycINFO; PsycARTICLES and EMBASE and grey literature search engines. A search strategy with predefined inclusion criteria was used to uncover relevant research in this area. Screening and data collection were done in duplicate.

RESULTS

47 631 articles were obtained through searching. However, only 25 articles met the inclusion criteria and were included in the analysis. Three dominant themes emerged from the literature: (1) the reorganisation of space for managing increased capacity; (2) increased staffing and support; and (3) the resulting challenges.

CONCLUSION

COVID-19 has strained institutional resources across the globe. To relieve the burden on intensive care units (ICUs), some PICUs adjusted their units to care for critically ill adults, with other PICUs making significant changes, including the redeployment of staff to adult ICUs to provide extra care for adults. Overall, PICUs were collectively well equipped to care for adult patients, with care enhanced by implementing elements of holistic, family-centred PICU practices. The pandemic fostered a collaborative approach among PICU teams and wider hospital communities. However, specific healthcare guidelines had to be created to safely care for adult patients.

Asymmetry in the peak in Covid-19 daily cases and the pandemic R-parameter

Within the context of the standard SIR model of pandemics, we show that the asymmetry in the peak in recorded daily cases during a pandemic can be used to infer the pandemic R-parameter. Using only daily data for symptomatic, confirmed cases, we derive a universal scaling curve that yields: (i) reff, the pandemic R-parameter; (ii) Leff, the effective latency, the average number of days an infected individual is able to infect others and (iii) α , the probability of infection per contact between infected and susceptible individuals. We validate our method using an example and then apply it to estimate these parameters for the first phase of the SARS-Cov-2/Covid-19 pandemic for several countries where there was a well separated peak in identified infected daily cases. The extension of the SIR model developed in this paper differentiates itself from earlier studies in that it provides a simple method to make an a-posteriori estimate of several useful epidemiological parameters, using only data on confirmed, identified cases. Our results are general and can be applied to any pandemic.

Early protective effect of a ("pan") coronavirus vaccine (PanCoVac) in Roborovski dwarf hamsters after single-low dose intranasal administration

Introduction

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the danger posed by human coronaviruses. Rapid emergence of immunoevasive variants and waning antiviral immunity decrease the effect of the currently available vaccines, which aim at induction of neutralizing antibodies. In contrast, T cells are marginally affected by antigen evolution although they represent the major mediators of virus control and vaccine protection against virus-induced disease.

Materials and methods

We generated a multi-epitope vaccine (PanCoVac) that encodes the conserved T cell epitopes from all structural proteins of coronaviruses. PanCoVac contains elements that facilitate efficient processing and presentation of PanCoVac-encoded T cell epitopes and can be uploaded to any available vaccine platform. For proof of principle, we cloned PanCoVac into a non-integrating lentivirus vector (NILV-PanCoVac). We chose Roborovski dwarf hamsters for a first step in evaluating PanCoVac in vivo. Unlike mice, they are naturally susceptible to SARS-CoV-2 infection. Moreover, Roborovski dwarf hamsters develop COVID-19-like disease after infection with SARS-CoV-2 enabling us to look at pathology and clinical symptoms.

Results

Using HLA-A^*0201-restricted reporter T cells and U251 cells expressing a tagged version of PanCoVac, we confirmed in vitro that PanCoVac is processed and presented by HLA-A^*0201. As mucosal immunity in the respiratory tract is crucial for protection against respiratory viruses such as SARS-CoV-2, we tested the protective effect of single-low dose of NILV-PanCoVac administered via the intranasal (i.n.) route in the Roborovski dwarf hamster model of COVID-19. After infection with ancestral SARS-CoV-2, animals immunized with a single-low dose of NILV-PanCoVac i.n. did not show symptoms and had significantly decreased viral loads in the lung tissue. This protective effect was observed in the early phase (2 days post infection) after challenge and was not dependent on neutralizing antibodies.

Conclusion

PanCoVac, a multi-epitope vaccine covering conserved T cell epitopes from all structural proteins of coronaviruses, might protect from severe disease caused by SARS-CoV-2 variants and future pathogenic coronaviruses. The use of (HLA-) humanized animal models will allow for further efficacy studies of PanCoVac-based vaccines in vivo.

The importance of equally accessible genomic surveillance in the age of pandemics

Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe.

Immune evasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); molecular approaches

In December 2019, a new betacoronavirus, known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), caused an outbreak at the Wuhan seafood market in China. The disease was further named coronavirus disease 2019 (COVID-19). In March 2020, the World Health Organization (WHO) announced the disease to be a pandemic, as more cases were reported globally. SARS-CoV-2, like many other viruses, employs diverse strategies to elude the host immune response and/or counter immune responses. The infection outcome mainly depends on interactions between the virus and the host immune system. Inhibiting IFN production, blocking IFN signaling, enhancing IFN resistance, and hijacking the host's translation machinery to expedite the production of viral proteins are among the main immune evasion mechanisms of SARS-CoV-2. SARS-CoV-2 also downregulates the expression of MHC-I on infected cells, which is an additional immune-evasion mechanism of this virus. Moreover, antigenic modifications to the spike (S) protein, such as deletions, insertions, and also substitutions are essential for resistance to SARS-CoV-2 neutralizing antibodies. This review assesses the interaction between SARS-CoV-2 and host immune response and cellular and molecular approaches used by SARS-CoV-2 for immune evasion. Understanding the mechanisms of SARS-CoV-2 immune evasion is essential since it can improve the development of novel antiviral treatment options as well as vaccination methods.

Patient-derived monoclonal antibodies to SARS-CoV-2 nucleocapsid protein N-terminal and C-terminal domains cross-react with their counterparts of SARS-CoV, but not other human betacoronaviruses

Introduction

SARS-CoV-2 nucleocapsid (N) protein plays a key role in multiple stages of the viral life cycle such as viral replication and assembly. This protein is more conserved than the Spike protein of the virus and can induce both humoral and cell-mediated immune responses, thereby becoming a target for clinical diagnosis and vaccine development. However, the immunogenic characteristics of this protein during natural infection are still not completely understood.

Methods

Patient-derived monoclonal antibodies (mAbs) against SARS-CoV-2 N protein were generated from memory B cells in the PBMCs using the antigen-specific B cell approach. For epitope mapping of the isolated hmAbs, a panel of series-truncated N proteins were used , which covered the N-terminal domain (NTD, aa 46-174 ) and C-terminal domain (CTD, aa 245-364 ), as well as the flanking regions of NTD and CTD. NTD- or CTD-specific Abs in the plasma from COVID-19 patients were also tested by ELISA method. Cross-binding of hmAbs or plasma Abs in COVID-19 patients to other human β-CoV N proteins was determined using the capture ELISA.

Results

We isolated five N-specific monoclonal antibodies (mAbs) from memory B cells in the peripheral blood of two convalescent COVID-19 patients. Epitope mapping revealed that three of the patient-derived mAbs (N3, N5 and N31) targeted the C-terminal domain (CTD), whereas two of the mAbs (N83 and 3B7) targeted the N-terminal domain (NTD) of SARS-CoV-2 N protein. All five patient-derived mAbs were cross-reactive to the N protein of SARS-CoV but showed little to no cross-reactivity to the N proteins of other human beta coronaviruses (β-CoVs). We also tested 52 plasma samples collected from convalescent COVID-19 patients for Abs against the N proteins of human β-CoVs and found that 78.8% of plasma samples showed detectable Abs against the N proteins of SARS-CoV-2 and SARS-CoV. No plasma sample had cross-reactive Abs to the N protein of MERS-CoV. Cross-reactive Abs to the N proteins of OC43 and HKU1 were detected in 36.5% (19/52) and 19.2% (10/52) of plasma samples, respectively.

Discussion

These results suggest that natural SARS-CoV-2 infection elicits cross-reactive Abs to the N protein of SARS-CoV and that the five patient-derived mAbs to SARS-CoV-2 N protein NTD and CTD cross-react with their counterparts of SARS-CoV, but not other human β-CoVs. Thus, these five patient-derived mAbs can potentially be used for developing the next generation of COVID-19 At-Home Test kits for rapid and specific screening of SARS-CoV-2 infection.

Impact of COVID-19 on ports, multimodal logistics and transport sector in India: Responses and policy imperatives

The COVID-19 pandemic spread rapidly in 2020 and led to full or partial lockdowns worldwide. The restrictions led to most economies contracting in the April-June quarter of 2020. As per the IMF World Economic Outlook of June 2020, the global economy was expected to contract by 4.9% in 2020, whereas the Indian economy was expected to contract by 4.5%, affecting a population of more than 1.3 billion. This led to disruption in the global supply chain network, adversely hitting all modes of transport, including ports and multimodal logistics. Based on the survey results of 98 respondents in the Indian ports, multimodal logistics and transport ("PMT") sector conducted during the lockdown in May-June 2020, an adverse impact on profitability, employment, operations and capital expenditure was identified, which is consistent with observations from previous economic crises. Additionally, we have estimated the financial impact on different categories of organisations in the industry. Based on these impacts, this study identified key factors required to support the sector and build resilience for the future through technology interventions, developing multimodal transport systems, and providing financial support and employment support for small and medium enterprises (SMEs). By providing an analysis of the impact of COVID-19 on the different categories of organisations based on data collected during and shortly after the lockdown, the study makes a novel contribution to understanding the impact of such crises on the PMT industry at a granular level and the aggregate-level impacts with guidance for policy and managers and in particular, in an emerging economy context.

Tracing the origin of Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): A systematic review and narrative synthesis

The aim of the study was to trace and understand the origin of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through various available literatures and accessible databases. Although the world enters the third year of the coronavirus disease 2019 pandemic, health and socioeconomic impacts continue to mount, the origin and mechanisms of spill-over of the SARS-CoV-2 into humans remain elusive. Therefore, a systematic review of the literature was performed that showcased the integrated information obtained through manual searches, digital databases (PubMed, CINAHL, and MEDLINE) searches, and searches from legitimate publications (1966-2022), followed by meta-analysis. Our systematic analysis data proposed three postulated hypotheses concerning the origin of the SARS-CoV-2, which include zoonotic origin (Z), laboratory origin (L), and obscure origin (O). Despite the fact that the zoonotic origin for SARS-CoV-2 has not been conclusively identified to date, our data suggest a zoonotic origin, in contrast to some alternative concepts, including the probability of a laboratory incident or leak. Our data exhibit that zoonotic origin (Z) has higher evidence-based support as compared to laboratory origin (L). Importantly, based on all the studies included, we generated the forest plot with 95% confidence intervals (CIs) of the risk ratio estimates. Our meta-analysis further supports the zoonotic origin of SARS/SARS-CoV-2 in the included studies.

The COVID-19 pandemic - How many times were we warned before?

Infectious diseases are known to act in both predictable and unpredictable ways, which leads to the notions of emerging and reemerging infectious diseases. Emerging diseases with their disastrous consequences might be surprising and unpredictable, but they could be foreseen. For instance, some emerging diseases and recently the coronavirus disease 2019 (COVID-19) were the reason for papers published by the World Health Organization (WHO) and other researchers addressing the likely pathogens causing future outbreaks, according to the reports of the WHO in 2016 and 2018. Although it might seem like a wisdom in retrospect, several studies had already indicated possible future outbreaks caused by coronaviruses. Announcements, which may be viewed as "warnings," appeared since the emergence of the first coronavirus-related outbreak caused by severe acute respiratory syndrome coronavirus (SARS-CoV) in the winter of 2002-2003 and a later outbreak caused by the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012-2013. Therefore, we were curious to review the medical literature prior to the COVID-19 pandemic with an aim to enumerate and evaluate studies addressing and warning against future outbreaks, and surprisingly pandemics, of members of coronaviruses. Interestingly, we found numerous studies that correctly predicted the current pandemic of COVID-19. While this part is highly interesting, how authorities reacted and prepared for warnings, if any, and how will they get prepared for the next warnings are our main messages. Taking these points into serious consideration will certainly aid in analyzing reports regarding possible future outbreaks as well as in developing various strategies for prevention and coping with such epidemics.

A literature review on quantitative models for supply chain risk management: Can they be applied to pandemic disruptions?

Supply chain risk management is considered a topic of increasing interest worldwide and its focus has evolved over time. The recent coronavirus pandemic (known as COVID-19) has forced business to handle a new global crisis and rapidly adapt to unexpected challenges. In an attempt to help companies counteract the pandemic risk, as well as to fuel the scientific discussion about this topic, this paper proposes a systematic literature review on risk management and disruptions in the supply chain focusing on quantitative models and paying a particular attention to highlighting the potentials of the studies reviewed for being applied to counteract pandemic emergencies. An appropriate query was made on Scopus and returned, after a manual screening, a useful set of 99 papers that proposed models for supply chain risk management. The relevant aspects of pandemics risk management have been first identified and mapped; then, the studies reviewed have been analysed with the aim of evaluating their suitability of being applied to sanitary crises. In carrying out this review of the literature, the study moves from previous, more general, reviews about risk management and updates them, starting from the lines of research that have been covered in recent years and evaluating their consistency with future research directions emerging also as a consequence of the pandemic crisis. Gaps and limitations of the existing models are identified and future research directions for pandemics risk management are suggested.

Diagnostic Tools for Rapid Screening and Detection of SARS-CoV-2 Infection

The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has severely impacted human health and the health management system globally. The ongoing pandemic has required the development of more effective diagnostic strategies for restricting deadly disease. For appropriate disease management, accurate and rapid screening and isolation of the affected population is an efficient means of containment and the decimation of the disease. Therefore, considerable efforts are being directed toward the development of rapid and robust diagnostic techniques for respiratory infections, including SARS-CoV-2. In this article, we have summarized the origin, transmission, and various diagnostic techniques utilized for the detection of the SARS-CoV-2 virus. These higher-end techniques can also detect the virus copy number in asymptomatic samples. Furthermore, emerging rapid, cost-effective, and point-of-care diagnostic devices capable of large-scale population screening for COVID-19 are discussed. Finally, some breakthrough developments based on spectroscopic diagnosis that could revolutionize the field of rapid diagnosis are discussed.

Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations

For the last two years, the COVID-19 pandemic has continued to bring consternation on most of the world. According to recent WHO estimates, there have been more than 5.6 million deaths worldwide. The virus continues to evolve all over the world, thus requiring both vigilance and the necessity to find and develop a variety of therapeutic treatments, including the identification of specific antiviral drugs. Multiple studies have confirmed that SARS-CoV-2 utilizes its membrane-bound spike protein to recognize human angiotensin-converting enzyme 2 (ACE2). Thus, preventing spike-ACE2 interactions is a potentially viable strategy for COVID-19 treatment as it would block the virus from binding and entering into a host cell. This work aims to identify potential drugs using an in silico approach. Molecular docking was carried out on both approved drugs and substances previously tested in vivo. This step was followed by a more detailed analysis of selected ligands by molecular dynamics simulations to identify the best molecules that thwart the ability of the virus to interact with the ACE2 receptor. Because the SARS-CoV-2 virus evolves rapidly due to a plethora of immunocompromised hosts, the compounds were tested against five different known lineages. As a result, we could identify substances that work well on individual lineages and those showing broader efficacy. The most promising candidates among the currently used drugs were zafirlukast and simeprevir with an average binding affinity of -22 kcal/mol for spike proteins originating from various lineages. The first compound is a leukotriene receptor antagonist that is used to treat asthma, while the latter is a protease inhibitor used for hepatitis C treatment. From among the in vivo tested substances that concurrently exhibit promising free energy of binding and ADME parameters (indicating a possible oral administration) we selected the compound BDBM50136234. In conclusion, these molecules are worth exploring further by in vitro and in vivo studies against SARS-CoV-2.

Induction of high affinity monoclonal antibodies against SARS-CoV-2 variant infection using a DNA prime-protein boost strategy

BACKGROUND

Calls for the coronavirus to be treated as an endemic illness, such as the flu, are increasing. After achieving high coverage of COVID-19 vaccination, therapeutic drugs have become important for future SARS-CoV-2 variant outbreaks. Although many monoclonal antibodies have been approved for emergency use as treatments for SARS-CoV-2 infection, some monoclonal antibodies are not authorized for variant treatment. Broad-spectrum monoclonal antibodies are unmet medical needs.

METHODS

We used a DNA prime-protein boost approach to generate high-quality monoclonal antibodies. A standard ELISA was employed for the primary screen, and spike protein-human angiotensin-converting enzyme 2 blocking assays were used for the secondary screen. The top 5 blocking clones were selected for further characterization, including binding ability, neutralization potency, and epitope mapping. The therapeutic effects of the best monoclonal antibody against SARS-CoV-2 infection were evaluated in a hamster infection model.

RESULTS

Several monoclonal antibodies were selected that neutralize different SARS-CoV-2 variants of concern (VOCs). These VOCs include Alpha, Beta, Gamma, Delta, Kappa and Lambda variants. The high neutralizing antibody titers against the Beta variant would be important to treat Beta-like variants. Among these monoclonal antibodies, mAb-S5 displays the best potency in terms of binding affinity and neutralizing capacity. Importantly, mAb-S5 protects animals from SARS-CoV-2 challenge, including the Wuhan strain, D614G, Alpha and Delta variants, although mAb-S5 exhibits decreased neutralization potency against the Delta variant. Furthermore, the identified neutralizing epitopes of monoclonal antibodies are all located in the receptor-binding domain (RBD) of the spike protein but in different regions.

CONCLUSIONS

Our approach generates high-potency monoclonal antibodies against a broad spectrum of VOCs. Multiple monoclonal antibody combinations may be the best strategy to treat future SARS-CoV-2 variant outbreaks.

Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS-CoV-2 variants

INTRODUCTION

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic revealed a worldwide lack of effective molecular surveillance networks at local, state, and national levels, which are essential to identify, monitor, and limit viral community spread. SARS-CoV-2 variants of concern (VOCs) such as Alpha and Omicron, which show increased transmissibility and immune evasion, rapidly became dominant VOCs worldwide. Our objective was to develop an evidenced-based genomic surveillance algorithm, combining reverse transcription polymerase chain reaction (RT-PCR) and sequencing technologies to quickly identify highly contagious VOCs, before cases accumulate exponentially.

METHODS

Deidentified data were obtained from 508,969 patients tested for coronavirus disease 2019 (COVID-19) with the TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) in four CLIA-certified clinical laboratories in Puerto Rico (n = 86,639) and in three CLIA-certified clinical laboratories in the United States (n = 422,330).

RESULTS

TaqPath data revealed a frequency of S Gene Target Failure (SGTF) > 47% for the last week of March 2021 in both, Puerto Rico and US laboratories. The monthly frequency of SGTF in Puerto Rico steadily increased exponentially from 4% in November 2020 to 47% in March 2021. The weekly SGTF rate in US samples was high (>8%) from late December to early January and then also increased exponentially through April (48%). The exponential increase in SGFT prevalence in Puerto Rico was concurrent with a sharp increase in VOCs among all SARS-CoV-2 sequences from Puerto Rico uploaded to Global Influenza Surveillance and Response System (GISAID) (n = 461). Alpha variant frequency increased from <1% in the last week of January 2021 to 51.5% of viral sequences from Puerto Rico collected in the last week of March 2021.

CONCLUSIONS

According to the proposed evidence-based algorithm, approximately 50% of all SGTF patients should be managed with VOCs self-quarantine and contact tracing protocols, while WGS confirms their lineage in genomic surveillance laboratories. Our results suggest this workflow is useful for tracking VOCs with SGTF.

Single-Domain Antibodies as Therapeutics for Respiratory RNA Virus Infections

Over the years, infectious diseases with high morbidity and mortality disrupted human healthcare systems and devastated economies globally. Respiratory viruses, especially emerging or re-emerging RNA viruses, including influenza and human coronavirus, are the main pathogens of acute respiratory diseases that cause epidemics or even global pandemics. Importantly, due to the rapid mutation of viruses, there are few effective drugs and vaccines for the treatment and prevention of these RNA virus infections. Of note, a class of antibodies derived from camelid and shark, named nanobody or single-domain antibody (sdAb), was characterized by smaller size, lower production costs, more accessible binding epitopes, and inhalable properties, which have advantages in the treatment of respiratory diseases compared to conventional antibodies. Currently, a number of sdAbs have been developed against various respiratory RNA viruses and demonstrated potent therapeutic efficacy in mouse models. Here, we review the current status of the development of antiviral sdAb and discuss their potential as therapeutics for respiratory RNA viral diseases.

Viral Inactivation and Biocompatibility Study of Electrically Activated Water Mist

In addition to the ongoing global problem of healthcare-acquired infections, the COVID-19 pandemic continues to pose a serious threat to the health of the global population. This unprecedented pandemic situation has reinforced the need for the development of technologies that can curb the transmission of viruses among human beings and help to control the infection. Existing disinfection techniques using either ultraviolet light or harsh chemicals pose safety risks and are not suitable for use in the presence of humans. Thus, the need for a safe and effective disinfection technique that can be used in the presence of humans to control viral transmission is evident. A technique that can continuously disinfect air and surfaces in indoor environments, where the chances of viral transmission are high, can be an indispensable tool to fight such a pandemic. The Airlens Minus Corona (AMC) device provided by Persapien Innovations has been developed to achieve this goal. In this study, the antiviral functionality and biocompatibility of AMC were evaluated. Activated water mist (AWM) generated from this device was tested in vitro and in vivo for its toxicity to cell lines and in animal model. The AWM was found to be non-cytotoxic to L-929 cell lines and had no sign of clinical toxicity in an animal model (rabbit). This device was further used to inactivate animal viruses and bacteriophages. The AWM was found to be effective in the complete inactivation of influenza A H1N1 virus within 5 minutes of direct treatment. This device was also found to be effective in inactivating >90% of bacteriophage particles.

Structural Dynamics and Molecular Evolution of the SARS-CoV-2 Spike Protein

The ongoing coronavirus disease 2019 (COVID-19) pandemic demonstrates the threat posed by novel coronaviruses to human health. Coronaviruses share a highly conserved cell entry mechanism mediated by the spike protein, the sole product of the S gene. The structural dynamics by which the spike protein orchestrates infection illuminate how antibodies neutralize virions and how S mutations contribute to viral fitness. Here, we review the process by which spike engages its proteinaceous receptor, angiotensin converting enzyme 2 (ACE2), and how host proteases prime and subsequently enable efficient membrane fusion between virions and target cells. We highlight mutations common among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern and discuss implications for cell entry. Ultimately, we provide a model by which sarbecoviruses are activated for fusion competency and offer a framework for understanding the interplay between humoral immunity and the molecular evolution of the SARS-CoV-2 Spike. In particular, we emphasize the relevance of the Canyon Hypothesis (M. G. Rossmann, J Biol Chem 264:14587-14590, 1989) for understanding evolutionary trajectories of viral entry proteins during sustained intraspecies transmission of a novel viral pathogen.

Severe Acute Respiratory Syndrome Type 2-Causing Coronavirus: Variants and Preventive Strategies

COVID-19 vaccines have constituted a substantial scientific leap in countering severe acute respiratory syndrome type 2-causing coronavirus (SARS-CoV-2), and worldwide implementation of vaccination programs has significantly contributed to the global pandemic effort by saving many lives. However, the continuous evolution of the SARS-CoV-2 viral genome has resulted in different variants with a diverse range of mutations, some with enhanced virulence compared with previous lineages. Such variants are still a great concern as they have the potential to reduce vaccine efficacy and increase the viral transmission rate. This review summarizes the significant variants of SARS-CoV-2 encountered to date (December 2021) and discusses a spectrum of possible preventive strategies, with an emphasis on physical and materials science.

Using postal change-of-address data to predict second waves in infections near pandemic epicentres

We propose that postal Change-of-Address (CoA) data can be used to monitor/predict likely second wave caseloads in viral infections around urban epicentres. To illustrate the idea, we focus on the tri-state area consisting of New York City (NYC) and surrounding counties in New York, New Jersey and Connecticut States. NYC was an early epicentre of the coronavirus disease 2019 (Covid-19) pandemic, with a first peak in daily cases in early April 2020, followed by the second peak in May/June 2020. Using CoA data from the US Postal Service (USPS), we show that, despite a quarantine mandate, there was a large net movement of households from NYC to surrounding counties in the period April-June 2020. This net outward migration of households was strongly correlated with both the timing and the number of cases in the second peaks in Covid-19 cases in the surrounding counties. The timing of the second peak was also correlated with the distance of the county from NYC, suggesting that this was a directed flow and not random diffusion. Our analysis shows that CoA data is a useful method in tracking the spread of an infectious pandemic agent from urban epicentres.

Tracing the connections between international business and communicable diseases

We posit that international business and the emergence and spread of communicable diseases are intrinsically connected. To support our arguments, we first start with a historical timeline that traces the connections between international business and communicable diseases back to the sixth century. Second, following the epidemiology of communicable diseases, we identify two crucial transitions related to international business: the emergence of epidemics within a host country and the shift from epidemics to global pandemics. Third, we highlight international business contextual factors (host country regulatory quality, urbanization, trade barriers, global migration) and multinationals' activities (foreign direct investment, corporate political activity, global supply chain management, international travel) that could accelerate each transition. Finally, building on public health insights, we suggest research implications for business scholars on how to integrate human health challenges into their studies and practical implications for global managers on how to help prevent the emergence and spread of communicable diseases.

Disrupted Sleep During a Pandemic

The COVID-19 pandemic affected sleep in several people. Though most of the studies argued that age, gender, employment, finances, responsibilities, and exposure to sunlight governed sleep-wake schedule and sleep disturbances, there is also scientific evidence to suggest that these issues could have aroused because of the infiltration of the central nervous system (CNS) by SARS-CoV-2. Sleep disturbances must be addressed during the pandemic as sleep disturbances and systemic inflammation run in a vicious cycle; quality of sleep and timing of vaccination can influence the immune response to vaccination and subjects having obstructive sleep apnea (OSA) are at higher risk for having SARS-CoV-2 infection-related complications.

SARS-CoV-2-host cell surface interactions and potential antiviral therapies

In this review, we reveal the latest developments at the interface between SARS-CoV-2 and the host cell surface. In particular, we evaluate the current and potential mechanisms of binding, fusion and the conformational changes of the spike (S) protein to host cell surface receptors, especially the human angiotensin-converting enzyme 2 (ACE2) receptor. For instance, upon the initial attachment, the receptor binding domain of the S protein forms primarily hydrogen bonds with the protease domain of ACE2 resulting in conformational changes within the secondary structure. These surface interactions are of paramount importance and have been therapeutically exploited for antiviral design, such as monoclonal antibodies. Additionally, we provide an insight into novel therapies that target viral non-structural proteins, such as viral RNA polymerase. An example of which is remdesivir which has now been approved for use in COVID-19 patients by the US Food and Drug Administration. Establishing further understanding of the molecular details at the cell surface will undoubtably aid the development of more efficacious and selectively targeted therapies to reduce the burden of COVID-19.

Fabrication of Ag-doped ZnO/PAN composite nanofibers by electrospinning: Photocatalytic and antiviral activities

Ag-doped ZnO nanoparticles (AZNs) were directly synthesized using sol-gel method to embed into polyacrylonitrile (PAN) nanofibers by electrospinning. The synthesized AZNs were optically and structurally characterized by UV-VIS spectroscopy, photoluminescence spectroscopy, high resolution HR-TEM and XRD. The photocatalytic activity of the AZNs was examined by photocatalytic degradation of methylene blue to correlate with their antiviral efficacy in PAN nanofibers fabricated via electrospinning technique. The PAN nanofibers containing AZNs were characterized using SEM and EDS. Finally, antiviral activity of AZNs/PAN nanofibers was investigated by using virus ϕx174 under visible light irradiation. As a result, the antiviral efficacy of nanofibers increased as the concentration of Ag in AZNs increased. The results show that better antiviral efficacy was obtained in AZNs/PAN nanofibers prepared with AZNs of higher photocatalytic performance.

A novel STING agonist-adjuvanted pan-sarbecovirus vaccine elicits potent and durable neutralizing antibody and T cell responses in mice, rabbits and NHPs

The emergence of SARS-CoV-2 variants and potentially other highly pathogenic sarbecoviruses in the future highlights the need for pan-sarbecovirus vaccines. Here, we discovered a new STING agonist, CF501, and found that CF501-adjuvanted RBD-Fc vaccine (CF501/RBD-Fc) elicited significantly stronger neutralizing antibody (nAb) and T cell responses than Alum- and cGAMP-adjuvanted RBD-Fc in mice. Vaccination of rabbits and rhesus macaques (nonhuman primates, NHPs) with CF501/RBD-Fc elicited exceptionally potent nAb responses against SARS-CoV-2 and its nine variants and 41 S-mutants, SARS-CoV and bat SARSr-CoVs. CF501/RBD-Fc-immunized hACE2-transgenic mice were almost completely protected against SARS-CoV-2 challenge, even 6 months after the initial immunization. NHPs immunized with a single dose of CF501/RBD-Fc produced high titers of nAbs. The immunized macaques also exhibited durable humoral and cellular immune responses and showed remarkably reduced viral load in the upper and lower airways upon SARS-CoV-2 challenge even at 108 days post the final immunization. Thus, CF501/RBD-Fc can be further developed as a novel pan-sarbecovirus vaccine to combat current and future outbreaks of sarbecovirus diseases.

COVID-19 "asymptomatic" patients: an old wives' tale

INTRODUCTION

A novel virus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reported via nucleic acid identification in December, 2019. "Asymptomatic cases" have arised as an obstacle for an accurate diagnosis, curtailing the elimination of the ongoing pandemic.

AREAS COVERED

In this review, we analyze the definition of symptoms and the principles of diagnosing COVID-19. Also, we explore the major reasons for cases presenting a phenotype with mild symptoms. Host, viral and environmental aspects for a COVID-19 infection leading to mild symptoms are being highlighted. A final aspect regarding a rational primary asymptomatic COVID-19 infection is presumed.

EXPERT OPINION

Diagnosing a pandemic via a sole test can be risky. Epidemiological administration should be more accurate and precise, not only for the societal pandemic levels and following policies, but for the same scientific community, that studies SARS-CoV-2 and its mutants. Several other issues should be answered before analyzing human genome for the asymptomatic scenario.

Insights Into the Changing Landscape of Coronavirus Disease 2019

Coronavirus disease 2019 (COVID-19) is a highly contagious, infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in late 2019 in Wuhan China. A year after the World Health Organization declared COVID-19 a global pandemic, over 215 million confirmed cases and approximately 5 million deaths have been reported worldwide. In this multidisciplinary review, we summarize important insights for COVID-19, ranging from its origin, pathology, epidemiology, to clinical manifestations and treatment. More importantly, we also highlight the foundational connection between genetics and the development of personalized medicine and how these aspects have an impact on disease treatment and management in the dynamic landscape of this pandemic.

Multidrug resistance crisis during COVID-19 pandemic: Role of anti-microbial peptides as next-generation therapeutics

The decreasing effectiveness of conventional drugs due to multidrug-resistance is a major challenge for the scientific community, necessitating development of novel antimicrobial agents. In the present era of coronavirus 2 (COVID-19) pandemic, patients are being widely exposed to antimicrobial drugs and hence the problem of multidrug-resistance shall be aggravated in the days to come. Consequently, revisiting the phenomena of multidrug resistance leading to formulation of effective antimicrobial agents is the need of the hour. As a result, this review sheds light on the looming crisis of multidrug resistance in wake of the COVID-19 pandemic. It highlights the problem, significance and approaches for tackling microbial resistance with special emphasis on anti-microbial peptides as next-generation therapeutics against multidrug resistance associated diseases. Antimicrobial peptides exhibit exceptional mechanism of action enabling rapid killing of microbes at low concentration, antibiofilm activity, immunomodulatory properties along with a low tendency for resistance development providing them an edge over conventional antibiotics. The review is unique as it discusses the mode of action, pharmacodynamic properties and application of antimicrobial peptides in areas ranging from therapeutics to agriculture.

Uncovering a conserved vulnerability site in SARS-CoV-2 by a human antibody

An essential step for SARS-CoV-2 infection is the attachment to the host cell receptor by its Spike receptor-binding domain (RBD). Most of the existing RBD-targeting neutralizing antibodies block the receptor-binding motif (RBM), a mutable region with the potential to generate neutralization escape mutants. Here, we isolated and structurally characterized a non-RBM-targeting monoclonal antibody (FD20) from convalescent patients. FD20 engages the RBD at an epitope distal to the RBM with a KD of 5.6 nM, neutralizes SARS-CoV-2 including the current Variants of Concern such as B.1.1.7, B.1.351, P.1, and B.1.617.2 (Delta), displays modest cross-reactivity against SARS-CoV, and reduces viral replication in hamsters. The epitope coincides with a predicted "ideal" vulnerability site with high functional and structural constraints. Mutation of the residues of the conserved epitope variably affects FD20-binding but confers little or no resistance to neutralization. Finally, in vitro mode-of-action characterization and negative-stain electron microscopy suggest a neutralization mechanism by which FD20 destructs the Spike. Our results reveal a conserved vulnerability site in the SARS-CoV-2 Spike for the development of potential antiviral drugs.

COVID-19 and breastfeeding: can SARS-CoV-2 be spread through lactation?

SARS-CoV-2 is a new betacoronavirus that was first reported in the Hubei province, China, in December 2019. The virus is likely transmitted through air droplets. However, there are reported cases where SARS-CoV-2-RNA was found in other samples, such as blood or stool. Nonetheless, there is limited information concerning the presence of viral RNA in pregnancy-related samples, specifically breast milk. However unlikely, there is still uncertainty regarding the possibility of vertical transmission from mother to infant through breastfeeding. This review aims to synthetize the literature written so far on this topic. Despite not being extensively researched, vertical transmission through breast milk seems unlikely. Case series showed that milk samples from mothers with COVID-19 were almost entirely negative. So far, there have been only 9 recorded cases of viral shedding in milk samples, uncertain however of the viability of the particles. Furthermore, WHO and UNICEF strongly encourage commencing breastfeeding after parturition, underlining the benefits of lactation. Moreover, some studies have proven the existence of IgG and IgA anti-SARS-CoV-2-antibodies in the maternal milk that could possibly play an important part in the neonate’s protection against the virus. Vertical transmission through lactation seems unlikely, most studies pointing towards the safety of breastfeeding. However, further larger-scale studies need to be performed in order to clarify a yet uncertain matter.

A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice

[Figure: see text].

CT of Post-Acute Lung Complications of COVID-19

The acute course of COVID-19 is variable and ranges from asymptomatic infection to fulminant respiratory failure. Patients recovering from COVID-19 can have persistent symptoms and CT abnormalities of variable severity. At 3 months after acute infection, a subset of patients will have CT abnormalities that include ground-glass opacity (GGO) and subpleural bands with concomitant pulmonary function abnormalities. At 6 months after acute infection, some patients have persistent CT changes to include the resolution of GGOs seen in the early recovery phase and the persistence or development of changes suggestive of fibrosis, such as reticulation with or without parenchymal distortion. The etiology of lung disease after COVID-19 may be a sequela of prolonged mechanical ventilation, COVID-19-induced acute respiratory distress syndrome (ARDS), or direct injury from the virus. Predictors of lung disease after COVID-19 include need for intensive care unit admission, mechanical ventilation, higher inflammatory markers, longer hospital stay, and a diagnosis of ARDS. Treatments of lung disease after COVID-19 are being investigated, including the potential of antifibrotic agents for prevention of lung fibrosis after COVID-19. Future research is needed to determine the long-term persistence of lung disease after COVID-19, its impact on patients, and methods to either prevent or treat it. © RSNA, 2021.

Implementation status of national airborne infection control guidelines in the health care facilities of a North Indian State: A mixed method study

Objective

Healthcare-acquired infection (HCAIs), have become a significant cause of morbidity as well as mortality among the hospitalized patients and health care workers. The implementation of air-borne infection control measures play an important role in prevention of health care acquired infections (HCAIs). Hence, this study was planned to assess the implementation status of National Airborne Infection Control Guidelines in the health care settings of a North Indian State.

Study design

A mixed method study was planned in all the 13 health facilities of Himachal Pradesh having both the Anti-Retroviral Therapy (ART) Centre and Directly observed Treatment Short course (DOTS) for TB center in the same facility.

Methods

The implementation of airborne infection control measures was evaluated using a Standardized Health Care Facility Airborne Infection Risk Assessment Tool and an observational checklist. In-depth interviews are conducted with hospital staff. At all health facilities, risk assessment and implementation of airborne infection control was evaluated by using a pretested semi-structured questionnaire. The qualitative data was analyzed manually and transcripts prepared from hand written notes and audio tape records were analyzed thematically.

Results

Only 5 out of 13 health facilities were having specially designated airborne infection control committee. The incidence of tuberculosis among hospital staff was 2.32% at secondary level health care facilities and 0.35% at tertiary care level health facilities. Among the tuberculosis cases, maximum were nursing staff (59.5%) as compared to other categories of health care workers. Improper functioning of health care system and individual factors were main reasons for deficiencies in the implementation of air-borne infection control measures.

Conclusion

The health care facilities were not implementing the infection control measure to the fullest both at secondary and tertiary care health facilities. There is a need to set up the surveillance of airborne infections in the hospital and especially the passive surveillance of tuberculosis among health care workers.

•

The implementation of airborne infection control measures was evaluated by using standardized tools and checklist.

•

In-depth interviews were conducted with the hospital staff.

•

There were gaps in implementation at all the three levels i.e. administrative, environmental and individual levels.

•

There is a need to set up the surveillance of air borne infections in the hospitals.

•

Passive surveillance of tuberculosis among health care workers should be implemented.

Current Understanding of the Innate Control of Toll-like Receptors in Response to SARS-CoV-2 Infection

The global coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection, threatens the entire world. It has affected every aspect of life and increased the burden on both healthcare and socioeconomic systems. Current studies have revealed that excessive inflammatory immune responses are responsible for the severity of COVID-19, which suggests that anti-inflammatory drugs may be promising therapeutic treatments. However, there are currently a limited number of approved therapeutics for COVID-19. Toll-like receptors (TLRs), which recognize microbial components derived from invading pathogens, are involved in both the initiation of innate responses against SARS-CoV-2 infection and the hyperinflammatory phenotype of COVID-19. In this review, we provide current knowledge on the pivotal role of TLRs in immune responses against SARS-CoV-2 infection and demonstrate the potential effectiveness of TLR-targeting drugs on the control of hyperinflammation in patients with COVID-19.

Handheld plasmonic biosensor for virus detection in field-settings

After World Health Organization (WHO) announced COVID-19 outbreak a pandemic, we all again realized the importance of developing rapid diagnostic kits. In this article, we introduced a lightweight and field-portable biosensor employing a plasmonic chip based on nanohole arrays integrated to a lensfree-imaging framework for label-free detection of viruses in field-settings. The platform utilizes a CMOS (complementary metal-oxide-semiconductor) camera with high quantum efficiency in the spectral window of interest to monitor diffraction field patterns of nanohole arrays under the uniform illumination of an LED (light-emitting diode) source which is spectrally tuned to the plasmonic mode supported by the nanohole arrays. As an example for the applicability of our biosensor for virus detection, we could successfully demonstrate the label-free detection of H1N1 viruses, e.g., swine flu, with medically relevant concentrations. We also developed a low-cost and easy-to-use sample preparation kit to prepare the surface of the plasmonic chip for analyte binding, e.g., virus-antibody binding. In order to reveal a complete biosensor technology, we also developed a user friendly Python™ - based graphical user interface (GUI) that allows direct access to biosensor hardware, taking and processing diffraction field images, and provides virus information to the end-user. Employing highly sensitive nanohole arrays and lensfree-imaging framework, our platform could yield an LOD as low as 10³ TCID₅₀/mL. Providing accurate and rapid sensing information in a handheld platform, weighing only 70 g and 12 cm tall, without the need for bulky and expensive instrumentation, our biosensor could be a very strong candidate for diagnostic applications in resource-poor settings. As our detection scheme is based on the use of antibodies, it could quickly adapt to the detection of different viral diseases, e.g., COVID-19 or influenza, by simply coating the plasmonic chip surface with an antibody possessing affinity to the virus type of interest. Possessing this ability, our biosensor could be swiftly deployed to the field in need for rapid diagnosis, which may be an important asset to prevent the spread of diseases before turning into a pandemic by isolating patients from the population.

Not everything is as it seems: Digital technology affordance, pandemic control, and the mediating role of sociomaterial arrangements

An overly favorable narrative has developed around the role played by digital technologies in containing Covid-19, which oversimplifies the complexity of technology adoption. This narrative takes sociomaterial arrangements for granted and conceptualizes technology affordance - the problem-solving capability of a technology - as a standard built-in feature that automatically activates during technology deployment, leading to undiversified and predetermined collective benefits. This paper demonstrates that not everything is as it seems; implementing a technology is a necessary but insufficient condition for triggering its potential problem-solving capability. The potential affordance and effects of a technology are mediated by the sociomaterial arrangements that users assemble to connect their goals to the materiality of technological artifacts and socio-organizational context in which technology deployment takes place. To substantiate this argument and illustrate the mediating role of sociomaterial arrangements, we build on sociomateriality and technology affordance theory, and we present the results of a systematic review of Covid-19 literature in which 2187 documents are examined. The review combines text data mining, co-occurrence pattern recognition, and inductive coding, and it focuses on four digital technologies that public authorities have deployed as virus containment measures: infrared temperature-sensing devices; ICT-based surveillance and contact-tracing systems; bioinformatic tools and applications for laboratory testing; and electronic mass communications media. Reporting on our findings, we add nuances to the academic debate on sociomateriality, technology affordance, and the governance of technology in public health crises. In addition, we provide public authorities with practical recommendations on how to strengthen their approach to digital technology deployment for pandemic control.

Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 and SARS-CoV-2 in 2019 highlights the need to develop universal vaccination strategies against the broader Sarbecovirus subgenus. Using chimeric spike designs, we demonstrate protection against challenge from SARS-CoV, SARS-CoV-2, SARS-CoV-2 B.1.351, bat CoV (Bt-CoV) RsSHC014, and a heterologous Bt-CoV WIV-1 in vulnerable aged mice. Chimeric spike messenger RNAs (mRNAs) induced high levels of broadly protective neutralizing antibodies against high-risk Sarbecoviruses. By contrast, SARS-CoV-2 mRNA vaccination not only showed a marked reduction in neutralizing titers against heterologous Sarbecoviruses, but SARS-CoV and WIV-1 challenge in mice resulted in breakthrough infections. Chimeric spike mRNA vaccines efficiently neutralized D614G, mink cluster five, and the UK B.1.1.7 and South African B.1.351 variants of concern. Thus, multiplexed-chimeric spikes can prevent SARS-like zoonotic coronavirus infections with pandemic potential.

Herramientas biotecnológicas en el diagnóstico, prevención y tratamiento frente a pandemias

Las pandemias son consideradas como un problema emergente de salud pública a nivel mundial, las cuales además de caracterizarse por tasas altas de morbilidad y mortalidad, ocasionan conflictos en los aspectos sociales, económicos y políticos. Las herramientas biotecnológicas, por su parte, han ido evolucionando conforme al avance tecnológico-científico, lo que ha permitido optimizar métodos de diagnóstico con alta sensibilidad y especificidad, además de mejorar el desarrollo de productos biológicos para la prevención y terapia de enfermedades. El objetivo de esta revisión es identificar la actualización de las herramientas biotecnológicas en el diagnóstico, tratamiento terapéutico y profiláctico frente a los patógenos causantes de las enfermedades pandémicas a lo largo de la historia, mediante la recopilación de información científica. Con este estudio se logró establecer que las herramientas y productos de origen biotecnológico han constituido un papel fundamental en el control de pandemias a través de la innovación constante que ha permitido alcanzar resultados eficientes tanto en diagnóstico como en el tratamiento.

Bibliometric Analysis of SARS, MERS, and COVID-19 Studies from India and Connection to Sustainable Development Goals

India is ranked fifth in the world in terms of COVID-19 publications accounting for 6.7% of the total. About 60% of the COVID-19 publications in the year 2020 are from United States, China, UK, Italy, and India. We present a bibliometric analysis of the publication trends and citation structure along with the identification of major research clusters. By performing network analysis of authors, citations, institutions, keywords, and countries, we explore semantic associations by applying visualization techniques. Our study shows lead taken by the United States, China, UK, Italy, India in COVID-19 research may be attributed to the high prevalence of COVID-19 cases in those countries witnessing the first outbreak and also due to having access to COVID-19 data, access to labs for experimental trials, immediate funding, and overall support from the govt. agencies. A large number of publications and citations from India are due to co-authored publications with countries like the United States, UK, China, and Saudi Arabia. Findings show health sciences have the highest number of publications and citations, while physical sciences and social sciences and humanities counts were low. A large proportion of publications fall into the open-access category. With India as the focus, by comparing three major pandemics—SARS, MERS, COVID-19—from a bibliometrics perspective, we observe much broader involvement of authors from multiple countries for COVID-19 studies when compared to SARS and MERS. Finally, by applying bibliometric indicators, we see an increasing number of sustainable development-related studies from the COVID-19 domain, particularly concerning the topic of good health and well-being. This study allows for a deeper understanding of how the scholarly community from a populous country like India pursued research in the midst of a major pandemic which resulted in the closure of scientific institutions for an extended time.

The Role of Indoor Plants in air Purification and Human Health in the Context of COVID-19 Pandemic: A Proposal for a Novel Line of Inquiry

The last two decades have seen the discovery of novel retroviruses that have resulted in severe negative consequences for human health. In late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged with a high transmission rate and severe effects on human health, with 5% infected persons requiring hospitalisation and 3.81 million deaths to date globally. Aerosol particles containing virions are considered the main source of SARS CoV-2 transmission in this pandemic, with increased infection rates in confined spaces. Consequently, public and private institutions had to institute mitigation measures including the use of facial masks and social distancing to limit the spread of the virus. Moreover, the role of air purification and bio-decontamination is understood as being essential to mitigate viral spread. Various techniques can be applied to bio-decontaminate the air such as the use of filtration and radiation; however, these methods are expensive and not feasible for home use. Another method of air purification is where indoor plants can purify the air by the removal of air pollutants and habituated airborne microbes. The use of indoor plants could prove to be a cost-efficient way of indoor air-purification that could be adapted for a variety of environments with no need for special requirements and can also add an aesthetic value that can have an indirect impact on human health. In this review, we discuss the emergence of the COVID-19 pandemic and the currently used air purification methods, and we propose the use of indoor plants as a new possible eco-friendly tool for indoor air purification and for reducing the spread of COVID-19 in confined places.

Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice

The emergence of SARS-CoV in 2003 and SARS-CoV-2 in 2019 highlights the need to develop universal vaccination strategies against the broader Sarbecovirus subgenus. Using chimeric spike designs, we demonstrate protection against challenge from SARS-CoV, SARS-CoV-2, SARS-CoV-2 B.1.351, bat CoV (Bt-CoV) RsSHC014, and a heterologous Bt-CoV WIV-1 in vulnerable aged mice. Chimeric spike mRNAs induced high levels of broadly protective neutralizing antibodies against high-risk Sarbecoviruses. In contrast, SARS-CoV-2 mRNA vaccination not only showed a marked reduction in neutralizing titers against heterologous Sarbecoviruses, but SARS-CoV and WIV-1 challenge in mice resulted in breakthrough infection. Chimeric spike mRNA vaccines efficiently neutralized D614G, UK B.1.1.7., mink cluster five, and the South African B.1.351 variant of concern. Thus, multiplexed-chimeric spikes can prevent SARS-like zoonotic coronavirus infections with pandemic potential.

Profile of Circulatory Cytokines and Chemokines in Human Coronaviruses: A Systematic Review and Meta-Analysis

BACKGROUND

SARS, MERS, and COVID-19 share similar characteristics. For instance, the genetic homology of SARS-CoV-2 compared to SARS-CoV and MERS-CoV is 80% and 50%, respectively, which may cause similar clinical features. Moreover, uncontrolled release of proinflammatory mediators (also called a cytokine storm) by activated immune cells in SARS, MERS, and COVID-19 patients leads to severe phenotype development.

AIM

This systematic review and meta-analysis aimed to evaluate the inflammatory cytokine profile associated with three strains of severe human coronavirus diseases (MERS-CoV, SARS-CoV, and SARS-CoV-2).

METHOD

The PubMed, Embase, and Cochrane Library databases were searched for studies published until July 2020. Randomized and observational studies reporting the inflammatory cytokines associated with severe and non-severe human coronavirus diseases, including MERS-CoV, SARS-CoV, and SARS-CoV-2, were included. Two reviewers independently screened articles, extracted data, and assessed the quality of the included studies. Meta-analysis was performed using a random-effects model with a 95% confidence interval to estimate the pooled mean of inflammatory biomarkers.

RESULTS

A high level of circulating IL-6 could be associated with the severity of infection of the three coronavirus strains. TNF, IL-10, and IL-8 are associated with the severity of COVID-19. Increased circulating levels of CXCL10/IP10 and CCL2/MCP-1 might also be related to the severity of MERS.

CONCLUSION

This study suggests that the immune response and immunopathology in the three severe human coronavirus strains are somewhat similar. The findings highlight that nearly all studies reporting severe cases of SARS, MERS, and COVID-19 have been associated with elevated levels of IL-6. This could be used as a potential therapeutic target to improve patients' outcomes in severe cases.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration 94 number: CRD42020209931.