The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control

Beyond the Pandemic Era: Recent Advances and Efficacy of SARS-CoV-2 Vaccines Against Emerging Variants of Concern

Vaccination has been instrumental in curbing the transmission of SARS-CoV-2 and mitigating the severity of clinical manifestations associated with COVID-19. Numerous COVID-19 vaccines have been developed to this effect, including BioNTech-Pfizer and Moderna's mRNA vaccines, as well as adenovirus vector-based vaccines such as Oxford-AstraZeneca. However, the emergence of new variants and subvariants of SARS-CoV-2, characterized by enhanced transmissibility and immune evasion, poses significant challenges to the efficacy of current vaccination strategies. In this review, we aim to comprehensively outline the landscape of emerging SARS-CoV-2 variants of concern (VOCs) and sub-lineages that have recently surfaced in the post-pandemic years. We assess the effectiveness of existing vaccines, including their booster doses, against these emerging variants and subvariants, such as BA.2-derived sub-lineages, XBB sub-lineages, and BA.2.86 (Pirola). Furthermore, we discuss the latest advancements in vaccine technology, including multivalent and pan-coronavirus approaches, along with the development of several next-generation coronavirus vaccines, such as exosome-based, virus-like particle (VLP), mucosal, and nanomaterial-based vaccines. Finally, we highlight the key challenges and critical areas for future research to address the evolving threat of SARS-CoV-2 subvariants and to develop strategies for combating the emergence of new viral threats, thereby improving preparedness for future pandemics.

Co-infections and Reactivation of some Herpesviruses (HHV) and Measles Virus (MeV) in Egyptian Cancer Patients infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

BACKGROUND

Coinfections and reactivation of persistent or latent viral infections such as herpesviruses (HHV) and/or measles virus (MeV) have been reported among COVID-19 patients. However, there is limited information regarding cancer patients who experienced severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). The primary purpose of this study was to investigate the interplay between SARS-CoV-2, HHV and MeV in cancer patients, aiming to provide insights into the pathophysiology of these infections and to enhance the patients' health outcomes.

METHODS

A prospective observational study was conducted on 4 groups (n = 147): newly diagnosed cancer patients infected with SARS-CoV-2 (n = 37), newly diagnosed cancer patients non-infected with SARS-CoV-2 (n = 13), apparently normal individuals infected with SARS-CoV-2 (n = 82) and finally a normal control group (n = 15). All samples were tested for SARS-CoV-2 infection using the real-rime quantitative reverse transcription polymerase chain reaction (qRT-PCR). Antibody responses were analyzed using indirect enzyme-linked immunosorbent assay (ELISA), and antibody levels were compared between patients and controls. Potential re-activation was investigated using fourfold (i.e. 400%) rise model criterion.

RESULTS

In all positive cases of SARS-CoV-2, recent infections or re-infection of herpes simplex viruses 1 and 2 (HSV1/2 or HHV1-2) were found to be significantly increased approximately three-fold higher in COVID-19 patients (p = 0.007) identified via pooled HSV1/2 IgM levels in plasma. Furthermore, reactivation of HSV1/2 was 29.7% in cancer/COVID-19 patients (n = 37) versus 0.0% of normal/COVID-19 group (n = 22) (p = 0.008). Likewise, Epstein-Barr Nuclear Antigen-1 (EBNA-1) IgG levels showed a ≥ fourfold increase in 20% (p = 0.034) of cancer patients (n = 50) versus 4.9% of controls (n = 41) for reactivation of Epstein-Barr virus (EBV or HHV-4). Obviously, MeV IgG levels increased up to 78.0% in cancer patients (n = 50) versus 17.5% in non-cancerous group (n = 40, p < 0.001). Reactivation of MeV in cancer and COVID-19 patients was 43.2% versus 30.8% cancer non-COVID-19 group, 3.3% normal COVID-19, and 0.0% in healthy volunteers (p < 0.001).

CONCLUSION

Cancer patients infected with SARS-CoV-2 were at increased risk of HHV and MeV co-infection and reactivation.

A small-molecule SARS-CoV-2 inhibitor targeting the membrane protein

The membrane (M) protein of betacoronaviruses is well conserved and has a key role in viral assembly1,2. Here we describe the identification of JNJ-9676, a small-molecule inhibitor targeting the coronavirus M protein. JNJ-9676 demonstrates in vitro nanomolar antiviral activity against SARS-CoV-2, SARS-CoV and sarbecovirus strains from bat and pangolin zoonotic origin. Using cryogenic electron microscopy (cryo-EM), we determined a binding pocket of JNJ-9676 formed by the transmembrane domains of the M protein dimer. Compound binding stabilized the M protein dimer in an altered conformational state between its long and short forms, preventing the release of infectious virus. In a pre-exposure Syrian golden hamster model, JNJ-9676 (25 mg per kg twice per day) showed excellent efficacy, illustrated by a significant reduction in viral load and infectious virus in the lung by 3.5 and 4 log10-transformed RNA copies and 50% tissue culture infective dose (TCID50) per mg lung, respectively. Histopathology scores at this dose were reduced to the baseline. In a post-exposure hamster model, JNJ-9676 was efficacious at 75 mg per kg twice per day even when added at 48 h after infection, when peak viral loads were observed. The M protein is an attractive antiviral target to block coronavirus replication, and JNJ-9676 represents an interesting chemical series towards identifying clinical candidates addressing the current and future coronavirus pandemics.

Immunohistochemical identification of ACE-2 (SARS-COV II entry mechanism) in the gastrointestinal tract, kidney and lung of rhesus monkeys (Macaca mulatta) and squirrel monkeys (Saimiri sciureus)

SARS-Cov-2 is a corona virus that causes COVID-19 disease, a viral infection responsible for the pandemic decreed by the World Health Organization in March 2020. Angiotensin-converting enzyme 2 (ACE-2) functions as the main receptor for SARS-Cov-2. The study aimed to detect the expression of ACE-2 in the gastrointestinal tract, kidney, and lung in the rhesus monkeys and squirrel monkeys. The sections from 18 rhesus monkey and 17 squirrel monkeys were incubated with rabbit polyclonal antibody to ACE2 (ab65863). In the lung of the rhesus monkeys, the presence of ACE-2 was noted in the bronchial mucosa of the respiratory epithelium. In the kidney, there was irregular in the proximal convoluted tubules. In the pyloric stomach, duodenum and in the large intestine it was observed on the surface of the lining epithelium. In the lung of the squirrel monkeys, this marking was present in both the ciliated cylindrical and goblet cell sof the bronchi. In the kidney light marking was observed along the surfasse of the cubic epithelium of the proximal convoluted tubules and in the renal glomerulus. No markings were observed throughout the stomach and intense staining was observed along the surfasse of the intestinal epithelium of the duodenum, jejunum and ileum, as well as in the intestinal glands. In our study, we can observe not able differences in the distribution of ACE2 between the two species of primates analysed. These differences must be considered in experimental studies on this disease, which continues to be a topic of notable importance for Public Health.

Nanophotonic biosensors for COVID-19 detection: advances in mechanisms, methods, and design

The growing societal impact of coronavirus disease 2019 (COVID-19) has underscored the urgent need for innovative strategies to address the ongoing challenges posed by the pandemic. While rapid therapeutic interventions remain critical for short-term mitigation, equally vital is the development of accessible and efficient diagnostic tools to curb viral transmission. In this context, optical sensing technologies have emerged as foundational tools for detection and diagnosis, owing to their rapid response, user-friendliness, and adaptability. These attributes strengthen their indispensable role in identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. This review systematically outlines the structural components of SARS-CoV-2 virions and their respective biological functions, classifies optical biosensors according to their underlying principles and evaluates the advantages and limitations of each methodology in real-world diagnostic applications. By addressing current detection challenges, these optical platforms not only enhance our capacity to manage SARS-CoV-2 but also establish a framework for deploying optical sensing technologies in future pandemic scenarios.

Investigating the mechanisms of ethanol-induced disruption of COVID-19 lipid bilayers through molecular dynamics simulations

CONTEXT

The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, began in December 2019 in Wuhan, China. To mitigate the spread of COVID-19, public health officials strongly recommended preventive measures such as disinfectants, alcohol-based hand sanitizers, and face masks. The effect of ethanol on virus structure and inactivation remains unclear, and its molecular mechanism needs to be elucidated. This study elucidates how ethanol solutions interact with the lipid bilayer of the COVID-19 virus utilizing molecular dynamics (MD) simulations. Its findings indicated that ethanol can deactivate the virus through two primary mechanisms. First, when ethanol penetrates the viral membrane, it disrupts the structural integrity of the lipid bilayer, leading to membrane disruption. This alteration in morphology is critical as it compromises the virus's ability to maintain its structure and function.

METHODS

For the simulation, a lipid bilayer containing the spike protein of SARS-CoV-2 was constructed. The interaction between the viral membrane and ethanol solution was then simulated using GROMACS 5.1.4 for molecular dynamics (MD) analysis. Also, visual molecular dynamics (VMD1.9.3) was used for visualization. The study calculated the Lennard-Jones (LJ) and electrostatic interactions between ethanol and the lipid bilayer, and it analyzed the conformational changes in the spike protein following ethanol adsorption. Additionally, the effects of ethanol penetration on the morphology of the lipid bilayer were evaluated.

Prevalence and pattern of adverse events following COVID-19 vaccination among adult population in Sokoto metropolis, northwest, Nigeria

BACKGROUND

COVID-19 still poses a major public health challenge worldwide and vaccination remains one of the major interventions to control the disease. Different types of vaccines approved by the World Health Organization (WHO) are currently in use across the world to protect against the disease. This study assessed the prevalence and pattern of adverse events following immunization (AEFI) after receiving COVID-19 vaccine (the Oxford-AstraZeneca vaccine) among the adult population in Sokoto metropolis, North-west, Nigeria.

METHODS

We conducted a cross-sectional study among 230 adults in Sokoto metropolis who received COVID-19 vaccines. Data was collected using a structured questionnaire administered via personal phone calls to respondents who were selected via a systematic sampling technique. For data analysis, IBM SPSS version 25.0 was used.

RESULTS

The majority of the participants [183 (79.7%)] experienced AEFI. The most common adverse events were body weakness [157 (85%)], fever [111 (60.3%)] and headache [103 (56%)]. Up to half of the respondents that experienced AEFI said it occurred within minutes and a few hours, whereas 75 (40.8%) said it was within 2-3 days. Up to 66.3% of the adverse reactions were mild and lasted between a few hours (37.5%) and one day (31.5%); however, 15.2% of the respondents had severe reactions of which 22.7% were admitted to a health facility. The development of AEFI was linked to the presence of an underlying medical condition (p = 0.001), a previous history of AEFI (p = 0.017), and a history of drug reaction (p = 0.005).

CONCLUSION

The majority of respondents reported adverse events following vaccination with the Oxford-AstraZeneca vaccine; body weakness, fever, and headache being the most common AEFIs. History of underlying medical condition as well as a history of adverse drug reactions were predictors of the development of adverse reactions following COVID-19 vaccination. Service providers at each COVID-19 vaccination point should always take the time to explain to vaccine recipients that adverse reactions are possible; however, they should reassure them that most ARs resolve within a few hours to a few days.

Trends and gaps in hydroxychloroquine and COVID-19 research (2020-2023): Performance and conceptual mapping

BACKGROUND

Hydroxychloroquine and Chloroquine (CQ) and Hydroxychloroquine (HCQ) are antimalarial drugs with well-known anti-inflammatory and antiviral effects used to treat various diseases, with few side effects. After COVID-19 emergence, numerous researches from around the world have examined the potential of using CQ or HCQ as potential treatment of COVID-19. However, conflicting outcomes have been found in COVID-19 clinical trials after treatment with CQ or HCQ. This study aims to evaluate research on CQ and HCQ for COVID-19 treatment and prophylaxis control using bibliometric methods.

METHODS

We analyzed bibliometric data on HCQ and COVID-19 (HCQ-C19) quantitatively and semantically (2020-2023) using the Scopus database VOSviewer, Bibliometrix, and MS Excel.

RESULTS

Analyses of 7471 original and conference articles revealed that the total number of publications has continually increased. The country producing the most articles in this field was the United States, followed by Italy, India, and Spain. The top-productive authors on HCQ-C19 are Mussini, C., and Raoult, D. (Italy) with 23 and 21 articles, respectively. The top-impactful organization is IHU Méditerranée Infection, France. A Bibliometrix's network analysis based on the co-occurrence of keywords revealed the following themes HCQ-C19, including "clinical research/practice," "COVID-19," "thrombosis," "HCQ," "epidemiology," and "infectious disease."

CONCLUSION

In conclusion, the analysis reveals a growing interest in HCQ-C19 research. Prominent contributions come from the United States, Italy, India, and Spain. Key themes include clinical research/practice, COVID-19, thrombosis, HCQ, epidemiology, and infectious disease. Future recommendations include conducting well-designed clinical trials and fostering collaborative interdisciplinary efforts.

One Health and planetary health research landscapes in the Arab world

This review explored research trends in One Health and planetary health in the Arab world, a region confronting major sustainability challenges. These fields are crucial in combating global pressing concerns like infectious diseases, biodiversity loss, antimicrobial resistance, climate change, and air pollution. The COVID-19 pandemic stressed their significance to global health and sustainable development. This analysis assessed the Arab world's contributions to these concepts applying performance analysis and visualization mapping, revealing that One Health outperformed planetary health in terms of productivity and number of contributed countries. Egypt, Saudi Arabia, and the United Arab Emirates have emerged as leading contributors to One Health and planetary health research in the Arab world. Meanwhile, the United States and the United Kingdom, as non-Arab nations, play a pivotal role in fostering collaborative efforts with the region. The trajectory of One Health research has indeed shown remarkable exponential growth, especially since the beginning of the COVID-19 pandemic in 2019, which is an indication of increasing relevance in the address of global health challenges. Conversely, planetary health presents an irregular growth pattern, with a strong point in the development of this area standing out in 2023. The unique set of social, cultural, governance, and agricultural attributes of the Arab region are joined by major environmental challenges that define the focus of both One Health and planetary health research efforts. Climate change, environmental contexts, and public health feature prominently in both One Health and planetary health, with One Health focusing mainly on infectious diseases and planetary health addressing the implications of climate change on human health. Advancing these concepts demands the establishment of a regional governing body to oversee an integrated One Health and planetary health strategy, foster regional research communities and alliances, secure political will and funding, and ensure the integration of these concepts into policy and academic frameworks.

Revolutionizing Nanovaccines: A New Era of Immunization

Infectious diseases continue to pose a significant global health threat. To combat these challenges, innovative vaccine technologies are urgently needed. Nanoparticles (NPs) have unique properties and have emerged as a promising platform for developing next-generation vaccines. Nanoparticles are revolutionizing the field of vaccine development, offering a new era of immunization. They allow the creation of more effective, stable, and easily deliverable vaccines. Various types of NPs, including lipid, polymeric, metal, and virus-like particles, can be employed to encapsulate and deliver vaccine components, such as mRNA or protein antigens. These NPs protect antigens from degradation, target them to specific immune cells, and enhance antigen presentation, leading to robust and durable immune responses. Additionally, NPs can simultaneously deliver multiple vaccine components, including antigens, and adjuvants, in a single formulation, simplifying vaccine production and administration. Nanovaccines offer a promising approach to combat food- and water-borne bacterial diseases, surpassing traditional formulations. Further research is needed to address the global burden of these infections. This review highlights the potential of NPs to revolutionize vaccine platforms. We explore their mechanisms of action, current applications, and emerging trends. The review discusses the limitations of nanovaccines, innovative solutions and the potential role of artificial intelligence in developing more effective and accessible nanovaccines to combat infectious diseases.

Short-Time Preamplification-Assisted One-Pot CRISPR Nucleic Acid Detection Method with Portable Self-Heating Equipment for Point-of-Care Diagnosis

Infectious diseases, especially respiratory infections, have been significant threats to human health. Therefore, it is essential to develop rapid, portable, and highly sensitive diagnostic methods for their control. Herein, a short-time preamplified, one-pot clustered regularly interspaced short palindromic repeats (CRISPR) nucleic acid detection method (SPOC) is developed by combining the rapid recombinase polymerase amplification (RPA) with CRISPR-Cas12a to reduce the mutual interference and achieve facile and rapid molecular diagnosis. SPOC can reduce the detection time and stably detect up to 1 copy/μL of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA without affecting the detection sensitivity. A highly sensitive one-pot assay integrated with reverse transcription RPA is achieved by wrapping paraffin with a specific melting point on the lyophilized CRISPR reagent surface. A self-heating pack is designed based on thermodynamic principles to melt the paraffin and release CRISPR reagents, enabling low-cost and time-saving detection. Notably, the designed system, coupled with RNA extraction-free technology, can achieve "sample-in-answer-out" detection of the SARS-CoV-2 Orf1ab gene within 22 min using smartphone imaging. The developed assay is validated on 12 clinical samples, and the results 100% correlate with real-time polymerase chain reaction. SPOC is time-saving, is easy to operate, and can eliminate centrifugal and complex hardware devices, satisfying the demand for point-of-care diagnostics in resource-constrained settings.

Conformational dynamics of the membrane protein of MERS-CoV in comparison with SARS-CoV-2 in ERGIC complex

The present study explores the conformational dynamics of the membrane protein of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) within the Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC) complex using an all-atomistic molecular dynamics simulation approach. Significant structural changes were observed in the N-terminal, C-terminal, transmembrane, and beta-sheet sandwich domains of the MERS-CoV membrane protein. This study also highlights the structural similarities between the MERS-CoV and the SARS-CoV-2 membrane proteins, particularly in how both exhibit a distinct kink in the transmembrane helix caused by aromatic residue-lipid interactions. A structural expansion below the transmembrane and above the beta-sheet sandwich domain within the dimer was observed in all the M-proteins. This site on the beta-sheet sandwich domains near the C-terminal end could serve as a potential drug-binding site. Notably, a stable helical structure was identified in the C-terminal domain of the MERS-CoV membrane protein, whereas a proper secondary structural conformation was not observed in the SARS-CoV-2 membrane protein. Further, the SARS-CoV-2 membrane protein exhibited stronger binding to the lipid bilayer than the MERS-CoV, indicating its greater structural stability within the ERGIC complex. The structural similarity between the membrane protein of MERS-CoV and SARS-CoV-2 suggests the feasibility of employing a common inhibitor against these beta-coronaviruses. Furthermore, this analysis enhances our understanding of the membrane protein's interactions with proteins and lipids, paving the way for therapeutic developments against these viruses.

Ahmed L. Chamomile in combating SARS-Cov-2

Traditional herbal medicine is of known history for the complementary treatment of viral infections and was recently suggested for COVID-19. Therefore, it is of interest to investigate chamomile decoction for its neutralizing activity against SARS-CoV-2 In vitro. Our experiments highlight the potential antiviral effect of chamomile. In vitro results show a significant inhibition of SARS-CoV-2. Our results recommend the use of chamomile as a potential natural remedy for COVID-19.

Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA

The nucleocapsid (N) protein is one of the four structural proteins in SARS-CoV-2, playing key roles in viral assembly, immune evasion, and stability. One of its primary functions is to protect viral RNA by forming the nucleocapsid. However, the precise mechanisms by which the N protein interacts with viral RNA and assembles into a nucleocapsid remain unclear. Compared to other SARS-CoV-2 components, targeting the N protein has several advantages: it exhibits higher sequence conservation, lower mutation rates, and stronger immunogenicity, making it an attractive target for antiviral drug development and diagnostics. Therefore, a detailed understanding of the N protein's structure is essential for deciphering its role in viral assembly and developing effective therapeutics. In this study, we report the expression and purification of a soluble recombinant N protein, along with a 1.55 Å resolution crystal structure of its nucleic acid-binding domain (N-NTD) in complex with ssDNA. Our structure revealed new insights into the conformation and interaction of the flexible N-arm, which could aid in understanding nucleocapsid assembly. Additionally, we identified residues that are critical for ssDNA interaction.

COVID-AMD database for coronavirus-infected animal models with comparative analysis tools

Respiratory infections caused by coronaviruses have posed serious and unpredictably public health threats; reliable animal models continue to be essential for advancing our understanding of the virus's transmission, pathophysiology, and immunological mechanisms. In response to the critical need for centralized resources in coronavirus research, the COVID-AMD database (Coronavirus Disease Animal Model Database, https://www.uc-med.net/CoV-AMD ) has been developed as an integrated platform. Data was gathered from public literature databases, refined and integrated using ETL (Extract, Transform, Load) methodology. After data conversion and cleaning, COVID-AMD was implemented using MySQL relational database with jQuery and JBoss. COVID-AMD database consolidates comprehensive data on animal models infected with various CoVs, including MERS-CoV, SARS-CoV, and SARS-CoV-2, featuring methodologies for establishing infection models, clinical features, and phenotypic data. It catalogs 869 animal models across 29 species and 312 virus strains, covering five diseases and ten infection routes. With global and advanced search capabilities, it facilitated data preprocessing, integration, analysis, and visualization, and provided tools for comparative analysis, model recommendation and omics analysis based on model and phenotype data. The open access to this rich repository aims to enable rapid identification of animal models for CoVs, thereby accelerating the development and clinical trial progression of prospective therapeutics and vaccines.

Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors

SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (Kdimer) 2-3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ∼10 to 30%, relative to that of the wild-type enzyme, without altering Kdimer. Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MProWT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MProWT-ensitrelvir. Chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.

Robust immune response to COVID-19 vaccination in the island population of Greenland

BACKGROUND

In Greenland, the COVID-19 pandemic was characterised by a late onset of community transmission and a low impact on the healthcare system, hypothesised as being partly due to a high uptake of vaccinations. To underpin this description, we aimed to assess the SARS-CoV-2 immune response post-vaccination in a Greenlandic population.

METHODS

In this observational cohort study, we included 430 adults in Greenland who had received a complete two-dose SARS-CoV-2 vaccination at enrolment. The total plasma SARS-CoV-2 spike glycoprotein Ig antibodies (S-Ab) induced by either the BNT162b2 or mRNA-1273 vaccine, was measured up to 11 months after the second vaccine dose. In addition, total salivary S-Abs were examined in 107 participants, and the T-cell response to the spike glycoprotein was assessed in 78 participants out of the entire study cohort.

RESULTS

Here we demonstrate that two months after the second vaccine dose, 96% of participants have protective plasma S-Ab levels. By 11 months, 98% have protective levels, with prior SARS-CoV-2 infection particularly enhancing S-Ab levels by 37% (95% CI 25-51%). Among individuals aged 60 years and older, we observe a 21% (95% CI 7-33%) reduction in antibody response. Total salivary S-Ab levels are detectable in all participants and significantly correlate with plasma levels. Moreover, all participants exhibit a robust SARS-CoV-2-specific T-cell response 11 months post-primary vaccination.

CONCLUSIONS

Our findings show that Greenlanders exhibit a robust and lasting immune response, both humoral and cellular, comparable to other population groups up to at least 11 months after the second vaccine dose. These results corroborate the hypothesis that vaccines contributed to the mild impact of the COVID-19 pandemic in the Greenlandic population.

3-chymotrypsin-like protease in SARS-CoV-2

Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is a highly pathogenic human coronavirus that has caused the coronavirus disease 2019 (COVID-19) pandemic. It has led to a global viral outbreak with an exceptional spread and a high death toll, highlighting the need for effective antiviral strategies. 3-Chymotrypsin-like protease (3CLpro), the main protease in SARS-CoV-2, plays an indispensable role in the SARS-CoV-2 viral life cycle by cleaving the viral polyprotein to produce 11 individual non-structural proteins necessary for viral replication. 3CLpro is one of two proteases that function to produce new viral particles. It is a highly conserved cysteine protease with identical structural folds in all known human coronaviruses. Inhibitors binding with high affinity to 3CLpro will prevent the cleavage of viral polyproteins, thus impeding viral replication. Multiple strategies have been implemented to screen for inhibitors against 3CLpro, including peptide-like and small molecule inhibitors that covalently and non-covalently bind the active site, respectively. In addition, allosteric sites of 3CLpro have been identified to screen for small molecules that could make non-competitive inhibitors of 3CLpro. In essence, this review serves as a comprehensive guide to understanding the structural intricacies and functional dynamics of 3CLpro, emphasizing key findings that elucidate its role as the main protease of SARS-CoV-2. Notably, the review is a critical resource in recognizing the advancements in identifying and developing 3CLpro inhibitors as effective antiviral strategies against COVID-19, some of which are already approved for clinical use in COVID-19 patients.

COVID-19 Safety: Perspectives from Dental Students

BACKGROUND

The coronavirus (COVID-19) pandemic created challenges for healthcare providers, especially dental professionals in practices and universities. This study investigated dental students' concerns about COVID-19 and whether institutional communication influenced pandemic-related stressors.

METHODS

An online survey designed to elicit dental students' concerns about COVID-19 was distributed to all dental students enrolled at a private non-profit academic institution in the Western United States from 26 April 2021 to 25 August 2021. Descriptive statistics were used to characterize the respondents, and Chi-square test and z-test analyses were used to compare students' experiences.

RESULTS

A total of 92 dental students answered the survey. The respondents' ages ranged from 22 to 47 years. Slightly more than half (50.5%) were male and 93.3% were non-Hispanic or non-Latino. Over one-fourth of the students (27.5%) reported that they either often or always felt anxious that they might become infected with the COVID-19 virus, with 16.3% of the students expressing concern about contracting COVID-19 while on campus. There were no statistically significant differences in anxiety levels about contracting COVID-19 from clinic patients or while on campus between the group of students who perceived the institution communicated effectively and those who did not. However, students who felt that the dental school clearly communicated COVID-19 protocols were more likely to believe that students took protocols seriously and expressed less concern about contracting COVID-19 by touching dental school items.

CONCLUSIONS

About one-quarter of dental students expressed high levels of anxiety about being infected with COVID-19. Clear communication about COVID-19 protocols reduced students' fear of contracting COVID-19 from dental school items and strengthened their belief that other students followed protocols.

Antiviral Properties of Moringa oleifera Leaf Extracts against Respiratory Viruses

Moringa oleifera (M. oleifera) is a plant widely used for its beneficial properties both in medical and non-medical fields. Because they produce bioactive metabolites, plants are a major resource for drug discovery. In this study, two different cultivars of leaves of M. oleifera (Salento and Barletta) were obtained by maceration or microwave-assisted extraction (MAE). We demonstrated that extracts obtained by MAE exhibited a lower cytotoxic profile compared to those obtained by maceration at concentrations ranged from 25 to 400 µg/mL, on both Vero CCL-81 and Vero/SLAM cells. We examined their antiviral properties against two viruses, i.e., the human coronavirus 229E (HCoV-229E) and measles virus (MeV), which are both responsible for respiratory infections. The extracts were able to inhibit the infection of both viruses and strongly prevented their attack and entry into the cells in a range of concentrations from 50 to 12 µg/mL. Particularly active was the variety of Salento that registered a 50% inhibitory concentration (IC50) at 21 µg/mL for HCoV-229E and at 6 µg/mL for MeV. We identified the presence of several compounds through high performance liquid chromatography (HPLC); in particular, chlorogenic and neochlorogenic acids, quercetin 3-O-β-d-glucopyranoside (QGP), and glucomoringin (GM) were mainly observed. In the end, M. oleifera can be considered a promising candidate for combating viral infections with a very strong action in the early stages of viral life cycle, probably by destructuring the viral particles blocking the virus-cell fusion.

The burden and impact of COVID-19 among newborns in African countries: a study protocol for a systematic review and meta-analysis

The WHO, on 30 January 2020, declared the Chinese outbreak of coronavirus disease 2019 (COVID-19) a global community health emergency that poses a serious threat to vulnerable healthcare systems. This review protocol will be conducted to systematically review and to perform a meta-analysis on the impact of COVID-19 among newborns in Africa. All observational studies on the impact of COVID-19 among newborns in Africa will be included. A standard quest strategy to retrieve studies was conducted on several databases (Google Scholar, PubMed/MEDLINE, EMBASE, HINARI, Cochrane Library, WHO COVID-19 database, Africa Wide Knowledge and Web of Science). Two independent authors were tasked to extract key data and to assess the risk of bias. To assess possible publication bias, funnel plot test and Egger's test methods will be used. The description will be used to show the COVID-19 distribution data by interest variables such as residence, setting and person-level characteristics. The findings of this review will notify healthcare professionals about the burden and impact of COVID-19 and provide evidence to bring about the requisite improvements in clinical practice.

COVID19 Vaccination Considerations for Pregnant Women: A Systematic Review

Background

Following the coronavirus disease 2019 (COVID-19) pandemic, pregnant women are at a higher risk of developing severe COVID-19 disease. This study investigated whether pregnant women should get vaccinated against COVID-19 or not. Pregnant women in comparison with non-pregnant women.

Materials and Methods

This study was a systematic review that searched the PubMed, Embase, and Scopus databases using the keywords "COVID-19" OR "SARS-CoV-2" OR "Coronavirus Disease" OR "2019-nCoV" AND "pregnancy "OR "pregnant" AND "vaccine" OR "vaccination" from January 2020 to April 2022.

Results

Of the 37 selected studies, 15 (40.50%) declared positive views, 9 (24.30%) had inconclusive views, and 13 (35.20%) opposed vaccination due to a lack of adequate information.

Conclusions

Despite the discrepancies among the studies, one-third of the studies suggested that pregnant women be enrolled in clinical trials to investigate the outcomes of the COVID-19 vaccination on maternal and fetal outcomes. However, the majority of the studies recommended maternal immunization against COVID-19.

Social distancing and extremely preterm births in the initial COVID-19 pandemic period

HYPOTHESIS

Increased social distancing was associated with a lower incidence of extremely preterm live births (EPLB) during the initial COVID-19 pandemic period.

STUDY DESIGN

Prospective study at the NICHD Neonatal Research Network sites comparing EPLB (220/7-286/7 weeks) and extremely preterm intrapartum stillbirths (EPIS) rates during the pandemic period (March-July, weeks 9-30 of 2020) with the reference period (same weeks in 2018 and 2019), correlating with state-specific social distancing index (SDI).

RESULTS

EPLB and EPIS percentages did not significantly decrease (1.58-1.45%, p = 0.07, and 0.08-0.06%, p = 0.14, respectively). SDI was not significantly correlated with percent change of EPLB (CC = 0.29, 95% CI = -0.12, 0.71) or EPIS (CC = -0.23, 95% CI = -0.65, 0.18). Percent change in mean gestational age was positively correlated with SDI (CC = 0.49, 95% CI = 0.07, 0.91).

CONCLUSIONS

Increased social distancing was not associated with change in incidence of EPLB but was associated with a higher gestational age of extremely preterm births.

CLINICALTRIALS

GOV ID

Generic Database: NCT00063063.

Public Preference for Financing Preventive Vaccines in Health Shocks: The Case of COVID-19 Vaccines in a Middle-Income Country

BACKGROUND

To effectively manage health crises such as disease pandemics, health authorities require reliable information regarding people's preferences. This helps to ensure timely and targeted interventions and avoids increasing societal costs through developing evidence-based policies. This study investigates the Iranian people's preference for financing coronavirus disease 2019 (COVID-19) vaccines and the factors affecting this.

METHODS

A cross-sectional survey was performed during the third-wave peak of COVID-19 in Iran from 1 to 20 February 2021 utilizing various data collection methods. The public preference regarding imported and domestically produced vaccines, their willingness to fully or partially contribute to the financing of these vaccines, and their willingness to pay (WTP) for domestically produced vaccines using the contingent valuation method was assessed in different scenarios. The determinants of the probability of positive financing preferences were evaluated using an ordered probit regression model.

RESULTS

Among the 2071 survey respondents, approximately 60% stated willingness to contribute to vaccine financing in the form of partial or full user fee payments. Forty percent of respondents are willing to be vaccinated if it is provided for free by the government. Interestingly, people's preference for financing the vaccine was not related to the type of vaccine. The regression analysis showed that income, having supplementary insurance, being male, perceived COVID-19 risk, education, and working in the health sector are significantly related to a higher probability of contribution to vaccine financing.

CONCLUSIONS

Regardless of country of origin of COVID-19 vaccines, vaccination is very important for the Iranian people, and the majority of respondents in our study showed an inclination to contribute to vaccine funding, from partial to full user fees, to achieve higher protection against COVID-19 disease. Hence, ensuring timely access to vaccines during health crises such as pandemics is imperative, as it saves lives and reduces the economic burden of disease. This commitment from the health system can be supported by financial contributions from the general public. In this regard, considering public preferences is strongly advised to policymakers.

Impact of COVID-19 Vaccination on In Vitro Fertilization Outcomes: A Systematic Review

COVID-19 vaccination, especially vaccines that mimic the structure of the COVID-19 virus (mRNA vaccines), may be wrongly assumed to be disrupting factors affecting in vitro fertilization (IVF) outcome. This study aims to evaluate any significant impact of COVID-19 vaccination in women undergoing IVF to improve vaccine compliance and promote COVID-19 eradication. This was a systematic review study. We searched studies published between 2020 and 2022 using databases such as PubMed, Cochrane, PMC, and CINAHL. Selected studies were carefully analyzed to review the impact of the COVID-19 vaccine on IVF outcomes. Seven retrospective and prospective cohort studies, which involved 3232 female patients undergoing IVF, who also received full doses of COVID-19 vaccinations (mRNA), were included. All studies in the present review showed that despite presenting anti-SARS-CoV-2 antibodies after vaccination, there were no significant differences in IVF outcomes, implantation rates, and pregnancy rates. Contrary to the theory that presumed cross-reactivity between anti- SARS-CoV-2 antibodies and the human syncytin-1 protein could affect syncytiotrophoblast formation and embryo implantation. The present review concluded that COVID-19 vaccination does not result in any detrimental effects on IVF outcomes and is safe for women undergoing IVF treatment. The results of our study are important to tackle misinformation regarding COVID-19 vaccination and infertility that may cause vaccine hesitancy in women of reproductive age.

Remdesivir versus Favipiravir in Hospitalized Patients with Moderate to Severe COVID-19 Pneumonia: A Propensity Score-Matched Retrospective Cohort Study

Background

Remdesivir treatment was associated with a reduced 28-day mortality and recovery time among patients hospitalized with severe COVID-19. Favipiravir is broadly used to treat COVID-19. However, various studies have had conflicting results on the efficacy of favipiravir for COVID-19. We hypothesized that remdesivir is more effective in clinical outcomes regarding the 29-day mortality rates, length of stay, and recovery rate than favipiravir in patients with moderate to severe COVID-19 pneumonia.

Methods

We performed a retrospective cohort study that included adult hospitalized COVID-19 pneumonia patients with hypoxemia. Patients were classified into two groups according to the antiviral drugs. Age, oxygen saturation, fraction of inspired oxygen, and Charlson comorbidity index were used for propensity score matching. The primary objective was to determine whether the type of antiviral agent is associated with 29-day mortality. Other outcomes were the 15-day recovery rate and the length of intensive care unit or hospital stay.

Results

A total of 249 patients with moderate to severe COVID-19 pneumonia were included. With an adjustment for propensity score-matched, there were 204 patients for further analysis (102 patients in each antiviral drug group). Remdesivir patients had higher Radiographic Assessment of Lung Edema (RALE) scores on Chest X-ray (14.32±9.08 vs 11.34±8.46; standardized mean difference =33.9%). The Charlson Comorbidity Index Scores were comparable. The prevalences of diabetes, obesity, hypertension, and non-HIV immunocompromised state were higher in the remdesivir group. Regarding the primary outcomes, after adjusting by diabetes, obesity, and RALE score, there was no difference in the 29-day mortality rate between both groups [26 patients (25.5%) in the remdesivir group vs 28 patients (27.5%) in the favipiravir group]. The Kaplan-Meier curve analysis at 29 days indicated no significant difference in cumulative survival rate. The two groups' adjusted hazard ratio was 0.72; 95% CI, 0.41 to 1.25, p=0.24. A Kaplan-Meier analysis on the 15-day cumulative survival rate observed a trend towards a higher survival rate in the remdesivir group (adjusted hazard ratio 0.41; 95% CI, 0.20 to 0.84; p= 0.02) The proportion of patients who recovered on day 15, the length of intensive care unit(ICU) stays, and the hospital stay were not different between remdesivir and favipiravir groups (62 patients (60.8%) vs 56 patients (54.9%), p=0.39; 11.48 ± 11.88 days vs 10.87 ± 9.31 days, p=0.69; and 16.64±14.28 days vs 16.59 ±11.31 days, p=0.98, respectively).

Conclusion

In patients with moderate to severe COVID-19 pneumonia, Remdesivir did not demonstrate superior benefits over Favipiravir regarding 29-day mortality, 15-day recovery rates, or hospital and ICU stay lengths. However, further investigation into the 15-day cumulative survival rate revealed a trend towards improved survival in the Remdesivir group.

Investigating the antiviral therapeutic potentialities of marine polycyclic lamellarin pyrrole alkaloids as promising inhibitors for SARS-CoV-2 and Zika main proteases (Mpro)

The new coronavirus variant (SARS-CoV-2) and Zika virus are two world-wide health pandemics. Along history, natural products-based drugs have always crucially recognized as a main source of valuable medications. Considering the SARS-CoV-2 and Zika main proteases (Mpro) as the re-production key element of the viral cycle and its main target, herein we report an intensive computer-aided virtual screening for a focused list of 39 marine lamellarins pyrrole alkaloids, against SARS-CoV-2 and Zika main proteases (Mpro) using a set of combined modern computational methodologies including molecular docking (MDock), molecule dynamic simulations (MDS) and structure-activity relationships (SARs) as well. Indeed, the molecular docking studies had revealed four promising marine alkaloids including [lamellarin H (14)/K (17)] and [lamellarin S (26)/Z (39)], according to their notable ligand-protein energy scores and relevant binding affinities with the SARS-CoV-2 and Zika (Mpro) pocket residues, respectively. Consequentially, these four chemical hits were further examined thermodynamically though investigating their MD simulations at 100 ns, where they showed prominent stability within the accommodated (Mpro) pockets. Moreover, in-deep SARs studies suggested the crucial roles of the rigid fused polycyclic ring system, particularly aromatic A- and F- rings, position of the phenolic -OH and δ-lactone functionalities as essential structural and pharmacophoric features. Finally, these four promising lamellarins alkaloids were investigated for their in-silico ADME using the SWISS ADME platform, where they displayed appropriated drug-likeness properties. Such motivating outcomes are greatly recommending further in vitro/vivo examinations regarding those lamellarins pyrrole alkaloids (LPAs).Communicated by Ramaswamy H. Sarma.

COVID-19 Hierarchical Classification Using a Deep Learning Multi-Modal

Coronavirus disease 2019 (COVID-19), originating in China, has rapidly spread worldwide. Physicians must examine infected patients and make timely decisions to isolate them. However, completing these processes is difficult due to limited time and availability of expert radiologists, as well as limitations of the reverse-transcription polymerase chain reaction (RT-PCR) method. Deep learning, a sophisticated machine learning technique, leverages radiological imaging modalities for disease diagnosis and image classification tasks. Previous research on COVID-19 classification has encountered several limitations, including binary classification methods, single-feature modalities, small public datasets, and reliance on CT diagnostic processes. Additionally, studies have often utilized a flat structure, disregarding the hierarchical structure of pneumonia classification. This study aims to overcome these limitations by identifying pneumonia caused by COVID-19, distinguishing it from other types of pneumonia and healthy lungs using chest X-ray (CXR) images and related tabular medical data, and demonstrate the value of incorporating tabular medical data in achieving more accurate diagnoses. Resnet-based and VGG-based pre-trained convolutional neural network (CNN) models were employed to extract features, which were then combined using early fusion for the classification of eight distinct classes. We leveraged the hierarchal structure of pneumonia classification within our approach to achieve improved classification outcomes. Since an imbalanced dataset is common in this field, a variety of versions of generative adversarial networks (GANs) were used to generate synthetic data. The proposed approach tested in our private datasets of 4523 patients achieved a macro-avg F1-score of 95.9% and an F1-score of 87.5% for COVID-19 identification using a Resnet-based structure. In conclusion, in this study, we were able to create an accurate deep learning multi-modal to diagnose COVID-19 and differentiate it from other kinds of pneumonia and normal lungs, which will enhance the radiological diagnostic process.

Paving the way for COVID survivors' psychosocial rehabilitation: Mining topics, sentiments, and their trajectories over time from Reddit

Objective: This study examined major themes and sentiments and their trajectories and interactions over time using subcategories of Reddit data. The aim was to facilitate decision-making for psychosocial rehabilitation. Materials and Methods: We utilized natural language processing techniques, including topic modeling and sentiment analysis, on a dataset consisting of more than 38,000 topics, comments, and posts collected from a subreddit dedicated to the experiences of people who tested positive for COVID-19. In this longitudinal exploratory analysis, we studied the dynamics between the most dominant topics and subjects' emotional states over an 18-month period. Results: Our findings highlight the evolution of the textual and sentimental status of major topics discussed by COVID survivors over an extended period of time during the pandemic. We particularly studied pre- and post-vaccination eras as a turning point in the timeline of the pandemic. The results show that not only does the relevance of topics change over time, but the emotions attached to them also vary. Major social events, such as the administration of vaccines or enforcement of nationwide policies, are also reflected through the discussions and inquiries of social media users. In particular, the emotional state (i.e., sentiments and polarity of their feelings) of those who have experienced COVID personally. Discussion: Cumulative societal knowledge regarding the COVID-19 pandemic impacts the patterns with which people discuss their experiences, concerns, and opinions. The subjects' emotional state with respect to different topics was also impacted by extraneous factors and events, such as vaccination. Conclusion: By mining major topics, sentiments, and trajectories demonstrated in COVID-19 survivors' interactions on Reddit, this study contributes to the emerging body of scholarship on COVID-19 survivors' mental health outcomes, providing insights into the design of mental health support and rehabilitation services for COVID-19 survivors.

Timing and Predictors of Loss of Infectivity Among Healthcare Workers With Mild Primary and Recurrent COVID-19: A Prospective Observational Cohort Study

BACKGROUND

There is a need to understand the duration of infectivity of primary and recurrent coronavirus disease 2019 (COVID-19) and identify predictors of loss of infectivity.

METHODS

Prospective observational cohort study with serial viral culture, rapid antigen detection test (RADT) and reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal specimens of healthcare workers with COVID-19. The primary outcome was viral culture positivity as indicative of infectivity. Predictors of loss of infectivity were determined using multivariate regression model. The performance of the US Centers for Disease Control and Prevention (CDC) criteria (fever resolution, symptom improvement, and negative RADT) to predict loss of infectivity was also investigated.

RESULTS

In total, 121 participants (91 female [79.3%]; average age, 40 years) were enrolled. Most (n = 107, 88.4%) had received ≥3 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine doses, and 20 (16.5%) had COVID-19 previously. Viral culture positivity decreased from 71.9% (87/121) on day 5 of infection to 18.2% (22/121) on day 10. Participants with recurrent COVID-19 had a lower likelihood of infectivity than those with primary COVID-19 at each follow-up (day 5 odds ratio [OR], 0.14; P < .001]; day 7 OR, 0.04; P = .003]) and were all non-infective by day 10 (P = .02). Independent predictors of infectivity included prior COVID-19 (adjusted OR [aOR] on day 5, 0.005; P = .003), an RT-PCR cycle threshold [Ct] value <23 (aOR on day 5, 22.75; P < .001) but not symptom improvement or RADT result.The CDC criteria would identify 36% (24/67) of all non-infectious individuals on day 7. However, 17% (5/29) of those meeting all the criteria had a positive viral culture.

CONCLUSIONS

Infectivity of recurrent COVID-19 is shorter than primary infections. Loss of infectivity algorithms could be optimized.

Research progress in cell therapy for oral diseases: focus on cell sources and strategies to optimize cell function

In recent years, cell therapy has come to play an important therapeutic role in oral diseases. This paper reviews the active role of mesenchymal stem cells, immune cell sources, and other cells in oral disorders, and presents data supporting the role of cell therapy in oral disorders, including bone and tooth regeneration, oral mucosal disorders, oral soft tissue defects, salivary gland dysfunction, and orthodontic tooth movement. The paper will first review the progress of cell optimization strategies for oral diseases, including the use of hormones in combination with stem cells, gene-modified regulatory cells, epigenetic regulation of cells, drug regulation of cells, cell sheets/aggregates, cell-binding scaffold materials and hydrogels, nanotechnology, and 3D bioprinting of cells. In summary, we will focus on the therapeutic exploration of these different cell sources in oral diseases and the active application of the latest cell optimization strategies.

Overview of the different methods for RNA preparation in COVID-19 diagnosis process during the pandemic

The COVID-19 pandemic brought to light the impact of a widespread disease on various aspects of human relationships, communities, and economies. One notable consequence was the increased demand for diagnostic kits, laboratory reagents, and personal health equipment. This surge in testing capacity worldwide led to shortages in the supply of essential items, including RNA extraction kits, which are crucial for detecting COVID-19 infections. To address this scarcity, researchers have proposed alternative and cost-effective strategies for RNA extraction, utilizing both chemical and physical solutions and extraction-free methods. These approaches aim to alleviate the challenges associated with the overwhelming number of tests being conducted in laboratories. The purpose of this review is intends to provide a comprehensive summary of the various kit-free RNA extraction methods available for COVID-19 diagnosis during the pandemic.

Identification of SARS-CoV-2 Main Protease Inhibitors Using Chemical Similarity Analysis Combined with Machine Learning

SARS-CoV-2 Main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome, which is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development. Herein, we performed a large-scale virtual screening by comparing multiple structural descriptors of reference molecules with reported anti-coronavirus activity against a library with >17 million compounds. Further filtering, performed by applying two machine learning algorithms, identified eighteen computational hits as anti-SARS-CoV-2 compounds with high structural diversity and drug-like properties. The activities of twelve compounds on Mpro's enzymatic activity were evaluated by fluorescence resonance energy transfer (FRET) assays. Compound 13 (ZINC13878776) significantly inhibited SARS-CoV-2 Mpro activity and was employed as a reference for an experimentally hit expansion. The structural analogues 13a (ZINC4248385), 13b (ZNC13523222), and 13c (ZINC4248365) were tested as Mpro inhibitors, reducing the enzymatic activity of recombinant Mpro with potency as follows: 13c > 13 > 13b > 13a. Then, their anti-SARS-CoV-2 activities were evaluated in plaque reduction assays using Vero CCL81 cells. Subtoxic concentrations of compounds 13a, 13c, and 13b displayed in vitro antiviral activity with IC50 in the mid micromolar range. Compounds 13a-c could become lead compounds for the development of new Mpro inhibitors with improved activity against anti-SARS-CoV-2.

Impact of COVID-19 quarantines on clozapine-induced constipation: Experience of utilizing a clozapine-induced constipation protocol at a state forensic psychiatric facility

Objective

Since 2017, Fulton State Hospital (FSH) has implemented a clozapine-induced constipation protocol. In March 2020, FSH initiated unit quarantines to minimize the spread of coronavirus disease (COVID-19). The objective of this study was to evaluate the impact of these quarantines on medical referrals for constipation, the Bristol Stool Chart ratings, utilization of as-needed (PRN) laxatives, and adherence rates with scheduled constipation medication regimens.

Methods

Patients on the clozapine-induced constipation protocol from May 1, 2019 to December 31, 2020, were included, with 10-month pre- and mid-quarantine implementation. Data collected included patient demographics, primary psychiatric diagnosis, and outcome variables. Descriptive statistics and paired t-tests were performed.

Results

A total of 31 patients were included. Most were male (93.5%), with a median age of 40 years. The most common primary diagnosis was schizophrenia. Compared with the pre-quarantine implementation period, there were fewer medical referral contacts per person, less use of PRN laxatives, and slightly lower adherence rates to scheduled constipation medication regimens during the mid-quarantine implementation period.

Conclusion

Compared with the pre-quarantine implementation period, there were fewer medical referrals per person during the mid-quarantine implementation period.

Knowledge of and Self-Expressed Stigma for COVID-19 Vaccination among Pre-University Students in a College in South India: A Cross-Sectional Study

Background

Coronavirus disease 2019 (COVID-19) is a contagious infection characterized by severe acute respiratory syndrome (SARS-CoV-2). Safe and effective vaccines are game-changers in the global vision of marking an end to the challenges posed by the COVID-19 pandemic. However, vaccine hesitancy due to perceived stigma and misinformation is a grave cause of concern.

Objectives

To assess pre-university students' self-expressed stigma regarding COVID-19 vaccination and its association with their knowledge.

Materials and Methods

A cross-sectional study was adopted for this research. A structured questionnaire approach was used to gather data from 384 students purposively at the selected pre-university college. The structured questionnaire consisted of three sections that explored the socio-demographic characteristics of the study participants, knowledge of vaccination, and self-expressed stigma, respectively. A total of 384 respondents took part in the study.

Results

The study observes a low positive relationship (r = 0.25, P < 0.01) between knowledge and self-expressed stigma toward vaccination. Further, it was observed that participants from rural backgrounds had lower knowledge and self-expressed stigma scores than participants from urban settings. It is pertinent to note that participants with other sources of information had higher knowledge than those who used the internet, friends/peers, or newspapers. Both of the aforementioned findings are statistically significant.

Conclusion

The interventions should revive trust in national health authorities, structured awareness campaigns by government agencies, and media coverage about the safety and efficacy of vaccines. In addition, it is also important to support citizens in ensuring that they have access to the right information from authentic sources in times of crisis.

Salmonellosis: An Overview of Epidemiology, Pathogenesis, and Innovative Approaches to Mitigate the Antimicrobial Resistant Infections

Salmonella is a major foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Salmonella is highly pathogenic and encompasses more than 2600 characterized serovars. The transmission of Salmonella to humans occurs through the farm-to-fork continuum and is commonly linked to the consumption of animal-derived food products. Among these sources, poultry and poultry products are primary contributors, followed by beef, pork, fish, and non-animal-derived food such as fruits and vegetables. While antibiotics constitute the primary treatment for salmonellosis, the emergence of antibiotic resistance and the rise of multidrug-resistant (MDR) Salmonella strains have highlighted the urgency of developing antibiotic alternatives. Effective infection management necessitates a comprehensive understanding of the pathogen's epidemiology and transmission dynamics. Therefore, this comprehensive review focuses on the epidemiology, sources of infection, risk factors, transmission dynamics, and the host range of Salmonella serotypes. This review also investigates the disease characteristics observed in both humans and animals, antibiotic resistance, pathogenesis, and potential strategies for treatment and control of salmonellosis, emphasizing the most recent antibiotic-alternative approaches for infection control.

Retrospective Cohort Study on Determinants of Mechanical Ventilation Duration of COVID-19 ICU Patients

Background In the face of the ongoing global health crisis posed by COVID-19, it becomes imperative to understand the disease's dynamics, particularly in specific regions. This study provides a detailed examination of the factors influencing mechanical ventilation (MV) duration among COVID-19 patients in an intensive care setting, focusing on a diverse patient cohort from the Al Hassa region of Saudi Arabia. The primary aim of this study was to identify key demographic factors, clinical outcomes, and comorbidities that affect the duration of MV among ICU patients with COVID-19. This understanding is crucial for enhancing patient care and informing healthcare strategies in the context of the pandemic. Methods A retrospective cohort study was conducted involving patients diagnosed with COVID-19 and admitted to the ICU in the Al Hassa region. The total number of participants was 1,259. Using a systematic sampling method, these participants were chosen to create a representative sample that reflects the prevailing treatment protocols in ICUs across these hospitals. Data encompassed patient demographics, comorbidities, clinical outcomes, and MV duration. Statistical analyses were employed to explore the associations between these variables. Results Our findings reveal a total of 1,259 participants significant associations between MV duration and various factors, including nationality, legal status, travel history, and comorbidities like heart failure and immunocompromised status. These insights are instrumental in understanding the nuances of COVID-19 management in critical care. Conclusion The study provides valuable insights into the determinants of MV duration in severe COVID-19 cases, emphasizing the need for individualized patient care approaches. It highlights the complexity of managing COVID-19 in ICU settings and underscores the importance of tailored healthcare responses to this global health challenge, particularly in the Al Hassa region.

Novel Federated Decision Making for Distribution of Anti-SARS-CoV-2 Monoclonal Antibody to Eligible High-Risk Patients

Context: When the epidemic first broke out, no specific treatment was available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The urgent need to end this unusual situation has resulted in many attempts to deal with SARS-CoV-2. In addition to several types of vaccinations that have been created, anti-SARS-CoV-2 monoclonal antibodies (mAbs) have added a new dimension to preventative and treatment efforts. This therapy also helps prevent severe symptoms for those at a high risk. Therefore, this is one of the most promising treatments for mild to moderate SARS-CoV-2 cases. However, the availability of anti-SARS-CoV-2 mAb therapy is limited and leads to two main challenges. The first is the privacy challenge of selecting eligible patients from the distribution hospital networking, which requires data sharing, and the second is the prioritization of all eligible patients amongst the distribution hospitals according to dose availability. To our knowledge, no research combined the federated fundamental approach with multicriteria decision-making methods for the treatment of SARS-COV-2, indicating a research gap. Objective: This paper presents a unique sequence processing methodology that distributes anti-SARS-CoV-2 mAbs to eligible high-risk patients with SARS-CoV-2 based on medical requirements by using a novel federated decision-making distributor. Method: This paper proposes a novel federated decision-making distributor (FDMD) of anti-SARS-CoV-2 mAbs for eligible high-risk patients. FDMD is implemented on augmented data of 49,152 cases of patients with SARS-CoV-2 with mild and moderate symptoms. For proof of concept, three hospitals with 16 patients each are enrolled. The proposed FDMD is constructed from the two sides of claim sequencing: central federated server (CFS) and local machine (LM). The CFS includes five sequential phases synchronised with the LMs, namely, the preliminary criteria setting phase that determines the high-risk criteria, calculates their weights using the newly formulated interval-valued spherical fuzzy and hesitant 2-tuple fuzzy-weighted zero-inconsistency (IVSH2-FWZIC), and allocates their values. The subsequent phases are federation, dose availability confirmation, global prioritization of eligible patients and alerting the hospitals with the patients most eligible for receiving the anti-SARS-CoV-2 mAbs according to dose availability. The LM independently performs all local prioritization processes without sharing patients’ data using the provided criteria settings and federated parameters from the CFS via the proposed Federated TOPSIS (F-TOPSIS). The sequential processing steps are coherently performed at both sides. Results and Discussion: (1) The proposed FDMD efficiently and independently identifies the high-risk patients most eligible for receiving anti-SARS-CoV-2 mAbs at each local distribution hospital. The final decision at the CFS relies on the indexed patients’ score and dose availability without sharing the patients’ data. (2) The IVSH2-FWZIC effectively weighs the high-risk criteria of patients with SARS-CoV-2. (3) The local and global prioritization ranks of the F-TOPSIS for eligible patients are subjected to a systematic ranking validated by high correlation results across nine scenarios by altering the weights of the criteria. (4) A comparative analysis of the experimental results with a prior study confirms the effectiveness of the proposed FDMD. Conclusion: The proposed FDMD has the benefits of centrally distributing anti-SARS-CoV-2 mAbs to high-risk patients prioritized based on their eligibility and dose availability, and simultaneously protecting their privacy and offering an effective cure to prevent progression to severe SARS-CoV-2 hospitalization or death.

The risk of pet animals in spreading severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and public health importance: An updated review

Since the outbreak of SARS-CoV-2 was first identified in 2019, it has been reported that the virus could infect a variety of animals either naturally or experimentally. This review discusses the occurrence SARS-CoV-2 in dogs and cats and the role of these animals in transmitting coronavirus disease 2019 (COVID-19) to their owners. The data were collected from epidemiological studies and case reports that focused on studying the occurrence of SARS-CoV-2 in pet animals and their owners. Epidemiological studies and case reports indicate that dogs and cats are infected with SARS-CoV-2 either naturally or experimentally; however, the global number of naturally infected animals is far lower than the number of people who have COVID-19. These studies demonstrate that pet animals acquire the infection from direct contact with COVID-19-infected owners. Currently, there are no studies reporting that dogs and cats can transmit SARS-CoV-2 to other animals and humans, under natural conditions. The emergence of SARS-CoV-2 infection in companion animals (dogs and cats) in different countries worldwide raises concerns that pets are at higher risk for spreading and transmitting SARS-CoV-2 to humans and other animals, which poses a hazard to the public health. Therefore, investigating the role of dogs and cats in the transmission and epidemiology of SARS-CoV-2 will help us to design and implement appropriate preventive measures against the further transmission of SARS-CoV-2.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) primer design based on Indonesia SARS-CoV-2 RNA sequence

BACKGROUND

The COVID-19 pandemic has highlighted the importance of tracking cases by using various methods such as the Reverse transcription loop-mediated isothermal amplification (RT-LAMP) which is a fast, simple, inexpensive, and accurate mass tracker. However, there have been no reports about the development of RT-LAMP primer designs that use genome sequences of viruses from Indonesia. Therefore, this study aimed to design an RT-LAMP primer using SARS-CoV-2 genome sequences from Indonesia and several other countries representing five continents in the world, as well as genomes from five Variants of Concern (VOC).

RESULT

The results showed that the consensus sequence of 70 SARS-CoV-2 virus sequences was obtained with a length of 29,982 bases. The phylogenetic test confirmed that the consensus sequence had a close kinship with the SARS-CoV-2 Wuhan Isolate. Furthermore, the SimPlot analysis showed that there was a high genetic diversity of sequences from the Coronaviridae tribal virus at base sequences of 1,500-5,000, 6,500-7,500, and 23,300-25,500. A total of 139 sets of primers were obtained from the primer design with 4 sets namely T1_6, T1_9, T4_7, and T4_52 having the best characteristics. Based on the secondary structure analysis test on 4 sets of primers, T1_6 and T1_9 were predicted not to form secondary structures at RT-LAMP operational temperatures. The primer set T1_9 showed better specificity in BLAST NCBI and eLAMP BLAST tests.

CONCLUSION

This study obtained a primer set of T1_9 with base sequence F3: CACTGAGACTCATTGATGCTATG, B3: CCAACCGTCTCTAAGAAACTCT, F2: GTTCACATCTGATTTGGCTACT, F1c: GAAGTCAACTGAACAACACCACCT, B2: CCTTCCTTAAACTTCTCTTCAAGC, B1c: GTGGCTAACTAACATCTTTGGCACT, LB: TGAAAACAAACCCGCCGTCCTTG, which meets the ideal parameters and has the best specificity. Therefore, it is recommended for use in further tests to recognize SARS-CoV-2 from Indonesia, other five continents, as well as five VOCs, including the new Omicron sub-variant.

A sensitive and simple RT-LAMP assay for sarbecovirus screening in bats

IMPORTANCE

We report the application of a colorimetric and fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to facilitate mass screening for sarbecoviruses in bats. The assay was evaluated using a total of 838 oral and alimentary samples from bats and demonstrated comparable sensitivity and specificity to quantitative reverse transcription PCR (qRT-PCR), with a simple setup. The addition of SYTO9, a fluorescent nucleic acid stain, also allows for quantitative analysis. The scalability and simplicity of the assay are believed to contribute to improving preparedness for detecting emerging coronaviruses by applying it to field studies and surveillance.

Electrochemical sensor for simultaneous determination of antiviral favipiravir drug, paracetamol and vitamin C based on host-guest inclusion complex of β-CD/CNTs nanocomposite

Favipiravir (FVI) is extensively used as an effective medication against several diverse infectious RNA viruses. It is widely administered as an anti-influenza drug. Combination therapy formed from FVI, paracetamol (PAR) and vitamin C (VC) is needed for treating patients diseased by RNA viruses. Thus, an efficient electrochemical sensor is developed for detecting FVI in human serum samples. The sensor is fabricated by casting a thin layer of carbon nanotubes (CNTs) over a glassy carbon (GC) electrode surface followed by electrodeposition of another layer of β-cyclodextrin (β-CD). Under optimized conditions, the sensor shows excellent catalytic effect for FVI, PAR and VC oxidation in the concentration ranges (0.08 µM → 80 µM), (0.08 µM → 50 µM) and (0.8 µM → 80 µM) with low detection limits of 0.011 μM, 0.042 μM and 0.21 μM, respectively. The combined effect of host-guest interaction ability of β-CD for the drugs, and a large conductive surface area of CNTs improves the sensing performance of the electrode. The sensor exhibits stable response over 4 weeks, good reproducibility, and insignificant interference from common species present in serum samples. The reliability of using the sensor in serum samples shows good recovery of FVI, PAR and VC.

Use of high-flow nasal oxygen for pregnant women with COVID-19 in the labour ward setting

The presentation and management of SARS-CoV-2 (COVID-19) infection in the obstetric population is affected by the hormonal and mechanical changes of pregnancy. The increased oxygen demands in pregnancy in the face of conventional oxygen therapy, risks of tracheal intubation and discomfort from non-invasive positive pressure ventilation all support the use of high-flow nasal oxygen (HFNO) as an alternative therapy. The lack of published guidance for the use of HFNO has led to the development of local-level guidance based on expert consensus. More evidence exploring the use of HFNO therapy in the pregnant population is required to assist in developing clinical guidelines.

A Review of Antibiotic Efficacy in COVID-19 Control

Severe acute respiratory disease is associated with chronic secondary infections that exacerbate symptoms and mortality. So far, many drugs have been introduced to treat this disease, none of which effectively control the coronavirus. Numerous studies have shown that mitochondria, as the center of cell biogenesis, are vulnerable to drugs, especially antibiotics. Antibiotics were widely prescribed during the early phase of the pandemic. We performed a literature review to assess the reasons, evidence, and practices on the use of antibiotics in coronavirus disease 2019 (COVID-19) in- and outpatients. The current research found widespread usage of antibiotics, mostly in an empirical context, among COVID-19 hospitalized patients. The effectiveness of this approach has not been established. Given the high death rate linked with secondary infections in COVID-19 patients and the developing antimicrobial resistance, further study is urgently needed to identify the most appropriate rationale for antibiotic therapy in these patients.

Typical phenotypes of patients with acute respiratory failure with and without COVID-19 and their relationship with outcomes: a cohort study

OBJECTIVE

To compare, within a cohort of patients with acute respiratory failure, the phenotypes of patients with and without COVID-19 in the context of the pandemic and evaluate whether COVID-19 is an independent predictor of intensive care unit mortality.

METHODS

This historical cohort study evaluated 1001 acute respiratory failure patients with suspected COVID-19 admitted to the intensive care unit of 8 hospitals. Patients were classified as COVID-19 cases and non-COVID-19 cases according to real-time polymerase chain reaction results. Data on clinical and demographic characteristics were collected on intensive care unit admission, as well as daily clinical and laboratory data and intensive care unit outcomes.

RESULTS

Although the groups did not differ in terms of APACHE II or SOFA scores at admission, the COVID-19 group had more initial symptoms of fever, myalgia and diarrhea, had a longer duration of symptoms, and had a higher prevalence of obesity. They also had a lower PaO2/FiO2 ratio, lower platelet levels than non-COVID-19 patients, and more metabolic changes, such as higher levels of blood glucose, C-reactive protein, and lactic dehydrogenase. Patients with non-COVID-19 acute respiratory failure had a higher prevalence of chronic obstructive pulmonary disease/asthma and cardiopathy. Patients with COVID-19 stayed in the hospital longer and had more complications, such as acute kidney failure, severe acute respiratory distress syndrome and severe infection. The all-cause mortality rate was also higher in this group (43.7% in the COVID-19 group versus 27.4% in the non-COVID-19 group). The diagnosis of COVID-19 was a predictor of intensive care unit mortality (odds ratio, 2.77; 95%CI, 1.89 - 4.07; p < 0.001), regardless of age or Charlson Comorbidity Index score.

CONCLUSION

In a prospective cohort of patients admitted with acute respiratory failure, patients with COVID-19 had a clearly different phenotype and a higher mortality than non-COVID-19 patients. This may help to outline more accurate screening and appropriate and timely treatment for these patients.

Changing patterns and clinical outcomes of hospitalized patients with COVID-19 severe pneumonia treated with remdesivir according to vaccination status: results from a real-world retrospective study

Since the beginning of Coronavirus Disease 2019 (COVID-19) pandemic, many drugs have been purposed for the treatment of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Remdesivir emerged as an encouraging antiviral drug for patients with documented severe COVID-19-related pneumonia. Although several studies about remdesivir effectiveness exist, no study investigated the effect of the combination of remdesivir with the vaccination status. The aim of this study was to assess whether the administration of remdesivir could show some differences in terms of clinical outcomes in patients vaccinated against SARS-CoV-2 versus those who were not. The primary outcome was the in-hospital mortality. The secondary outcomes were 30-days mortality, the need for ICU admission and for oxygen supplementation. This is a retrospective cohort study including all consecutive adult patients hospitalized for severe COVID-19 at the Padua University Hospital (Italy), between September 1st, 2020, and January 31st, 2022, and who received a 5-days course of remdesivir. A total of 708 patients were included, 467 (66%) were male, and the median age was 67 (IQR: 56-79) years. To better estimate the outcomes of interest, a propensity score weighted approach was implemented for vaccination status. A total of 605/708 patients (85.4%) did not complete the vaccination schedule. In-hospital mortality rate was 5.1% (n = 36), with no statistically significant difference between the unvaccinated (n=29, 4.8%) and vaccinated (n=7, 6.8%; p=0.4) patients. After propensity score matching, mortality between the two groups remained similar. However, both the need for ICU and oxygen supplementation were significantly lower in the vaccinated group. Our finding suggests that a complete vaccination course could have an impact in reducing the need for transfer in ICU and for high-flow therapy in moderate-to-severe COVID-19 patients treated with remdesivir.

Comparative analysis of SARS-CoV-2 detection methods using stool, blood, and nasopharyngeal swab samples

Introduction

as a public health policy, the ongoing global coronavirus disease 2019 vaccination drives require continuous tracking, tracing, and testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnostic testing is important in virus detection and understanding its spread for timely intervention. This is especially important for low-income settings where the majority of the population remains untested. This is well supported by the fact that of about 9% of the Kenyan population had been tested for the virus.

Methods

this was a cross-sectional study conducted at the Kisumu and Siaya Referral Hospitals in Kenya. Here we report on the sensitivity and specificity of the rapid antigen detection test (Ag-RDT) of SARS-CoV-2 compared with the quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) using stool and nasopharyngeal swab samples. Further, the mean Immunoglobulin M (IgM) and Immunoglobulin G (IgG) antibody levels among symptomatic and asymptomatic individuals in western Kenya were evaluated.

Results

the sensitivity and specificity of Ag-RDT were 76.3% (95% CI, 59.8-88.6%) and 96.3% (95% CI, 87.3-99.5%) with a negative and positive predictive value of 85% (95% CI, 73.8%-93.0%) and 93% (95% CI, 78.6%-99.2%) respectively. There was substantial agreement of 88% (Kappa value of 0.75, 95% CI, 0.74-0.77) between Ag-RDT and nasopharyngeal swab RT-qPCR, and between stool and nasopharyngeal swab RT-qPCR results (83.7% agreement, Kapa value 0.62, 95% CI 0.45-0.80). The mean IgM and IgG antibody response to SARS-CoV-2 were not different in asymptomatic individuals, 1.11 (95% CI, 0.78-1.44) and 0.88 (95% CI, 0.65-1.11) compared to symptomatic individuals 4.30 (95% CI 3.30-5.31) and 4.16 (95% CI 3.32 -5.00).

Conclusion

the choice of an appropriate SARS-CoV-2 diagnostic, screening, and surveillance test should be guided by the specific study needs and a rational approach for optimal results.

When antivirals backfire: An evaluation of favipiravir's clinical outcomes in critically ill patients with COVID-19: A multicenter cohort study

BACKGROUND

Favipiravir is an oral antiviral, that might treat COVID-19 by enhancing viral eradication, particularly in patients with mild-to-moderate disease. Yet, the findings on the use of favipiravir in critically ill patients with COVID-19 are inconsistent. Therefore, this study aimed to assess the effectiveness and safety of favipiravir in critically ill patients with COVID-19.

METHOD

A multicenter retrospective cohort study includes critically ill adult patients with COVID-19 admitted to the intensive care units (ICUs) was conducted from March 2020 to July 2021. Patients were categorized based on favipiravir use (control vs. favipiravir). The primary outcome was in-hospital mortality. Secondary outcomes included mechanical ventilation (MV) duration, 30-day mortality, ICU length of stay (LOS), hospital LOS, and complications during the stay.

RESULTS

After propensity score (PS) matching (1:1 ratio), 146 patients were included in the final analysis. A higher in-hospital and 30-day mortality were observed in patients receiving favipiravir compared to the control group at crude analysis (65.3% vs. 43.8%; P-value=0.009 and 56.3% vs. 40.3; P-value=0.06, respectively); however, no differences were observed using multivariable Cox proportional hazards regression analysis (HR 1.17; 95% CI 0.73, 1.87; P-value =0.51 and HR 0.86; 95% CI 0.53, 1.39; P-value=0.53, respectively). Conversely, the MV duration and ICU LOS were longer in patients who received favipiravir than the control group (β coefficient 0.51; CI 0.09, 0.92; P-value = 0.02, β coefficient 0.41; CI 0.17, 0.64; P-value = 0.0006, respectively). Complications during the stay were comparable between the two groups.

CONCLUSION

The use of favipiravir in critically ill patients with COVID-19 did not demonstrate a reduction in mortality; instead, it was linked with longer MV duration and ICU stay. This finding suggests limiting favipiravir use to infections where it is more effective, other than COVID-19. Further randomized clinical trials are needed to confirm these findings.

Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches

3CLpro is a viable target for developing antiviral therapies against the coronavirus. With the urgent need to find new possible inhibitors, a structure-based virtual screening approach was developed. This study recognized 75 pharmacologically bioactive compounds from our in-house library of 1052 natural product-based compounds that satisfied drug-likeness criteria and exhibited good bioavailability and membrane permeability. Among these compounds, three promising sulfonamide chalcones were identified by combined theoretical and experimental approaches, with SWC423 being the most suitable representative compound due to its competitive inhibition and low cytotoxicity in Vero E6 cells (EC50 = 0.89 ± 0.32 μM; CC50 = 25.54 ± 1.38 μM; SI = 28.70). The binding and stability of SWC423 in the 3CLpro active site were investigated through all-atom molecular dynamics simulation and fragment molecular orbital calculation, indicating its potential as a 3CLpro inhibitor for further SARS-CoV-2 therapeutic research. These findings suggested that inhibiting 3CLpro with a sulfonamide chalcone such as SWC423 may pave the effective way for developing COVID-19 treatments.

Regulation of coronavirus nsp15 cleavage specificity by RNA structure

SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, has had an enduring impact on global public health. However, SARS-CoV-2 is only one of multiple pathogenic human coronaviruses (CoVs) to have emerged since the turn of the century. CoVs encode for several nonstructural proteins (nsps) that are essential for viral replication and pathogenesis. Among them is nsp15, a uridine-specific viral endonuclease that is important in evading the host immune response and promoting viral replication. Despite the established endonuclease function of nsp15, little is known about other determinants of its cleavage specificity. In this study we investigate the role of RNA secondary structure in SARS-CoV-2 nsp15 endonuclease activity. Using a series of in vitro endonuclease assays, we observed that thermodynamically stable RNA structures were protected from nsp15 cleavage relative to RNAs lacking stable structure. We leveraged the s2m RNA from the SARS-CoV-1 3'UTR as a model for our structural studies as it adopts a well-defined structure with several uridines, two of which are unpaired and thus highly probable targets for nsp15 cleavage. We found that SARS-CoV-2 nsp15 specifically cleaves s2m at the unpaired uridine within the GNRNA pentaloop of the RNA. Further investigation revealed that the position of uridine within the pentaloop also impacted nsp15 cleavage efficiency suggesting that positioning within the pentaloop is necessary for optimal presentation of the scissile uridine and alignment within the nsp15 catalytic pocket. Our findings indicate that RNA secondary structure is an important determinant of nsp15 cleavage and provides insight into the molecular mechanisms of RNA recognition by nsp15.