Air pollution is a major global environment and health concern. Recent studies have suggested an association between air pollution and COVID-19 mortality and morbidity. In this context, a close association between increased levels of air pollutants such as particulate matter ≤2.5 to 10 µM, ozone and nitrogen dioxide and SARS-CoV-2 infection, hospital admissions and mortality due to COVID 19 has been reported. Air pollutants can make individuals more susceptible to SARS-CoV-2 infection by inducing the expression of proteins such as angiotensin converting enzyme (ACE)2 and transmembrane protease, serine 2 (TMPRSS2) that are required for viral entry into the host cell, while causing impairment in the host defence system by damaging the epithelial barrier, muco-ciliary clearance, inhibiting the antiviral response and causing immune dysregulation. The aim of this review is to report the epidemiological evidence on impact of air pollutants on COVID 19 in an up-to-date manner, as well as to provide insights on in vivo and in vitro mechanisms.

Understanding SARS-CoV-2 epidemiology in companion animals is critical for evaluating their role in viral transmission and their potential as sentinels for human infections. This large-scale serosurvey analyzed serum samples from 706 cats and 2,396 dogs collected across the USA in 2023 using a surrogate virus neutralization test (sVNT) to detect SARS-CoV-2 antibodies. Overall, 5.7% of cats and 4.7% of dogs tested positive for antibodies, with younger animals (under 12 months) showing significantly lower seropositivity rates (p = 0.0048). Additionally, we analyzed 153 positive samples for variant-specific antibody responses using six sVNT kits targeting the Delta variant and five Omicron sublineages. Among cats, 67.5% showed antibodies to Delta, with positivity rates for Omicron sublineages as follows: BA.1 (62.5%), BA.2 (42.5%), BA.4/BA.5 (77.5%), XBB (52.5%), and XBB.1.5 (45.0%). In dogs, 55.8% were positive for Delta, and Omicron sublineage rates were BA.1 (46.0%), BA.4/BA.5 (37.2%), XBB (58.4%), BA.2 (13.3%), and XBB.1.5 (9.7%). Given the close contact between companion animals and humans, and the persistence of antibodies against various SARS-CoV-2 variants and sublineages, our findings suggest that seroprevalence in cats and dogs may serve as valuable tool for tracking COVID-19 epidemiology.

Considering that bat ecology alterations may be linked with pathogen spillover, research on bat coronaviruses, particularly on the infection and transmission pattern among bats in relation with their ecology, is essential. We captured bats distributed in Korea from 2021 to 2022, examined coronaviruses in oral swabs, feces, urine, and ectoparasites, and were able to detect alphacoronavirus. We investigated coronaviruses, but noted no substantial differences in the body condition index in the coronavirus-positive bats. Binary logistic regression analysis revealed that bat ecological factors that were significantly associated with coronavirus-positive were roost type, sample type, and bat species. Coronavirus-positive ectoparasite cases suggested additional study on the potential role of them as the viral transmission vectors or fomites. Reinfection of a different coronavirus in recaptured bats was evident, suggesting the possibility that coronavirus circulation can evade the potential protective immunity acquired from previous coronavirus infections. The present findings provide comprehensive information on the coronaviruses transmission dynamics within bat populations linked with bat ecology.

Since winter 2019, SARS-CoV-2 has emerged, spread, and evolved all around the globe. We explore 4 y of evolutionary epidemiology of this virus, ranging from the applied public health challenges to the more conceptual evolutionary biology perspectives. Through this review, we first present the spread and lethality of the infections it causes, starting from its emergence in Wuhan (China) from the initial epidemics all around the world, compare the virus to other betacoronaviruses, focus on its airborne transmission, compare containment strategies ("zero-COVID" vs. "herd immunity"), explain its phylogeographical tracking, underline the importance of natural selection on the epidemics, mention its within-host population dynamics. Finally, we discuss how the pandemic has transformed (or should transform) the surveillance and prevention of viral respiratory infections and identify perspectives for the research on epidemiology of COVID-19.

N6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotic RNA and is also present in various viral RNAs, where it plays a crucial role in regulating the viral life cycle. However, the molecular mechanisms through which viruses regulate host RNA m6A methylation are not fully understood. In this study, we reveal that SARS-CoV-2 and HCoV-OC43 infection enhance host m6A modification by activating the mTORC1 signalling pathway. Specifically, the viral non-structural protein nsp14 upregulates the expression of S-adenosylmethionine synthase MAT2A in an mTORC1-dependent manner. This mTORC1-MAT2A axis subsequently stimulates the synthesis of S-adenosylmethionine (SAM). The increase of SAM then enhances the m6A methylation of host RNA and facilitates viral replication. Our findings uncover a molecular mechanism by which viruses regulate host m6A methylation and provide insights into how SARS-CoV-2 hijacks host cellular epitranscriptomic modifications to promote its replication.

The COVID-19 pandemic underscores the urgent need to develop broad-spectrum antivirals against coronaviruses (CoVs) to prepare for future outbreaks. In this study, we presented a systematic approach to developing broad-spectrum Mpro inhibitors, with a focus on high-risk CoVs. We optimised S-217622 as a lead compound, with the goal of enhancing conserved interactions within the S1, S2, and S3/S4 pockets of Mpro, leading to significantly improved inhibitory potency against representative CoVs. Compound 25 exhibited submicromolar activity across all ten CoVs, with IC50 values below 0.1 μM for six of them. The X-ray co-crystal structure of SARS-CoV-2 Mpro in complex with compound 25 revealed the structural basis of conserved interactions contributing to its broad-spectrum activity. This study demonstrates the feasibility of reinforcing conserved interactions to develop Mpro inhibitors with broad-spectrum activity and provides valuable strategies for combating future pandemics caused by unknown CoVs.

Packaging signals (PSs) of coronaviruses (CoVs) are specific RNA elements recognized by nucleocapsid (N) proteins that direct the selective packaging of genomic RNAs (gRNAs). These signals have been identified in the coding regions of the nonstructural protein 15 (Nsp 15) in CoVs classified under Embecovirus, a subgenus of betacoronaviruses (beta-CoVs). The PSs in other alpha- and beta-CoVs have been proposed to reside in the 5'-proximal regions of gRNAs, supported by comprehensive phylogenetic evidence. However, experimental data remain limited. In this study, we investigated the interactions between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) 5'-proximal gRNA transcripts and N proteins using electrophoretic mobility shift assays (EMSAs). Our findings revealed that the in vitro synthesized 5'-proximal gRNA transcripts of CoVs can shift from a major conformation to alternative conformations. We also observed that the conformer comprising multiple stem-loops (SLs) is preferentially bound by N proteins. Deletions of the 5'-proximal structural elements of CoV gRNA transcripts, SL1 and SL5a/b/c in particular, were found to promote the formation of alternative conformations. Furthermore, we identified RNA-binding peptides from a pool derived from SARS-CoV N protein. These RNA-interacting peptides were shown to preferentially bind to wild-type SL5a RNA. In addition, our observations of N protein condensate formation in vitro demonstrated that liquid-liquid phase separation (LLPS) of N proteins with CoV-5'-UTR transcripts was influenced by the presence of SL5a/b/c. In conclusion, these results collectively reveal previously uncharacterized binding features between the 5'-proximal transcripts of CoV gRNAs and N proteins.

Viral infectious diseases have been seriously affecting human life and health. SARS-CoV-2 was the pathogen that caused Coronavirus Disease 2019 (COVID-19), and the impact of COVID-19 is still existing. Enterovirus 71 (EV71) is the primary pathogen of hand, foot, and mouth disease (HFMD), and no effective direct-acting antiviral drugs targeting EV71 has been approved yet. Innate antiviral strategies play an important role in preventing virus infections depending on the powerful immune regulatory system of body, while viruses have evolved to exploit diverse methods to overcome immune response. Viral proteases, which are known in cleaving viral polyproteins, have also been found to modulate the innate immunity of host cells, thereby promoting viral proliferation. Herein, we reviewed the current development of SARS-CoV-2 3CLpro, PLpro, and EV71 3Cpro and 2Apro, mainly including structure, function, modulation of immune response, and inhibitors of these four proteases, to further deepen the understanding of viral pathogenesis and provide a new perspective for subsequent corresponding drug development.

The global outbreak of the novel coronavirus has renewed interest in related viral pathogens, including canine coronavirus (CCoV), which causes severe gastroenteritis, diarrhea, and vomiting in dogs worldwide. While cases of CCoV have been reported in China, specific instances in the Guangxi Zhuang Autonomous Region-a major center for dog breeding and consumption-have not been documented. In this study, we collected spleen tissue samples from dogs in Yulin city and conducted meta-transcriptomic sequencing. Bioinformatics analysis confirmed CCoV presence in these samples. Furthermore, virus screening and phylogenetic analyses identified the circulation of two CCoV genotypes within the dog population, revealing an overall prevalence of 14.2 %, with CCoV-IIb being the predominant genotype. Notably, two significant recombination events were detected among the analyzed strains. These findings provide valuable insights into the presence and genetic diversity of CCoV Yulin's dog populations, enhancing the understanding of its genetic variation and evolution.

It has been five years since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and we are also approaching the five-year mark of the COVID-19 pandemic. The vaccine is a significant weapon in combating infectious diseases like SARS-CoV-2. Several vaccines were developed against SARS-CoV-2, and they demonstrated efficacy and safety during these five years. The rapid development of multiple next-generation vaccine candidates in different platforms with very little time is the success story of the vaccine development endeavor. This remarkable success of rapid vaccine development is a new paradigm for fast vaccine development that might help develop infectious diseases and fight against the pandemic. With the completion of five years since the beginning of SARS-CoV-2 origin, we are looking back on the five years and reviewing the milestones, vaccine platforms, animal models, clinical trials, successful collaborations, vaccine safety, real-world effectiveness, and challenges. Lessons learned during these five years will help us respond to public health emergencies and to fight the battle against future pandemics.

Vaccines based on mRNA have been fundamental in facing the COVID-19 pandemic, however, they still raise concerns about stability and long-term efficacy. Thus, protein-based vaccines remain valid options and hence the study of effective adjuvants is crucial. Here, we developed a COVID-19 vaccine based on the receptor-binding domain (RBD) of SARS-CoV-2 Spike protein, which is covalently conjugated to the natural polymer hyaluronan (HA) that acts as an immunological adjuvant. Vaccination of K18-hACE2 mice with HA-RBD was well tolerated, and elicited high and sustained titres of RBD-binding antibodies and SARS-CoV-2-neutralizing antibodies, without the addition of other immunostimulatory compounds. Most importantly, HA-RBD vaccination conferred long-term protection to K18-hACE2 mice after challenge with SARS-CoV-2, also in the case of two consequent infections driven by different variants. These findings demonstrate the efficacy of HA-based vaccination against COVID-19 disease, and support the promising use of HA as an efficient and well tolerated adjuvant.

In recent years, the role of the intestinal microbiota in regulating host health and immune balance has attracted widespread attention. This study provides an in-depth analysis of the close relationship between the intestinal microbiota and respiratory system diseases, with a focus on three common respiratory virus infections, including respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and influenza virus. The research indicates that during RSV infection, there is a significant decrease in intestinal microbial diversity, suggesting the impact of the virus on the intestinal ecosystem. In SARS-CoV-2 infection, there are evident alterations in the intestinal microbiota, which are positively correlated with the severity of the disease. Similarly, influenza virus infection is associated with dysbiosis of the intestinal microbiota, and studies have shown that the application of specific probiotics exhibits beneficial effects against influenza virus infection. Further research indicates that the intestinal microbiota exerts a wide and profound impact on the occurrence and development of respiratory system diseases through various mechanisms, including modulation of the immune system and production of short-chain fatty acids (SCFAs). This article comprehensively analyzes these research advances, providing new perspectives and potential strategies for the prevention and treatment of future respiratory system diseases. This study not only deepens our understanding of the relationship between the intestinal microbiota and respiratory system diseases but also offers valuable insights for further exploring the role of host-microbiota interactions in the development of diseases.

The genus Phlomis contains more than 100 species distributed in North Africa and the Mediterranean region. This review highlights Phlomis-derived compounds' biological and pharmacological properties and their essential oils, with a special emphasis on anticancer activities. Relevant data was collected from scientific sources including Google Scholar, Science Direct, PubMed, and Springer Link by using the keyword "Phlomis". Also, the latest version of the plants' names was checked by www.worldfloraonline.org. Important Phytochemicals compounds like flavonoids, iridoids, and alkaloids, which were isolated from different Phlomis species showed significant biological activity, and inhibitory effects on various cancer cells (MCF-7, A549, HepG2, HT-29, etc.) via different mechanisms. The collected data strongly underpins the viewpoint that species belonging to the Phlomis genus have diverse biological and pharmaceutical activities to treat various diseases, including cancer, and their remarkable antimicrobial properties with no or minimal health and environmental hazards.

mRNA-based technology has been evaluated in clinical trials for rapid control and prevention of emergencies and diseases. HC009, a mRNA vaccine encoding the full-length SARS-CoV-2 spike protein delivered via the QTsome platform, was tested in rats for immunogenicity, toxicity, and biodistribution. For immunogenicity and toxicity, rats received three intramuscular injections of HC009 at 3-week intervals followed by a 4-week observation period. In the biodistribution study, rats received a single intramuscular injection, with mRNA levels measured in organs at various time points. Results showed that HC009 elicited effective, long-lasting humoral immunity and Th1-biased cellular responses. The mRNA primarily localized to the injection site and spleen, with no observed vaccine-related toxicological reactions. These findings support HC009's potential for inducing an effective immune response with a favorable safety profile, warranting further clinical investigation.

The SARS-CoV-2 spike protein is synthesized in the endoplasmic reticulum of host cells, from where it undergoes export to the Golgi and the plasma membrane or retrieval from the Golgi to the endoplasmic reticulum. Elucidating the fundamental principles of this bidirectional secretion are pivotal to understanding virus assembly and designing the next generation of spike genetic vaccine with enhanced export properties. However, the widely used strategy of C-terminal affinity tagging of the spike cytosolic tail interferes with proper bidirectional trafficking. Hence, the structural and biophysical investigations of spike protein trafficking have been hindered by a lack of appropriate spike constructs. Here we describe a strategy for the internal tagging of the spike protein. Using sequence analyses and AlphaFold modeling, we identified a site down-stream of the signal sequence for the insertion of a twin-strep-tag, which facilitates purification of an ecto-domain construct from the extra-cellular medium of mammalian Expi293F cells. Mass spectrometry analyses show that the internal tag has minimal impact on N-glycan modifications, which are pivotal for spike-host interactions. Single particle cryo-electron microscopy reconstructions of the spike ecto-domain reveal conformational states compatible for ACE2 receptor interactions, further solidifying the feasibility of the internal tagging strategy. Collectively, these results present a substantial advance towards reagent development for the investigations of spike protein trafficking during coronavirus infection and genetic vaccination.

SARS-CoV-2 infection affects the respiratory system but also many tissues and organs that may be adversely compromised. Accordingly, recent evidence has assessed virus ability to infect different cell phenotypes, translate viral proteins and promote virus replication. Among them, Envelope (E) proteins sustain virus replication, promote inflammatory processes and remodelling of host cells. However, despite advances on structure and sequence, E-protein specific location and effects in human host cells are still controversial and poorly investigated. Using lentiviral vectors, we established HEK293 and hiPS cell lines stably expressing E-protein. Immunocytochemistry showed E-protein mainly locates within the endoplasmic reticulum, the ERGIC and the Golgi compartments, while only HEK293 cells display some protein staining in cell periphery suggesting a possible insertion into the plasmalemma. Electrophysiological recordings in HEK293 cells revealed E-protein self-assembles in the plasma membrane to mediate a cation efflux pore that is sensitive to amantadine blockade. Calcium fluorescence imaging in HEK293 and hiPS cells demonstrated E-protein expression induces a marked depletion of thapsigargin-sensitive intracellular calcium stores. The altered calcium homeostasis associates to reduced cell metabolic activity, mitochondrial potential, proliferation rate and promotes ER stress. Finally, trilineage differentiation of hiPS cells indicated E-protein expression preserves cell pluripotency while selectively impairs mesodermal differentiation. These results unveil a critical role of stable E-viroporin expression that through alteration of ER Ca²⁺ homeostasis, metabolic activity and induction of ER stress affects important cellular functions, including the differentiative process from pluripotent to mesodermal progenitors, a critical cell population in self-repair and homeostasis of most human tissue and organs.

Porcine hemagglutinating encephalomyelitis virus (PHEV) is a member of the genus Betacoronavirus, known for its impact on the central and peripheral nervous systems in pigs. Traditionally associated with vomiting and wasting disease (VWD) and encephalomyelitis, PHEV was first reported in Canada in the late 1950s and has since been identified in numerous countries. Although serologic studies indicate global dissemination, the prevalence of PHEV remains unclear due to sporadic reporting and lack of active surveillance. Neonatal pigs are particularly vulnerable, with outbreaks resulting in high morbidity and mortality. Histopathological findings typically include non-suppurative encephalomyelitis and lymphoplasmacytic perivascular cuffs, gliosis, and neuronal degeneration. Recent observations have suggested a potential role for PHEV in respiratory disease, a hypothesis prompted by cases of influenza-like symptoms in pigs in Michigan in 2015 and corroborated by subsequent reports. This study aims to explore this possibility through a combination of clinical outbreak analysis and retrospective investigation. PHEV was confirmed via qPCR in 83.33 % of pigs examined for respiratory disease, with histological lesions such as necrotizing bronchitis and bronchiolitis. In-situ hybridization (ISH) confirmed the presence of PHEV mRNA in respiratory epithelium, and immunohistochemical analysis revealed significant macrophage infiltration in affected lung. Phylogenetic analysis indicated that PHEV strains from respiratory cases cluster closely with historical respiratory strains, though distinct from neurologic strains. This genetic differentiation suggests possible phenotypic variation contributing to respiratory tropism. The retrospective study identified PHEV in 7.62 % of cases with necrotizing bronchitis or bronchiolitis, reinforcing the virus's potential role in respiratory disease. Notably, PHEV co-infection with other respiratory pathogens such as PRRSV was observed, suggesting it may contribute to the porcine respiratory disease complex (PRDC). These findings suggest that PHEV is a significant respiratory pathogen in swine, warranting its inclusion in the differential diagnosis for respiratory disease in nursery pigs. Future research should focus on elucidating the pathogenesis of PHEV in respiratory disease, host-virus interactions, and the virus's impact on immune response and secondary infections. Understanding these factors will be crucial in developing effective preventive and therapeutic strategies against PHEV in swine.

The persistence and infectivity of respiratory viruses in cadavers remain poorly characterized, posing significant biosafety risks for forensic and healthcare professionals. This study systematically evaluates the post-mortem stability and transmission potential of SARS-CoV-2, influenza A virus (IAV), and respiratory syncytial virus (RSV) under varying environmental conditions, providing critical insights into viral kinetics.

To assess the post-mortem stability of SARS-CoV-2, tissue samples were collected from infected cadavers at 4 ℃, room temperature (RT, 20-22 ℃), and 37 ℃ over a predetermined timeframe. Viral kinetics were analyzed using quantitative assays, while histopathology and immunohistochemistry characterized tissue-specific distribution. Additionally, comparative analyses were conducted both in vitro and in cadaveric tissues to characterize the survival dynamics of IAV and RSV under identical conditions.

SARS-CoV-2 exhibited prolonged post-mortem infectivity, persisting for up to 5 days at RT and 37 ℃ and over 7 days at 4 ℃, with the highest risk of transmission occurring within the first 72 h at RT and 24 h at 37 ℃. In contrast, RSV remained viable for 1-2 days, while IAV persisted for only a few hours post-mortem. Viral decay rates were temperature-dependent and varied across tissues, demonstrating distinct post-mortem survival kinetics.

This study presents the first comprehensive analysis of viral persistence in cadavers, revealing prolonged SARS-CoV-2 stability compared to IAV and RSV. These findings underscore the need for enhanced post-mortem biosafety protocols to mitigate occupational exposure risks in forensic and clinical settings. By elucidating viral decay dynamics across environmental conditions, this research establishes a critical foundation for infection control strategies, informing biosafety policies for emerging respiratory pathogens.

Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To perform these often amazing tasks, proteins must move and we must think of them as dynamic ensembles of three dimensional structures formed first by folding the polypeptide chains so as to minimize the conflicts between the interactions of their constituent amino acids. It is apparent however that, even when completely folded, not all conflicting interactions have been resolved so the structure remains 'locally frustrated'. Over the last decades it has become clearer that this local frustration is not just a random accident but plays an essential part of the inner workings of protein molecules. We will review here the physical origins of the frustration concept and review evidence that local frustration is important for protein physiology, protein-protein recognition, catalysis and allostery. Also, we highlight examples showing how alterations in the local frustration patterns can be linked to distinct pathologies. Finally we explore the extensions of the impact of frustration in higher order levels of organization of systems including gene regulatory networks and the neural networks of the brain.

The zoonotic potential has been well studied for SARS-CoV-2 and its earlier variants, but the information for Omicron variants and SARS-CoV is lacking. In this study, we generated lentivirus-based pseudoviruses carrying spike protein (S) of SARS-CoV-2, parental and Omicron variants including BA.1.1, BA.4/5, XBB.1 and JN.1 to assess the entry into cells expressing human or animal ACE2 including dogs, cats and white-tailed deer. Using these pseudoviruses, along with pseudoviruses carrying S of MERS-CoV and SARS-CoV, we assessed the protease processing of these various S through western blotting, entry/inhibition assays, and fusion assays. The results showed that overall, pseudotyped viruses carrying each S of SARS-CoV-2 Omicron strains efficiently entered cells expressing human or animal ACE2 comparably (BA.1.1 and JN.1) or better (BA.4/5 and XBB.1) than those with parental strain. In addition, the entries of pseudotyped viruses carrying S of SARS-CoV were also efficient the cells expressing human or animal ACE2. The presence of TMPRSS2 significantly increased the entry of all tested pseudoviruses including those with S of MERS-CoV, SARS-CoV and SARS-CoV-2, with BA.1.1, JN1, and XBB.1 Omicron having the largest fold increase. When cathepsin inhibitors were examined to assess their inhibitory effects on entry of parental and Omicron variants, they were significantly less effective in the entry of Omicron variants compared to parent strain, suggesting Omicron strains do not depend on the endosomal route compared to parental strain.

SARS-CoV-2 undergoes continuous mutations during transmission, resulting in a variety of Omicron subvariants. Currently, SARS-CoV-2 BA.2.86 and its descendants JN.1, KP.2, KP.1.1 have been identified as the primary variants spreading globally. These emerging Omicron variants have increased transmissibility, potentially elevating the risk of viral reinfection in the population. However, the biological characteristics of newly-emerged Omicron subvariants in infecting host cells remain unclear. In this study, we assessed the neutralization effect of BA.2.86 and its descendant JN.1, as well as D614G, BA.2, BA.4/5, XBB.1.5, EG.5.1, HV.1, HK.3, JD.1.1 and JG.3 on convalescent sera obtained from individuals infected with BA.5 or XBB.1.5 strain. We evaluated the biological characteristics of variants spike proteins by measuring viral infectivity, affinity for receptors, and membrane fusion. Compared to XBB-related subvariants, BA.2.86 exhibited a diminished immune escape response, but JN.1 displayed a markedly augmented immune escape capability, which was closely related to its rapid transmission. BA.2.86 was less infectious in susceptible cells, while the JN.1 variant exhibited relatively high infectivity. Notably, BA.2.86 and JN.1 exhibited low fusion activity in 293 T-ACE2 cells, but relatively high fusogenicity in transmembrane protease serine 2 (TMPRSS2) overexpression cells. This study explored the evolutionary characteristics of emerging Omicron subvariants in host adaptation, and provided new strategies for the prevention and treatment of coronavirus disease 2019 (COVID-19).

The COVID-19 pandemic caused a major public health crisis, with severe impacts on global health and the economy. Machine learning (ML) has been crucial in developing new technologies to address challenges posed by the pandemic, particularly in identifying high-risk COVID-19 patients. This identification is vital for efficiently allocating hospital resources and controlling the virus's spread. Comprehensive validation of these intelligent approaches is necessary to confirm their clinical usefulness and help create future strategies for managing viral outbreaks. Here we present a prospective study to evaluate the performance of state-of-the-art ML models designed to identify high-risk COVID-19 patients across four clinical stages. Using artificial neural networks trained with historical patient data from Mexico, we assess the models' accuracy across six epidemiological waves without retraining them. We then compare their performance against neural networks trained with cumulative historical data up to the end of each wave. The findings reveal that models trained on early data can effectively predict high-risk patients in later waves, despite changes in vaccination rates, viral strains, and treatments. These results suggest that artificial intelligence-based patient classification methods could be robust tools for future pandemics, aiding in predicting clinical outcomes under evolving conditions.

The JAK family, particularly JAK3, plays a crucial role in immune signaling and inflammatory responses. Dysregulated JAK3 activation in SARS-CoV-2 infections has been associated with severe inflammation and respiratory complications, making JAK inhibitors a viable therapeutic option. However, their use raises concerns regarding immunosuppression, which could increase susceptibility to secondary infections. While long-term adverse effects are less of a concern in acute COVID-19 treatment, patient selection and monitoring remain critical. Furthermore, adverse effects associated with oral JAK3 inhibitors necessitate the exploration of alternative strategies to optimize therapeutic efficacy while minimizing risks. This review highlights the role of JAK3 in immune and epithelial cells, examines the adverse effects of oral JAK3 inhibitors in COVID-19 and other treatments, and discusses alternative therapeutic strategies for improving patient outcomes.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced impaired antiviral immunity and excessive inflammatory responses cause lethal pneumonia. However, the in vivo roles of key pattern recognition receptors that elicit protective antiviral and fatal inflammatory responses, specifically in the lungs, are not well described. Coronaviruses possess single-stranded RNA genome that activates TLR7/8 to induce an antiviral interferon (IFN) and robust inflammatory cytokine response. Here, using wild-type and TLR7-deficient (TLR7-/-) mice infected with mouse-adapted SARS-CoV-2 (MA-CoV-2), we examined the role of TLR7 in the lung antiviral and inflammatory response and severe pneumonia. We showed that TLR7 deficiency significantly increased lung virus loads and morbidity/mortality, which correlated with reduced levels of type I IFNs (Ifna/b), type III IFNs (Ifnl), and IFN-stimulated genes (ISGs) in the lungs. A detailed evaluation of MA-CoV-2-infected lungs revealed increased neutrophil accumulation and lung pathology in TLR7-/- mice. We further showed that blocking type I IFN receptor (IFNAR) signaling enhanced SARS-CoV-2 replication in the lungs and caused severe lung pathology, leading to 100% mortality compared to infected control mice. Moreover, immunohistochemical assessment of the lungs revealed increased numbers of SARS-CoV-2 antigen-positive macrophages, pneumocytes, and bronchial epithelial cells in TLR7-/- and IFNAR-deficient mice compared to control mice. In summary, we conclusively demonstrated that despite TLR7-induced robust lung inflammation, TLR7-induced IFN/ISG responses suppress lung virus replication and pathology and provide protection against SARS-CoV-2-induced fatal pneumonia. Additionally, given the similar disease outcomes in control, TLR7-/-, and IFNAR-deficient MA-CoV-2-infected mice and coronavirus disease 2019 (COVID-19) patients, we propose that MA-CoV-2-infected mice constitute an excellent model for studying COVID-19.IMPORTANCESevere coronavirus disease 2019 (COVID-19) is caused by a delicate balance between a strong antiviral and an exuberant inflammatory response. A robust antiviral immunity and regulated inflammation are protective, while a weak antiviral response and excessive inflammation are detrimental. However, the key host immune sensors that elicit protective antiviral and inflammatory responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge are poorly defined. Here, we examined the role of viral RNA-mediated TLR7 activation in the lung antiviral and inflammatory responses in SARS-CoV-2-infected mice. We demonstrate that TLR7 deficiency led to a high rate of morbidity and mortality, which correlated with an impaired antiviral interferon (IFN)-I/III response, enhanced lung virus replication, and severe lung pathology. Furthermore, we show that blocking IFN-I signaling using anti-IFN receptor antibody promoted SARS-CoV-2 replication in the lungs and caused severe disease. These results provide conclusive evidence that TLR7 and IFN-I receptor deficiencies lead to severe disease in mice, replicating clinical features observed in COVID-19 patients.

Despite the diminishing global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus continues to circulate and undergo mutations, posing ongoing challenges for public health. A comprehensive understanding of virus entry mechanisms is crucial for managing new epidemic strains. However, the cellular processes post-endocytosis remain largely unexplored. This study employs proximity labeling to examine proteins near ACE2 post-viral infection and identified syntaxin-6 (STX6) as a factor that inhibits SARS-CoV-2 infection by impeding the endocytic release of the virus. SARS-CoV-2 infection enhances early endosome recruitment of STX6. STX6 appears to hinder the maturation of viral particles-laden early endosomes into late endosomes, from which the virus could escape. Instead, it promotes the trafficking of the virus toward the autophagy-lysosomal degradation pathway. STX6 exhibits a broad-spectrum effect against various SARS-CoV-2 variants and several other viruses that enter via endocytosis. We report for the first time the function of STX6 as a restrictive factor in viral infection.IMPORTANCEVirus entry is the first step of the virus life cycle, and the exploitation of the endo-lysosome pathway for cellular entry by viruses has been well documented. Meanwhile, the intrinsic defense present within cells interferes with virus entry. We identified STX6 as a host restriction factor for viral entry by facilitating the virus trafficking to the autophagy-lysosomal degradation pathway. Notably, STX6 exhibits broad-spectrum antiviral activity against diverse severe acute respiratory syndrome coronavirus 2 variants and other viruses employing endocytosis for entry.

The main protease (Mpro) is essential for the replication of SARS-CoV-2, making it one of the major therapeutic targets for COVID-19 treatment. Here, we explored the conformational dynamics and energetics of the catalytic residue His41 in Mpro, as revealed by a rare conformational shift observed in the cocrystal structures of Mpro bound by certain inhibitors. Using steered molecular dynamics combined with umbrella sampling, we demonstrated that π-cation interactions between these inhibitors and the ionized catalytic dyad significantly reduced the energy barrier for the conformational flip of the His41 side chain. To further investigate the structure-activity relationship linked to this conformational change, we designed and synthesized a series of covalent inhibitors that control His41 flipping. Among these, compound H102-7 exhibited remarkable inhibitory activity with an IC50 of 5 nM. Drug resistance studies revealed that these inhibitors displayed improved resistance profiles compared to the clinically approved Mpro covalent inhibitor, Nirmatrelvir. This study integrates computational simulations, medicinal chemistry, and molecular biology to uncover an interesting allosteric effect of a key catalytic residue of SARS-CoV-2 Mpro and yields new promising molecules for the further development of Mpro-targeted therapeutic intervention.

To explore the association between perioperative SARS-CoV-2 infection and the postoperative complications during the breakout of the Omicron epidemic wave.

Observational retrospective cohort study. Multivariable logistic regression was performed to explore the association between the duration from surgery to COVID-19 diagnosis and the likelihood of postoperative complications.

A general hospital in China.

7927 patients aged 18 years and older who underwent surgical treatment between 1 December 2022 and 28 February 2023.

The outcome was a composite of postoperative adverse events that occurred within the initial 30 postoperative days.

Of all patients, 420 (11.76%) experienced postoperative complications. Compared with No COVID-19, preoperative COVID-19 within 1 week (pre-1w) exhibited a high risk of postoperative complications (adjusted OR (aOR), 2.67; 95% CI 1.50 to 4.78), followed by patients with pre-2w (aOR, 2.14; 95% CI 1.20 to 3.80). For patients with postoperative COVID-19 within 1 week (post-1w), the aOR was 2.48 (95% CI 1.48 to 4.13), followed by patients with post-2w (aOR 1.95; 95% CI 1.10 to 3.45), and those with post-3w (aOR 2.25; 95% CI 1.27 to 3.98). The risks of postoperative complications decreased roughly with the increase of the time interval between the surgery date and SARS-CoV-2 infection. Stratification analyses suggested that perioperative COVID-19 increased the risk of postoperative complications in older patients, smokers, those with comorbidities or experiencing moderate or severe COVID-19 symptoms.

Our findings reveal a significant time-dependent relationship between perioperative COVID-19 and postoperative complications, highlighting the importance of tailored preoperative risk evaluations, enhanced postoperative surveillance, and the implementation of effective postoperative COVID-19 prevention measures.

ChiCTR2300072473.

This narrative review examines the critical nexus between climate change, coronavirus emergence, and Long COVID-a triad that may shape public health outcomes for generations. Climate change disrupts ecological balances that have historically limited viral spillover events, creating novel interfaces between wildlife reservoirs and human populations. The coronavirus family presents particular concern due to its diversity, adaptability, and demonstrated capacity for cross-species transmission. With over 200 coronaviruses identified in bat populations alone, this vast reservoir of genetic diversity, combined with the family's propensity for recombination, creates substantial pandemic potential that climate disruption may further amplify. Long COVID has revealed another dimension of the coronavirus threat: the potential for significant chronic disease burden following acute infection. This complex multisystem condition affects a substantial portion of SARS-CoV-2 infected individuals, with mechanisms including viral persistence, autoimmunity, microclot formation, and mitochondrial dysfunction. Future projections suggest that climate change could increase global viral spillover risk by 30-45% by 2070, particularly in Southeast Asia, Central Africa, and parts of South America. Artificial intelligence offers promising tools for addressing these interconnected challenges through enhanced surveillance, accelerated therapeutic development, and optimized healthcare delivery. Understanding the climate-coronavirus-chronic illness nexus has become essential to the development of resilient health systems and effective planetary health policies face to an uncertain future.

Being widespread across the globe, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) keeps evolving and generating new variants and continuously poses threat to public health, especially to the population with chronic comorbidities. Diabetes mellitus is one of high-risk factors for severe outcome of coronavirus disease 2019 (COVID-19). Establishment of animal models that parallel the clinical and pathological features of COVID-19 complicated with diabetes is thus highly essential. Here, in this study, we constructed leptin receptor gene knockout hamsters with the phenotype of diabetes mellitus (db/db), and revealed that the diabetic hamsters were more susceptible to SARS-CoV-2 and its variants than wild-type hamsters. SARS-CoV-2 and its variants induced a stronger immune cytokine response in the lungs of diabetic hamsters than in wild-type hamsters. Comparative histopathology analyses also showed that infection of SARS-CoV-2 and the variants caused more severe lung tissue injury in diabetic hamsters, and may induce serious complications such as diabetic kidney disease and cardiac lesions. Our findings demonstrated that despite the decreased respiratory pathogenicity, the SARS-CoV-2 variants were still capable of impairing other organs such as kidney and heart in diabetic hamsters, suggesting that the risk of evolving SARS-CoV-2 variants to diabetic patients should never be neglected. This hamster model may help better understand the pathogenesis mechanism of severe COVID-19 in patients with diabetes. It will also aid in development and testing of effective therapeutics and prophylactic treatments against SARS-CoV-2 variants among these high-risk populations.

Zoonotic viruses originating from small mammals pose significant challenges to public health on a global scale. Insectivores, serving as natural reservoirs for a diverse array of zoonotic viruses, are known to carry a multitude of viral species. However, compared to the extensive research conducted on rodents (Rodentia) and bats (Chiroptera), the role of insectivores in harboring and transmitting unknown pathogens remains underexplored, which may lead to a severe underestimation of their contributions and impact to global public health.

This study employed a meta-transcriptomic approach to profile the viromes of 214 individual insectivores, encompassing 13 species from the families Soricidae, Erinaceidae, and Talpidae, collected across 12 counties in Yunnan Province, a recognized zoonotic hotspot. Based on virus reads, the analysis identified 42 viral families associated with vertebrates, highlighting significant virome diversity and host-specific viral tropisms among shrews, hedgehogs, and moles, along with notable geographic and environmental specificity of the viruses. Shrews exhibited greater viral richness and abundance compared to hedgehogs and moles, with variations influenced predominantly by host taxonomy, altitude, and geographic location. A total of 114 RNA-dependent RNA polymerase sequences were obtained, leading to the identification of 68 viruses, including 57 novel species. Instances of host jumping were observed in 11 viruses, with potential pathogenic viruses related to Mojiang paramyxovirus and members of the Hantaviridae family. Cross-species transmission was predominantly observed in viruses carried by shrews, while moles may play a pivotal role in facilitating viral transmission among insectivores.

This study enhances the understanding of the high diversity of mammalian viruses among insectivores in a relatively confined region and underscores the associations between virome composition and related zoonotic risks, providing a foundation for proactive measures to prevent and control the spillover of emerging zoonotic pathogens and potential future outbreaks. Video Abstract.

Infection and transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to pose a global public health concern. Using electromagnetic waves represents an alternative strategy to inactivate pathogenic viruses such as SARS-CoV-2. However, whether electromagnetic waves reduce SARS-CoV-2 infectivity is unclear. Here, we adapted a coplanar waveguide (CPW) to identify frequencies that could potentially neutralize SARS-CoV-2 virus-like particles (SC2-VLPs). Treatment of SC2-VLPs at frequencies between 2.5 and 3.5 GHz and an electric field of 413 V/m reduced infectivity. Exposure of SC2-VLPs to a frequency of 3.1 GHz -and to a lesser extent, 5.9 GHz- reduced their binding to antibodies targeting the SARS-CoV-2 Spike S1 receptor-binding domain (RBD) but did not alter the total levels of Spike, Nucleocapsid, Envelope, or Membrane proteins in virus particles. These results suggest that electromagnetic waves alter the conformation of Spike, thereby reducing viral attachment and entry. Overall, this data provides proof-of-concept in using electromagnetic waves for sanitation and prevention efforts to curb the transmission of SARS-CoV-2 and potentially other pathogenic enveloped viruses.

Neurological symptoms involving the central nervous system (CNS) and peripheral nervous system (PNS) are common complications of acute COVID-19 as well as post-COVID conditions. Most research into these neurological sequalae focuses on the CNS, disregarding the PNS. Guinea pigs were previously shown to be useful models of disease during the SARS-CoV-1 epidemic. However, their suitability for studying SARS-CoV-2 has not been experimentally demonstrated. To assess the suitability of guinea pigs as models for SARS-CoV-2 infection and the impact of SARS-CoV-2 infection on the PNS, and to determine routes of CNS invasion through the PNS, we intranasally infected wild-type Dunkin-Hartley guinea pigs with ancestral SARS-CoV-2 USA-WA1/2020. We assessed PNS sensory neurons (trigeminal ganglia, dorsal root ganglia), autonomic neurons (superior cervical ganglia), brain regions (olfactory bulb, brainstem, cerebellum, cortex, hippocampus), lungs, and blood for viral RNA (RT-qPCR), protein (immunostaining), and infectious virus (plaque assay) at three- and six-days post infection. We show that guinea pigs, which have previously been used as a model of SARS-CoV-1 pulmonary disease, are not susceptible to intranasal infection with ancestral SARS-CoV-2, and are not useful models in assessing neurological impacts of infection with SARS-CoV-2 isolates from the early pandemic.

To investigate the epidemiological and genetic features of common human coronaviruses (HCoVs) in Beijing in the context of the COVID-19 pandemic.

We collected clinical samples from patients with acute respiratory tract infections (ARTIs) in 35 sentinel hospitals from 2015 to 2023. HCoVs were detected via multiple real-time PCRs, and S gene sequencing and phylogenetic analysis were subsequently performed.

From 2015 to 2023, the combined detection rate of HCoVs was 1.55% (909/58,550). During the COVID-19 pandemic, a significant increase in HCoVs detection was observed (P < 0.001). Overall, the epidemic season of four HCoVs was from July to October, and each HCoV showed different epidemic seasons. Notably, HCoV-NL63 and HCoV-229E exhibited pronounced annual alternations in prevalence. The highest combined detection rates of HCoVs were in the ≥60 years age group (1.85%), followed by the 0-5 years age group (1.48%). HCoV-229E was more prevalent in patients with severe community-acquired pneumonia (sCAP) (P=0.001). Phylogenetic analyses revealed that the four HCoVs were subjected to negative selection pressure, and multiple high-frequency amino acid site mutations were observed. HCoV-229E formed an emerging lineage after 2021.

This nine-year multicenter study in Beijing systematically elucidated that the four HCoVs exhibit distinct epidemiological characteristics, susceptible populations, and common mutations in amino acid sites, especially in the context of COVID-19. Therefore, continuous epidemiological surveillance and genetic characterization studies are imperative for predictive warning and timely identification of emerging coronavirus.