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.

Since the emergence of Severe Acute Respiratory Syndrome (SARS) in 2002, bats have been recognized as important reservoirs of diverse coronaviruses (CoVs). Despite extensive research on the broad geographic transmission of bat CoVs, there is a notable gap in understanding the transmission dynamics within sympatric bat communities. Using a phylogeographic Bayesian statistical framework, we examined CoV transmission patterns and their determinants in a region where four bat roosting caves coexist and CoVs circulate persistently. Our findings reveal that two subgenera of CoVs, α-CoVs and β-CoVs dominate different bat caves at varying times. Notably, β-CoVs show more frequent cross-species transmission events among the dominant reservoir hosts, bats of Rhinolophidae. Phylogenetic distance between host species emerges as the key influence factor of viral cross-species transmission, whereas cohabitation duration and the number of hosts sharing caves do not significantly influence viral transmission. In addition, we emphasize that the compositional similarity of species in the roosting caves is critical for the inter-cave transmission of bat-CoVs, rather than the distance between cave. These results provide novel insights into the complex transmission dynamics of bat CoVs within sympatric bat communities.

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.

The human coronavirus HKU1 uses both sialoglycoconjugates and the protein transmembrane serine protease 2 (TMPRSS2) as receptors. Carbohydrate binding leads to the spike protein up conformation required for TMPRSS2 binding, an outcome suggesting a distinct mechanism for driving fusion of the viral and host cell membranes. Nevertheless, the conformational changes promoted by carbohydrate binding have not been fully elucidated and the basis for HKU1's carbohydrate binding specificity remains unknown. Reported here are high resolution cryo-EM structures of the HKU1 spike protein trimer in its apo form and in complex with the carbohydrate moiety of a candidate carbohydrate receptor, the 9-O-acetylated GD3 ganglioside. The structures show that the spike monomer can exist in four discrete conformational states and that progression through them would promote the up conformation upon carbohydrate binding. We also show that a six-amino-acid insert is a determinant of HKU1's specificity for gangliosides containing a 9-O-acetylated α2-8-linked disialic acid moiety and that HKU1 shows weak affinity for the 9-O-acetylated sialic acids found on decoy receptors such as mucins.

The Dinga Dinga Virus (DDV) has emerged as a mysterious disease gripping women in Uganda, raising alarm due to its unusual and distressing "dancing" like symptoms. These symptoms, characterized by involuntary movements resembling dance, suggest possible neurological involvement, though the exact pathogen remains unidentified. The causative agent for DDV is still unknown. We hypothesized that the possible microorganism could be a virus, bacteria, or vector-borne origin. Therefore, comprehensive research is urgently needed to confirm its cause.

We performed a comprehensive literature search in Scopus and Web of Science related to the different outbreaks of viruses. We collected relevant information from appropriate articles for this review.

The unique representation of the disease is spreading rapidly in localized areas that have the potential to escalate into a broader public health crisis. Preventive measures focused on symptom monitoring, public awareness, and isolation of suspected cases to limit transmission. Authorities emphasize hygiene practices, using personal protective equipment (PPE), and early reporting to manage the outbreak effectively. Simultaneously, global health organizations are being called to collaborate on diagnostic development, therapeutic interventions, and vaccine research. The disproportionate impact on women has brought social and cultural dynamics into the spotlight, as stigma and misinformation exacerbate the outbreak's challenges. Immediate and long-term strategies must address these aspects by strengthening healthcare infrastructure and enhancing disease surveillance systems.

As the world recovers from the COVID-19 pandemic, the DDV is a stark reminder of the ongoing threat of emerging infectious diseases. Proactive, science-driven efforts are critical to understanding and mitigating this enigmatic disease, ensuring it does not escalate into another global health crisis.

The continuous evolution of SARS-CoV-2 through accumulating mutations, combined with the persistent risk of zoonotic sarbecovirus transmission events, highlights the critical demand for broadly protective vaccines. Building on our previous findings that a heterodimeric receptor-binding domain (RBD) design substantially improves cross-reactive immunogenicity in vaccine candidates, we propose this strategy as a foundation for developing pan-sarbecovirus vaccines with cross-neutralizing capacity against diverse and emerging variants. In this study, we developed a sarbecovirus immunogen, utilizing a heterodimeric strategy incorporating the RBDs from both SARS-CoV and SARS-CoV-2. Pseudovirus neutralization assays revealed that mice immunized with the SARS-CoV-2 prototype (PT)-SARS-CoV heterodimer (PT-SARS) developed 39.9- to 305.6-fold higher neutralizing antibody (NAb) titers against SARS-CoV-2 sub-variants compared to the SARS-CoV RBD homodimer (SARS-SARS). Furthermore, PT-SARS elicited 17.6- and 31.2-fold enhanced neutralization against WIV1 and SARS-CoV, respectively, relative to the SARS-CoV-2 PT homodimer (PT-PT). To address evolving Omicron sub-variants, we further updated BA.1-SARS and BA.2-SARS immunogens. Notably, BA.2-SARS exhibited a 6.2-fold increase in neutralizing potency against BA.2.86 compared to PT-SARS. Crucially, the heterodimeric immunogen induced balanced and broadly reactive NAbs against multiple sarbecoviruses, including RaTG13, Pangolin GD, SARS-CoV, and SARS-CoV-2 variants/sub-variants, demonstrating its potential as a sarbecovirus immunogen candidate.

Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV) and porcine deltacoronavirus (PDCoV) cause highly contagious gastrointestinal damage to piglets with high coinfection in clinical. However, there is no available trivalent vaccine against the three viruses. Here, a trivalent subunit vaccine by combining PEDV-SCOE, TGEV-SAD, and PDCoV-RBD proteins with ISA 201 adjuvant was effectively prepared, and the immunogenicity was evaluated. The detection results showed that the vaccine induced specific humoral IgG, neutralizing antibodies, and increased levels of Th1 and Th2 cytokines. Splenocytes proliferation and specific cytotoxic T lymphocytes (CTL) were activated. Furthermore, the three antigenic proteins up-regulated CD4+ and CD8+ T lymphocytes, activated the germinal center (GC) through the Tfh-GC axis, and promoted the differentiation of GC B cells in to plasma cells and memory B cells. Overall, the three antigenic proteins will provide helpful information for further exploration of trivalent vaccines against PEDV, TGEV, and PDCoV.

Replicon RNA (RepRNA) represents a cutting-edge technology in the field of vaccinology, fundamentally transforming vaccine design and development. This innovative approach facilitates the induction of robust immune responses against a range of infectious diseases and cancers. RepRNA vaccines leverage the inherent capabilities of RNA-dependent RNA polymerase associated with self-replicating repRNA, allowing for extreme replication within host cells. This process enhances antigen production and subsequently stimulates adaptive immunity. Additionally, the generation of double-stranded RNA during RNA replication can activate innate immune responses. Numerous studies have demonstrated that repRNA vaccines elicit potent humoral and cellular immune responses that are broader and more durable than those generated by conventional mRNA vaccines. These significant immune responses have been shown to provide protection in various models for infectious diseases and cancers. This article will explore the design and delivery of RepRNA vaccines, the mechanisms of immune activation, preclinical studies addressing infectious diseases and tumors, and related clinical trials that focus on safety and immunogenicity.

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COVID-19, caused by SARS-CoV-2 virus, has emerged as a global threat to human health. The main protease (Mpro) of SARS-CoV-2 is an excellent target for the development of antiviral drugs against COVID-19, and various protease biosensors have been developed to evaluate anti-coronavirus drugs. However, the application of these protease biosensors was limited due to high background fluorescence, poor signal-to-noise ratios, and constraints in enzyme activity thresholds for accessing live viruses. In this study, we rationally designed a highly conserved Mpro cleavage site sequence among different coronaviruses (CoVs) with high proteolytic activity, and described an intracellular coronavirus Mpro proteolytic (ICMP) reporter system that takes advantage of virus-encoded Mpro expressed in infected cells to reform the NanoBiT fluorescent protein. The system can be used to visualize and identify cells infected with coronavirus, and demonstrated high compatibility with various Mpro proteins from 13 different mammalian coronaviruses (covering α, β, γ, and δ CoVs), exhibiting at least a 1,030-fold increase in luminescence. Stronger Nluc signals were detectable with CoV 229E virus infection at a MOI of 0.001. Additionally, the system proved suitable for evaluating and screening of antiviral compounds, including lufotrelvir, GC376, Nirmatrelvir, X77, MG-101, and the potential inhibitor Cynaroside. The ICMP system is not only an invaluable tool for the detection of live coronaviruses, but also for the discovery of antivirals against current and future pandemic coronaviruses.

SARS-CoV-2 variant recurrence has emphasized the imperative prerequisite for effective antivirals. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication, making it one of the prime and promising antiviral targets. Mpro features several druggable sites, including active sites and allosteric sites near the dimerization interface, that regulate its catalytic activity. This study identified six highly efficacious antiviral SARS-CoV-2 compounds (WIN-62577, KT185, bexarotene, ledipasvir, diacerein, and simepervir) using structure-based virtual screening of compound libraries against Mpro. Using SPR and ITC, the binding of selected inhibitory compounds to the target Mpro was validated. The FRET-based protease assay demonstrated that the identified molecules effectively inhibit Mpro with IC50 values in the range from 0.64 to 11.98 μM. Additionally, in vitro cell-based antiviral assays showed high efficacy with EC50 values in the range of 1.51 to 18.92 μM. The crystal structure of the Mpro-minocycline complex detailed the possible inhibition mechanism of minocycline, an FDA-approved antibiotic. Minocycline binds to an allosteric site, revealing residues critical for the loss of protease activity due to destabilization of molecular interactions at the dimeric interface, which are crucial for the proteolytic activity of Mpro. The study suggests that the binding of minocycline to the allosteric site may play a role in Mpro dimer destabilization and direct the rational design of minocycline derivatives as antiviral drugs.

Schizophrenia is a chronic and complex mental disorder resulting from interactions between cumulative and synergistic genetic and environmental factors. Viral infection during the prenatal stage constitutes one of the most relevant risk factors for the development of schizophrenia later in adulthood.

A narrative review was conducted to explore the link between viral infections and schizophrenia, as well as the neuropsychiatric effects of antiviral drugs, particularly in the context of this specific mental condition. Literature searches were performed using the PubMed, Scopus, and Web of Science databases.

Several viral infections, such as herpesviruses, influenza virus, Borna disease virus, and coronaviruses, can directly or indirectly disrupt normal fetal brain development by modifying gene expression in the maternal immune system, thereby contributing to the pathophysiological symptoms of schizophrenia. In addition, neuropsychiatric effects caused by antiviral drugs are frequent and represent significant adverse outcomes for viral treatment.

Epidemiological evidence suggests a potential relationship between viruses and schizophrenia. Increases in inflammatory cytokine levels and changes in the expression of key genes observed in several viral infections may constitute potential links between these viral infections and schizophrenia. Furthermore, antivirals may affect the central nervous system, although for most drugs, their mechanisms of action are still unclear, and a strong relationship between antivirals and schizophrenia has not yet been established.

To address the increasing demand for high-quality pork protein, it is essential to implement strategies that enhance diets and produce pigs with excellent production traits. Selective breeding and crossbreeding are the primary methods used for genetic improvement in modern agriculture. However, these methods face challenges due to long breeding cycles and the necessity for beneficial genetic variation associated with high-quality traits within the population. This limitation restricts the transfer of desirable alleles across different genera and species. This article systematically reviews past and current research advancements in porcine molecular breeding. It discusses the screening of clustered regularly interspaced short palindromic repeats (CRISPR) to identify resistance loci in swine and the challenges and future applications of genetically modified pigs.

The emergence of transgenic and gene editing technologies has prompted researchers to apply these methods to pig breeding. These advancements allow for alterations in the pig genome through various techniques, ranging from random integration into the genome to site-specific insertion and from target gene knockout (KO) to precise base and prime editing. As a result, numerous desirable traits, such as disease resistance, high meat yield, improved feed efficiency, reduced fat deposition, and lower environmental waste, can be achieved easily and effectively by genetic modification. These traits can serve as valuable resources to enhance swine breeding programmes.

In the era of genome editing, molecular breeding of pigs is critical to the future of agriculture. Long-term and multidomain analyses of genetically modified pigs by researchers, related policy development by regulatory agencies, and public awareness and acceptance of their safety are the keys to realizing the transition of genetically modified products from the laboratory to the market.

In the context of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), metabolic research has become crucial for in-depth exploration of viral infection mechanisms and in searching for therapeutic strategies. This paper summarizes the interrelationships between carbohydrate, lipid, and amino acid metabolism and COVID-19 infection, discussing their roles in infection progression. SARS-CoV-2 infection leads to insulin resistance and increased glycolysis, reducing glucose utilization and shifting metabolism to use fat as an energy source. Fat is crucial for viral replication, and imbalances in amino acid metabolism may interfere with immune regulation. Consequently, metabolic changes such as hyperglycemia, hypolipidemia, and deficiency of certain amino acids following SARS-CoV-2 infection can contribute to progression toward severe conditions. These metabolic pathways not only have potential value in prediction and diagnosis but also provide new perspectives for the development of therapeutic strategies. By monitoring metabolic changes, infection severity can be predicted early, and modulating these metabolic pathways may help reduce inflammatory responses, improve immune responses, and reduce the risk of thrombosis. Research on the relationship between metabolism and SARS-CoV-2 infection provides an important scientific basis for addressing the global challenge posed by COVID-19, however, further studies are needed to validate these findings and provide more effective strategies for disease control.

Globally, over 768 million confirmed cases and 6.9 million deaths had been documented as of July 17, 2023. Coronaviruses have a relatively large RNA genome. As with other viruses, SARS-CoV-2 does have an envelope film produced from host cells that are assisted by virally encoded glycoproteins that are required for infectivity, immunological assault, and viral particle production. Although the intermediate source of origin and transmission to humans is unexplained, rapid transmission from human to human has been established. This review focuses on the mechanistic framework for understanding the SARS-CoV-2 viral infection. Additionally, it discusses the origins and implications of COVID-19 using direct quotations from the published scientific literature to avoid misinterpretation of this catastrophic event that resulted in a massive loss of human life and impact on the global economy. The current available information unfolds large number of topics related with COVID-19 and/or the coronavirus (SARS-CoV-2) responsible of the disease. This review article also delves into the multifaceted aspects of COVID-19 and SARS-CoV-2, with a specific focus on a controversial yet essential issue: the possible association between SARS-CoV-2's origin and aldose reductase, an enzyme known for its role in diabetic retinopathy. Exploring this connection holds utmost significance, offering valuable insights into COVID-19's pathogenesis and unlocking new avenues for therapeutic interventions. It is important to trace back the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19).

Betacoronavirus is a causative agent of respiratory and enteric diseases in humans and animals. Several ruminants are recognized to be intermediate hosts in the transmission of emerging coronaviruses from reservoir hosts to humans. Here, we first report a novel Betacoronavirus isolated from goats suffering from diarrhea in China, putatively named caprine coronavirus (cpCoV). Full-genome characterization and nuclear acid comparisons demonstrated that this virus is an evolutionarily distinct Betacoronavirus belonging to the subgenus Embecovirus and is a Betacoronavirus 1 species. Notably, on phylogenetic trees based on complete genomes and RdRp, S, and N genes, the cpCoVs were grouped into a clade distinct from other Betacoronavirus strains and were closely related to the HKU23- and HKU23-associated coronaviruses. CpCoV possessed a unique genome organization with a truncated NS4a protein and an elongated NS4b protein that showed no significant matches in the GenBank database. The homology of the S and NS4a-4b genes between cpCoV and Embecovirus was less than 95%. Analysis revealed possible recombination events occurred during the evolution of cpCoV and HKU23, and there are striking similarities between the two viruses in evolutionary terms. In addition, cpCoV showed a narrow cell tropism, replicating in human- and bovine-origin cells in vitro, and caused diarrhea and enteric pathologic changes in goats and calves in vivo. We have provided epidemiological, virological, evolutionary, and experimental evidence that cpCoV is a novel etiological agent for enteric disease in goats. Evidently, a spilling-over event might have occurred between ruminants, including goats, camels, cattle, and wild animals. This study highlights the importance of identifying coronavirus diversity and inter-species transmission in ruminants worldwide, broadens our understanding of the ecology of coronaviruses, and aids in the prevention of animal-to-human transmission and outbreaks.

Human coronavirus 229E (HCoV-229E) is the earliest CoV found to infect humans. It binds to the human aminopeptidase N (hAPN) through the receptor binding domain (RBD) of its spike (S) protein to achieve host recognition. We present the cryo-electron microscopy structure of two HCoV-229E S protein in complex with a dimeric hAPN to provide structural insights on how the HCoV-229E S protein opens up its RBD to engage with its host receptor, information that is currently missing among alphacoronaviruses to which HCoV-229E belong. We quantitatively profile the glycosylation of HCoV-229E S protein and hAPN to deduce the glyco-shielding effects pertinent to antigenicity and host recognition. Finally, we present an atomic model of fully glycosylated HCoV-229E S in complex with hAPN anchored on their respective membrane bilayers to recapitulate the structural basis of the first step of host infection by HCoV-229E.

Maintenance of genomic integrity is a fundamental characteristic of viruses, however, RNA-dependent RNA Polymerase (RdRp) lacks exonuclease activity for proofreading. To facilitate genomic proofreading in viruses, an independent exonuclease domain assists RdRp to maintain fidelity during replication. In contrast to high fidelity in DNA viruses, RNA viruses have to evolve into new variants through comparatively delicate mutagenesis activity for genetic diversity. Coronavirideae, a family of single positive-stranded RNA (+ ssRNA) viruses, meticulously sustain a balance between genetic diversity and large-size RNA genome. In coronaviruses, the proofreading activity is accomplished by an exonuclease (ExoN) domain located at the N-terminal of non-structural protein 14 (nsp14). ExoN is responsible for the new variants and antiviral resistance towards nucleotide analogs. Here, we provide an evolutionary characterization of ExoN by using a well-defined phylogenetic pipeline and structural analysis based on host and habitat. We carried out a phylogenetic analysis on ExoN, methyltransferase domain, nsp14, and whole genomes of ExoN-containing viruses. Furthermore, a three-dimensional structural comparison of the ExoN domain from various sources is also carried out to understand structural preservation. Our study has unveiled the evolutionary trajectories and structural conservation of the ExoN domain within the Coronaviridae family, highlighting its distinct evolutionary path independent of other domains. Structural analyses revealed minimal variance in RMSD values, underscoring the conserved nature of ExoN despite diverse ecological settings.

In 2021, at the height of the COVID-19 pandemic, coronavirus research spiked, with over 83,000 original research articles related to the word "coronavirus" added to the online resource PubMed. Just 2 years later, in 2023, only 30,900 original research articles related to the word "coronavirus" were added. While, irrefutably, the funding of coronavirus research drastically decreased, a possible explanation for the decrease in interest in coronavirus research is that projects on SARS-CoV-2, the causative agent of COVID-19, halted due to the challenge of establishing a good cellular or animal model system. Most laboratories do not have the capabilities to culture SARS-CoV-2 'in house' as this requires a Biosafety Level (BSL) 3 laboratory. Until recently, BSL 2 laboratory research on endemic coronaviruses was arduous due to the low cytopathic effect in isolated cell culture infection models and the lack of means to quantify viral loads. The purpose of this review article is to compare the human coronaviruses and provide an assessment of the latest techniques that use the endemic coronaviruses-HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1-as lower-biosafety-risk models for the more pathogenic coronaviruses-SARS-CoV-2, SARS-CoV, and MERS-CoV.

Coronaviruses (CoVs) are a diverse group of RNA viruses that cause respiratory and gastrointestinal diseases in humans and animals. Over the past two decades, outbreaks of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and bovine coronavirus (BCoV) have affected animal populations, especially in regions with close animal-human interactions, such as the Arabian Peninsula and Iraq. Given the potential for zoonotic transmission, understanding the prevalence and spread of CoVs among livestock is essential for managing potential risks to animal and human health.

This study aimed to investigate the prevalence of MERS-CoV in camels and BCoV in bovines within the Wasit Governorate of Iraq to assess the infection rates and potential interspecies transmission risks.

One hundred and fifty nasal swab samples (75 from camels and 75 from bovines) were collected between November 2022 and April 2023. The samples were analyzed for the presence of MERS-CoV and BCoV using real- time quantitative reverse transcription PCR (qRT-PCR) targeting the nucleocapsid (N) gene for each virus. Standard procedures for RNA extraction were followed, and qRT-PCR assays were conducted using specific primers to ensure high sensitivity and specificity.

MERS-CoV was present in (42%) of the camel samples, whereas BCoV was detected in (34%) of the bovine samples. Statistical analysis indicated a significant difference (p < 0.05) in infection rates between camels and bovines, with a higher prevalence observed in camels. The clinical signs observed in infected camels included fever, nasal discharge, and appetite loss, whereas infected bovines exhibited symptoms such as diarrhea and respiratory distress.

The high prevalence of MERS-CoV and BCoV in camels and bovines in the Wasit region indicates a substantial risk for the continued spread of these viruses within animal populations. These findings underscore the importance of surveillance and biosecurity measures to control the spread of coronavirus among livestock, potentially reducing zoonotic transmission risks. Further research is required to understand the transmission dynamics of CoVs in mixed livestock farming systems.

HCoV-HKU1 diversity and evolution were scarcely studied. We performed next-generation sequencing (NGS) and analysis of HCoV-HKU1 genomes over 5 years. NGS used Illumina technology on NovaSeq 6000 following whole genome PCR amplification by an in-house set of primers designed using Gemi and PrimalScheme. Genome assembly and analyses used CLC Genomics, Mafft, BioEdit, Nextstrain, Nextclade, MEGA, and iTol bioinformatic tools. Spike molecular modeling and dynamics simulations used Molegro Molecular Viewer and Hyperchem programs. Twenty-eight PCR systems allowed obtaining 158 HCoV-HKU1 genomes including 69 and 89 of genotypes A and B, respectively. Both genotypes co-circulated during the study period but one predominated each year. A total of 1683 amino acid substitutions including 80 in ≥ 10 genomes were detected in genotype A relatively to a 2004 reference. H512R in spike, first detected in 2009 and reported as involved in antibody neutralization, was found in all genotype A, almost always with V387I and K478N, and was predicted here to significantly improve cellular TMPRSS2 protein binding. Also, 1802 amino acid substitutions including 64 in ≥ 10 genomes were detected in genotype B relatively to a 2005 reference. This study substantially expands the global set of HCoV-HKU1 genomes. Genomics with protein structural analyses contributed to our understanding of HCoV-HKU1 evolution.

The transmission bottleneck, defined as the number of viruses shed from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission bottleneck remains poorly characterized. We adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes, infected donor hamsters with this pool, and exposed contact hamsters to paired infected donors, varying the duration and route of exposure. Following exposure, the nasal turbinates, trachea, and lungs were collected and the number of barcodes in each tissue was enumerated. We found that longer and more direct exposures increased the transmission bottleneck and that the upper airway is the primary source of transmitted virus in this model. Together, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission.

Future pandemic threats may be caused by novel coronaviruses and influenza A viruses. Here we show that when directly added to a cell culture, 12mer guanine RNA (G12) and its phosphorothioate-linked derivatives (G12(S)), rapidly entered cytoplasm and suppressed the propagation of human coronaviruses and influenza A viruses to between 1/100 and nearly 1/1000 of normal virus infectivity without cellular toxicity and induction of innate immunity. Moreover, G12(S) alleviated the weight loss caused by coronavirus infection in mice. G12(S) might exhibit a stable G-tetrad with left-handed parallel-stranded G-quadruplex, and inhibit the replication process by impeding interaction between viral nucleoproteins and viral RNA in the cytoplasm. Unlike previous antiviral strategies that target the G-quadruplexes of the viral genome, we now show that excess exogenous G-quadruplex-forming small RNA displaces genomic RNA from ribonucleoprotein, effectively inhibiting viral replication. The approach has the potential to facilitate the creation of versatile middle-molecule antivirals featuring lipid nanoparticle-free delivery.

The 2019 COVID-19 pandemic had a global impact, leading to numerous deaths, long recovery times, and economic challenges worldwide, especially in countries with limited financial resources like Ethiopia. In Ethiopia, Hawassa lacks viral shedding information. Identifying predictors can help ease economic impact of illness.Therefore, this research aimed to examine the demographics, clinical features, and recovery time of COVID-19 patients, as well as determine predictive markers for severe adverse outcomes.

Study at Hawassa University Comprehensive Speciality Hospital COVID-19 quarantine and therapy facility in Ethiopia (Sep 24, 2020 - Nov 26, 2021) with 804 patients. Extracted clinical, epidemiological, demographic info from medical records. Researchers used statistical tests like T tests, Chi-square tests, and Fisher's exact tests to analyze relationships between variables. They also used a Cox PH model to identify risk factors for COVID-19 patient recovery time. Significance level was set at 0.05 for all analyses.

Out of 804 COVID-19 patients, 74% recovered at an average age of 44.8 years, with 64.1% being male. Severe and critical cases were 24.1% and 21.4% of the population, respectively, with only 16.0% of critical cases and 19.5% of severe cases recovering. Average length of stay was 12.3 days. 88.4% of recovered patients had symptoms, with chest pain (66.7%), cough (64.4%), shortness of breath (59.2%), and fever (57.1%) being common. Nearly half had comorbidities, with diabetes (15.9%) and hypertension (15.2%) prevalent. Male patients had higher recovery rates, while severe/critical patients had lower rates. Patients over 39 age category had lower recovery chance. Existence of at least one comorbidities, diabetes, fever, and hypertension impacted recovery. Fever with gender and shortness of breath affected recovery. Assumptions were met with no multicollinearity.

Recent studies found that about 95% of COVID-19 patients recover within 30 days, with a median of 12 days. Severe cases, elderly, and those with comorbidities may take longer to recover. By effectively managing hypertension and diabetes, individuals can improve their prognosis and facilitate a quicker recovery. Public health concerns persist regarding COVID-19, especially for comorbidities like diabetic and hypertension. Early detection of fever and treatment of hypertension may expedite recovery.

The continued evolution of SARS-CoV-2 variants capable of subverting vaccine and infection-induced immunity suggests the advantage of a broadly protective vaccine against betacoronaviruses (β-CoVs). Recent studies have isolated monoclonal antibodies (mAbs) from SARS-CoV-2 recovered-vaccinated donors capable of neutralizing many variants of SARS-CoV-2 and other β-CoVs. Many of these mAbs target the conserved S2 stem region of the SARS-CoV-2 spike protein, rather than the receptor binding domain contained within S1 primarily targeted by current SARS-CoV-2 vaccines. One of these S2-directed mAbs, CC40.8, has demonstrated protective efficacy in small animal models against SARS-CoV-2 challenge. As the next step in the pre-clinical testing of S2-directed antibodies as a strategy to protect from SARS-CoV-2 infection, we evaluated the in vivo efficacy of CC40.8 in a clinically relevant non-human primate model by conducting passive antibody transfer to rhesus macaques (RM) followed by SARS-CoV-2 challenge. CC40.8 mAb was intravenously infused at 10mg/kg, 1mg/kg, or 0.1 mg/kg into groups (n = 6) of RM, alongside one group that received a control antibody (PGT121). Viral loads in the lower airway were significantly reduced in animals receiving higher doses of CC40.8. We observed a significant reduction in inflammatory cytokines and macrophages within the lower airway of animals infused with 10mg/kg and 1mg/kg doses of CC40.8. Viral genome sequencing demonstrated a lack of escape mutations in the CC40.8 epitope. Collectively, these data demonstrate the protective efficiency of broadly neutralizing S2-targeting antibodies against SARS-CoV-2 infection within the lower airway while providing critical preclinical work necessary for the development of pan-β-CoV vaccines.

The molecular mechanisms regulating coronavirus pathogenesis are complex, including virus-host interactions associated with replication and innate immune control. However, some genetic and epigenetic conditions associated with comorbidities increase the risk of hospitalization and can prove fatal in infected patients. This systematic review will provide insight into host genetic and epigenetic factors that interfere with COVID-19 expression in light of available evidence.

This study conducted a systematic review to examine the genetic and epigenetic susceptibility to COVID-19 using a comprehensive approach. Through systematic searches and applying relevant keywords across prominent online databases, including Scopus, PubMed, Web of Science, and Science Direct, we compiled all pertinent papers and reports published in English between December 2019 and June 2023.

The findings reveal that the host's HLA genotype plays a substantial role in determining how viral protein antigens are showcased and the subsequent immune system reaction to these antigens. Within females, genes responsible for immune system regulation are found on the X chromosome, resulting in reduced viral load and inflammation levels when contrasted with males. Possessing blood group A may contribute to an increased susceptibility to contracting COVID-19 as well as a heightened risk of mortality associated with the disease. The capacity of SARS-CoV-2 involves inhibiting the antiviral interferon (IFN) reactions, resulting in uncontrolled viral multiplication.

There is a notable absence of research into the gender-related predisposition to infection, necessitating a thorough examination. According to the available literature, a significant portion of individuals affected by the ailment or displaying severe ramifications already had suppressed immune systems, categorizing them as a group with elevated risk.

Porcine deltacoronavirus (PDCoV) and transmissible gastroenteritis coronavirus (TGEV), the two causative agents of porcine diarrhea, have been reported to be at risk of cross-species transmission, including to humans. However, the potential host range in which these two CoVs interact remains unclear. We screened 16 animal counterparts for porcine aminopeptidase N (APN), the receptor of PDCoV and TGEV, and found that APNs from eight of 17 animals could bind to the receptor-binding domains (RBDs) of PDCoV and TGEV. Furthermore, the animal APNs that could bind to the RBDs could mediate cellular infection by both viruses. Dog APN (dAPN) has been identified as the animal receptor with the highest capability to mediate the virus infection. We further resolved the complex structures of dAPN bound to the PDCoV RBD/TGEV RBD, respectively, establishing its divergent receptor-binding modes. We identified R325 of dAPN as an important residue in the PDCoV RBD-dAPN interaction, and found the central role of Q746 and T749 in dAPN in the interaction with the TGEV RBD. These findings provide the molecular basis of the potential cross-species transmission of these two porcine CoVs and shed light on future surveillance of these CoVs.

To investigate determinants of new onset diabetes after COVID-19 (NODAC) and its recovery at 6 months.

This was an observational follow up study conducted from August, 2020 to July, 2023, recruiting patients with preexisting DM and COVID 19 patients with no history of DM. Multivariate regression analysis was used to determine the factors responsible for severity of COVID 19 infection in preexisting DM group. Clinical, laboratory and glycometabolic parameters were estimated at baseline and 6 months in NODAC and euglycemic group to determine the factors responsible for NODAC and its persistence at 6 months.

Of 1310 patients, 855 (65.3%) COVID 19 patients were further divided based on their glycemic status: preexisting DM (19%), NODAC (8.5%) and euglycemia (72.5%). Older age and male gender were independent risk factors for severe COVID 19 disease in patients with preexisting diabetes. Prevalence of NODAC in present study was 8.5%. Patients with NODAC had higher mean fasting blood glucose (FBG), random blood glucose (RBG) and HbA1c at baseline as compared to COVID with euglycemic group with no difference in serum C-peptide levels. Female gender, family history of DM, signs of insulin resistance, higher BMI, WHR, HbA1c, serum insulin levels, FBG and RBG predicted persistence of NODAC at 6 months.

Preexisting DM is a risk factor for severe COVID 19 disease. Patients with NODAC have evidence of persistence insulin resistance on follow up, underscoring the need for long term glycemic monitoring.

Multinucleated cells are present in lung tissues of patients infected by SARS-CoV-2. Although the spike protein can cause the fusion of infected cells and ACE2-expressing cells to form syncytia and induce damage, how host cell responses to this damage and the role of DNA damage response (DDR) signals in cell fusion are still unclear. Therefore, we investigated the effect of SARS-CoV-2 spike protein on the fusion of homologous and heterologous cells expressing ACE2 in vitro models, focusing on the protein levels of ATR and ATM, the major kinases responding to DNA damage, and their substrates CHK1 and CHK2. We found that both homologous and heterologous cell fusion activated the ATR-CHK1 and ATM-CHK2 signaling axis and induced the aggregation of γH2AX, 53BP1 and RAD51 in syncytia. In addition, siRNA or inhibitors of ATM and ATR suppressed syncytia formation by decreasing the level of S protein. These results showed the important role of DDR in stabilizing the S protein and in favoring its induction of cell fusion and syncytium formation, suggesting that the virus exploits the host DDR to facilitate its spread among infected cells.

The SARS-CoV-2 is the causative agent of COVID-19 whose evolutionary path with geographical context forms the focus of present study. The first reported sequence from each of the 161 countries was downloaded from the GISAID database. Multiple sequence alignment was performed using MAFFT v.7, and a TCS-based network was constructed using PopART v.1.7. A total of 27 proteins were analyzed including structural and non-structural proteins. NSP3 and NSP12, responsible for viral replication and RNA synthesis, respectively, had the highest mutation incidence and frequency among non-structural proteins. The spike (S) protein, critical for viral attachment and entry, had the highest prevalence and frequency of mutations. ORF3a had the highest mutation incidence and frequency among accessory proteins. The phylogeogenomic network identified six haplogroups containing 35 sequences, while the remaining sequences belonged to different haplotypes. The virus's genetic distinctiveness was higher in European genomes, with four haplogroups dominated by Europe-linked sequences. The triangular-shaped pattern observed in the virus's evolutionary path suggests that it spread to different continents from Asia. Multiple transmission pathways connecting different countries affirm the virus's ability to emerge in multiple countries by early 2020. The possibility of new species emergence through "saltation" due to the pandemic is also discussed.

3CLPro is crucial to the life cycle of SARS-CoV-2 and exhibits high sequence similarity with other coronaviruses, while being absent in human proteases. This makes it an ideal target for developing broad-spectrum antiviral drugs. Ensitrelvir (S-217622) is the only launched non-covalent, non-peptidomimetic 3CLPro inhibitor, offering certain advantages in terms of dosage and metabolism. Using S-217622 as the lead, we designed and synthesized 43 pyrimidone derivatives and conducted a systematic evaluation of their structure-activity relationships. Among them, A36 exhibited strong inhibitory activity against several β-coronaviruses and demonstrated low cytotoxicity. A36 also displayed moderate stability in mouse liver microsomes. Co-crystal structure analysis of 3CLPro in complex with A36 revealed the similar binding mode with S-217622. A36 shows strong potential as a promising lead for broad-spectrum anti-coronavirus therapy, warranting further investigation.

Infectious laryngotracheitis (ILT) is a highly contagious disease, usually controlled by vaccination with live attenuated vaccines. However, the latent infection and adverse reactions caused by the live attenuated vaccines against infectious laryngotracheitis virus (ILTV) have limited its use in poultry. Infectious bronchitis virus (IBV) is considered a potential vector for vaccine development, but the issue of poor stability in recombinant IBV expressing foreign genes has not yet been resolved. In this study, we designed a multi-epitope cassette (gD-T/B) containing multiple T and B cell epitopes of ILTV gD protein. The genetic stability of the full-length gD gene and the gD-T/B multi-epitope cassette replacing non-essential genes in IBV was systematically analyzed. We found that, at the same insertion site, the stability of inserting gD-T/B multi-epitope cassette was consistently higher compared to the full-length gD gene. This difference may be related to the presence of more signals affecting virus replication or transcription in larger heterologous genes. In addition, the stability of recombinant IBV varied depending on the genome region being replaced. When the gene 5 was replaced, rH120-Δ5ab-gD-T/B was maintained up to at least passage 20 (P20). Compared with the parental virus H120 strain, rH120-Δ5ab-gD-T/B showed similar growth kinetics. Clinical observations and scoring of clinical signs in the vaccination-challenge experiment showed that rH120-Δ5ab-gD-T/B provided 90% protection against virulent ILTV, effectively alleviating clinical signs caused by infection with a virulent strain of ILTV. Furthermore, rH120-Δ5ab-gD-T/B significantly reduced the replication and shedding of ILTV in the trachea. Overall, this study suggests that rH120-Δ5ab-gD-T/B is a promising candidate vaccine against ILTV.