Ecological drivers of evolution of swine influenza in the United States: a review

Influenza A viruses (IAVs) pose a major public health threat due to their wide host range and pandemic potential. Pigs have been proposed as "mixing vessels" for avian, swine, and human IAVs, significantly contributing to influenza ecology. In the United States, IAVs are enzootic in commercial swine farming operations, with numerous genetic and antigenic IAV variants having emerged in the past two decades. However, the dynamics of intensive swine farming systems and their interactions with ecological factors influencing IAV evolution have not been systematically analysed. This review examines the evolution of swine IAVs in commercial farms, highlighting the role of multilevel ecological factors. A total of 61 articles published after 2000 were reviewed, with most studies conducted after 2009 in Midwestern US, followed by Southeast and South-central US. The findings reveal that ecological factors at multiple spatial scales, such as regional transportation networks, interconnectedness of swine operations, farm environments, and presence of high-density, low-genetic diversity herds, can facilitate virus transmission and enhance virus evolution. Additionally, interactions at various interfaces, such as between commercial swine and feral swine, humans, or wild birds contribute to the increase in genetic diversity of swine IAVs. The review underscores the need for comprehensive studies and improved data collection to better understand the ecological dynamics influencing swine IAV evolution. This understanding is crucial for mitigating disease burden in swine production and reducing the risk of zoonotic influenza outbreaks.

The highly pathogenic strain of porcine deltacoronavirus disrupts the intestinal barrier and causes diarrhea in newborn piglets

Porcine deltacoronavirus (PDCoV) is increasingly prevalent in newborn piglets with diarrhea. With the development of research on the virus and the feasibility of PDCoV cross-species transmission, the biosafety and the development of pig industry have been greatly affected. In this study, a PDCoV strain CH/LNFX/2022 was isolated from diarrheal newborn piglets at a farm in China. A genome-wide based phylogenetic analysis suggests that 97.5% to 99.2% homology existed in the whole genomes of other strains. Five amino acid mutations are seen for the first time in the S protein. By constructing 3D models, it was found that the S1-NTD/CTD and S2-HR-C regions produced structural alterations. Protein functional analysis showed that the structural changes of the three regions changed the epitope of S protein, the O-GalNAc glycosylation site and the 3C-like protease cleavage site. In addition, oral administration of 107 TCID50 CH/LNFX/2022 to newborn piglets successfully reproduced obvious clinical signs of piglets, such as diarrhea and dehydration. Meanwhile, PDCoV antigen was detected by immunofluorescence in the small intestine, and microscopic lesions and intestinal mucosal barrier destruction were detected by histological observation and scanning electron microscopy. Our study confirmed that porcine coronavirus strains increased pathogenicity through evolution, damaged the intestinal barrier of newborn piglets, and caused diarrhea in pigs. This study provided the candidate strains and theoretical basis for establishing the prevention and control system of vaccine and diagnostic methods for piglet diarrhea.

Precursor of H-type II histo-blood group antigen and subterminal sialic acids on gangliosides are significantly implicated in cell entry and infection by a porcine P[11] rotavirus

Rotaviruses, non-enveloped viruses with a double-stranded RNA genome, are the leading etiological pathogen of acute gastroenteritis in young children and animals. The P[11] genotype of rotaviruses exhibits a tropism for neonates. In the present study, a binding assay using synthetic oligosaccharides demonstrated that the VP8* protein of P[11] porcine rotavirus (PRV) strain 4555 binds to lacto-N-neotetraose (LNnT) with the sequence Galβ1,4-GlcNAcβ1,3-Galβ1,4-Glc, one of the core parts of histo-blood group antigen (HBGA) and milk glycans. However, infections were significantly inhibited by blocking of endogenous monosialoganglioside (GM) GM1a with cholera toxin B subunit and preincubation of the virus with exogenous GM1a, suggesting that GM1a is involved in the infection of P[11] PRV 4555. In addition to GM1a, preincubation of the virus with exogenous disialogangliosides (GD) GD1a, GD1b, and trisialoganglioside (GT) GT1b also prevented infection. In contrast, exogenous ganglioside GM3 only inhibited infections at an early time point, and exogenous asyalosphingolipids GA1 and LacCer did not show any inhibitory effect on infections. This indicates that P[11] PRV 4555 preferentially utilizes gangliosides containing subterminal sialic acids. Further experiments revealed that P[11] PRV 4555 infections were prevented by preincubation of the virus with Neu5Ac and Neu5Gc. These results confirmed that sialic acids are essential for P[11] PRV 4555 cell entry, despite the classification as NA-resistant strain. Overall, our results proved that P[11] rotavirus not only binds to the Gal-GlcNAc motif but also utilizes gangliosides containing subterminal sialic acids.

Umbrella review of the safety of Chikungunya vaccine platforms used in other vaccines

Chikungunya virus (CHIKV), transmitted through Aedes mosquitoes, is a significant global health concern. Various vaccine platforms have been explored to combat CHIKV, including formalin inactivation, live-attenuated strains, virus-like particles (VLPs), viral vectors, and mRNA technologies. This umbrella review synthesizes evidence on the safety profiles of vaccine platforms used in Chikungunya vaccines that have been applied in other vaccines, focusing on adverse events of special interest (AESI) in pregnant persons, children, and adolescents. A comprehensive overview of systematic reviews (SRs) was conducted. Results: Seven systematic reviews were included and complemented with primary studies. Vaccines like influenza, human papillomavirus (HPV), and COVID-19, which share platforms with Chikungunya vaccines, showed no significant increase in AESI. Moderate-to high-quality SRs supported favorable safety profiles. Vaccines sharing platforms with Chikungunya vaccines generally exhibit acceptable safety profiles in pregnant persons, children, and adolescents.

Diagnostic investigation of porcine hemagglutinating encephalomyelitis virus as potential pathogen associated with respiratory clinical signs and pulmonary lesions in pigs

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.

Coinfection with bacterial pathogens and genetic modification of PRRSV-2 for suppression of NF-κB and attenuation of proinflammatory responses

Porcine reproductive and respiratory syndrome virus (PRRSV) infects pulmonary alveolar macrophages and induces inflammation in the respiratory system. In swine farms, coinfection with PRRSV and bacterial pathogens is common and can result in clinically complicated outcomes, including porcine respiratory disease complex. Coinfection can cause excessive expressions of proinflammatory mediators and may lead to cytokine-storm-like syndrome. An immunological hallmark of PRRSV-2 is the bidirectional regulation of NF-κB with the nucleocapsid (N) protein identified as the NF-κB activator. We generated an NF-κB-silencing mutant PRRSV-2 by mutating the N gene to block its binding to PIAS1 [protein inhibitor of activated STAT-1 (signal transducer and activator of transcription 1)]. PIAS1 functions as an NF-κB repressor, and thus, the PIAS1-binding modified N-mutant PRRSV-2 became NF-κB activation-resistant in its phenotype. During coinfection of pigs with PRRSV-2 and Streptococcus suis, the N-mutant PRRSV-2 decreased the expression of proinflammatory cytokines and showed clinical attenuation. This review describes the coinfection of pigs with various pathogens, the generation of mutant PRRSV for NF-κB suppression, inflammatory profiles during bacterial coinfection, and the potential application of these findings to designing a new vaccine candidate for PRRSV-2.

The consequences of SARS-CoV-2 within-host persistence

SARS-CoV-2 causes an acute respiratory tract infection that resolves in most people in less than a month. Yet some people with severely weakened immune systems fail to clear the virus, leading to persistent infections with high viral titres in the respiratory tract. In a subset of cases, persistent SARS-CoV-2 replication results in an accelerated accumulation of adaptive mutations that confer escape from neutralizing antibodies and enhance cellular infection. This may lead to the evolution of extensively mutated SARS-CoV-2 variants and introduce an element of chance into the timing of variant evolution, as variant formation may depend on evolution in a single person. Whether long COVID is also caused by persistence of replicating SARS-CoV-2 is controversial. One line of evidence is detection of SARS-CoV-2 RNA and proteins in different body compartments long after SARS-CoV-2 infection has cleared from the upper respiratory tract. However, thus far, no replication competent virus has been cultured from individuals with long COVID who are immunocompetent. In this Review, we consider mechanisms of viral persistence, intra-host evolution in persistent infections, the connection of persistent infections with SARS-CoV-2 variants and the possible role of SARS-CoV-2 persistence in long COVID. Understanding persistent infections may therefore resolve much of what is still unclear in COVID-19 pathophysiology, with possible implications for other emerging viruses.

SARS-CoV-2 Vaccines and Multiple Sclerosis: An Update

The highly contagious zoonosis coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a pandemic by the World Health Organization on March 11, 2020, and has led to a global health crisis with nearly 777 million confirmed infections and over 7 million deaths worldwide by November 10, 2024.1-3 Over time, various variants emerged, with Omicron and its sublines dominating the world over the past 3 years.4 In addition, there is increasing evidence regarding the immune response of SARS-CoV-2 vaccines, especially for people with multiple sclerosis (MS) receiving disease-modifying therapies. Hence, with this review, we aim to provide an updated overview and recommendations for clinical practice regarding MS and SARS-CoV-2 vaccines, including efficacy and safety, SARS-CoV-2 variants, vaccine hesitancy, and the immune response under treatment with respective disease-modifying therapies.

Population and pan-genomic analyses of Staphylococcus pseudintermedius identify geographic distinctions in accessory gene content and novel loci associated with AMR

Staphylococcus pseudintermedius is a common representative of the normal skin microbiota of dogs and cats but is also a causative agent of a variety of infections. Although primarily a canine/feline bacterium, recent studies suggest an expanded host range including humans. This paper details population genomic analyses of the largest yet assembled and sequenced collection of S. pseudintermedius isolates from across the USA and Canada and assesses these isolates within a larger global population genetic context. We then employ a pan-genome-wide association study analysis of over 1,700 S. pseudintermedius isolates from sick dogs and cats, covering the period 2017-2020, correlating loci at a genome-wide level, with in vitro susceptibility data for 23 different antibiotics. We find no evidence from either core genome phylogenies or accessory genome content for separate lineages colonizing cats or dogs. Some core genome geographic clustering was evident on a global scale, and accessory gene content was noticeably different between various regions, some of which could be linked to known antimicrobial resistance (AMR) loci for certain classes of antibiotics (e.g., aminoglycosides). Analysis of genes correlated with AMR was divided into different categories, depending on whether they were known resistance mechanisms, on a plasmid, or a putatively novel resistance mechanism on the chromosome. We discuss several novel chromosomal candidates for follow-up laboratory experimentation, including, for example, a bacteriocin (subtilosin), for which the same protein from Bacillus subtilis has been shown to be active against Staphylococcus aureus infections, and for which the operon, present in closely related Staphylococcus species, is absent in S. aureus.IMPORTANCEStaphylococcus pseudintermedius is an important causative agent of a variety of canine and feline infections, with recent studies suggesting an expanded host range, including humans. This paper presents global population genomic data and analysis of the largest set yet sequenced for this organism, covering the USA and Canada as well as more globally. It also presents analysis of in vitro antibiotic susceptibility testing results for the North American (NA) isolates, as well as genetic analysis for the global set. We conduct a pan-genome-wide association study analysis of over 1,700 S. pseudintermedius isolates from sick dogs and cats from NA to correlate loci at a genome-wide level with the in vitro susceptibility data for 23 different antibiotics. We discuss several chromosomal loci arising from this analysis for follow-up laboratory experimentation. This study should provide insight regarding the development of novel molecular treatments for an organism of both veterinary and, increasingly, human medical concern.

Molecular characteristics of the immune escape of coronavirus PEDV under the pressure of vaccine immunity

Coronaviruses have undergone evolutionary changes and mutations in response to the immune pressures exerted by vaccines and environmental factors, resulting in more severe consequences during breakthrough infections. Nevertheless, the specific correlation between the evolutionary mutations of coronaviruses and immune pressures remains ambiguous. Swine coronavirus-porcine epidemic diarrhea virus (PEDV)-has existed for decades. This study utilized in vivo preparation of polyclonal antibodies against the PEDV and identified critical neutralizing epitopes through serial in vitro passaging. Then, the recombinant mutated strains were successfully constructed. In vitro experiments confirmed the ability of the rA1273P strain to escape neutralization by polyclonal antibodies. Both in vitro cell studies and in vivo animal experiments revealed that the strain maintains virulence and pathogenicity while evading antibody pressure post-vaccination. The pathogenicity of the strain while evading immune pressure is comparable to wild-type strains. A comparison of the S protein gene between vaccine strains and clinical strains identified mutations in 1273 amino acid positions in clinical strains. In conclusion, this study identified a novel PEDV S protein neutralizing site under immune pressure through serial passaging, indicating that the 1,273th amino acid position is prone to mutation under prolonged antibody pressure, enhancing the virus's ability to escape hosts. This study offers new insights into the interpretation of coronavirus escape immune pressure and provides technical support for monitoring and predicting the variation and evolution of coronavirus.IMPORTANCECoronaviruses represent an ongoing public health threat because of high variability. Since 2010, the emergence of highly pathogenic porcine epidemic diarrhea virus (PEDV) strains has resulted in significant economic losses to the global pig industry. PEDV undergoes evolution and mutation under external immune pressure, rendering it an increasingly challenging target for prevention and control measures. Here, we prepared the polyclonal antibodies against PEDV and identified a novel neutralization epitope on the S protein (1,273th amino acids) through serial in vitro passaging. Furthermore, our findings indicate that the mutation of A1273P in the S protein did not alter the virulence of the PEDV but significantly enhanced its ability to escape and infect the host in vitro and in vivo. Finally, we found that the 1,273 amino acid position of the S gene has been mutated to varying degrees in clinical PEDV strains. This work provides a specific correlation between the evolutionary mutations of coronaviruses and immune pressures.

LDHB suppresses the PDCoV proliferation by targeting viral nucleocapsid protein for autophagic degradation

Porcine deltacoronavirus (PDCoV) is a newly identified enteric coronavirus that causes serious diarrhea and vomiting in pigs, leading to substantial economic losses globally. Studying the molecular interactions between virus and host proteins is crucial for developing new anti-PDCoV strategies. Here, the role and mechanism of lactate dehydrogenase B (LDHB) in PDCoV replication were investigated. LDHB suppresses PDCoV replication in a dose-dependent manner, whereas the knockdown of LDHB via RNA interference enhances virus proliferation in LLC-PK1 cells. Mechanistically, LDHB directly interacts with PDCoV N protein in the cytoplasm. LDHB mediated the autophagic degradation of PDCoV N protein, thereby inhibiting viral replication. To our interests, PDCoV infection or PDCoV N protein expression significantly reduces LDHB expression in cells. Further studies showed that PDCoV N protein, dependent on its LIR motif, binds to the LC3. It facilitates LDHB degradation, possibly as a strategy for viral evasion from host cell cytosolic defense mechanisms. Overall, the present study provided a novel regulatory mechanism of LDHB in PDCoV infection and suggested new avenues for the antiviral strategy.

IMPORTANCE

This study elucidates the intricate interaction between the PDCoV N protein and LDHB within the context of viral infection and immune evasion strategies. By demonstrating that LDHB can suppress PDCoV replication through a novel mechanism involving the autophagic degradation of the viral N protein, the research highlights the potential of targeting such interactions for antiviral strategies. The findings not only expand our understanding of how PDCoV manipulates host cell pathways to its advantage but also open up new avenues for therapeutic interventions that could mitigate the impact of this and similar viral pathogens.

Abortive PDCoV infection triggers Wnt/β-catenin pathway activation, enhancing intestinal stem cell self-renewal and promoting chicken resistance

Porcine deltacoronavirus (PDCoV) is an emerging coronavirus causing economic losses to swine industries worldwide. PDCoV can infect chickens under laboratory conditions, usually with no symptoms or mild symptoms, and may cause outbreaks in backyard poultry and wildfowl, posing a potential risk of significant economic loss to the commercial poultry industry. However, the reasons for such a subdued reaction after infection are not known. Here, using chicken intestinal organoid monolayers, we found that although PDCoV infects them nearly as well as porcine intestinal organoid monolayers, infection did not result in detectable amounts of progeny virus. In ex vivo and in vivo experiments using chickens, PDCoV infection failed to initiate interferon and inflammatory responses. Additionally, infection did not result in a disrupted intestinal barrier nor a reduced number of goblet cells and mucus secretion, as in pigs. In fact, the number of goblet cells increased as did the secreted mucus, thereby providing an enhanced protective barrier. Ex vivo PDCoV infection in chicken triggered activation of the Wnt/β-catenin pathway with the upregulation of Wnt/β-catenin pathway genes (Wnt3a, Lrp5, β-catenin, and TCF4) and Wnt target genes (Lgr5, cyclin D1, and C-myc). This activation stimulates the self-renewal of intestinal stem cells (ISCs), accelerating ISC-mediated epithelial regeneration by significant up-regulation of PCNA (transiently amplifying cells), BMI1 (ISCs), and Lyz (Paneth cells). Our data demonstrate that abortive infection of PDCoV in chicken cells activates the Wnt/β-catenin pathway, which facilitates the self-renewal and proliferation of ISCs, contributing to chickens' resistance to PDCoV infection.IMPORTANCEThe intestinal epithelium is the main target of PDCoV infection and serves as a physical barrier against pathogens. Additionally, ISCs are charged with tissue repair after injury, and promoting rapid self-renewal of intestinal epithelium will help to re-establish the physical barrier and maintain intestinal health. We found that PDCoV infection in chicken intestinal organoid monolayers resulted in abortive infection and failed to produce infectious virions, disrupt the intestinal barrier, reduce the number of goblet cells and mucus secretion, and induce innate immunity, but rather increased goblet cell numbers and mucus secretion. Abortive PDCoV infection activated the Wnt/β-catenin pathway, enhancing ISC renewal and accelerating the renewal and replenishment of shed PDCoV-infected intestinal epithelial cells, thereby enhancing chicken resistance to PDCoV infection. This study provides novel insights into the mechanisms underlying the mild or asymptomatic response to PDCoV infection in chickens, which is critical for understanding the virus's potential risks to the poultry industry.

Shortened SARS-CoV-2 Viral RNA Shedding in Saliva During Early Omicron Compared to Wild-Type Pandemic Phase

This study compared the dynamics of SARS-CoV-2 viral shedding in saliva between wild-type virus-infected and Omicron-infected household cohorts. Preexisting immunity in participants likely shortens the viral RNA shedding duration and lowers viral load peaks. Frequent saliva sampling can be a convenient tool to study viral load dynamics.

Discovery of 3,4-dihydropyrimidine derivatives as novel Anti-PEDV agents targeting viral internalization through a unique calcium homeostasis disruption mechanism

Porcine epidemic diarrhea virus (PEDV) poses critical challenges to global swine production, with current vaccines showing limited efficacy against emerging strains. To address this gap, we designed 41 novel 3,4-dihydropyrimidine derivatives via systematic structure-activity relationship (SAR) optimization. Compound D39, incorporating a C-4 2'-substituted biphenyl, C-2 thione, C-6 phenyl, and C-5 isopropanol substituents, emerged as the most potent anti-PEDV agent (EC50 = 0.09 μM, SI = 358.9), outperforming remdesivir (EC50 = 3.14 μM, SI > 40.8) by 35-fold. D39 exhibited broad-spectrum anti-coronavirus activity (FIPV, IDV) at micromolar levels and demonstrated acceptable metabolic stability (T1/2 = 78.75 min, Clint = 8.8 μL/min/mg) in porcine liver microsomes. Mechanistic studies revealed the antiviral actions was achieved by blocking PEDV early internalization via intracellular Ca2+ homeostasis modulation. These findings highlight D39 as a first-in-class anti-PEDV candidate with a unique dihydropyrimidine scaffold and a calcium-targeting mechanism, offering a promising therapeutic strategy against coronaviral infections.

Study of coronavirus diversity in wildlife in Northern Cambodia suggests continuous circulation of SARS-CoV-2-related viruses in bats

Since SARS-CoV-2's emergence, studies in Southeast Asia, including Cambodia, have identified related coronaviruses (CoVs) in rhinolophid bats. This pilot study investigates the prevalence and diversity of CoVs in wildlife from two Cambodian provinces known for wildlife trade and environmental changes, factors favoring zoonotic spillover risk. Samples were collected from 2020 to 2022 using active (capture and swabbing of bats and rodents) and non-invasive (collection of feces from bat caves and wildlife habitats) methods. RNA was screened for CoVs using conventional pan-CoVs and real-time Sarbecovirus-specific PCR systems. Positive samples were sequenced and phylogenetic analysis was performed on the partial RdRp gene. A total of 2608 samples were collected: 867 rectal swabs from bats, 159 from rodents, 41 from other wild animals, and 1541 fecal samples. The overall prevalence of CoVs was 2.0%, with a 3.3% positive rate in bats, 2.5% in rodents, and no CoVs detected in other wildlife species. Alpha-CoVs were exclusive to bats, while Beta-CoVs were found in both bats and rodents. Seven SARS-CoV-2-related viruses were identified in Rhinolophus shameli bats sampled in August 2020, March 2021, and December 2021. Our results highlight diverse CoVs in Cambodian bats and rodents and emphasize bats as significant reservoirs. They also suggest continuous circulation of bat SARS-CoV-2-related viruses may occur in a region where ecological and human factors could favor virus emergence. Continuous surveillance and integrated approaches are crucial to managing and mitigating emerging zoonotic diseases.

HDAC4 suppresses porcine epidemic diarrhea virus infection through negatively regulating MEF2A-GLUT1/3 axis- mediated glucose uptake

Porcine epidemic diarrhea virus (PEDV), a porcine enteropathogenic coronavirus, causes severe diarrhea and death in neonatal piglets. Histone deacetylase 4 (HDAC4), a member of class IIa deacetylases, controls a wide range of physiological processes, but, little is known about its role in PEDV infection. Here, we report a novel strategy by which PEDV manipulates HDAC4. First, HDAC4 expression was examined, and showed a significant down-regulation in PEDV-infected Vero and IPEC-J2 cells. Subsequently, knockdown of HDAC4 by specific small interfering RNA (siRNA) led to an increase in viral infection, whereas overexpression of HDAC4 remarkably suppressed PEDV infection. Mechanistically, we showed that HDAC4 significantly reduced glucose uptake, as glucose is required for PEDV infection. Through screening, we identified glucose transporters 1 and 3 (GLUT1 and GLUT3) as responsible for glucose uptake during PEDV infection. We further confirmed that HDAC4 regulated GLUT1 and GLUT3 expression through its converging hub, myocyte enhancer factor 2 A (MEF2A). Taken together, these findings contribute to a better understanding of a novel function of HDAC4 in regulating glucose uptake via MEF2A-GLUT1/3 to limit PEDV infection, and provide new strategies for the development of anti-PEDV drugs.

Carnitine palmitoyltransferase 2 as a novel prognostic biomarker and immunoregulator in colorectal cancer

BACKGROUND

Metabolic interventions are critical for enhancing immunotherapy efficacy, but reliable metabolic targets remain absent for colorectal cancer (CRC). This study aims to investigate the interplay between metabolic and immunological factors in CRC, identify metabolic immunoregulatory molecules, and propose targets for prognostic and therapeutic applications.

METHODS

Immune infiltration and metabolic pathways in CRC were analyzed using CIBERSORT and gene set variation analyses. Cox regression identified survival-related metabolic genes, forming a metabolic-related gene prognostic index (MRGPI), which was validated through survival analysis, timeROC, GSEA, CIBERSORT, and TIDE. Hub genes in the MRGPI were assessed using enrichment and co-expression network analyses. The expression of carnitine palmitoyltransferase 2 (CPT2) was validated through multiplex immunofluorescence of tissue microarrays. While its role was examined by western blot, CCK-8 assay, flow cytometry, qRT-PCR, Elisa, chemotaxis assays, etc. RESULTS: Fatty acid oxidation (FAO) pathways were significantly altered in CRC and correlated with immune cell infiltration and patient survival. The MRGPI, constructed from five survival-related metabolic genes, demonstrated strong prognostic and immunotherapeutic predictive value. Moreover, CPT2, a key hub gene in the MRGPI, whose lower expression in plasma cells predicts unfavorable patients' survival and could be an independent prognostic indicator, while its knockout in tumor cells significantly increases the infiltrating levels of CD8+ T cells via promoting the release of CCL25.

CONCLUSION

The FAO-dominated MRGPI is a promising biomarker for predicting patient outcomes and immunotherapy response. CPT2 holds potential as a prognostic marker and therapeutic target for CRC metabolic immunotherapy.

Capsid and genome damage are the leading inactivation mechanisms of aerosolized porcine respiratory coronavirus at different relative humidities

Relative humidity (RH) varies widely in indoor environments based on temperature, outdoor humidity, heating systems, and other environmental conditions. This study explored how RH affects aerosolized porcine respiratory coronavirus (PRCV), a model for coronaviruses, over a time range from 0 min to a maximum of 1 h, and the molecular mechanism behind viral infectivity reduction. These questions were answered by quantifying: (i) viral-host receptor interactions, (ii) capsid integrity, (iii) viral genome integrity, and (iv) virus infectivity. We found RH did not alter PRCV-receptor interactions. RHs 45-55% and 65-75% damaged viral genomes (2 log10 reduction and 1 log10 reduction, respectively, in terms of median sample value), whereas RHs 55-65% decreased capsid integrity (2 log10 reduction). No apparent virion damage was observed in RH 75-85%. Two assays were used to quantify virus presence: qPCR for detecting the viral genomes and plaque-forming unit assay for detecting the virus replication. Our results indicated that the qPCR assay overestimated the concentrations of infectious viruses, and RNase treatment with long-range RT-qPCR performed better than one-step RT-qPCR. We propose that understanding the influence of RH on the stability of aerosolized viruses provides critical information for detecting and preventing the indoor transmission of coronaviruses.

IMPORTANCE

Indoor environments can impact the stability of respiratory viruses, which can then affect the transmission rates. The mechanisms of how relative humidity (RH) affects virus infectivity still remain unclear. This study found RH inactivates porcine respiratory coronavirus by damaging its capsid and genome. The finding highlights the potential role of controlling indoor RH levels as a strategy to reduce the risk of coronavirus transmission.

Protein structure prediction via deep learning: an in-depth review

The application of deep learning algorithms in protein structure prediction has greatly influenced drug discovery and development. Accurate protein structures are crucial for understanding biological processes and designing effective therapeutics. Traditionally, experimental methods like X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy have been the gold standard for determining protein structures. However, these approaches are often costly, inefficient, and time-consuming. At the same time, the number of known protein sequences far exceeds the number of experimentally determined structures, creating a gap that necessitates the use of computational approaches. Deep learning has emerged as a promising solution to address this challenge over the past decade. This review provides a comprehensive guide to applying deep learning methodologies and tools in protein structure prediction. We initially outline the databases related to the protein structure prediction, then delve into the recently developed large language models as well as state-of-the-art deep learning-based methods. The review concludes with a perspective on the future of predicting protein structure, highlighting potential challenges and opportunities.

Mycoplasma gallisepticum and Mycoplasma synoviae in commercial poultry: current control strategies and future challenges

Mycoplasma gallisepticum (Mg) and Mycoplasma synoviae (Ms) are regarded as the most important avian mycoplasma species for today's chicken and turkey farming industry from clinical and economical perspectives. Control strategies for Mg and Ms have become more efficient due to investments in mycoplasma research over the last 70 years. These investments have contributed to the further implementation of serological and molecular testing, the development of vaccines, and the improvement of antimicrobial treatment strategies. However, the increasing spotlight on welfare, the pressure on prudent use of antimicrobials, and the expected global increase in poultry production, are going to have an impact on the future control of avian mycoplasmas in commercial poultry. In this paper a group of avian mycoplasma experts discuss the future challenges in mycoplasma control considering the background of these expected changes and the relevance for future avian mycoplasma research.

A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata

OBJECTIVE

In recent years, COVID-19 has placed enormous burdens on healthcare systems. Currently, hundreds of thousands of new cases are reported monthly. World Health Organization is managing COVID-19 as a long-term disease, indicating that an efficient and low-cost detection method remains necessary. Previous studies have shown competitive results on cough-based COVID-19 detection combined with deep learning methods. However, most studies have focused only on improving classification performance on single-source data while neglecting the impact of various factors in real-world applications.

METHODS

To this end, we collected clinical and large-scale crowdsourced cough audios with abundant metadata to comprehensively validate the performance differences among different groups. Specifically, we leveraged self-supervised learning for pre-training and fine-tuned the model with data from different sources. Then based on the metadata, we compared the effects of factors such as cough types, symptoms, and infection stages on detection performance. Moreover, we recorded clinical indicators of viral load and antibody levels and observed the correlation between predicted probabilities and indicator values for the first time. Several open-source datasets were tested to verify the model generalizability.

RESULTS

The area under receiver operating characteristic curve is 0.79 for clinical data and 0.69 for crowdsourced data, indicating differences between clinical validation and real-world application. The performance in detecting symptomatic COVID-19 subjects is usually better than detecting asymptomatic COVID-19 subjects. The prediction results show weak correlation with clinical indicators on a small number of clinical data. Poor detection performance in recovery individuals and open-source datasets shows a limitation of existing cough-based detection models.

CONCLUSION

Our study validated the model performance and limitations using multi-source data with abundant metadata, which helped researchers evaluate the feasibility of cough-based COVID-19 detection model in practical applications.

Detection of SARS-CoV-2- specific antibodies in domestic cats using different ELISA tests

The emergence of SARS-CoV-2 raised concerns about the potential for interspecies transmission, particularly among domestic animals. We evaluated the seroprevalence of SARS-CoV-2 antibodies in domestic cats from various sites in North America. A total of 216 serum samples collected between December 2019 and February 2022, were analyzed using four different enzyme-linked immunosorbent assays (ELISAs), including a commercial surrogate virus neutralization test (sVNT), a commercial double antigen test (dN ELISA), and two in-house developed indirect ELISAS based on receptor-binding domain (RBD iELISA) and the nucleocapsid (N iELISA) proteins, respectively. Seropositive samples in the commercial ELISAs were subject to virus neutralization test (cVNT) employing the Wuhan-like USA-WA1/2020 SARS-CoV-2 isolate. Our findings revealed that, 6 % (12/216) of the cat serum samples tested positive by the sVNT, while 4 % (9/216) tested positive for the dN-ELISA. Interestingly, the N iELISA showed a higher seroprevalence, with 31 % of the samples testing positive, possibly due to cross-reactive antibodies against the N protein of other coronavirus commonly found in cats. There was a high concordance between sVNT, cVNT, and RBD iELISA. Among positive sVNT cat serum samples, 75 % (9/12) exhibited neutralizing titers with all samples also being positive by RBD iELISA. Notably, the RBD iELISA and sVNT demonstrated high sensitivity and specificity in detecting SARS-CoV-2 antibodies (100 and 79 %; 100 and 90 %, respectively). In conclusion, our study provides important insights into the seroprevalence of SARS-CoV-2 antibodies in domestic cats, highlighting the potential for interspecies transmission and the need for continued monitoring of SARS-CoV-2 in animal populations.

Distribution of aminopeptidase N coronavirus receptors in the respiratory and digestive tracts of domestic and wild artiodactyls and carnivores

Aminopeptidase N (APN) is a transmembrane protein that mediates the attachment of the spike protein of several clinically important coronaviruses (CoVs) responsible for respiratory and intestinal diseases in animals and humans. To assess the potential for APN-mediated viral tropism, we characterized APN receptor distribution in the respiratory and intestinal tissues of various artiodactyls (cervids, bovids, camelids and suids) and carnivores (canids, felids, mustelids and phocids) using immunohistochemistry. In the lungs, APN expression was limited to artiodactyls, with strong expression in the bronchiolar epithelium and weaker expression in pneumocytes. Nasal turbinate and tracheal samples, where available, showed stronger APN expression in artiodactyls over carnivores. APN was consistently detected on the microvilli of enterocytes in the small intestine across multiple taxa, while the presence in the colon was more variable. Of the animals examined, pig and alpaca consistently expressed the most abundant APN in the upper and lower respiratory tract. In silico evaluation of APN orthologue sequences from humans, artiodactyls and carnivores identified distinct evolutionary relationships. Further in silico binding predictions for alpaca alphacoronavirus and human coronavirus 229E with cognate and heterologous alpaca and human APN revealed substantial overlapping binding footprints with high conservation of amino acid residues, suggesting an evolutionary divergence and subsequent adaptation of a 229E-like or ancestral virus within a non-human animal host. This combined anatomical and in silico approach enhances understanding of host susceptibility, tissue tropism and viral transmission mechanisms in APN-dependent CoVs and has the potential to inform future strategies for disease modelling, surveillance and control.

Vaccine efficacy of NVX-CoV2373 against SARS-CoV-2 infection in adolescents in the USA: an ancillary study to a phase 3, observer-blinded, randomised, placebo-controlled trial

BACKGROUND

Although existing COVID-19 vaccines are known to be highly effective against severe disease and death, data are needed to assess their ability to reduce SARS-CoV-2 infection. We aimed to estimate the efficacy of the NVX-CoV2373 protein subunit vaccine against SARS-CoV-2 infection, regardless of symptoms, among adolescents.

METHODS

We performed an ancillary observational study (SNIFF) to the phase 3, observer-blinded, randomised, placebo-controlled PREVENT-19 trial that assessed vaccine efficacy against symptomatic COVID-19 in the USA. Participants in the PREVENT-19 trial included healthy adolescents aged 12-17 years and with no history of laboratory-confirmed SARS-CoV-2 infection. They were randomly assigned (2:1) to receive either the NVX-CoV2373 (Novavax, Gaithersburg, MD, USA) vaccine (immediate NVX-CoV2373 group) or placebo (delayed NVX-CoV2373 group) on days 0 and 21 (initial series). After 2 months, in a crossover series, participants received two doses, 21 days apart, of the intervention that they did not receive in their initial series. Participants at 47 of the PREVENT-19 sites were invited to participate in the SNIFF study and self-collect nasal swabs at home twice weekly for SARS-CoV-2 testing to assess vaccine efficacy against SARS-CoV-2 infection. This primary outcome was defined as the first identification of SARS-CoV-2 detected by RT-PCR, regardless of symptoms, with onset within 4 weeks after the second dose of the initial vaccination series until the second dose of the crossover series. Secondary outcomes were vaccine efficacy against asymptomatic and minimally symptomatic SARS-CoV-2 infection, durability of vaccine efficacy against SARS-CoV-2 infection, and durability of vaccine efficacy against asymptomatic and minimally symptomatic infections. Outcomes were analysed in the modified intention-to-treat population, which included all participants without previous SARS-CoV-2 infection and was restricted to participants enrolled within 4 weeks of the second dose of the primary (primary analysis population) or crossover (post-crossover analysis population) series. This study is registered with ClinicalTrials.gov (NCT04611802).

FINDINGS

Between June 1 and Dec 17, 2021, 1196 (53·2%) of the 2247 adolescent participants recruited in the PREVENT-19 trial enrolled in the SNIFF study. The primary analysis population included 471 participants in the immediate NVX-CoV2373 group and 220 in the delayed NVX-CoV2373 group. Incidence of SARS-CoV-2 infection was 14·9 cases per 100 person-years (95% CI 7·9-25·5) in the immediate group and 54·2 cases per 100 person-years (33·6-82·9) in the delayed group; vaccine efficacy was 73·5% (95% CI 47·1-86·7; p=0·0002). Incidence of minimally symptomatic or asymptomatic SARS-CoV-2 infection was 10·3 cases per 100 person-years (95% CI 4·7-19·6) in the immediate group and 36·1 cases per 100 person-years (19·8-60·7) in the delayed group; vaccine efficacy was 72·8% (95% CI 37·1-88·2; p=0·0023). After the second crossover dose, incidence of SARS-CoV-2 was 14·6 cases per 100 person-years (95% CI 8·6-23·0) in the immediate group (receiving placebo at crossover) and 9·1 cases per 100 person-years (3·0-21·3) in the delayed group, with a durability ratio of 160·3 (95% CI 59·5-431·6; p=0·35). Almost all infections after crossover were minimally symptomatic or asymptomatic, with a durability ratio of 151·4 (55·9-410·4; p=0·41).

INTERPRETATION

Among adolescents participating in the PREVENT-19 trial during the delta (B.1.617.2) variant wave of the COVID-19 pandemic, the NVX-CoV2373 vaccine was highly efficacious against SARS-CoV-2 infection regardless of symptoms, indicating its potential to reduce the reservoir of infections that contribute to community transmission.

FUNDING

US Department of Health and Human Services, Administration for Strategic Preparedness and Response, Biomedical Advanced Research and Development Authority, National Institute of Allergy and Infectious Diseases, and National Institutes of Health.

Isolation, phylogenetics, and characterization of a new PDCoV strain that affects cellular gene expression in human cells

Introduction

Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that causes acute diarrhea, vomiting, dehydration, and even death in piglets, resulting in serious economic losses to the pork industry worldwide. PDCoV has received much attention owing to its broad host range, including humans, posing a potential threat to public health. However, the prevalence, characteristics, and host cellular gene expression of PDCoV remain poorly understood.

Methods

In this study, a new PDCoV strain (CHN/SX-Y/2023, GenBank number PQ373831) was successfully isolated, identified, and subjected to phylogenetic tree and transcriptome analysis in human hepatoma (Huh7) cells following PDCoV infection.

Results

The results showed that the CHN/SX-Y/2023 strain belongs to the Chinese lineage and causes cytopathic effects in canonical cell lines (LLC-PK1 and ST cells) and other cell lines (Huh7 and LMH cells). However, HEK-293T, EEC, MDBK, and Vero-CCL81 cells were not found to be susceptible in this study. Based on transcriptome analysis, 1,799 differentially expressed genes (DEGs) were upregulated and 771 were downregulated during PDCoV infection.

Discussion

Among the upregulated genes, FCGR1A, VSIG1, TNFRSF9, and PLCXD3 are associated with immunity, inflammation, and lipid catabolism. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the upregulated DEGs were significantly enriched in the MAPK, TNF, and NF-κB signaling pathways and viral protein interactions with cytokines and cytokine receptors. Protein-protein interaction networks showed that the upregulated genes CXCL8, DUSP1, PTGS2, and IL15 were associated with inflammation and immunity. In addition, the protein levels of p-IRF3, LC3-II, and ACSL4 increased, suggesting that PDCoV infection in Huh7 cells induces an intrinsic immune response, cellular autophagy, and ferroptosis. Collectively, our findings provide new insights into the characteristics and mechanisms of PDCoV infection.

Review on biphasic blood drying method for rapid pathogen detection in bloodstream infections

Rapid and accurate detection of pathogenic microorganisms in blood is critical for diagnosing life-threatening conditions such as bloodstream infections (BSIs). Current methods for the detection and identification of bacteria from large volumes of blood (5 mL) involve culture steps followed by DNA extraction/purification/concentration and Polymerase Chain Reaction (PCR)-based nucleic acid amplification. DNA extraction and amplification directly from blood samples is hampered by the complexity of the blood matrix, resulting in time-consuming and labor-intensive processes. This review delves into recent advancements in molecular diagnostics based on blood drying, coined as 'biphasic reaction', and highlights this new technique that attempts to overcome the limitations of traditional sample preparation and amplification processes. The biphasic blood drying method, in combination with isothermal amplification methods such as loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA), has recently been shown to improve the sensitivity of detection of bacterial, viral, and fungal pathogens from ∼1 mL of whole blood, while minimizing DNA loss and avoiding the use of extraction/purification/concentration kits. Furthermore, the biphasic approach in combination with LAMP has been shown to be a culture-free method capable of detecting bacteria in clinical samples with a sensitivity of ∼1 CFU/mL in ∼2.5 h. This represents a significant reduction in detection and identification time compared to current clinical procedures based on bacterial culture prior to PCR amplification. This review paper aims to be a guide to identify new opportunities for future advancements and applications of the biphasic technology.

LAMP Assay Coupled with a Pyrococcus furiosus Argonaute System for the Rapid Detection of Porcine Epidemic Diarrhea Virus

Porcine epidemic diarrhea virus (PEDV) infection can lead to serious acute intestinal infectious disease, bringing huge economic losses to the pig industry. In addition to triggering an extremely high mortality rate for lactating piglets, there is currently a lack of effective treatments and vaccines. Therefore, rapid, accurate, sensitive, and specific detection of PEDV is critical for timely control. In this study, a nucleic acid detection method combining reverse transcription loop-mediated isothermal amplification (RT-LAMP) and Pyrococcus furiosus Argonaute (PfAgo) was established for the detection of PEDV and performed after optimizing the system (mainly for the design and screening of the LAMP primers and PfAgo gDNA). The optimized system had a detection limit as low as 2.4 copies/μL. To reach more timely on-site detection of PEDV and overcome the reliance on bulky and complex equipment, a lateral flow strip was introduced into the system, which could detect the target as low as 24 copies/μL. This RT-LAMP-PfAgo system took about 35 min to react, and the results could be observed and clarified with the naked eyes. Moreover, the method was highly specific and had no cross-reactivity with other swine pathogens. The detection results for the clinical samples were consistent with those obtained by the gold standard method, reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), proving its applicability. In conclusion, the established RT-LAMP-PfAgo system can provide a new solution for the development of a portable, visual PEDV testing platform.

Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance

In a subset of SARS-CoV-2-infected individuals treated with the antiviral nirmatrelvir-ritonavir, the virus rebounds following treatment. The mechanisms driving this rebound are not well understood. We used a mathematical model to describe the longitudinal viral load dynamics of 51 individuals treated with nirmatrelvir-ritonavir, 20 of whom rebounded. Target cell preservation, either by a robust innate immune response or initiation of N-R near the time of symptom onset, coupled with incomplete viral clearance, appears to be the main factor leading to viral rebound. Moreover, the occurrence of viral rebound is likely influenced by the time of treatment initiation relative to the progression of the infection, with earlier treatments leading to a higher chance of rebound. A comparison with an untreated cohort suggests that early treatments with nirmatrelvir-ritonavir may be associated with a delay in the onset of an adaptive immune response. Nevertheless, our model demonstrates that extending the course of nirmatrelvir-ritonavir treatment to a 10-day regimen may greatly diminish the chance of rebound in people with mild-to-moderate COVID-19 and who are at high risk of progression to severe disease. Altogether, our results suggest that in some individuals, a standard 5-day course of nirmatrelvir-ritonavir starting around the time of symptom onset may not completely eliminate the virus. Thus, after treatment ends, the virus can rebound if an effective adaptive immune response has not fully developed. These findings on the role of target cell preservation and incomplete viral clearance also offer a possible explanation for viral rebounds following other antiviral treatments for SARS-CoV-2.

IMPORTANCE

Nirmatrelvir-ritonavir is an effective treatment for SARS-CoV-2. In a subset of individuals treated with nirmatrelvir-ritonavir, the initial reduction in viral load is followed by viral rebound once treatment is stopped. We show that the timing of treatment initiation with nirmatrelvir-ritonavir may influence the risk of viral rebound. Nirmatrelvir-ritonavir stops viral growth and preserves target cells but may not lead to full clearance of the virus. Thus, once treatment ends, if an effective adaptive immune response has not adequately developed, the remaining virus can lead to rebound. Our results provide insights into the mechanisms of rebound and can help develop better treatment strategies to minimize this possibility.

Amplification-free, OR-gated CRISPR-Cascade reaction for pathogen detection in blood samples

Rapid and accurate detection of DNA from disease-causing pathogens is essential for controlling the spread of infections and administering timely treatments. While traditional molecular diagnostics techniques like PCR are highly sensitive, they include nucleic acid amplification and many need to be performed in centralized laboratories, limiting their utility in point-of-care settings. Recent advances in CRISPR-based diagnostics (CRISPR-Dx) have demonstrated the potential for highly specific molecular detection, but the sensitivity is often constrained by the slow trans-cleavage activity of Cas enzymes, necessitating preamplification of target nucleic acids. In this study, we present a CRISPR-Cascade assay that overcomes these limitations by integrating a positive feedback loop that enables nucleic acid amplification-free detection of pathogenic DNA at atto-molar levels and achieves a signal-to-noise ratio greater than 1.3 within just 10 min. The versatility of the assay is demonstrated through the detection of bloodstream infection pathogens, including Methicillin-Sensitive Staphylococcus aureus (MSSA), Methicillin-Resistant Staphylococcus aureus (MRSA), Escherichia coli, and Hepatitis B Virus (HBV) spiked in whole blood samples. Additionally, we introduce a multiplexing OR-function logic gate, further enhancing the potential of the CRISPR-Cascade assay for rapid and accurate diagnostics in clinical settings. Our findings highlight the ability of the CRISPR-Cascade assay to provide highly sensitive and specific molecular detection, paving the way for advanced applications in point-of-care diagnostics and beyond.

Spike gene variability in porcine epidemic diarrhea virus as a determinant for virulence

Porcine epidemic diarrhea virus (PEDV) is a pathogenic coronavirus that targets the swine intestinal tract, leading to acute diarrhea and high mortality in neonatal piglets. PEDV is categorized into different genotypes based on genetic variations, especially in the spike (S) gene. The S protein is crucial for viral entry and a major immune target. Significant differences in virulence have been observed among PEDV genotypes, particularly between classical strains and newly emerging strains. In this study, we explored the impact of spike gene variability on PEDV pathogenicity. Using targeted RNA recombination, we generated recombinant PEDV (rPEDV) variants carrying spike genes from contemporary strains (moderately virulent strain UU and highly virulent strain GDU), all within the genetic background of the avirulent DR13 vaccine strain. Pathogenicity was assessed in 3-day-old piglets. The rPEDV carrying the DR13 spike gene was nonpathogenic, with no detectable viral RNA in feces. The rPEDV with the UU spike gene induced mild to severe diarrhea, with moderate viral shedding but no mortality. Conversely, the rPEDV with the GDU spike gene caused severe diarrhea, high viral titers, and high mortality. These findings highlight the critical role of the spike protein in PEDV virulence, informing future development of effective control strategies, including the design of live-attenuated vaccines.IMPORTANCEThis study significantly advances our understanding of how genetic variations in the spike (S) protein of porcine epidemic diarrhea virus (PEDV) influence its ability to cause disease. By engineering viruses with spike genes from different PEDV strains, variations in this protein could be directly linked to differences in disease severity. We found that the spike protein from highly virulent strains caused severe diarrhea and high mortality in piglets, while that from less virulent strains led to milder symptoms. These findings emphasize the central role of the spike protein in determining PEDV virulence, which may enable the design of more effective vaccines to combat PEDV and reduce its impact on the swine industry.

Isolation and pathogenicity of a novel recombinant pseudorabies virus from the attenuated vaccine and classical strains

Pseudorabies (PR) remains one of the most important swine diseases in China. Live attenuated vaccines have been widely deployed and have proven highly effective in controlling PR in the field. However, recent concerns regarding the evolution and recombination events involving pseudorabies virus (PRV) vaccine strains have raised substantial attention. In the present study, a novel recombinant PRV strain named HN2201 was isolated from one stillbirth case in Henan province in 2022. To assess the genetic and evolutionary features, the major immunogenic and virulence-associated genes, including gB, gC, gD, gG, gE and TK, were sequenced and analyzed. Phylogenetic and nucleotide homology analysis revealed that gB, gC, gD and gG genes of HN2201 displayed close relationship with Chinese classical strains. However, the TK gene of HN2201 contained a continuous deletion of 205 nucleotides, sharing the highest nucleotide homology (99.9%) with HB-98 vaccine strain. Additionally, a similar deletion was observed in the promoter region of the gE gene in both HN2201 and HB-98. Pathogenicity studies on 9-week-old piglets demonstrated that HN2201 exhibited attenuated virulence, characterized by transient clinical signs. The above results suggest that the naturally isolated HN2201 likely resulted from recombination events between the PRV classical strain and the HB-98 vaccine strain. Our findings provide valuable insights into the evolution of PRV in China and underscore the necessity of scientific and cautious use of PRV vaccines in the field.

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

BACKGROUND

The molecular underpinnings of organ dysfunction in severe COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we perform single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents.

RESULTS

We identify hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells, and a central role in a pro-fibrotic TGFβ signaling cell-cell communications network. Integrated analysis and comparisons with healthy controls reveal extensive changes in the cellular composition and expression states in COVID-19 liver, providing the underpinning of hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis characteristic of COVID-19 cholangiopathy. We also observe Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition is dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells.

CONCLUSIONS

Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.

Molecular breeding of pigs in the genome editing era

BACKGROUND

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.

MAIN BODY

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.

CONCLUSION

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.

Prediction of drug target interaction based on under sampling strategy and random forest algorithm

Drug target interactions (DTIs) play a crucial role in drug discovery and development. The prediction of DTIs based on computational method can effectively assist the experimental techniques for DTIs identification, which are time-consuming and expensive. However, the current computational models suffer from low accuracy and high false positive rate in the prediction of DTIs, especially for datasets with extremely unbalanced sample categories. To accurately identify the interaction between drugs and target proteins, a variety of descriptors that fully show the characteristic information of drugs and targets are extracted and applied to the integrated method random forest (RF) in this work. Here, the random projection method is adopted to reduce the feature dimension such that simplify the model calculation. In addition, to balance the number of samples in different categories, a down sampling method NearMiss (NM) which can control the number of samples is used. Based on the gold standard datasets (nuclear receptors, ion channel, GPCRs and enzymes), the proposed method achieves the auROC of 92.26%, 98.21%, 97.65%, 99.33%, respectively. The experimental results show that the proposed method yields significantly higher performance than that of state-of-the-art methods in predicting drug target interaction.

Advances in porcine epidemic diarrhea virus research: genome, epidemiology, vaccines, and detection methods

Porcine epidemic diarrhea (PED) is a highly contagious intestinal disease caused by the porcine epidemic diarrhea virus (PEDV). The economic impact of PEDV on the global pig industry has been significant, resulting in considerable losses. This paper presents a review of the latest research progress on PEDV genome, molecular epidemiology, vaccine development, and molecular detection methods. It was determined that the genetic diversity of the PEDV spike (S) gene was closely associated with the epidemiological trend of PEDV. The prevalence of S gene variants of different genotypes exhibited variability across regions and pig populations. Epidemiological analyses have demonstrated that PEDV can be transmitted via multiple routes, including direct contact, airborne aerosol, and water source contamination. With regard to vaccine research, the available vaccines can be classified into several categories, including live-attenuated vaccines, inactivated vaccines, subunit vaccines, bacterial vector vaccines, viral vector vaccines, mRNA vaccines, etc. Each of these has distinctive characteristics in terms of immunogenicity, protection efficiency, and safety. Molecular detection methods, including PCR-based methods, isothermal amplification techniques, immunological assays, and biosensors, play an important role in the diagnosis and monitoring of PEDV. Furthermore, this paper examines the current developments in PEDV research and identifies the key areas of future investigation. The objective of this paper is to establish a theoretical foundation for the prevention and control strategies of PED, and to provide a point of reference for further research on the genomics, epidemiology, vaccine development and detection methods of PEDV.

Modeling natural coinfection in a bat reservoir shows modulation of Marburg virus shedding and spillover potential

The Egyptian rousette bat (ERB) is a natural reservoir for Marburg virus (MARV; family Filoviridae), a putative reservoir for Sosuga virus (SOSV; family Paramyxoviridae), and a vertebrate reservoir for Kasokero virus (KASV; family Orthonairoviridae); however, the effect of naturally occurring coinfection by those viruses on MARV shedding and spillover potential is unknown. To answer this question, we experimentally infected one cohort of captive-bred ERBs with SOSV+MARV (n=12 bats) or MARV only (n=12 bats) and a second cohort with KASV+MARV (n=12 bats) or MARV only (n=12 bats), and then collected blood, oral swab, and rectal swab specimens throughout the course of infection to monitor viral shedding. Compared to the MARV-monoinfected bat group, the SOSV+MARV-coinfected bat group exhibited a significantly shortened duration of MARV oral shedding and a significantly decreased anti-MARV IgG response, which may increase the capacity for MARV reinfection. In contrast, relative to the MARV-monoinfected bat group, the KASV+MARV-coinfected bat group exhibited significantly increased peak magnitudes and durations of MARV viremia and oral shedding, as well as a significantly increased anti-MARV IgG response. Correspondingly, cumulative MARV shedding loads, a measure of infectiousness, were significantly higher in the KASV+MARV-coinfected bat group than the MARV-monoinfected bat group. Four of the KASV+MARV-coinfected bats were classified as MARV supershedders, together accounting for 72.5% of the KASV-MARV experimental cohort's total shedding. Our results demonstrate that SOSV+MARV and KASV+MARV coinfection of ERBs differentially modulates MARV shedding and anti-MARV IgG responses, thereby implicating MARV coinfection as playing a critical role in bat-to-bat MARV transmission dynamics and spillover potential.

Validation of two multiplex lateral flow devices for the rapid detection and typing of foot-and-mouth disease viruses

Lateral Flow Devices (LFDs) represent a simple tool for the rapid diagnosis of FMD, particularly in endemic regions, often lacking adequate and equipped laboratories. Other experimental prototypes offer a user-friendly FMD confirmation tool, but serotype identification is crucial for transmission patterns evaluation and for vaccine selection and their serotyping capacity was limited. This study describes the validation of two multiplex devices based on well-characterized monoclonal antibodies: LFD1 (O, A and Asia1) and LFD2 (SAT1 and SAT2). First, the ability of the LFDs to recognize the widest spectrum of strains was assessed. Eighty-three tissue-cultured FMDV strains were tested with LFD1 and 15 with LFD2, confirming the capability to recognize and serotype a broad range of lineages and sub-lineages belonging to all 7 endemic pools. The diagnostic sensitivity related to FMDV detection was evaluated using 224 real-time RT-PCR positive samples collected in endemic countries, resulting in 87.5 % for LFD1 (140/160 detected) and 70 % for LFD2 (45/64 detected). The diagnostic sensitivity of serotyping capabilities was assessed by testing field samples in parallel with an antigen-ELISA kit: applied on 178 samples, LFD1 correctly typed 96 %, 94 % and 83 % of samples positive for type O (n = 95), A (n = 54) and Asia1 (n = 29) respectively, while LFD2 correctly typed 77 % SAT1 (n = 52) and 82 % SAT2 (n = 40) in 92 positive field samples. A 100 % diagnostic specificity was found testing 60 epithelium homogenates collected from animals negative for FMD. Obtained data highlighted the devices' potential value for field use to support the enhanced surveillance of FMD.

Streptococcus hillyeri isolated from septic pleuritis in a horse

Here we report the isolation of Streptococcus hillyeri from a thoracic sample from a horse. A 17-y-old Hungarian Sport Horse mare was referred to the equine clinic of the University of Veterinary Medicine Budapest, Hungary, with suspected pleuritis. Upon arrival, the horse was febrile and had tachycardia, severe inspiratory dyspnea, and tachypnea. Thoracic ultrasonography revealed severe bilateral pleural effusion, and a large area of lung consolidation. After sampling of both hemithoraces, 66 L of turbid exudate were drained. Based on these findings, a tentative diagnosis of septic pleuritis was made, and the horse was immediately started on a course of broad-spectrum antibiotics, a NSAID, an anticoagulant, and intravenous fluids. Despite intensive care, the clinical parameters deteriorated, and the horse was euthanized 6 d later. Cytology confirmed septic pleuritis, with short chains or groups of coccoid bacteria. Anaerobic culture yielded gram-positive cocci from both hemithoraces in almost pure culture, which we identified as S. hillyeri by 16S rDNA and whole-genome analysis. Additionally, we identified 4 previously unassigned Streptococcus sp. sequences as S. hillyeri. Of these, 3 were obtained from aborted equine fetuses and a fourth from a donkey mastitis case, supporting the pathogenic nature of S. hillyeri in these host species.

Enhanced testing can substantially improve defense against several types of respiratory virus pandemic

Mass testing to identify and isolate infected individuals is a promising approach for reducing harm from the next acute respiratory virus pandemic. It offers the prospect of averting hospitalizations and deaths whilst avoiding the need for indiscriminate social distancing measures. To understand scenarios where mass testing might or might not be a viable intervention, here we modeled how effectiveness depends both on characteristics of the pathogen (R0, time to peak viral load) and on the testing strategy (limit of detection, testing frequency, test turnaround time, adherence). We base time-dependent test sensitivity and time-dependent infectiousness on an underlying viral load trajectory model. We show that given moderately high public adherence, frequent testing can prevent as many transmissions as more costly interventions such as school or business closures. With very high adherence and fast, frequent, and sensitive testing, we show that most respiratory virus pandemics could be controlled with mass testing alone.

Role of admission rapid antigen testing (RATs) for COVID-19 on patients transferred from acute hospitals to a postacute rehabilitation setting

BACKGROUND

Rapid antigen tests (RATs) are suitable for point-of-care testing, require no laboratory time, and give immediate results. However, are RATs useful for detecting asymptomatic COVID-19 infection when compared with polymerase chain reaction (PCR) testing in health care settings?

METHODS

RAT testing was carried out on all new admissions without a history of confirmed COVID-19 infection within 3 months of admission. PCR testing was carried out on all patients with a positive RAT for confirmation purposes. The cycle threshold values of COVID-19-detected results on PCR testing were examined to determine the utility of the RATs.

RESULTS

A total of 1,403 patients were transferred to the postacute rehabilitation unit from January to December 2023. The results of the study revealed an 85% accuracy of RATs with a 15% rate of false-negative results at the time of admission. All patients who had a positive RAT at the time of admission also had a positive PCR test.

CONCLUSIONS

This testing algorithm resulted in early detection and prompt isolation of positive cases reducing the likely spread of COVID-19 infection, hospital outbreaks, and bed/ward closures.

Refining genetic classification of global porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) and investigating their geographic and temporal distributions

Porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) primarily circulates in Europe but is also detected in North America and Asia. Based on ORF5 sequences, previous studies classified PRRSV-1 into four subtypes. Subtype 1 was further classified into 12 clades (A-L) or into three lineages with lineage 1 including clades 1A-1G and lineage 3 including clades 3A-3G, but the systems are inconsistent and have not been adopted. In this study, we proposed a statistically supported PRRSV-1 genetic classification system based on 10,446 global PRRSV-1 ORF5 sequences spanning 1991-2023. We replaced the colloquial "subtype" designation with "lineage" to reflect evolutionary history and, subsequently, PRRSV-1 was classified into four lineages (L1-L4) with L1 including 18 sublineages (L1.1 to L1.18). The proposed classification system is flexible and may be amended if additional lineages, sublineages, or more granular classifications are needed to reflect contemporary PRRSV-1 detections and evolution. Geographic distributions of PRRSV-1 at lineage and sublineage levels were distinct, with L1 globally distributed and L2, L3 and L4 more restricted. Temporal dynamic changes in some countries were quantified. Classification and ORF5 nucleotide identity of six commercial PRRSV-1 vaccines to each lineage and sublineage and detection frequency of vaccine-like viruses were determined. The phylogenies based on whole-genome and ORF5 sequences demonstrated slightly different tree topologies. Recombination of PRRSV-1 was observed at within-sublineage and between-sublineage levels. A set of ORF5 reference sequences representing the refined classification is available for future diagnostic and epidemiological applications. This study provides a benchmark delineating the current genetic diversity of PRRSV-1 and introduces a refined classification system to support the global standardization and application of ORF5-based genetic classification for PRRSV-1.

Estimating Mean Viral Load Trajectory From Intermittent Longitudinal Data and Unknown Time Origins

Viral load (VL) in the respiratory tract is the leading proxy for assessing infectiousness potential. Understanding the dynamics of disease-related VL within the host is of great importance, as it helps to determine different policies and health recommendations. However, normally the VL is measured on individuals only once, in order to confirm infection, and furthermore, the infection date is unknown. It is therefore necessary to develop statistical approaches to estimate the typical VL trajectory. We show here that, under plausible parametric assumptions, two measures of VL on infected individuals can be used to accurately estimate the VL mean function. Specifically, we consider a discrete-time likelihood-based approach to modeling and estimating partial observed longitudinal samples. We study a multivariate normal model for a function of the VL that accounts for possible correlation between measurements within individuals. We derive an expectation-maximization (EM) algorithm which treats the unknown time origins and the missing measurements as latent variables. Our main motivation is the reconstruction of the daily mean VL, given measurements on patients whose VLs were measured multiple times on different days. Such data should and can be obtained at the beginning of a pandemic with the specific goal of estimating the VL dynamics. For demonstration purposes, the method is applied to SARS-Cov-2 cycle-threshold-value data collected in Israel.

Presence of anti-SARS-CoV-2 antibodies in European bison (Bison bonasus) in Poland, 2019-2023

BACKGROUND

The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unknown. However, it is likely that the virus spillover occurred from an animal reservoir to humans. Identifying animal species susceptible to SARS-CoV-2 is crucial for understanding cross-species transmission to humans. This study distinguishes itself by focusing on the susceptibility of the European bison (Bison bonasus), an endangered species, to SARS-CoV-2. The objective of this study was to investigate the occurrence of SARS-CoV-2 antibodies in a substantial number (n = 238) of both free-living and captive Polish European bison using an in-house ELISA method and virus neutralization test (VNT).

RESULTS

The seroprevalence of SARS-CoV-2 infection was found to be 1.29% (3/232). None of the seropositive European bison tested positive in the virus neutralization test. All seropositive animals were part of captive herds.

CONCLUSIONS

This study represents the first report of SARS-CoV-2 seroprevalence in both free-ranging and captive European bison in Poland. Based on these findings, the European bison appears to be a less susceptible species to SARS-CoV-2. The most probable route of transmission was from humans to European bison, as all seropositive animals belonged to captive herds with contact with indirect human sources, such as tourists and keepers.

Boswellic Acids Reduce Systemic Inflammation in Patients with Moderate COVID-19 Through Modulation of NF-κB Pathway

Prevention and/or management of the dysregulated immune response in patients with COVID-19 is expected to help in the treatment of COVID-19. Boswellic acids (BAs) have great therapeutic potential because they have anti-inflammatory and immunomodulatory effects. Here, we aimed to investigate the mechanism of action of a BA formulation, Inflawell syrup, which was previously shown to be effective in reducing disease symptoms in patients who suffer from mild to moderate COVID-19. Patients with mild to moderate COVID-19 were treated with either Inflawell containing boswellic acids or a placebo for 14 days. The serum levels of inflammatory cytokines, including tumor necrosis factor-alpha (TNF-α), interleukin (IL)-8, IL-1α, IL-17, IL-1Ra, and Monocyte Chemoattractant Protein-1 (MCP-1), were measured both at study onset and on day 14 after treatment started. In addition, to further investigate the signaling pathway(s) underlying the changes in cytokine levels, we evaluated the expression of tumor necrosis factor receptor 1 (TNFR1), tumor necrosis factor receptor 2 (TNFR2), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) p65 mRNAs and phospho-inhibitor of nuclear factor kappa B (IκB) and IκB proteins. In our study, a significant decrease in the serum levels of IL-1α (p < .009), IL-8 (p < .04), TNF-α (p < .0001), and MCP-1 (p < .007) was detected in patients treated with Inflawell. Additionally, our data revealed a decrease in phospho-IκB protein levels (p < .02) and NF-κB p65 mRNA levels (p < .002), whereas the amount of IκB protein (p < .01) in the Inflawell group was significantly greater than that in the placebo group. Furthermore, despite the decreasing trend in the expression of TNFR1 and TNFR2 in the Inflawell group, there was no statistically significant difference compared with that in the placebo group. In general, treatment with Inflawell syrup led to a lower level of proinflammatory cytokines and a decrease in the activity of the TNF-α/NF-κB signaling pathway.

A comprehensive review of current insights into the virulence factors of SARS-CoV-2

The evolution of SARS-CoV-2 pathogenicity has been a major focus of attention. However, the determinants of pathogenicity are still unclear. Various hypotheses have attempted to elucidate the mechanisms underlying the evolution of viral pathogenicity, but a definitive conclusion has yet to be reached. Here, we review the potential impact of all proteins in SARS-CoV-2 on the viral pathogenic process and analyze the effects of their mutations on pathogenicity evolution. We aim to summarize which virus-encoded proteins are crucial in influencing viral pathogenicity, defined as disease severity following infection. Mutations in these key proteins, which are the virulence factors in SARS-CoV-2, may be the driving forces behind the evolution of viral pathogenicity. Mutations in the S protein can impact viral entry and fusogenicity. Mutations in proteins such as NSP2, NSP5, NSP14, and ORF7a can alter the virus's ability to suppress host protein synthesis and innate immunity. Mutations in NSP3, NSP4, NSP6, N protein, NSP5, and NSP12 may alter viral replication efficiency. The combined effects of mutations in the S protein and NSP6 can significantly reduce viral replication. In addition, various viral proteins, including ORF3a, ORF8, NSP4, Spike protein, N protein, and E protein, directly participate in the inflammatory process. Mutations in these proteins can modulate the levels of inflammation following infection. Collectively, these viral protein mutations can influence SARS-CoV-2 pathogenicity by impacting viral immune evasion, replication capacity, and the level of inflammation mediated by infection. In conclusion, the evolution of SARS-CoV-2 pathogenicity is likely determined by multiple virulence factors.

A novel neutralizing antibody recognizing a conserved conformational epitope in PDCoV S1 protein and its therapeutic efficacy in piglets

Porcine deltacoronavirus (PDCoV) is an enteric pathogen that burdens the global pig industry and is a public health concern. The development of effective antiviral therapies is necessary for the prevention and control of PDCoV, yet to date, there are few studies on the therapeutic potential of PDCoV-neutralizing antibodies. Here, we investigate the therapeutic potential of a novel monoclonal antibody (mAb 4A6) which targets the PDCoV S1 protein and effectively neutralizes PDCoV, both pre- and post-attachment on cells, with IC50 values of 0.537 and 8.487 µg/mL, respectively. A phage-display peptide library was used to determine the epitope recognized by mAb 4A6, and two mimotopes, QYPVSYA (P1) and FPHWPTI (P2), were identified. KLH-P1 reacted with PDCoV-positive sera but failed to induce PDCoV-specific IgG and neutralizing antibodies in mice, suggesting P1 does not fully mimic the conformational epitope. Molecular docking and alanine scanning mutagenesis revealed that S461, P462, T463, E465, and Y467 on the S protein are essential for mAb 4A6 binding. Antibody therapy experiments in PDCoV-infected piglets showed that administering mAb 4A6 once or twice could delay the onset of diarrhea symptoms, reduce the severity of diarrhea, and decrease virus shedding. Taken together, our findings demonstrate that mAb 4A6 holds promise as a treatment against PDCoV, and the amino acids recognized by mAb 4A6 will be valuable for developing novel epitope-based vaccines or antiviral drugs.

IMPORTANCE

Porcine deltacoronavirus (PDCoV) is a novel swine enteropathogenic coronavirus that poses a potential threat to public health. Developing effective antiviral therapies is crucial for its prevention and control. Here, we demonstrated that mAb 4A6 shows promise as a treatment against PDCoV. Antibody therapy experiments conducted on PDCoV-infected piglets revealed that administering mAb 4A6 once or twice could delay the onset of diarrhea symptoms, reduce the severity of diarrhea, and decrease virus shedding. Furthermore, we characterized the conformational epitope (S461, P462, T463, E465, and Y467) recognized by mAb 4A6 through an integrated approach involving phage display peptide library, molecular docking, and alanine scanning mutagenesis. More importantly, mAb 4A6 exhibits a broad-spectrum neutralizing activity against different PDCoV strains. These findings indicate that mAb 4A6 has promising therapeutic value for PDCoV-infected piglets, and the identification of mAb 4A6 recognized epitope may provide a new idea for the identification of conformational epitopes.

SARS-CoV-2 outbreak in lions, tigers, and hyenas at Denver Zoo

In late 2019, SARS-CoV-2 spilled over from an animal host into humans, where it efficiently spread, resulting in the COVID-19 pandemic. Through both natural and experimental infections, we learned that many animal species are susceptible to SARS-CoV-2. Importantly, animals in close proximity to humans, including companion, farmed, and those at zoos and aquariums, became infected, and many studies demonstrated transmission to/from humans in these settings. In this study, we first review the literature of SARS-CoV-2 infections in tigers and lions and compare species, sex, age, virus and antibody detection assay, and types, frequency, and length of clinical signs, demonstrating broad heterogeneity among infections. We then describe a SARS-CoV-2 outbreak in lions, tigers, and hyenas at Denver Zoo in late 2021. Animals were tested for viral RNA (vRNA) for 4 months. Lions had significantly more vRNA in nasal swabs than both tigers and hyenas, and many individual lions experienced viral recrudescence after weeks of undetectable vRNA. Infectious virus was correlated with high levels of vRNA and was more likely to be detected earlier during infection. Four months post-infection, all tested animals generated robust neutralizing antibody titers. Animals were infected with Delta lineage AY.20 identical to a variant circulating at less than 1% in Colorado humans at that time, suggesting a single spillover event from an infected human spread within and between species housed at the zoo. Better understanding of epidemiology and susceptibility of SARS-CoV-2 infections in animals is critical to limit the current and future spread and protect animal and human health.IMPORTANCESurveillance and experimental testing have shown many animal species, including companion, wildlife, and conservatory, are susceptible to SARS-CoV-2. Early in the COVID-19 pandemic, big cats at zoological institutions were among the first documented cases of naturally infected animals; however, challenges in the ability to collect longitudinal samples in zoo animals have limited our understanding of SARS-CoV-2 kinetics and clearance in these settings. We measured SARS-CoV-2 infections over 4 months in lions, tigers, and hyenas at Denver Zoo and detected viral RNA, infectious virus, neutralizing antibodies, and recrudescence after initial clearance. We found lions had longer and higher levels of virus compared to the other species. All animals were infected by a rare viral lineage circulating in the human population, suggesting a single spillover followed by interspecies transmission. These data are important in better understanding natural SARS-CoV-2 spillover, spread, and infection kinetics within multiple species of zoo animals.

Disease dynamics and mortality risk in tapirs (Perissodactyla: Tapiridae) through a systematic literature review: Implications for preventive medicine and conservation

The impact of diseases on tapir mortality and potential implications for preventive medicine and conservation remain unclear. A systematic literature review was conducted using seven databases and grey literature to address these gaps. The PRISMA statement was adopted to report results, and boosted regression tree models were employed for data analysis. After screening 5323 records and removing duplicates, the title and abstract of 2484 records were assessed. Out of 502 eligible studies, only 206 met all inclusion criteria. These were published between 1924 and 2023 in ten languages, comprising mainly case reports (45.1 %) and cross-sectional studies (41.3 %). Infectious diseases were found in 72.9 % of the reports, and 27.2 % presented clinical signs. The most affected systems were gastroenteric (22.7 %), integumentary (22.1 %), and respiratory (17.5 %). Respiratory diseases were associated with increased mortality. Factors affecting tapir mortality included species (relative influence 41.5 %), followed by geographic location (23.5 %) and captivity (16.8 %). Clinical signs were the least important variable (4 %). While infectious diseases were associated with higher mortality risk, tapirs were more likely to become ill from non-infectious than infectious diseases. Captive individuals were also more likely to present with illness than their wild counterparts. When considering external causes, vehicle collisions represented the most significant cause of death (52.2 %), followed by hunting (38.2 %). Diseases (8.7 %) were the third most important, with bacterial infections the leading cause of death. This review represents the most comprehensive overview on tapir health to date and provides novel ways to collate epidemiological data from disparate study designs.

Identification and pathogenicity of avian hepatitis E virus from quail

BACKGROUND

Avian hepatitis E virus (HEV) has caused economic losses in the poultry industry and has shown a broad spectrum of infections. In 2022, a quail farm (YangLing, China) exhibited a decrease in egg production, an increase in mortality and hepatosplenomegaly. These characteristics were similar to those of avian HEV infection. To determine whether avian HEV existed on this farm and further clarify the pathogenicity caused by avian HEV under experimental conditions, the livers and spleens were collected from the diseased quails in the field for gross lesion observation and avian HEV detection; then, the pathogenicity was characterized.

RESULTS

In the field, the results showed enlargement of the liver and spleen and hemorrhage spots on the liver, and the amplified fragment (330-bp length) of HEV shared 100% identity with the Chinese avian HEV strain. The pathogenicity of this virus in quail was characterized by decreased egg production, seroconversion, viremia, fecal virus shedding, liver lesions and HEV antigen in the liver under experimental conditions. These differences indicated that there may be other pathogens or factors causing this disease together on the quail farm in addition to avian HEV, and further detection should be performed.

CONCLUSIONS

Overall, this is the first study to detect HEV RNA in quails, and an avian HEV strain can successfully infect quails under experimental conditions.