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.

The role and implication of rotavirus VP8∗ in viral infection and vaccine development

Rotaviruses (RVs) are major causative agents of diarrhea in both humans and animals worldwide. Despite the successful development of live attenuated vaccines, the efficacy of these vaccines remains low in developing countries and RV infections still result in more than 200,000 deaths in children under 5 years old globally each year. These viruses are also an enteric pathogen for agricultural animals and have caused substantial economic losses annually to the animal livestock industry. Frequent reassortment and the emergence of new RV strains continue to pose a significant challenge to human and agricultural animal health. Attachment to susceptible cells by recognizing cell surface glycans is the first step of the RV lifecycle, which is directed by the RV spike protein VP8∗. VP8∗-host glycan receptor interactions are thought to be strain-specific and play an important role in RV replication fitness, tropism, and cross-species transmission. This review will summarize the current understanding of the roles of VP8∗ in engagement of glycan receptors and its functional consequences in impacting RV replication fitness and host ranges. The current progress towards developing a VP8∗-based RV vaccine is also discussed in the review.

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.

Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia

BACKGROUND

Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.

METHODS

Fecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.

RESULTS

The metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.

CONCLUSIONS

To our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.

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.

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.

Daidzein effectively mitigates amyloid-β-induced damage in SH-SY5Y neuroblastoma cells and C6 glioma cells

Alzheimer's disease (AD) is the most debilitating form of dementia, characterized by amyloid-β (Aβ)-related toxic mechanisms such as oxidative stress, neuroinflammation, and mitochondrial dysfunction. The development of AD is influenced by environmental factors linked to lifestyle, including physical and mental inactivity, diet, and smoking, all of which have been associated with the severity of the disease and Aβ-related pathology. In this study, we used differentiated SH-SY5Y neuroblastoma and C6 glioma cells to investigate the neuroprotective and anti-inflammatory effects of daidzein, a naturally occurring isoflavone, in the context of Aβ oligomer-related toxicity. We observed that pre-treatment with daidzein prevented Aβ-induced cell viability loss, increased oxidative stress, and mitochondrial membrane potential decline in both SH-SY5Y and C6 cells. Furthermore, daidzein application reduced elevated levels of MAPK pathway proteins, pro-inflammatory molecules (cyclooxygenase-2 and IL-1β), and pyroptosis markers, including caspase-1 and gasdermin D, all of which were increased by Aβ exposure. These findings strongly suggest that daidzein alleviates inflammation and toxicity caused by Aβ oligomers. Our results indicate that daidzein could be a potential therapeutic agent for AD and other Aβ-related neurodegenerative diseases.

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.

Genomic characteristics and epidemic trends of NADC30-like PRRSV in China

BACKGROUND

NADC30-like PRRSV was first identified in China in 2012 and had become the predominant circulating strain since 2016. Currently, the recombination patterns of NADC30-like PRRSV in China exhibit a high degree of complexity, characterized by low whole-genome sequence homology. The genomic features and epidemiological trends of these strains remain to be elucidated.

RESULTS

To evaluate the prevalence of NADC30-like PRRSV in China, this study acquired 30 whole-genome sequences of NADC30-like strains via Next-Generation Sequencing (NGS). These sequences were subsequently integrated with 224 whole-genome sequences from China available in the GenBank database. A comprehensive analysis of the genomic characteristics of contemporary NADC30-like PRRSV strains in China was conducted. Recombinant analysis indicated a yearly increase in the number of NADC30-like strains exhibiting recombination signals, whereas nonrecombinant NADC30-like strains have become nearly extinct. Among the recombination events, those involving L1C and L8E as parental strains are most prevalent. Based on the results of recombination and phylogenetic analyses, this study classified 120 Chinese NADC30-like strains with similar recombination characteristics into groups NADC30-R1 to R12. The intra-group genetic distances of the NADC30-R1 to R12 groups approximately 5.73% (SD ± 1.68), while the inter-group genetic distances between different groups are usually stably greater than 10%. The amino acid alignment of Nsp2 demonstrated that all NADC30-R1 to R12 strains exhibit a discontinuous deletion of 131 amino acids. These classifications do not exhibit consistent pathogenic characteristics within groups, with most NADC30-like PRRSVs showing moderate virulence. Geographical distribution analysis indicated that NADC30 whole-genome sequences in China originated from 19 provinces. Notably, the NADC30-R1 and NADC30-R2 strains are the most widely distributed and abundant, suggesting that these variants have established localized epidemics in specific regions.

CONCLUSION

In summary, the vast majority of NADC30-like strains in our country have undergone recombination, L1C + L8E is the most common recombination mode. The NADC30-like strains in China can be classified into 12 different recombination patterns, NADC30-R1 and NADC30-R2 strains are already showing pandemic trends. These findings provide a critical foundation for future NADC30-like PRRSV prevention and control strategies.

Binding of transmissible gastroenteritis virus and porcine respiratory coronavirus to human and porcine aminopeptidase N receptors as an indicator of cross-species transmission

Coronaviruses have the ability to overcome interspecies barriers and adapt to new hosts, posing significant epidemic risks in cases of zoonotic transmission to humans. A critical factor in this process is the interaction between coronavirus spike proteins and host cell surface receptors, which plays an important role in infection and disease progression. This study focused on two representatives of coronaviruses: transmissible gastroenteritis virus (TGEV) and its mutant, porcine respiratory coronavirus (PRCV), both of which naturally cause disease in pigs. A phylogenetic analysis of previously identified strains of these viruses was performed, and the conservation of receptor-binding domain (RBD) sequences within their spike proteins was evaluated. In silico modeling was performed for complexes of the RBDs from 16 virus strains with porcine aminopeptidase N (APN), as well as for putative complexes with the human APN receptor. The binding free energy of these modeled complexes was evaluated, along with the impact of more than 500 theoretical mutations in the RBD. The computational results suggest that the TGEV 133 strain exhibits the highest affinity for both porcine and human receptors, with only two additional mutations required to further enhance this affinity. Molecular dynamics simulations were conducted for porcine and human APN complexes with known TGEV strains (Purdue and 133) as well as a theoretical mutated strain. These simulations reveal differences in the dynamic behavior of complexes with porcine and human receptors and support the hypothesis that mutagenesis at a few key amino acid residues in the RBD could enable TGEV to achieve affinity for human APN comparable to that of its natural host receptor. The findings underscore a theoretical risk of zoonotic transmission of these coronaviruses to humans, emphasizing the importance of further monitoring these pathogens.

Occurrence and Epidemiology of Bovine Coronavirus in Cattle in Kazakhstan

Bovine coronavirus (BCoV) causes gastrointestinal and respiratory diseases in cattle, but its prevalence in Kazakhstan remains unknown. This nationwide cross-sectional study aimed to assess BCoV prevalence in cattle and to investigate its epidemiological characteristics. Between April and August 2024, serum, nasal and rectal swab samples were collected from 2,237 clinically healthy cattle across 390 farms in 17 oblasts of Kazakhstan. None of the farm owners reported vaccinating against BCoV. Serum samples were tested for BCoV-specific antibodies using a commercially available ELISA, while nested RT-PCR assays were performed on pooled nasal and rectal swabs to detect BCoV RNA. Sequencing and phylogenetic analysis were performed following RT-PCR testing. A univariate GEE model was used to assess the risk factors and a multivariate model was employed to refine the discovered associations. The animal-level seroprevalence of BCoV was 88.2% (95% CI: 84.3%-92.0%), while the herd-level seroprevalence was 89.6% (95% CI: 85.4%-92.9%). The eastern region of Kazakhstan had the lowest seroprevalence compared to other regions. Seropositivity was not associated with age, sex or breed, but correlated with the proportion of cattle in backyards, cattle density and farm size. BCoV shedding was detected in 2.4% (95% CI: 1.4 5% - 3.4%) of sampled animals and in 7.8% (95%CI: 5.3% - 11.0%) of cattle operations across 12 oblasts. Phylogenetic analysis of the complete hemagglutinin/esterase and spike genes revealed that the Kazakhstani BCoV strains belonged to the GIIa group. This first report on BCoV in Kazakhstan confirms its endemic presence, highlighting the need for a national control program.

Development and identification of porcine monoclonal antibodies against PEDV from single B cells

Porcine epidemic diarrhea virus (PEDV) is a swine enteropathogenic coronavirus causing severe diarrhea and high mortality in neonatal piglets. Pigs of all ages are susceptible to PEDV, and the humoral immune response plays an important role in preventing PEDV infection. However, there is little information on monoclonal antibodies (mAbs) against PEDV derived from single B cells of pigs. In this study, we aimed to develop mAbs using antigen-specific single B cells from peripheral blood mononuclear cells (PBMCs) of pigs via fluorescence-activated cell sorting (FACS). Subsequently, the variable region genes of pig-derived mAbs were amplified and cloned into the plasmid pcDNA3.4 bearing the constant region gene of porcine-derived antibody. Pig-derived mAbs were expressed by transfecting the resultant antibody plasmids into HEK293F cells and validated using indirect Enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence assay (IFA), and Western blotting. The results showed 60 double-positive (antigen+ and IgG+) single B cells were obtained by flow sorting, of which 36 were positive for PEDV and 24 were positive for the N protein of PEDV. A total of 21 mAbs were expressed and purified. Indirect ELISA results showed that 20 bound specifically to PEDV, 19 recognized the N protein, and none reacted with S1D protein. Seven mAbs reacted with PEDV HN2021, as revealed by IFA. Western blotting showed that three N protein-specific mAbs identified linear epitopes, while the remaining 16 N protein-specific mAbs may recognize conformational epitopes. This study laid a foundation for the structural analysis of PEDV and the development of diagnostic reagents and antiviral drug.

Post-recovery viral shedding shapes wastewater-based epidemiological inferences

BACKGROUND

The prolonged viral shedding from the gastrointestinal tract is well documented for numerous pathogens, including SARS-CoV-2. However, the impact of prolonged viral shedding on epidemiological inferences using wastewater data is not yet fully understood.

METHODS

To gain a better understanding of this phenomenon at the population level, we extended a wastewater-based modeling framework that integrates viral shedding dynamics, viral load data in wastewater, case report data, and an epidemic model.

RESULTS

Our results indicate that as an outbreak progresses, the viral load from recovered individuals gradually becomes predominant, surpassing that from the infectious population. This phenomenon leads to a dynamic relationship between model-inferred and reported daily incidence over the course of an outbreak. Sensitivity analyses on the duration and rate of viral shedding for recovered individuals reveal that accounting for this phenomenon can considerably advance prediction of transmission peak timing. Furthermore, extensive viral shedding from the recovered population toward the conclusion of an epidemic wave may overshadow viral signals from newly infected cases carrying emerging variants, which can delay the rapid recognition of emerging variants based on viral load.

CONCLUSIONS

These findings highlight the necessity of integrating post-recovery viral shedding to enhance the accuracy and utility of wastewater-based epidemiological analysis.

SARS-CoV-2 accessory proteins ORF3a and ORF6 alter the miRNome of human lung epithelial cells

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19. The accessory proteins of SARS-CoV-2 have been reported to attune host immune responses and viral pathogenicity. We have studied the effect of SARS-CoV-2 accessory proteins ORF3a and ORF6 on the expression pattern of miRNAs and their impact on cell signaling pathways in human lung epithelial cells.

METHODS AND RESULTS

The miRNA expression profiling of human lung epithelial cells revealed a subset of 14 and 19 differentially expressed miRNAs (DEMs) in response to SARS-CoV-2 ORF3a and ORF6, respectively. Target prediction tools and subsequent bioinformatic analysis revealed the involvement of DEMs in key signaling pathways like PI3K/AKT, TNF, MAPK, TGF-β, and NF-κB, as a bystander effect of SARS-CoV-2 ORF3a and ORF6. The target genes were validated using real-time PCR and immunoblotting techniques. The results demonstrate that SARS-CoV-2 ORF3a and ORF6 exploit host cellular miRNAs such as hsa-miR-101-3p, hsa-miR-4455, hsa-miR-10b-5p, hsa-miR-940, and hsa-miR-4483, etc. to modulate the key cellular signaling pathways like NF-κB, TGF-β, Ras, IL-17, MAPK, and TNF signaling pathways.

CONCLUSIONS

The present study demonstrates that SARS-CoV-2 ORF3a and ORF6 modulate the miRNA expression pattern in human lung epithelial cells. ORF3a exploits miRNAs to trigger a pro-inflammatory response, while ORF6 antagonizes IFN signaling via miRNA dysregulations to help SARS-CoV-2 in evading the host's immune response.

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.

Genomic sequencing and evolutionary analysis of bovine kobuvirus in Yunnan Province, China

BACKGROUND

Bovine Kobuvirus (BKV) is an emerging pathogen associated with diarrhea in cattle. Limited reports on its prevalence and genetic characteristics are available. To determine the epidemiology and genetic evolution of BKV strains circulating in Yunnan Province, China, 204 diarrheal samples were collected from cattle farms across five regions for screening for BKV infection.

RESULTS

RT-PCR analysis identified 40 BKV-positive samples, yielding an infection rate of 19.6%. Positive samples were inoculated into Vero cells for continuous passage, followed by molecular biology, immunofluorescence, and electron microscopy identification. Two BKV strains, BKV YN-1 2023 and YN-2 2023, were isolated. Whole-genome sequencing revealed genome lengths of 8289 bp and 8291 bp (GenBank No. PV410179 and PV410180), respectively. Phylogenetic analysis demonstrated that both strains belong to genotype B, the dominant genotype circulating in China, and are closely related to the previously reported Chinese strain BKV 13/2021. The genetic similarity of two BKV isolates was analyzed. Genome-wide nucleotide identities ranged from 39.9 to 93.9%, with the highest similarity to BKV13 2021 CHN. ORF analysis showed nucleotide and amino acid similarities of 48.7-93.9% and 29.3-98.5%, respectively. Compared to the BKV13 2021 CHN, both isolates exhibited high conservation in VP0, VP3, and nonstructural proteins (97.8-100%), while the L protein had the lowest similarity (94.7-95.2%). The 5' UTR showed lower conservation than the 3' UTR, suggesting regulatory variations.

CONCLUSIONS

These findings reveal that the circulating BKV strains in Yunnan belong to the globally prevalent genotype B and are widely distributed. This study provides valuable insights into the molecular epidemiology, genetic diversity and evolutionary dynamics of BKV, offering an important reference for developing diagnostics, vaccines and further studies on its pathogenesis.

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.

Genetic and Pathogenic Characterization of a Porcine Deltacoronavirus Strain Isolated in Zhejiang Province, China

Porcine deltacoronavirus (PDCoV) has emerged as a significant pathogen in swine, affecting animal health and posing potential risks for cross-species transmission. In this study, we successfully isolated a PDCoV strain named HZYH-2019 from the feces of diarrheal sows in Zhejiang Province, China. The viral growth curve demonstrated strong adaptation of this strain to cells, with particularly high replication efficiency observed in LLC-PK1 cells. Genomic analysis revealed a high degree of nucleotide sequence similarity between PDCoV HZYH-2019 and other PDCoV strains. A notable mutation at the tenth amino acid position of the spike protein altered the predicted signal peptide position. Phylogenetic analyses indicated that PDCoV HZYH-2019 clustered with Chinese strains, while four Chinese strains were grouped within the American spectrum, suggesting that the pork trade may facilitate cross-border virus transmission. Analysis of known PDCoV strains inferred that PDCoV may have originated in Asia and that there is cross-species transmission from birds to mammals. Notably, PDCoV HZYH-2019 caused diarrhea in piglets without mortality, although significant intestinal lesions were observed. These findings enhance our understanding of PDCoV's biological behavior and zoonotic potential, informing the development of effective vaccines and control measures to manage future outbreaks.

Epidemiological investigation, isolation, and pathogenicity of porcine epidemic diarrhea virus subtype G2c in Sichuan province

Continued outbreaks of porcine epidemic diarrhea are causing serious economic losses to the swine industry in China. To monitor the prevalence, genetic mutations, and pathogenicity of porcine epidemic diarrhea virus (PEDV), 172 samples were collected from eight cities in Sichuan Province from 2020 to 2022. RT-PCR analysis revealed that 25.0% (43/172) of samples were positive for PEDV. Phylogenetic analysis of 17 S gene sequences (encoding the spike protein) showed that G2c was the main genotype circulating in Sichuan. One strain, Leshan-s-2020 (G2a), was identified as a recombinant resulting from inter-lineage recombination between the KM609212/LYG/2015 (G2a) and MianYang-s-2020 (G2a) strains in the S2 domain. In addition, the G2c strain YB2201, which was highly virulent in 4-day-old piglets, was successfully isolated. The results of this study enrich our understanding of the epidemiology of PEDV, the genetic characteristics and pathogenicity of the PEDV strains circulating in China, and the role of recombination in their evolution. These findings may contribute to the development of antigen detection reagents and vaccines.

Dynamic Alterations of the Intestinal Microbiome and Metabolome During Transmissible Gastroenteritis Virus Infection in Weaned Pigs

Transmissible gastroenteritis virus (TGEV) infection induces diarrhea in piglets by targeting the small intestine, especially the jejunum and ileum. However, dynamic changes in the gut microbiota and metabolome during TGEV infection remain unclear. This study investigated these alterations and their association with intestinal damage in weaned pigs during early TGEV infection. Thirty 4-week-old pigs were allocated randomly into TGEV-inoculated and mock groups. On days 3, 5, and 7 postinoculation, intestinal tissue and fecal samples were collected. Full-length 16S rRNA sequencing and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC‒MS/MS) were employed to analyze microbiota composition and nontargeted metabolites. TGEV infection resulted in reduced villous height-to-crypt depth (VH:CD) ratios (P < 0.01) and significantly altered microbial diversity (P = 0.0091 in jejunum) and composition (P = 0.001). Notably, infected pigs showed increased abundances of Lactobacillus and Limosilactobacillus species. The VH:CD ratio correlated with the overall taxonomic composition in both the jejunum and ileum (r = 0.4, P < 0.001) and was positively associated with microbial functions such as aerobic chemoheterotrophy and chitinolysis in the jejunum. Fecal metabolomics revealed 1,815 and 892 differentially expressed metabolites in the jejunum and ileum, respectively, including amino acids, fatty acids, and intermediates of energy metabolism. Integrated analysis revealed that Lactobacillus amylovorus DSM20531 was positively correlated with linoleic acid, L-tyrosine, and citric acid, whereas Lactococcus lactis showed a negative correlation with isocitric acid and glutamine. This study enhances our understanding of the pathogenesis of TGEV and provides potential microbial and metabolic biomarkers for future diagnostic and preventive strategies.

Infectious potential and circulation of SARS-CoV-2 in wild rats

Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, a wide range of animal species (pets, mink…) have been naturally infected with this betacoronavirus. The emergence of new variants has increased the ability of SARS-CoV-2 to infect species that were not susceptible to the "original" SARS-CoV-2, such as mice and rats. This work attempted to evaluate the role of urban rats in the SARS-CoV-2 transmission by combining surveillance studies of rat populations in urban environments, in vivo experimental inoculation of SARS-CoV-2 and comparative viral-receptor interaction in silico analyses. We studied the circulation of SARS-CoV-2 in wild Rattus norvegicus (n = 401) captured in urban areas and sewage systems of several French cities. Except for 3 inconclusive samples (2/75 from Bordeaux and 1/261 from Lyon) none of the 353 sera tested showed anti-SARS-CoV-2 antibodies by microsphere immunoassay. However, the 3 inconclusive sera samples were negative by virus neutralisation assay. No SARS-CoV-2 viral RNA was detected in all lungs collected from the 401 captured urban brown rats. In complement, four rat groups (two wild-type colonies, Rattus norvegicus and Rattus rattus, and two laboratory strains, Sprague-Dawley and Wistar) were inoculated with the SARS-CoV-2 Omicron BA.5. At 4 days post-inoculation, no infectious viral particles were detected in the lungs and upper respiratory tract (URT) while viral RNA was detected at a low level only in the URT of all groups. In addition, seroconversion was observed 14 days after inoculation in the four groups. By molecular modelling, the Omicron BA.5 receptor binding domain (RBD) had lower affinities for Rattus norvegicus and Rattus rattus ACE2 than Homo sapiens ACE2. Based on these results the SARS-CoV-2 Omicron BA.5 was unable to infect laboratory and wild type rats. In addition, Rattus norvegicus collected for this study in different areas of France were not infected with SARS-CoV-2.

Tapping into Metabolomics for Understanding Host and Rotavirus Group A Interactome

Group A rotavirus continues to be a leading global etiological agent of severe gastroenteritis in young children under 5 years of age. The replication of this virus in the host is associated with the occurrence of Lewis antigens and the secretor condition. Moreover, histo-blood group antigens (HBGAs) act as attachment factors to the outer viral protein of VP4 for rotavirus. Therefore, in this study, we employed a metabolomic approach to reveal potential signature metabolic molecules and metabolic pathways specific to rotavirus P[8] strain infection (VP4 genotype), which is associated with the expression of HBGA combined secretor and Lewis (Le) phenotypes, specifically secretor/Le(a+b+). Further integration of the achieved metabolomics results with lipidomic and proteomics metadata analyses was performed. Saliva samples were collected from children diagnosed as negative or positive for rotavirus P[8] strain infection (VP4 genotype), which is associated with the HBGA combined secretor/Le(a+b+). A total of 22 signature metabolic molecules that were downregulated include butyrate, putrescine, lactic acid, and 7 analytes. The upregulated metabolic molecule was 2,3-Butanediol. Significant pathway alterations were also specifically observed in various metabolism processes, including galactose and butanoate metabolisms. Butyrate played a significant role in viral infection and was revealed to exhibit different reactions with glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, and fatty acyls. Moreover, butyrate might interact with protein receptors of free fatty acid receptor 2 (FFAR2) and free fatty acid receptor 3 (FFAR3). The revealed metabolic pathways and molecule might provide fundamental insight into the status of rotavirus P[8] strain infection for monitoring its effects on humans.

A single recall vaccination lapse in sows triggers PRRSV resurgence and boosts viral genetic diversity

BACKGROUND

Porcine reproductive and respiratory syndrome virus (PRRSV) persists on certain farms despite vaccination and control efforts, with genetic diversity suspected as a contributing factor. This study examined the evolution and persistence dynamics of PRRSV-1 on a farrow-to-fattening farm with 1,700 sows vaccinated quarterly, focusing on a summer vaccination lapse.

RESULTS

Over eight months, three farrowing batches were monitored from birth to nine weeks of age using virological (RT-qPCR, whole-genome, and ORF5 sequencing) and serological (ELISA and neutralizing antibody) analyses. An incident related to elevated temperatures during the summer involving unproper vaccine handling occurred during the last blanket vaccination, before sampling the third batch. Viral circulation was primarily confined to the nurseries, with a notable surge of incidence and mortality in this last batch, linked to lower maternal antibody levels likely due to vaccination failure. Phylogenetic analyses showed the persistence of the same viral strain throughout the study, with increased genetic diversity in Batch 3 driven by selection and recombination. Ultimately, reestablishing the vaccination program led to a PRRSV-positive-stable with vaccination status.

CONCLUSIONS

Overall, a single vaccination lapse caused increased PRRSV-1 incidence and genetic diversity in weaners, linked to declining maternal antibody levels, underscoring the importance of strict vaccination adherence.

Isolation and Characterization of Porcine Epidemic Diarrhea Virus G2c Strains Circulating in China from 2021 to 2024

Porcine epidemic diarrhea virus (PEDV) is a major pathogen responsible for viral diarrhea in pigs, causing particularly high mortality in neonatal piglets. In recent years, genetic variations in PEDV have resulted in alterations in both its virulence and antigenicity, leading to a reduced efficacy of existing vaccines. In this study, diarrheal samples were collected from four commercial pig farms in the Hubei, Guangxi, and Jiangxi provinces, China, which experienced vaccine failure. RT-qPCR confirmed PEDV infection, and three PEDV strains, 2021-HBMC, 2024-JXYX, and 2024-JXNC, were successfully isolated. Sequence analysis and phylogenetic tree construction classified these strains into the G2c genotype, the predominant subtype in China. The neutralization assays revealed a significant reduction in the neutralizing titers of these strains against the immune serum compared with the AJ1102 reference strain. Further amino acid sequence analysis of the spike (S) protein identified several mutations in key neutralizing epitopes compared with the AJ1102 strain, including S27L, E57A, N139D, M214T, and P229L in the S-NTD epitope; A520S, F539L, K566N, D569E, G612V, P634S, E636V/K in the COE epitope; and Y1376H in the 2C10 epitope, along with several deletions at N-glycosylation sites (347NSSD and 510NITV). Additionally, whole-genome sequencing and recombination analysis indicated that the 2021-HBMC strain may have resulted from a recombination event. The findings of this study underscore the challenge posed by the continuous genetic evolution of PEDV to vaccine efficacy and provide valuable insights for future vaccine development and control strategies.

Non-Secretor Status Due to FUT2 Stop Mutation Is Associated with Reduced Rotavirus Infections but Not with Other Enteric Pathogens in Rwandan Children

Enteric pathogens remain a health threat for children in low-income countries. A single nucleotide polymorphism (SNP) in the FUT2 gene that precludes the expression of fucosyltransferase 2 has been reported to influence the susceptibility to rotavirus and norovirus infections. The aim of this study was to investigate the association between G428A at rs601338 (stop codon variant) in the FUT2 gene and a range of enteric pathogens in children under 5 years of age. Rectal swab samples from 668 children (median age 13.6 months, 51% males, 93% rotavirus vaccinated, 468 with diarrhea) from Rwanda were analyzed via PCR for pathogen detection and SNP genotyping. A FUT2 stop codon ('non-secretor' status) was found in 19% of all children. Rotavirus was detected in 5.3% of non-secretors compared with in 13% of secretors (OR = 0.39, p = 0.019). Rotavirus P[8] was the predominant genotype and was found in 2.3% of non-secretors compared with 8.8% of secretors (p = 0.009). There was no association with any other pathogen, including noroviruses, of which 2 of 14 GII.4 infections were detected among non-secretors. Thus, the FUT2 stop codon variant was associated with rotavirus but not with any other pathogen.

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.

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.

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.

Evaluation of an N1 NA antibody-specific enzyme-linked lectin assay for detection of H5N1 highly pathogenic avian influenza virus infection in vaccinated birds

Unprecedented H5N1 highly pathogenic avian influenza (HPAI) outbreaks are occurring around the world and there is growing interest in the use of vaccines in affected regions. Vaccination when properly applied can contribute to HPAI control by significantly reducing virus shedding and breaking the transmission chain, but it requires robust surveillance to ensure that international trade is not affected. Thus, it is imperative to establish a test to differentiate vaccinated only animals from vaccinated and then infected animals (DIVA). In this study, we applied enzyme-linked lectin assay (ELLA) to specifically detect N1 neuraminidase (NA) antibody by inhibition of NA activity and provide a proof-of-concept bench validation using reference and experimental serum samples. We used a wild-type low pathogenic H7N1 virus of North American lineage as the ELLA antigen. The NA inhibition ELLA (NI-ELLA) was evaluated for its specificity and sensitivity using reference and experimental samples. The results demonstrated that the NI-ELLA was highly specific with low background NI activity against influenza-negative sera from different species although varying level of cross-reactivity was observed against sera of different NA subtypes with highest cross-reactivity against N4 subtype sera. Using a conservative positive cut-off threshold of 50 % NI activity, NI-ELLA provides 100 % specificity with all reference sera of 9 different NA subtypes. The relative sensitivity of NI-ELLA was evaluated in detecting H5N1 infection in vaccinated and then challenged birds and NI-ELLA showed higher detection rate of H5N1 infection compared with commercial NP ELISAs and real-time RT-PCR. Overall, the NI-ELLA shows high specificity and sensitivity and has the potential for application in DIVA surveillance with further validation.

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.

Current Evolutionary Dynamics of Porcine Epidemic Diarrhea Virus (PEDV) in the U.S. a Decade After Introduction

Porcine Epidemic Diarrhea Virus (PEDV) was introduced in the United States (U.S.) in 2013, spreading rapidly and leading to economic losses. Two strains, S-INDEL and non-S-INDEL, are present in the U.S. We analyzed 313 genomes and 556 Spike protein sequences generated since its introduction. PEDV case numbers were highest during the first two years after its introduction (epidemic phase), then declined and stabilized in the following years (endemic phase). Sequence surveillance was higher during the initial epidemic phase. Our results suggest the non-S-INDEL strain is the predominant strain in U.S. The non-S-INDEL sequences exhibit pairwise nucleotide identity percentages above 97.6%. Most non-S-INDEL sequences sampled after 2017 clustered into two sub-clades. No descendants derived from other clades present in the epidemic period were detected in the contemporary data, suggesting that these clades are no longer circulating in the U.S. The two clades currently circulating are restricted to two respective geographic regions and our results suggest limited inter-regional spread. This insight helps determine the risk of re-introduction of PEDV if it were regionally eliminated. Ongoing molecular surveillance is essential to confirming that some older clades no longer circulate anymore in the U.S., mapping the distribution and spread of recent clades, and understanding PEDV's evolutionary diversification.

Trends and Challenges in the Detection and Environmental Surveillance of the Hepatitis E Virus

The Hepatitis E virus (HEV) is responsible for causing Hepatitis E, a zoonotic disease that has emerged as a significant global health concern, accounting for about 20 million infections and 70,000 deaths annually. Although it is often recognized as a disease that is acute in low-income countries, HEV has also been recognized as a zoonotic disease in high-income countries. The zoonotic transmission requires flexible approaches to effectively monitor the virus, vectors, and reservoirs. However, the environmental monitoring of HEV presents additional challenges due to limitations in current detection methods, making it difficult to accurately assess the global prevalence of the virus. These challenges hinder efforts to fully understand the scope of the disease and to implement effective control measures. This review will explore these and other critical concerns, addressing gaps in HEV research and highlighting the need for improved strategies in the monitoring, prevention, and management of Hepatitis E using a One Health approach.

Immune Protection Gap Between Porcine Reproductive and Respiratory Syndrome Subunit Vaccine (N Protein) and Live Vaccine

Objectives: To evaluate the immunoprotective effect of a PRRSV N protein subunit vaccine on piglets using a live PRRSV vaccine as a control. Methods: The HEK-293T eukaryotic expression system was used to produce PRRSV N protein, and then PRRSV N protein was immunized with a commercial live PRRS vaccine. The immunoprotective effect of the PRRSV N protein subunit vaccine on piglets was evaluated by detecting the antibody level in the immunized piglets, and the clinical symptoms, pathological changes, and survival rate of the immunized piglets. Results: At 21 and 28 days after immunization, the serum N protein-specific antibody levels of piglets in the live PRRSV vaccine group were higher than those in the N protein group. After PRRSV infection, piglets in the N protein group and the DMEM group showed more severe clinical symptoms such as respiratory distress, loss of appetite, skin redness, and diarrhea than those in the live vaccine group. The rectal temperature of piglets in the live vaccine group remained below 40 °C, and only one piglet died on day 11 post-infection; in the PRRSV N protein group, the rectal temperature of some piglets exceeded 41 °C, and four piglets died on days 9, 11, 14, and 20 post-infection. In addition, pathologic damage to organs such as lungs, liver, lymph nodes, spleen, and kidneys was more severe in the N protein group than in the live vaccine group. Furthermore, histopathology and immunohistochemistry showed more pronounced organ damage (lungs, liver, lymph nodes, spleen, and kidneys) and higher viral loads in the N protein group compared to the live vaccine group. Conclusions: The PRRS subunit vaccine (N protein) expressed in the HEK-293T eukaryotic system did not protect piglets from heterologous PRRSV infection compared with the PRRS live vaccine.

Oral Delivery of Lactococcus lactis Expressing Full-Length S Protein via Alginate-Chitosan Capsules Induces Immune Protection Against PEDV Infection in Mice

Background/Objectives: Porcine epidemic diarrhea (PED) is a highly contagious enteric infectious disease that causes severe morbidity and mortality in piglets, posing significant economic losses to the swine industry worldwide. Oral vaccines based on Lactococcus lactis offer a promising approach due to their safety and genetic manipulability. This study aims to develop and evaluate an oral L. lactis-based vaccine expressing the full-length PEDV S protein. Methods: A recombinant L. lactis strain expressing the PEDV S protein was constructed and encapsulated in alginate-chitosan microcapsules. Vaccine stability was tested in simulated digestive fluids, and mice were orally immunized. Immune responses were evaluated by measuring specific antibodies, cytokines, and lymphocyte proliferation. Results: The recombinant L. lactis NZ3900/pNZ8149-S strain successfully expressed the full-length PEDV S protein and maintained stable plasmid inheritance. Oral immunization in mice induced detectable PEDV-specific immune responses. Both encapsulated and non-encapsulated vaccines stimulated the production of IgG and sIgA antibodies, as well as cytokines associated with Th1 and Th2 responses. Notably, encapsulation with alginate-chitosan significantly enhanced bacterial survival in digestive conditions and further amplified immune responses, including higher antibody titers, elevated levels of IFN-γ, IL-4, and IL-10, and greater lymphocyte proliferation, indicating improved immune memory. Conclusions: The oral L. lactis NZ3900/pNZ8149-S vaccine expressing the PEDV S protein effectively induced systemic and mucosal immunity in mice. Encapsulation with alginate-chitosan further enhanced its immunogenicity and stability in gastrointestinal conditions. These results suggest that both the engineered L. lactis strain and the encapsulation strategy contribute to the development of a promising oral vaccine platform for controlling PEDV in swine populations.

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.

Portable, quantitative, real-time isothermal nucleic acid amplification test using microfluidic device-coupled UV-LED photodiode detector

We report a stand-alone, automated, fully quantitative, and portable Microfluidics Integrated LED-Photodiode (MILP) sensing technology as a new molecular diagnostic platform for rapid point-of-care nucleic acid testing in real-time. The all-in-one device integrates a paper-based assay for nucleic acid purification using a polymer-based membrane filter, in-situ isothermal amplification, dual-mode optical detection, and fully quantitative signal analysis by capturing the photovoltaic response using electrical polarity and photocurrent measurements. Highly selective photovoltaic cut-offs may readily recognize test-gene-specific variations quantitatively without requiring further auxiliary instrumentation. The on-cartridge limit of detection (LoD) showed 10 copies/μL, which could diagnose SARS-CoV-2 samples with high clinical sensitivity (95%) and specificity (100%) with reference to real-time PCR-based gold-standard benchmark. Our findings emphasize the test's unique advantages for intensive health surveillance, enabling early disease screening, precise severity assessment, and real-time tracking of disease progression in resource-limited settings without the need for extensive and expensive laboratory infrastructure.

Novel Antibacterial Approaches and Therapeutic Strategies

The increase in multidrug-resistant organisms worldwide is a major public health threat driven by antibiotic overuse, horizontal gene transfer (HGT), environmental drivers, and deficient infection control in hospitals. In this article, we discuss these factors and summarize the new drugs and treatment strategies suggested to combat the increasing challenges of multidrug-resistant (MDR) bacteria. New treatments recently developed involve targeting key processes involved in bacterial growth, such as riboswitches and proteolysis, and combination therapies to improve efficacy and minimize adverse effects. It also tackles the challenges of the Gram-negative bacterial outer membrane, stressing that novel strategies are needed to evade permeability barriers, efflux pumps, and resistance mechanisms. Other approaches, including phage therapy, AMPs, and AI in drug discovery, are also discussed as potential alternatives. Finally, this review points out the urgency for continued research and development (R&D), industry-academic partnerships, and financial engines to ensure that MDR microbes do not exceed the value of antibacterial therapies.

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.

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.

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.

In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. Here we combine daily longitudinal sampling of individuals with replicate sequencing to increase the accuracy of and lower the threshold for variant calling. We sequenced 577 specimens from 105 individuals in a household cohort during the BA.1/BA.2 variant period. Individuals exhibited extremely low viral diversity, and we estimated a low within-host evolutionary rate. Within-host dynamics were dominated by genetic drift and purifying selection. Positive selection was rare but highly concentrated in spike. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 14 loci with 7 in spike, including S:448 and S:339. This detectable immune-mediated selection is unusual in acute respiratory infections and may be caused by the relatively narrow antibody repertoire in individuals during the early Omicron phase of the SARS-CoV-2 pandemic.

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.