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.

Castilho P, Cremer MJ, Vieira JV, Lemos GG, R. Moreira J, Rogge Renner GD, Kolesnikovas CKM, S. Peres N, Faita T, Pavaneli L, Ikeda J, Colosio AC, Marcondes MCC, Sánchez-Sarmiento AM, Barbosa CB, Ferioli RB, L. Ribeiro V, Bertozzi CP, F. Pessi C, Chupill H, Catão-Dias JL, B. Keid L. Morbillivirus and coronavirus survey in stranded cetaceans, Brazil

Since 2010, Guiana dolphin morbillivirus (GDMV; family Paramyxoviridae, genus Morbillivirus, species Morbillivirus ceti, syn. Cetacean morbillivirus) is recognized as the cause of death of multiple cetacean species along the Brazilian coast, including an unusual mortality event in Rio de Janeiro state. Coronaviruses of the genus Gammacoronavirus (family Coronaviridae) have been previously detected in cetaceans in the northern hemisphere. After the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic and with the potential to affect several mammal species, there is an increased concern about the risk of infection in aquatic mammals. The goal of this study was to molecularly screen the presence of morbillivirus and coronavirus infections in cetaceans stranded in several regions of the Brazilian coast in order to determine their occurrence rates, pathogenicity, and range of potentially susceptible cetacean species. We molecularly tested tissue samples of 118 cetaceans, belonging to 20 species, found stranded in Brazil, between 2015 and 2022. Overall, 2.5% (3/118) of the analyzed cetaceans were positive for GDMV infection: a Guiana dolphin (Sotalia guianensis), an Atlantic spotted dolphin (Stenella frontalis), and a humpback whale (Megaptera novaeangliae). None of the animals were positive for coronavirus. Our findings indicate that the morbillivirus sequence type identified in Indo-Pacific bottlenose dolphins (Tursiops aduncus) of Australia and our GDMV sequences from Brazil belong to the same strain. The systematic monitoring of cetacean morbilliviruses is recommended to properly estimate the occurrence rate, pathogenicity and evolution of these viruses, which may help anticipate novel epizooties and reduce their impact on endangered cetacean populations.

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.

Revisiting the roles of trypsin in the productive infection of porcine deltacoronavirus in porcine-derived cells

Porcine deltacoronavirus (PDCoV) is an emerging enteric coronavirus with the potential for interspecies transmission. Trypsin has been shown to play a positive role in the isolation and multiplication of PDCoV in vitro, however, the functions of trypsin during PDCoV replication cycle remain controversial. In this study, we revisited the roles of trypsin for PDCoV infection by utilizing two kinds of PDCoV, PDCoVT+ and PDCoVT-, which were prepared in the presence or absence of trypsin, respectively. We found that PDCoVT+ was able to continuously proliferate in the medium containing trypsin, achieving a higher titer as the infection progress in LLC-PK1 and other tested porcine-derived cells. However, its replication was only transiently improved at 12 hours post-infection, and lower viral titers were observed under trypsin-free culture conditions. Furthermore, the trypsin-mediated enhancement of viral replication could be inhibited by trypsin inhibitor SBTI, suggesting that the second-round viral reproduction of PDCoVT+ might be impeded without trypsin. We further investigated the replication dynamics of PDCoVT- in LLC-PK1 cells in the presence or absence of trypsin. The results indicated that PDCoVT- generated lower viral titers under trypsin-free culture conditions, while the addition of trypsin reverted the infectivity of PDCoVT-. Additionally, we demonstrated that trypsin cleaved the PDCoV spike protein, activating viral attachment and internalization. Moreover, trypsin promoted viral replication and release, accelerating PDCoV maturation and facilitating second-round infection. Taken together, this study systematically revaluated and emphasized an essential role of trypsin in PDCoV infection, providing mechanistic insights into the productive infection of PDCoV in porcine-derived cells.

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.

Towards developing multistrain PEDV vaccines: Integrating basic concepts and SARS-CoV-2 pan-sarbecovirus strategies

Porcine epidemic diarrhea virus (PEDV) is a major pathogen impacting the global pig industry, with outbreaks causing significant financial losses. The genetic variability of PEDV has posed challenges for vaccine development since its identification in the 1970s, a problem that intensified with its global emergence in the 2010s. Since current vaccines provide limited cross-protection against PEDV strains, and the development of multistrain PEDV vaccines remains an underexplored area of research, there is an urgent need for improved vaccine solutions. The rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and ongoing pan-sarbecovirus vaccine research, have demonstrated the potential of next-generation vaccine platforms and novel antigen design strategies. These advancements offer valuable insights for the development of multistrain PEDV vaccines. This review summarizes key aspects of PEDV virology and explores multistrain vaccine development considering SARS-CoV-2 vaccine innovations, proposing a framework for developing next-generation PEDV vaccine solutions.

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.

Transformative approaches in SARS-CoV-2 management: Vaccines, therapeutics and future direction

The global healthcare and economic challenges caused by the pandemic of COVID-19 reinforced the urgent demand for quick and effective therapeutic and preventative interventions. While vaccines served as the frontline of defense, antivirals emerged as adjunctive countermeasures, especially for people who developed infection, were immunocompromised, or were reluctant to be vaccinated. Beyond the serious complications of SARS-CoV-2 infection, the threats of long-COVID and the potential for zoonotic spillover continue to be significant health concerns that cannot be overlooked. Moreover, the incessant viral evolution, clinical safety issues, waning immune responses, and the emergence of drug-resistant variants pinpoint towards more severe viral threats in the future and call for broad-spectrum innovative therapies as a pre-pandemic preparedness measure. The present review provides a comprehensive up-to-date overview of the strategies utilized in the development of classical and next-generation vaccines against SARS-CoV-2, the clinical and experimental data obtained from clinical trials, while addressing safety risks that may arise. Besides vaccines, the review also covers recent breakthroughs in anti-SARS-CoV-2 drug discovery, emphasizing druggable viral and host targets, virus- and host-targeting antivirals, and highlighting mechanistically representative molecules that are either approved or are under clinical investigation. In conclusion, the integration of both vaccines and antiviral therapies, along with swift innovative strategies to address viral evolution and drug resistance is crucial to strengthen our preparedness against future viral outbreaks.

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.

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.

The ratio between SARS-CoV-2 RNA viral load and culturable viral titre differs depending on the stage of infection: a case study of household transmission in an adult male

Effective public health measures for communicable diseases rely on the ability to identify infectious individuals and prevent transmission from those individuals. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the presence of replication-competent virus in specimens from an individual is the gold standard for confirming infectiousness. However, viral culture from clinical specimens is difficult and infrequently performed. Instead, infectiousness may be inferred based on the abundance of viral RNA (or viral load) in a specimen, which is more easily assessed. For this reason, understanding the relationship between RNA viral load and infectious viral titre has important implications for public health strategy. In this case report, we quantified incident, longitudinal SARS-CoV-2 viral loads collected from saliva and nasal-swab specimens, and viral titre from nasal-swab specimens. We observed that the relationship between viral load and viral titre decreases by over five orders of magnitude throughout the course of the infection. Our work demonstrates the potential for infectious virus even in specimens with low viral loads collected during the early phases of infection.

Prevalence estimation of Pestivirus scrofae (atypical porcine pestivirus) among Hungarian pig herds and the effects of different sample types on detection rates

BACKGROUND

Atypical porcine pestivirus (APPeV), also known as Pestivirus scrofae, is a member of the Pestivirus genus within the Flaviviridae family. Experimental infections have directly linked APPeV to congenital tremor (CT) type A-II in congenitally infected piglets born to challenged sows. Here, we report the assessment of the prevalence of APPeV in Hungarian pig herds and the influence of different sample types on detection rates.

RESULTS

Altogether, 2650 blood serum, 198 oral fluid and 163 processing fluid samples were obtained via a systemic approach from 26 Hungarian farms and one Slovakian farm. The samples originated from different age groups and were analyzed via reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The estimated prevalence of APPeV was determined to be 66.67% in the sampled farms, indicating the widespread distribution of the virus within Hungary. Within the positive farms, APPeV genetic material was detected in the serum (21%), processing fluid (57%), and oral fluid (72%) samples. Notably, in some farms, the presence of APPeV was confirmed in only specific sample types, and five farms had APPeV in all three sample types. Age group analysis revealed that 10-week-old animals had the highest positivity rate in their blood serum (27%), whereas 20-week-old animals presented the highest rate in their oral fluid samples (59%). Processing fluid and oral fluid samples proved to be valuable for noninvasive diagnostic matrices, allowing for efficient population-level virus detection. We determined the partial NS2-3 coding region of 15 Hungarian strains and a Slovakian strain, and our phylogenetic analysis revealed that very similar strains can be found on different farms.

CONCLUSION

In conclusion, our study provides insights into APPeV prevalence in Hungarian pig herds, emphasizing the importance of different sample types for accurate diagnostics. These findings contribute to our understanding of the virus's distribution across different age groups.

Epidemiological Study and Genetic Diversity Assessment of Porcine Epidemic Diarrhea Virus (PEDV) in Yunnan Province, China

Porcine epidemic diarrhea virus (PEDV) is a highly contagious pathogen responsible for devastating enteric disease and lethal watery diarrhea, leading to significant economic losses in the global swine industry. Understanding the epidemiology and genetic diversity of PEDV over the past decade is crucial for the effective prevention and treatment of porcine epidemic diarrhea. In this study, 1851 fecal samples were collected from pigs exhibiting diarrhea symptoms across 11 cities in Yunnan Province between 2013 and 2022. The prevalence of PEDV, along with other common swine diarrhea viruses, including porcine transmissible gastroenteritis virus (TGEV), porcine rotavirus (PoRV), porcine Sapporo virus (PoSaV), porcine stellate virus (PaStV), and porcine delta coronavirus (PDCoV) was assessed using a polymerase chain reaction (PCR) assay. The results revealed a total detection rate of 52.94% (980/1851) for the six viruses, with PEDV accounting for 25.93% (480/1851) of cases. Further analysis showed that weaned piglets were more susceptible to PEDV than fattening pigs, with the highest prevalence observed in spring (61.52%, 275/447) and the lowest in summer (12.68%, 97/765). Dual infections were also identified, with PEDV + PoSaV being the most common combination (2.81%, 52/1851), followed by PEDV + PoRV, with a detection rate of 1.67% (31/1851). Phylogenetic analysis of the PEDV S genes revealed that the 28 epidemic strains in Yunnan Province shared a nucleotide sequence homology from 91.4% to 98.4% and an amino acid sequence homology ranging from 85.6% to 99.3%. All strains were classified as GII variant strains. This study provides a comprehensive overview of the epidemiology of PEDV and its co-infection patterns with other common diarrhea-causing viruses in the swine herds of Yunnan Province over the past decade. These findings offer valuable insights for the development of effective prevention and control strategies to mitigate the impact of PEDV and other enteroviruses on the swine industry in Yunnan Province.

Molecular structural arrangement in quorum sensing and bacterial metabolic production

Quorum sensing (QS) regulates bacterial behaviors such as biofilm formation, virulence, and metabolite production through signaling molecules like acyl-homoserine lactones (AHLs), peptides, and AI-2. These signals are pivotal in bacterial communication, influencing pathogenicity and industrial applications. This review explores the molecular architecture of QS signals and their role in metabolite production, emphasizing structural modifications that disrupt bacterial communication to control virulence and enhance industrial processes. Key findings highlight the development of synthetic QS analogs, engineered inhibitors, and microbial consortia as innovative tools in biotechnology and medicine. The review underscores the potential of molecular engineering in managing microbial behaviors and optimizing applications like biofuel production, bioplastics, and anti-virulence therapies. Additionally, cross-species signaling mechanisms, particularly involving AI-2, reveal new opportunities for regulating interspecies cooperation and competition. This synthesis aims to bridge molecular insights with practical applications, showcasing how QS-based technologies can drive advancements in microbial biotechnology and therapeutic strategies.

Multiplexed detection of respiratory virus RNA using optical pH sensors and injection-molded centrifugal microfluidics

The application is demonstrated of injection-molded centrifugal microfluidic chips with integrated optical pH sensors for multiplexed detection of respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, and influenza B RNA. The optical pH sensors generated sensitive fluorescent readouts from diagnostic reverse transcription loop-mediated isothermal amplification (RT-LAMP) reactions; limits of detection for influenzas A and B, and SARS-CoV-2 of 89, 245, and 38 RNA copies per reaction, respectively, were attained. Results were obtainable within 44 min for SARS-CoV-2 and influenza A, and 48 min for influenza B. We implemented a data processing strategy based on numerical derivatives of the fluorescence curves that allowed for reliable, quantitative thresholds for deciding reaction outcomes and enabled 100% specificity. This work demonstrates the utility of optical pH sensors and injection-molded centrifugal microfluidics for multiplexed infectious disease diagnostics with point-of-care applications.

Pseudovirus nanoparticles targeting the receptor binding HA1 domains of influenza viruses elicited high HA1-specific antibody responses and protected mice against mortality caused by influenza virus challenges

The continually high disease burden of influenza and the relatively low effectiveness of current influenza vaccines call for enhanced vaccine strategies. We previously generated unique S-HA1 pseudovirus nanoparticles (PVNPs) displaying the receptor binding HA1 antigens of the H7N9 subtype as an influenza vaccine candidate and characterized their features in biochemistry, biophysics, structure, and immune response. In this follow up study, we created new S-HA1 PVNPs displaying the HA1 antigens of other common influenza viruses, including two H1N1 strains, one H3N2 strain, and an influenza B virus, respectively. The recombinant PVNPs react well with antibodies against hemagglutinins (HAs) or mouse sera obtained after influenza virus challenge. 3D structural models were constructed to comprehend the structural features and size variations of the S-HA1 PVNPs. The PVNPs are immunogenic, eliciting high titers of HA1-specific serum antibodies that recognized commercial HA1 proteins. Importantly, the S-HA1 PVNP representing the H1N1 PR8 strain provided mice with 100 % protection against mortality caused by challenge with the mouse-adapted influenza virus of the same PR8 strain. The S-HA1 PVNP representing the H1N1 2009 pandemic strain conferred mice with 50 % protection against mortality caused by challenge with the 1934 PR8 strain, despite the two strains circulating 75 years apart. Our data demonstrated the feasibility of generating S-HA1 PVNPs to display HA1 antigens of diverse influenza A and B viruses. The readily available S-HA1 PVNPs hold promise as influenza vaccines, presenting a novel approach to combat the deadly influenza disease.

First detection of atypical porcine pestivirus in piglets affected by congenital tremor in Poland

Congenital tremors are neurological disorders of newborn piglets that may lead to serious health consequences, including increased mortality. Many reports have indicated that atypical porcine pestivirus (APPV), first identified in 2015, is a possible cause of this condition. In different countries, APPV was detected in farms affected by piglets' congenital tremors. There is a lack of data regarding the presence of this virus in Poland. However, swine veterinarians report outbreaks of congenital tremor with unestablished aetiology nationwide. Therefore, this study aimed to verify the presence of APPV in piglets with congenital tremors in Poland. Samples of blood (2), faecal swabs (7), brain (7), cerebellum (5), spinal cord, (7) lymph nodes (7), tonsil (7), thymus (6), tongue (7), heart (7), lung (7) and liver (7) were collected from piglets. Form sows' blood (5) and oral fluid (3, pooling samples) were collected. All samples have been derived from a commercial breeding farm reporting a case of congenital tremor and subjected to the qPCR via commercial kit (EXOone Atypical Porcine Pestivirus, Exopol, Spain). Six out of seven piglets tested positive for APPV, with the highest viral loads detected in the cerebellum and tonsils. All samples from sows were negative, emphasising the virus's specificity to piglets. To the authors' knowledge, this is the first report confirming APPV's presence in Poland. Given the potentially significant impact of APPV infections on swine health and production economics, further research evaluating the epidemiology and pathogenicity of APPV, as well as identifying preventive measures, is sorely needed.

Field Investigation Evaluating the Efficacy of Porcine Reproductive and Respiratory Syndrome Virus Type 2 (PRRSV-2) Modified Live Vaccines in Nursery Pigs Exposed to Multiple Heterologous PRRSV Strains

This study was conducted to evaluate the protective efficacy of modified live vaccines (MLVs) against porcine reproductive and respiratory syndrome (PRRS) in nursery pigs in a worst case scenario where MLV does not match the genetic profile of the field isolate, different MLVs are used for sows and piglets, and piglets are naturally exposed to genetically distinct heterologous PRRS virus (PRRSV) isolates. We divided 76,075, 2-week-old piglets from a seropositive sow herd vaccinated with US1-MLV into four groups. US1-MLV, US2-MLV, and US3-MLV groups were vaccinated with PRRSV-2 MLV including Ingelvac® PRRS MLV (Boehringer Ingelheim, Ingelheim am Rhein, Germany), HP-PRRSV-2 based MLV (Harbin Veterinary Research Institute, CAAS, Harbin, China), and Prime Pac® PRRS (MSD Animal Health, Rahway, NJ, USA), respectively. The NonVac group was left unvaccinated. At 0, 14, 28, and 56 days post-vaccination (DPV), sera were assayed for the presence of PRRSV-specific antibodies using ELISA and serum neutralization (SN), and PRRSV RNA using PCR. Average daily gain (ADG) and survival rates were compared between treatment groups. The results demonstrated vaccinated groups significantly improved in ADG compared to the non-vaccinated control group. Only US1-MLV and US3-MLV were able to significantly reduce mortality associated with field PRRSV infection in nursery pigs. Pigs vaccinated with US3-MLV displayed significantly lower mortality and higher ADG compared to all other groups. Field isolates were isolated and genetically compared to all three MLV vaccines at the start of the trial. The MLV with closest genetic similarity to the field isolate was US2-MLV by ORF5 gene comparison. This provided the lowest protection judging by ADG improvement and mortality reduction, as compared to US1-MLV and US3-MLV. Separately, strains of Thai PRRSV-2 isolates collected in 2017, 2019, and 2020 in the study area were investigated for evolutionary changes. Over time, we observed a shift in PRRSV-2 isolates from lineage 8.7 to lineage 1. The field isolates found shared 82.59-84.42%, 83.75-85.74%, and 84.25-85.90% nucleotide identity with the US1-MLV, US3-MLV and US2-MLV based vaccine, respectively. Our findings suggest genetic similarity between field viruses and vaccine strains should not be used as a predictor of field performance. We found that zootechnical performance of piglets was best in US3-MLV, despite sows being treated with a different vaccine The results also support that different MLVs can be used at different stages of production. Finally, we concluded that the shift from lineage 8.7 to lineage 1 was due to shifts in the worldwide prevalence of PRRSV isolates during that period of time and not due to vaccine recombination between isolates. Overall, MLV vaccine selection should be based on production performance and safety profile.

Associations Between Histo-blood Group Antigen Status in Mother-Infant Dyads and Infant Oral Rotavirus Vaccine Immunogenicity in Rural Zimbabwe

BACKGROUND

Histo-blood group antigen (HBGA) phenotypes may contribute to poor oral rotavirus vaccine (RVV) immunogenicity, since rotavirus binds intestinal epithelial HBGA glycans, while maternal HBGA status shapes breastmilk composition, which influences the composition of the infant microbiome. We investigated associations between maternal/infant HBGA phenotypes and RVV immunogenicity in rural Zimbabwe.

METHODS

We undertook salivary FUT2/FUT3 phenotyping in mother-infant pairs. Serum anti-rotavirus immunoglobulin A was measured by enzyme-linked immunosorbent assay. We explored adjusted associations between FUT2/FUT3 status and RVV seroconversion (primary outcome, n = 322) and seropositivity and geometric mean titer (secondary outcomes, n = 776).

RESULTS

Infants of FUT2- or FUT3-positive women were less likely to seroconvert post-RVV than infants of FUT2- or FUT3-negative women (FUT2 positive [20.1%] vs FUT2 negative [27.5%]: adjusted relative risk [aRR], 0.47; 95% CI, .26-.82; P = .008; FUT3 positive [18.1%] vs FUT3 negative [30.0%]: aRR, 0.45; 95% CI, .25-.78; P = .005). When compared with FUT2-positive infants with FUT2-positive mothers, FUT2-positive infants with FUT2-negative mothers were twice as likely to seroconvert (36.8% vs 21.9%; aRR, 2.12; 95% CI, 1.23-3.63; P = .006). When compared with FUT3-positive infants with FUT3-positive mothers, FUT3-positive infants with FUT3-negative mothers were 3 times as likely to seroconvert (48.3% vs 18.2%; aRR, 2.99; 95% CI, 1.82-4.90; P < .001).

CONCLUSIONS

Maternal and infant FUT2 and FUT3 status influences infant RVV immunogenicity.

Surveillance of antimicrobial resistance in hospitalized companion animals in China in 2022-23

Objectives

In this study, bacteria isolated from companion animals in China were taxonomically identified and assessed for antimicrobial susceptibility to evaluate the prevalence of antimicrobial resistance (AMR) in pets.

Methods

From October 2022 to October 2023, 5468 samples were collected from pets, predominantly from cats and dogs, in China, of which 5253 bacterial strains were identified (>98%). Antimicrobial susceptibility was assessed using the VITEK 2 COMPACT system and the Kirby-Bauer disc diffusion method.

Results

The most common bacterial species were Escherichia coli (14.5%) and Staphylococcus pseudintermedius (13.6%). E. coli exhibited high resistance to ampicillin and cefpodoxime (56.8%-73.2%) but moderate resistance to doxycycline, trimethoprim-sulfamethoxazole, enrofloxacin, gentamicin, and amoxicillin-clavulanate (18.1%-38.5%). Klebsiella spp. and Enterobacter spp. were resistance to several antimicrobials (32.2%-57.7%). High susceptibility to imipenem was noted in Proteus spp., Pseudomonas spp., and Acinetobacter spp. (91.7%-94.1%). Coagulase-positive Staphylococcus spp. demonstrated higher resistance than coagulase-negative strains. Enterococcus faecium showed greater resistance to some antimicrobials compared with E. faecalis. Streptococcus spp. exhibited low resistance to enrofloxacin (1.6%) and penicillin (1.1%).

Conclusions

The study demonstrates that AMR is widespread in companion animals in China, emphasizing the need for continuous surveillance. The accumulation of commercial antimicrobial susceptibility data can improve understanding of AMR and promote more effective antimicrobial stewardship and clinical practices in veterinary medicine.

Comparison of commercial next-generation sequencing assays to conventional culture methods for bacterial identification and antimicrobial susceptibility of samples obtained from clinical cases of canine superficial bacterial folliculitis

BACKGROUND

Bacterial identification and antimicrobial susceptibility testing is an important step in timely therapeutic decisions for canine superficial bacterial folliculitis (SBF), commonly caused by Staphylococcus pseudintermedius. Next-generation sequencing (NGS) offers the appeal of potentially expedited results with complete detection of bacterial organisms and associated resistance genes compared to culture. Limited studies exist comparing the two methodologies for clinical samples.

HYPOTHESIS/OBJECTIVES

To compare and contrast genotypic and phenotypic methods for bacterial identification and antimicrobial susceptibility from cases of canine SBF.

ANIMALS

Twenty-four client-owned dogs with lesions consistent with SBF were enrolled.

MATERIALS AND METHODS

A sterile culturette swab was used to sample dogs with SBF lesions. The swab was rinsed in 0.9 mL of sterile phosphate-buffered saline and vortexed to create a homogenous solution. Two swabs for NGS laboratories (Labs) and one swab for culture (Culture Lab) were randomly sampled from this solution and submitted for bacterial identification and antimicrobial susceptibility.

RESULTS

No statistical difference regarding turnaround time for NGS Labs compared to Culture Lab was found. NGS Lab 1 identified more organisms than NGS Lab 2 and Culture Lab, which were both statistically significant. There was no statistical difference in detection frequency for Staphylococcus spp. among all laboratories. There was poor agreement for the presence of meticillin resistance and most antimicrobials among all laboratories.

CONCLUSIONS AND CLINICAL RELEVANCE

Utilisation of NGS as a replacement for traditional culture when sampling canine SBF lesions is not supported at this time.

Genetic Epidemiology of Porcine Epidemic Diarrhea Virus Circulating in China From 2010 to 2024: Characterization of Phylogenetic and Genetic Diversity of S1-Based Genes

As a porcine alphacoronavirus, porcine epidemic diarrhea virus (PEDV) frequently undergoes mutations that significantly reduce the effectiveness of current prevention and control strategies, leading to recurrent outbreaks in China. This study investigates the genetic evolution and mutation patterns of the S1 protein to characterize PEDV variation in China. Genetic evolutionary analysis of 804 PEDV S1 genes, including 620 Chinese PEDV strains, revealed that 78.06% of the Chinese PEDV strains belong to the G2a-subgroup, further divided into seven branches (G2a-Clade 1-7), with the predominant strains from 2020 to 2024 being in G2a-Clade 4 (68.00%). From 2021 to 2024, 32 novel substitutions, 25 deletions, and 8 insertions were identified in the S1 protein of Chinese strains compared to those from 2010 to 2011. Notably, complete mutations were observed at amino acid sites N139D, H189Y, L229P, I287M, F345L, A361T, T499I, and A520S. Moreover, protein homology modeling analysis displayed that these deletion-insertion mutations significantly altered the surface structure of the S protein, particularly in the N-terminal domain (NTD) and receptor-binding domain (RBD) regions of S1 protein. The predictive analysis using AlphaFold3 indicated that deletion-insertion mutations in the S1-RBD region notably affected the binding affinity of the S protein to porcine DC-SIGN. These findings enhance our understanding of the genetic evolution of PEDV in China.

Immune responses to avian influenza viruses in chickens

Chickens are a key species in both the manifestation of avian influenza and the potential for zoonotic transmission. Avian influenza virus (AIV) infection in chickens can range from asymptomatic or mild disease with low pathogenic AIVs (LPAIVs) to systemic fatal disease with high pathogenic AIVs (HPAIVs). During AIV infection in chickens, Toll-like receptor 7 and melanoma differentiation-associated gene 5 are upregulated to detect the single-stranded ribonucleic acid genomes of AIV, triggering a signaling cascade that produces interferons (IFNs) and pro-inflammatory cytokines. These inflammatory mediators induce the expression of antiviral proteins and recruit immune system cells, such as macrophages and dendritic cells, to the infection site. AIV evades these antiviral responses primarily through its non-structural protein 1, which suppresses type I IFNs, influencing viral pathogenicity. The uncontrolled release of pro-inflammatory cytokines may contribute to the pathogenicity and high mortality associated with HPAIV infections. AIV modulates apoptosis in chicken cells to enhance its replication, with variations in apoptosis pathways influenced by viral strain and host cell type. The presentation of AIV antigens to T and B cells leads to the production of neutralizing antibodies and the targeted destruction of infected cells by CD8+ T cells, respectively, which enhances protection and establishes immunological memory. This review explores the diverse innate and adaptive immune responses in chickens to different AIVs, focusing on the dynamics of these responses relative to protection, susceptibility, and potential immunopathology. By understanding these immune mechanisms, informed strategies for controlling AIV infection and improving chicken health can be developed.

Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree

In metabarcoding research, such as taxon identification, phylogenetic placement plays a critical role. However, many existing phylogenetic placement methods lack comprehensive features for downstream analysis and visualization. Visualization tools often ignore placement uncertainty, making it difficult to explore and interpret placement data effectively. To overcome these limitations, we introduce a scalable approach using treeio and ggtree for parsing and visualizing phylogenetic placement data. The treeio-ggtree method supports placement filtration, uncertainty exploration, and customized visualization. It enhances scalability for large analyses by enabling users to extract subtrees from the full reference tree, focusing on specific samples within a clade. Additionally, this approach provides a clearer representation of phylogenetic placement uncertainty by visualizing associated placement information on the final placement tree.

SARS-CoV-2 drug resistance and therapeutic approaches

In light of the transition of COVID-19 from a pandemic to an endemic phase, there is still a dire need to address challenges associated with drug resistance, particularly among immunocompromised and high-risk populations. This review explores the current state of research on SARS-CoV-2 drug resistance and underscores the ongoing need for effective therapeutic strategies. It critically evaluates existing knowledge on resistance mechanisms and therapeutic options, aiming to consolidate information and highlight areas for future research. By examining the complex interactions between the virus and its host, the review advocates for a multifaceted approach, including combination therapies, targeted drug development, and continuous surveillance of viral mutations. It also emphasizes the impact of evolving viral variants on antiviral efficacy and suggests adaptive treatment protocols. This review aims to enhance our understanding of SARS-CoV-2 drug resistance and contribute to more effective management of COVID-19 through a discussion of promising strategies such as drug repurposing and combination therapies.

Multiple Co-Infecting Caliciviruses in Oral Fluid and Enteric Samples of Swine Detected by a Novel RT-qPCR Assay and a 3'RACE-PCR-NGS Method

Caliciviruses including noro- and sapoviruses of family Caliciviridae are important enteric human and swine pathogens, while others, like valoviruses, are less known. In this study, we developed a detection and typing pipeline for the most prevalent swine enteric caliciviruses-sapovirus GIII (Sw-SaV), norovirus GII (Sw-NoV), and valovirus GI (Sw-VaV). The pipeline integrates triplex RT-qPCR, 3'RACE semi-nested PCR, and next-generation sequencing (NovaSeq, Illumina) techniques. A small-scale epidemiological investigation was conducted on archived enteric and, for the first time, on oral fluid/saliva samples of diarrheic and asymptomatic swine of varying ages from Hungary and Slovakia. In enteric samples, Sw-SaV was the most prevalent, detected in 26.26% of samples, primarily in diarrheic pigs with low Cq values, followed by Sw-NoV (2.53%) in nursery pigs. In oral fluid samples, Sw-NoV predominated (7.46%), followed by Sw-SaV (4.39%). Sw-VaVs were sporadically found in both sample types. A natural, asymptomatic Sw-SaV outbreak was retrospectively detected where the transient shedding of the virus was <2 weeks. Complete capsid sequences (n = 59; 43 Sw-SaV, 13 Sw-NoV, and 3 Sw-VaV) including multiple (up to five) co-infecting variants were identified. Sw-SaV sequences belong to seven genotypes, while Sw-NoV and Sw-VaV strains clustered into distinct sub-clades, highlighting the complex diversity of these enteric caliciviruses in swine.

Development of a one-step multiplex RT-qPCR method for rapid detection of bovine diarrhea viruses

Introduction

Viral calf diarrhea poses a significant challenge to the cattle industry worldwide due to its high morbidity and mortality rates, leading to substantial economic losses. The clinical symptoms associated with various diarrhea pathogens often overlap, complicating accurate diagnosis; thus, there is an urgent need for rapid and precise diagnostic methods to improve prevention and treatment efforts. In this study, we developed a one-step multiplex reverse-transcription quantitative real-time polymerase chain reaction (mRT-qPCR) that enables the simultaneous detection of three key viral pathogens responsible for calf diarrhea: bovine kobuvirus (BKoV), bovine astrovirus (BoAstV), and bovine torovirus (BToV). However, development of accurate and rapid methods to distinguish these three viruses is helpful for the early detection, disease surveillance, and control of viral calf diarrhea.

Methods

Specific primers and minor groove binder (MGB)-based probes were designed targeting the 3D region of BKoV, ORF1 region of BoAstV, and N region of BToV. The sensitivity, specificity, and reproducibility ability were evaluated for the mRT-qPCR. Further, 80 bovine fecal samples were subjected to the mRT-qPCR, and the results were verified using conventional reverse-transcription PCR (RT-PCR) or PCR methods and sequencing methods.

Results

This novel method demonstrated high sensitivity and specificity,achieving a detection limit of 24 copies/mL for each pathogen. Furthermore, the assay exhibited excellent reproducibility, with coefficients of variation below 1.5%, a strong linear correlation (R2 > 0.996), and an amplification efficiency between 90% and 110%. Validation with 80 clinical samples from both diarrheic and non-diarrheic cattle across four farms in Shanghai showed a high degree of concordance with RT-PCR, with positive detection rates for BKoV, BoAstV, and BToV at 28.75%, 8.75%, and 3.75%, respectively, highlighting the predominance of BKoV and BoAstV. Notably, this study represents the first identification of BKoV, BoAstV, and BToV in the Shanghai region.

Discussion

The mRT-qPCR is a robust, rapid, and simple tool for identifying viral pathogens associated with calf diarrhea, facilitating the development of effective prevention and control measures that are vital for the future sustainability of the cattle industry.

Development of a portable multi-step microfluidic device for point-of-care nucleic acid diagnostics

BACKGROUND

The COVID-19 pandemic has significantly affected global health, economies, and societies, and highlighted the urgent need for rapid, sensitive, affordable, and portable diagnostic devices for respiratory diseases, especially in areas with limited resources. In recent years, there has been rapid development in integrated equipments using microfluidic chips and biochemical detection technologies. However, these devices are expensive and complex to operate, showing limited feasibility for in point of care tests (PoCTs). This study aims to develop a cost-effective, portable, and practical microfluidic nucleic acid PoCT device for rapid virus diagnosis.

RESULTS

Here, we developed a device based on freeze-dried reverse transcription loop-mediated isothermal amplification (RT-LAMP) reagents for rapid nucleic acid diagnostics. Homebrew RT-LAMP reagents were optimized to eliminate non-specific amplification. The multi-step device combines nucleic acid extraction, RT-LAMP and fluorescence detection in an integrated microfluidic chip, enabling sample-in, result-out diagnosis. This device showed satisfactory sensitivity in detecting SARS-CoV-2 and Trichomonas vaginalis RNA samples, with a limit of detection (LOD) of 400 copies/μL and 80 copies/μL respectively in 45 min. The LOD of cultured Trichomonas vaginalis samples were 0.32 cells/μL in 50 min. Additionally, the freeze-dried homebrew RT-LAMP can be stored at 4 °C for up to 30 days while still maintaining high sensitivity and detection capabilities. The cost of diagnosis was reduced to as low as 0.45 $ per reaction.

SIGNIFICANCE AND NOVELTY

Overall, by integrating freeze-dried homebrew RT-LAMP and microfluidic chip, the device achieves ready-to-use, laboratory-free, quick, resource-independent and cost-effective nucleic acid detection, and provides a feasible alternative to complex equipments. The device shows potentials for point-of-care testing of SARS-CoV-2 and other respiratory diseases in remote or resource-limited areas with proper implementation.

Duplex qPCR for detecting and differentiating porcine epidemic diarrhea virus GI and GII subtypes

Introduction

Porcine epidemic diarrhea virus (PEDV) is a pathogen that causes a highly contagious intestinal disease in pigs, which causes significant economic losses to the pig industry worldwide. PCR is the most commonly used technique for PEDV diagnosis in practical clinics, however, reported works still suffer from shortcomings, for example, most of them cannot differentiate GI and GII subtypes, they suffer from low sensitivity, and some primer sequences are no longer able to match the mutant strains.

Methods

To address these issues, we conducted a comprehensive analysis by comparing the sequences of the PEDV S protein in the existing NCBI database with a recently isolated epidemic strain of PEDV, named SX0818-2022, of subtype GIIa from Shanxi, China. The conserved sequences of GI and GII subtypes were retrieved to design the primers and probe. Leveraging this information, we developed a TaqMan probe-based quantitative real-time PCR (qPCR) assay that is uniquely tailored to detect both PEDV GI and GII subtypes.

Results

Additionally, this qPCR can identify PEDV GI and GII subtypes with high sensitivities of 90 copies/μL and 40 copies/μL, respectively (refers to the number of copies of the DNA target per microliter of template in the reaction system), much higher than the previously reported works and especially suitable for early diagnosis and prevention. Besides, excellent specificity and repeatability of the duplex qPCR were verified, thus supporting its potential applications in practical clinics.

Discussion

Therefore, this work presents a promising tool for PEDV diagnosis, prevention, and control.

Comparative Genomic and Biological Investigation of NADC30- and NADC34-Like PRRSV Strains Isolated in South Korea

Porcine reproductive and respiratory syndrome virus (PRRSV) is a globally endemic, costly swine arterivirus with wide genetic and antigenic variations, leading to the frequent appearance of novel virulent strains that hampers PRRSV control. Recently, NADC30-like (lineage 1C, L1C) and NADC34-like (lineage 1A, L1A) PRRSV strains were reported to be prevalent in mainland South Korea and became the main epidemic strains persistently attributed to PRRSV outbreaks nationwide, raising great concern in the domestic pork industry. Although the genotypic and pathotypic variability of NADC30- and NADC34-like viruses has been explored in the United States and China, their genomic and biological characteristics have been scarcely studied in South Korea. Here, NADC34-like GNU-2353 and NADC30-like GNU-2377 strains were independently identified from vaccinated swine herds experiencing high piglet mortality. Whole-genome sequencing and phylogenetic analysis revealed that GNU-2353 and GNU-2377 clustered into sublineages L1A (NADC34-like) and L1C (NADC30-like), respectively, sharing high genomic homology with their corresponding lineage-representative strains and harboring the same molecular signatures of continuous 100 and discontinuous 131 amino acid deletions in the nsp2-coding region, respectively. Recombination detection indicated that GNU-2353 and GNU-2377 were recombinants and evolved through natural interlineage recombination between NADC34-like (L1A, major parent) or NADC30-like (L1C, major parent) and RespPRRS modified live virus (MLV)-like (lineage 5, minor parent) strains, respectively. Both viruses displayed homogenous growth kinetics but replicated faster than the prototype VR-2332 in a porcine alveolar macrophage cell line (PAM-KNU). The transcriptional profiles of immune response genes in infected PAM-KNU cells varied between the isolates and VR-2332; particularly, interleukin-10 expression was dramatically upregulated in cells infected with GNU-2353 and GNU-2377. Piglets with GNU-2353 and GNU-2377 infection had high fever; weight loss; increased viremia and nasal shedding; viral distribution in various tissues; thymic atrophy; and apparent macroscopic and microscopic lung lesions, including interstitial pneumonia and viral colonization, compared with control piglets, suggesting that both isolates were virulent to pigs. Remarkably, GNU-2353 caused higher fever, mortality rate (40%) with cyanosis, viremia, and viral shedding within 2 weeks and significantly higher viral loads in several organs than GNU-2377 infection. Thus, NADC34-like GNU-2353 was more pathogenic than NADC30-like GNU-2377. Our findings provide insights into the current epizootic circumstance of NADC30- and NADC34-like PRRSV in South Korea and can aid in tailoring improved control strategies.