Search Results (345)

Porcine reproductive and respiratory syndrome virus remains one of the most economically significant pathogens in swine production, with PRRSV-2 being the dominant variant in the United States. While lineage classification has traditionally relied on ORF5 sequencing, recent studies suggest that this single-gene approach may overlook key evolutionary events such as recombination. In this study, we performed whole-genome sequencing and phylogenetic analysis of seven PRRSV-2 isolates collected in the U.S. between 2006 and 2024. Using reference-guided assembly, lineage assignment, and recombination detection with RDP5 and SIMplot, we identified discordant phylogenetic placements between ORF5 and whole genomes in four of the seven isolates. These discordances were explained by multiple recombination events affecting different genomic regions, particularly ORF2–ORF7. In contrast, three isolates showed phylogenetic concordance and no strong evidence of recombination. Our findings demonstrate that recombination plays a significant role in shaping PRRSV-2 evolution and highlight the limitations of ORF5-based lineage classification. Whole-genome surveillance is therefore essential to accurately track viral diversity, detect recombinant strains, and inform control strategies. This work underscores the need for a broader adoption of full-genome analysis in routine PRRSV surveillance and research. Full article

Canine morbillivirus (CDV), the cause of canine distemper, is a pathogen affecting many hosts. While modified live virus (MLV) vaccines are crucial for controlling the disease in dogs, cases of vaccine-related infections have been found in both domestic and wild animals. Specifically, the America-1 and Rockborn-like vaccine genotypes are concerning due to their spread and ability to transmit between different species. This study conducted a review and analysis of molecular detections of these strains in various carnivores (domestic, captive, synanthropic, and wild species). This study used a conceptual model considering host ecology and the domestic–wild interface to evaluate plausible transmission connections over time using Linear Directional Mean (LDM) and Weighted Mean Centre (WMC) methods. Statistical analyses examined the relationship between how likely a strain is to spread and factors like host type and vaccination status. The findings showed that the America-1 genotype spread in a more organised way, with domestic dogs being the main source and recipient, bridging different environments. Synanthropic mesocarnivores also played this same role, with less intensity. America-1 was most concentrated in the North Atlantic and Western Europe. In contrast, the Rockborn-like strain showed a more unpredictable and restricted spread, residual circulation from past use rather than ongoing spread. Species involved in vaccine-related infections often share characteristics like generalist behaviour, social living, and a preference for areas where domestic animals and wildlife interact. We did not find a general link between a host vaccination status and the likelihood of the strain spreading. The study emphasised the ongoing risk of vaccine-derived strains moving from domestic and synanthropic animals to vulnerable wild species, supporting the need for improved vaccination approaches. Mapping these plausible transmission routes can serve as a basis for targeted surveillance, not only of vaccine-derived strains, but of any other circulating genotype. Full article

Objectives: To confirm a conjecture from year 2020 of the SARS-CoV-2 (COVID-19) pandemic suggesting policy alternatives to substantially reduce mortality burden. Methods: Data from a global COVID-19 database comparing different countries on cumulative mortality and vaccination were analyzed in conjunction with surveys of seropositivity. Predictions of final mortality burden under an alternate policy scenario for Japan were calculated and the COVID-19 outcomes for China were assessed. Results: By 2025, Western countries (US, UK, Brazil and Italy) had cumulative mortality rates in the range of 3339–3548 deaths per million, about 6-fold higher than East Asian and New Zealand ‘zero-COVID’ countries. Moderate virus suppression in Japan produced the lowest cumulative mortality of the countries analyzed; if earlier policies had been maintained, the predicted cumulative mortality rate by 2025 would be one-tenth that of the US, UK, Brazil and Italy and one-half to one-third that of other zero-COVID countries. For China, transitioning from a zero-COVID policy in 2022–2023, the estimated 2025 cumulative mortality was 1607/million, half that of Western countries. Conclusions: To minimize COVID-19 mortality would require: (1) Innovation on systematic sampling of ambient airborne virus exposure to sustain low but non-zero virus levels across entire populations, and (2) seropositivity assessment (instead of mass PCR testing for new cases) for calibrating exposure management, and tracking and protecting high-risk populations. Full article

The emergence of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus closely related to SARS-CoV and officially known as Betacoronavirus pandemicum precipitated a substantial surge in vaccine development that culminated during the global COVID-19 pandemic. At present, there are dozens of vaccines for the prevention of SARS-CoV-2 being utilized across the globe. However, only 10 of these vaccines have been authorized by the World Health Organization (WHO). These include mRNA-based, viral vector, subunit and whole-virion inactivated vaccines. At the current end of the pandemic, there has been a decline in the global vaccination rate, both for the general population and for those most at risk of severe illness from the virus. This suggests that the effectiveness of the vaccines may be waning. The decline occurs alongside a decrease in testing and sequencing for SARS-CoV-2. Furthermore, the process of tracking viruses becomes increasingly complex, thereby providing a selective advantage for SARS-CoV-2 and allowing it to evolve stealthily. In this review, we provide a comprehensive overview of viral evolution and vaccine development. We also discuss ways to overcome viral variability and test universal vaccines for all SARS-CoV-2 variants. Full article

Dengue virus (DENV) poses a major global health concern, with over 6.5 million cases and 7300 deaths reported in 2023. Accurate serological assays are essential for tracking infection history, evaluating disease severity, and guiding vaccination strategies. However, existing assays are limited in their specificity, sensitivity, and cross-reactivity. Using optical modulation biosensing (OMB) technology and non-structural protein 1 (NS1) antigens from DENV-1–3, we developed highly sensitive and quantitative serotype-specific anti-DENV NS1 IgG serological assays. The OMB-based assays offered a wide dynamic range (~4-log), low detection limits (~400 ng/L), fast turnaround (1.5 h), and a simplified workflow. Using samples from endemic (Vietnam) and non-endemic (Israel) regions, we assessed intra-DENV and inter-Flavivirus cross-reactivity. Each assay detected DENV infection with a 100% sensitivity for the corresponding serotype and 64% to 90% for other serotypes. Cross-reactivity with Zika, Japanese encephalitis, and West Nile viruses ranged from 21% to 65%, reflecting NS1 antigen conservation. Our study provides valuable insights into the cross-reactivity of DENV NS1 antigens widely used in research and highlights the potential of OMB-based assays for quantitative and epidemiological studies. Ongoing efforts should aim to minimize cross-reactivity while maintaining sensitivity and explore integration with complementary platforms for improved diagnostic precision. Full article

Infectious diseases can spread through virus-laden respiratory droplets exhaled into the air. Ventilation systems are crucial in indoor settings as they can dilute or eliminate these droplets, underscoring the importance of understanding their efficacy in the management of indoor infections. Within the field of fluid dynamics methods, the dispersed droplets may be approached through either a Lagrangian framework or an Eulerian framework. In this study, various Eulerian methodologies are systematically compared against the Eulerian–Lagrangian (E-L) approach across three different scenarios: the pseudo-single-phase model (PSPM) for assessing the transport of gaseous pollutants in an office with displacement ventilation (DV), stratum ventilation (SV), and mixing ventilation (MV); the two-fluid model (TFM) for evaluating the transport of non-evaporating particles within an office with DV and MV; and the two-fluid model-population balance equation (TFM-PBE) approach for analyzing the transport of evaporating droplets in a ward with MV. The Eulerian and Lagrangian approaches present similar agreement with the experimental data, indicating that the two approaches are comparable in accuracy. The computational cost of the E-L approach is closely related to the number of tracked droplets; therefore, the Eulerian approach is recommended when the number of droplets required by the simulation is large. Finally, the performances of DV, SV, and MV are presented and discussed. DV creates a stratified environment due to buoyant flows, which transport respiratory droplets upward. MV provides a well-mixed environment, resulting in a uniform dispersion of droplets. SV supplies fresh air directly to the breathing zone, thereby effectively reducing infection risk. Consequently, DV and SV are preferred to reduce indoor infection. Full article

Many viruses mutate rapidly to adapt to host defenses, and for some of these viruses, the result is long-term infection in individual hosts. The work described here examines the infection and long-term maintenance of a newly identified virus, equine parvovirus-hepatitis (EqPV-H), in an individual horse. This description is possible because of a hypervariable region in the capsid gene; sequence variants were tracked by high-throughput sequencing of serum samples taken over a 16-year period. The data support the hypothesis that EqPV-H infection resulted in a sequence variant bottleneck. The continuing infection evolved into a complex viral population showing a pattern of emergence, dominance, and recession with replacement. This is the first temporal description of the capsid gene evolution of EqPV-H in a single animal. Full article

Streptococcus pyogenes is a bacterial pathogen known to be the causative agent in many different illnesses, with Group A Streptococcus (GAS) pharyngitis (strep throat), being one of the more prevalent. The spread and severity of GAS pharyngitis can grow exponentially if individuals are not taking the proper precautions. Wastewater surveillance has been used to test for numerous different pathogens that humans spread throughout a community and in this study, we utilized wastewater surveillance to monitor GAS pharyngitis in a small city. Over a year, 57 wastewater influent samples were tested for S. pyogenes and three commonly tested respiratory viruses (Respiratory Syncytial Virus (RSV), SARS-CoV-2, Influenza A). Three microbial indicators and population normalizers (CrAssphage, Pepper mild mottle virus (PMMoV), and Mycobacterium) were tested as well to compare and contrast each indicator’s value and range over time. Wastewater data was then compared to publicly available search term data as clinical data was not readily available. There was a high correlation between the collected molecular data and the publicly available search term data for Streptococcus pyogenes. Additionally, this study provided more information about the seasonal trend of S. pyogenes throughout the year through molecular data and allowed for the ability to track peak infection months in this small city. Overall, these results highlight the substantial benefits of using wastewater surveillance for the monitoring of GAS pharyngitis. This study also provides helpful insights into future studies about the prevalence of respiratory bacteria and their seasonal trends in wastewater, allowing for public health systems to provide mitigation strategies. Full article

African swine fever virus (ASFV), the causative agent of African swine fever (ASF), poses a catastrophic threat to global swine industries through its capacity for immune subversion and rapid evolution. Multigene family genes (MGFs)-encoded proteins serve as molecular hubs governing viral evolution, immune evasion, cell tropism, and disease pathogenesis. This review synthesizes structural and functional evidence demonstrating that MGFs-encoded proteins suppress both interferon signaling and inflammasome activation, while their genomic plasticity in variable terminal regions drives strain diversification and adaptation. Translationally, targeted deletion of immunomodulatory MGFs enables the rational design of live attenuated vaccines that improve protective efficacy while minimizing residual virulence. Moreover, hypervariable MGFs provide strain-specific signatures for PCR-based diagnostics and phylogeographic tracking, directly addressing outbreak surveillance challenges. By unifying virology with translational innovation, this review establishes MGFs as priority targets for next-generation ASF countermeasures. Full article

Infection with Zika virus (ZIKV) is a perinatal health problem and a vertical infection that promotes neurological fetal damage. ZIKV infects different cellular components at the maternal–fetal interface, including umbilical cord endothelial cells (HUVECs). Extracellular vesicles (EVs) are cellular components that mediate extracellular communication. Viruses have the capacity to hijack and modify the biogenesis machinery of EVs for their own benefit. The present work provides proteomic results (2D electrophoresis) that show the regulation of the expression of proteins involved in autophagy, oxidative stress, and exosome biogenesis in HUVECs infected with ZIKV. We confirmed that Alix and CD9 proteins were downregulated following the infection. Additionally, EVs isolated from infected cells showed the expression of Alix, and CD9 was increased in contrast to the mock condition. Interestingly, nanoparticle tracking and cryo-microscopy assays revealed that these EVs showed an increase in the quantity and size of ZIKV infection to differences in mock conditions. Furthermore, EVs isolated from infected cells showed infectivity, and both RNA and viral proteins were detected. Finally, our cryo-microscopy analysis revealed that the viral infection promoted morphological changes in these extracellular vesicles to identify vesicles with double and triple vesicles and electrodense and double membranes. In conclusion, our data suggest that ZIKV infection can modulate cellular factors involved in the formation and morphology of EVs in HUVECs. Furthermore, these EVs carry viral elements that may contribute to the dissemination of infection. Future studies aimed at the proteomic and lipidomic composition analyses of these EVs are needed to understand the biological implications in vertical infection. Full article

Polyomaviruses have the potential to cause significant morbidity not only in transplant medicine, but also in other forms of disease or variants of immunosuppression. In kidney transplant recipients or recipients of human stem cell transplants, the BK-Virus is the major proponent of manifestations such as BKPyV-associated nephropathy or hemorrhagic cystitis. As no polyomavirus-specific drug with proven in vivo effects has been developed so far, methods to screen for such drugs are important. This work describes the establishment of a virus-secreting cell line. By infecting a pre-established monkey kidney cell line (COS-1) with a non-rearranged human BK polyomavirus isolated from a kidney transplant patient suffering from BKPyV-associated nephropathy, a continuously replicating cell type with consistent virus secretion could be established and was termed COSSA. Measurements of BKPyV replication, virion production, and secretion were performed both intracellularly and in the cell supernatant. Viral proteins such as VP1 and LTAg were accurately tracked by confocal microscopy, as well as by immunoblot and qPCR. An intracellular flow cytometry (FACS) assay detecting VP1 protein was established and revealed an expanded range of positive intracellular signals. The viruses produced proved to be infectious in human tubular epithelial cell lines. Long-range sequencing of the COSSA genome using Oxford Nanopore Technology revealed a total of five distinct BKPyV integration events. One integration of a partial BKPyV genome was located upstream of the epidermal growth factor receptor gene. The second and third, both truncated forms of integration, were close to histocompatibility gene locuses, while the fourth was characterized by a ninefold and the fifth by a fourfold tandem repeat of the BKPyV genome. From both of the repeat forms, virus replicates were derived showing deletions/duplications on early and late genes and inversions within the non-coding control region (NCCR). This pattern of repetitive viral genome integration is a potential key driver of enhanced viral replication and increased virion assembly, ultimately supporting efficient virus egress. Quantitative PCR analysis confirmed the release of approximately 10⁸/mL viral units per 48 h from 2 × 10⁵ COSSA cells into the culture supernatant. Notably, the NCCR region of the most frequent copies of circular virus and the integrated tetrameric tandem repeat exhibited a rearranged configuration, which may contribute to the observed high replication dynamics. The establishment of a consistent methodology to generate and secrete BKPyV from a cell line is expected to significantly facilitate antiviral drug development. Full article

Infectious bronchitis virus (IBV) and low-pathogenic avian influenza virus (LPAIV) H9N2 are commonly identified in poultry, individually or in association with other pathogens. This study monitored 183 broiler farms affected by respiratory diseases across seven regions of Morocco from January 2021 to December 2023. Among these farms, 87.98% were vaccinated against IBV, while 57.92% were against AI H9N2. Abnormally high mortality rates were observed in 44.26% of the farms, with 24.69% of cases attributed to IBV, 50.62% to LPAI H9N2, and 13.58% due to coinfection with both IBV and H9N2. RT-PCR analysis of tissue samples and cloacal and tracheal swabs collected from 183 broiler farms revealed that 33.33% were positive for IBV and 34.97% for H9N2. Coinfection by IBV and H9N2 was detected in 12.57% of cases, peaking at 17% in 2022. Co-infected flocks exhibited severe clinical signs and lesions, such as reduced food consumption, diarrhea, and renal issues. The predominant lesions were in the respiratory tract, affecting 91.26% of infected broilers. Additionally, among the 183 flocks, 50 farms that tested positive for IBV infection were randomly selected from the seven regions of Morocco for further investigation of other respiratory pathogens, including Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), and infectious laryngotracheitis (ILT), using real-time RT-PCR. Detection rates for these pathogens were 26% for MG, 30% for MS, 4% for ILTv (vaccine strain), and 18% for ILTw (wild strain). Detection rates for single, dual, triple, and quadruple infections were 34%, 42%, 18%, and 4%, respectively. The most common dual and triple coinfections were IBV + H9N2 (14%) and IBV + MG + MS (10%). Phylogenetic analysis of the S gene identified two main IBV genotypes, namely, 793B and D181, with the latter being a strain circulating for the first time in Moroccan poultry. This underscores the urgent need to establish surveillance systems to track pathogen circulation and implement strategies to control virus spread, ensuring the protection of animals and public health. Full article

COVID-19, which is caused by the SARS-CoV-2 virus, has caused millions of cases and fatalities around the world. It is clearer and clearer how ex-COVID-19 patients endure neurological symptoms, such as headaches and cognitive impairment, in addition to respiratory problems. Long COVID refers to symptoms that continue after the acute phase, impacting millions of people and having severe socioeconomic consequences. The pathogenesis of neurological symptoms in long-term COVID is still unknown, making diagnosis and management difficult. The purpose of this review is to investigate the ophthalmological/neurological effects of prolonged COVID and the possibility of eye-tracking technology as an objective biomarker for diagnosis and monitoring. A scoping literature review was carried out, yielding 15 relevant studies. Several ophthalmological signals, such as saccadic movements and pupillary reflexes, were found to be significantly affected in patients with long COVID. These signals were measured using a variety of methods, including infrared cameras and eye-tracking systems. The study emphasises the need for more research to develop standardised biomarkers for long COVID diagnosis and monitoring. Understanding the ophthalmological impacts of long COVID can help develop novel tools for assessing and controlling this disorder. Full article

Porcine reproductive and respiratory syndrome virus (PRRSV) modified live virus (MLV) vaccination is used to control PRRSV. In China, farms conduct random sampling from sow herds every 4 to 6 months. They use the enzyme-linked immunosorbent assay (ELISA) method to monitor the immune status of the herd by tracking the positive rate or the sample-to-positive ratio. However, in farms that implement mass vaccination and have stable production, the positive rate of ELISA antibodies has decreased, especially in high-parity sows. This poses a considerable challenge to the current monitoring approach of PRRSV immunity. It remains unclear whether this reflects insufficient sensitivity of the kits for these special scenarios or the fact that the sows have truly lost immunity. In this study, 233 samples from four farms (A–D) across different regions of China were acquired. They were tested using four representative ELISA kits, two targeting the nucleocapsid protein (N) and two targeting the glycoprotein (GP) to evaluate PRRS immune status. The respective sample positive rates in A–D were 57.1–100%, 50.9–100%, 50–100%, and 75.7–100% using the kits. The positive rates using the four ELISA kits were 50.0–75.7%, 70.0–75.7%, 82.5–97.1%, and 100%, respectively, with poor agreement among them. The positive rates and humoral antibody levels for parity 1 and 2 sows were significantly lower than those with higher parities (>4). Eighty-eight ELISA-negative samples identified using ELISA kit A were verified using a viral neutralizing test (VNT), with only 15.9% of the samples testing negative. In conclusion, the ELISA antibody negativity issue existed, mostly occurring in specific farms tested using a specific kit. However, the low correlation with the VNT results and the poor agreements among the kits suggest that relying on one ELISA test is insufficient to monitor the immune status of PRRSV MLV-vaccinated herds. Full article

Introduction: Coronavirus (CoV) is an extremely contagious, enveloped positive-single-stranded RNA virus, which has become a global pandemic that causes several illnesses in humans and animals. Hence, it is necessary to investigate viral-induced reactions across diverse hosts. Herein, we propose utilizing naturally secreted extracellular vesicles (EVs), mainly focusing on exosomes to examine virus–host responses following CoV infection. Exosomes are small membrane-bound vesicles originating from the endosomal pathway, which play a pivotal role in intracellular communication and physiological and pathological processes. We suggested that CoV could impact EV formation, content, and diverse immune responses in vitro. Methods: In this study, we infected A-72, which is a canine fibroblast cell line, with a feline coronavirus (FCoV) and canine coronavirus (CCoV) independently in an exosome-free media at 0.001 multiplicity of infection (MOI), with incubation periods of 48 and 72 h. The cell viability was significantly downregulated with increased incubation time following FCoV and CCoV infection, which was identified by performing the 3-(4,5-dimethylthiazo-1-2yl)-2,5-diphenyltetrazolium bromide (MTT) assay. After the infection, EVs were isolated through ultracentrifugation, and the subsequent analysis involved quantifying and characterizing the purified EVs using various techniques. Results: NanoSight particle tracking analysis (NTA) verified that EV dimensions fell between 100 and 200 nm at both incubation periods. At both periods, total protein and RNA levels were significantly upregulated in A-72-derived EVs following FCoV and CCoV infections. However, total DNA levels were gradually upregulated with increased incubation time. Dot blot analysis indicated that the expression levels of ACE2, IL-1β, Flotillin-1, CD63, caspase-8, and Hsp90 were modified in A-72-derived EVs following both CoV infections. Conclusions: Our results indicated that FCoV and CCoV infections could modulate the EV production and content, which could play a role in the development of viral diseases. Investigating diverse animal CoV will provide in-depth insight into host exosome biology during CoV infection. Hence, our findings contribute to the comprehension and characterization of EVs in virus–host interactions during CoV infection. Full article