Viruses Infecting Cuban Honey Bees and Evolution of Deformed-Wing-Virus Variants

Viruses · 2026-01-22 · 1 citations

Cuba is in a unique situation in which it has a large (220,000 managed colonies) and isolated honey bee population due to a 60+ year ban on the importation of bees. Despite this, the ectoparasitic mite Varroa destructor arrived in 1996, and with it came deformed wing virus (DWV). In 2018, an island-wide survey detected varroa and DWV in 91% of colonies. In this study, we conducted a full-virome analysis on some of these samples, along with additional samples collected in 2021. For the first time, we detected two variants of Lake Sinai Virus and confirmed the absence of the normally widespread black queen cell virus in Cuba. We also detected both DWV-A and DWV-B master variants, with DWV-B being the dominant variant. Interestingly, the DWV-B/A recombinant was also detected, indicating that despite Cuba’s isolated nature, the pattern of DWV evolution mirrors that found in the USA and Europe. However, this pattern is not found in neighboring Latin America, China, or Japan, where the DWV-A master variant continues to be dominant. How and why two distinct evolutionary DWV pathways have arisen remain a mystery.

Determining farm surface porcine reproductive and respiratory syndrome virus (PRRSV) contamination through viability RT-qPCR

PLoS ONE · 2026-03-13

Porcine reproductive and respiratory syndrome (PRRS) continues to be a major threat to U.S. swine industry, as a substantial number of herds become positive and can pose a risk to other nearby farms, especially in post weaning farms as multiple of them may be overseen by one worker. Personnel moving between farms without adequate biosecurity measures, may play a role in viral spread acting as a fomite. The ability to detect and distinguish between the free PRRS virus (PRRSV) genomic RNA vs its genome found in a viable virus form on frequently touched surfaces in growing pig farms was assess in this study. Ten PRRSV positive growing pig farms in the Midwestern U.S. were visited to collect 20 environmental surface samples and eight oral fluids from each one. Environmental samples were analyzed using standard RT-qPCR and viability RT-qPCR, while oral fluids were assessed using the VetMAX™ PRRSV EU & NA v3.0 kit. The virus' RNA was commonly detected on metal and plastic (non-porous) surfaces (e.g., pig pen top rail, mortality handling equipment's handle) from all farms, with 80 out of 200 environmental samples testing positive. Viable virus was detected in 48 samples across six farms, with non-porous materials testing positive more frequently. A generalized linear mixed effect model suggested a negative association (OR = 0.005; 95% CI 0.00, 6.82; p-value = 0.18) between the proportion of positive oral fluids and detecting viable virus from sampled surfaces. Agreement between the detection of RNA and viable PRRSV from surface samples using Cohen's kappa yielded perfect agreement (κ = 1.00) from doorknobs of different locations, to low agreement (κ = 0.29) in the floor of a specific area, among others. These results indicate the presence of viable virus on surfaces that are frequently touched by the farm's personnel. This study highlights the importance of biosecurity measures applied to the personnel and their potential role of environmental contamination and PRRSV dissemination. The use of viability RT-qPCR to detect viable PRRSV offers a practical tool in field settings to improve biosecurity protocols to reduce indirect transmission of PRRSV in swine production systems.

Experimental evidence of vaccine-driven evolution of PRRSV-2 in pigs-to-pig infection chains

AASV Annual Meeting · 2025-02-15

Evaluating the Antiviral Activity of Termin-8 and Finio Against a Surrogate ASFV-like Algal Virus

Pathogens · 2025-07-08

The objective of this study was to evaluate the time-course of incubation for the potential preventative mitigation of megaviruses using Termin-8 (a formaldehyde-based product) and Finio (non-formaldehyde solution) from Anitox. Emiliania huxleyi virus (EhV), an algal surrogate for African swine fever virus (ASFV), was treated with the recommended concentrations of Termin-8 (0.1% to 0.3%) and Finio (0.05% to 0.2%), and both viability qPCR (V-qPCR) and standard PCR (S-qPCR) were used to quantify EhV concentrations at 1 h, 5 h, 24 h and day 7 post-inoculation. Overall, Finio, and to a lesser extent Termin-8, at their highest treatment concentrations, showed the greatest log reduction of 4.5 and 2 log10 units, respectively, at 1 h post-inoculation. Although Termin-8 efficacy did not improve with time, due to its fixing of viral particles and rendering them non-infectious, treatment with Finio showed 100% viable viral inactivation (>5 log10 reduction units) at the lowest concentration after 7 days of exposure. Our results demonstrate that both Termin-8 and Finio can be used as effective chemical mitigants against megaviruses such as EhV and ASFV and can be used as effective preventive or mitigation strategies to prevent the transmission of ASFV by reducing particle viability in contaminated feed, although additional research is warranted.

Distinct virome compositions and lack of viral diversification indicate that viral spillover is a dead-end between the western honey bee and the common eastern bumblebee

Communications Biology · 2025-06-16 · 3 citations

Pathogen spillover events are of global concern as they have the potential to cause significant harm to the novel host species. The potential of viral spillover from the western honey bee (Apis mellifera) to other insects is well established. New variants should inevitably emerge following a host expansion, yet to our knowledge no study has shown this within this system. To investigate the outcome of viral spillover, we sequenced the RNA biased viromes of sympatric A. mellifera (n = 389) and common eastern bumblebee Bombus impatiens (n = 117) over three years. Distinct viromes occurred within each bee species throughout the study duration, with only one of the well-characterized honey bee viruses, sacbrood virus, consistently found in the bumblebee virome. Viruses shared by both bees shared over 98% nucleotide identity, and no bumblebee-specific strains of honey bee viruses occurred, as expected if spillover led to a true host expansion involving bumblebee-bumblebee transmission. Honey bee viruses, namely deformed wing virus, black queen cell virus, and sacbrood virus, which were present in the bumblebees did not show evidence of diversification among hosts, suggesting environmental exposure or dead-end spillover, rather than spillover host expansion.

Characterization of Glycoprotein 5-Specific Response in Pigs Vaccinated with Modified Live Porcine Reproductive and Respiratory Syndrome Virus Vaccine Derived from Two Different Lineages

Vaccines · 2025-02-27 · 3 citations

BACKGROUND/OBJECTIVES: , which encodes a major surface glycoprotein GP5 containing both neutralizing and non-neutralizing linear epitopes. Several positively selected sites have been identified on the GP5 ectodomain, indicating host immune pressure on these sites. This present study aimed to investigate the kinetics of antibody responses to GP5 and to map the epitope-specific response to the GP5 ectodomain from different PRRSV lineages after vaccination with commercially available modified live virus (MLV) vaccines. METHODS: ). Animals were challenged with a heterologous (lineage 1A) strain at 64 days post-vaccination (dpv). Blood samples were collected at various times post-vaccination and challenge. Kinetics of antibody response to different PRRSV antigens were monitored and virus neutralization against archetypal and contemporary strains belonging to lineage 5 and 1A were evaluated. In addition, antibody responses to peptides derived from the GP5 ectodomain of different viral lineages were assessed. RESULTS: Our results showed that the GP5-specific antibody response observed between 18 and 35 dpv was delayed compared to responses to the viral nucleocapsid protein. The polyclonal antibody response in both vaccinated groups showed similar levels of binding to variant GP5 peptides from different sub-lineages. Notably, in both vaccinated groups, the antibody directed to a peptide representing the GP5 ectodomain of a lineage 1C strain (variant 1C.5) displayed a rise in titer at 64 dpv, which was further increased by the challenge with the lineage 1A strain. Less than 50% of animals developed heterologous neutralizing antibodies post-vaccination with both MLV vaccines. However, higher neutralization titers were observed in all vaccinated animal post-challenge. CONCLUSIONS: Together, these data provide insights into the antibody responses to the GP5 ectodomain in MLV-vaccinated swine herds.

Evaluating the inactivation of a surrogate ASFV-like algal virus in a pilot solvent extraction soybean processing facility

Frontiers in Animal Science · 2025-03-20 · 2 citations

Introduction African swine fever virus (ASFV) is extremely stable in the environment, and previous laboratory experiments and simulations have also shown it to be highly stable in animal feed ingredients. However, ASFV cannot be studied in real world demonstrations because it is a highly contagious virus. African swine fever virus is a member of the nucleocytoplasmic large DNA viruses (NCLDVs), and similar to Emiliania huxleyi virus (EhV), which has a restricted host range limited to a species of marine algae called Emiliania huxleyi . This algal NCLDV has many similar morphological and physical characteristics to ASFV, thereby making it a safe surrogate for generating experimental results that are applicable to ASFV and representative of real-world conditions. Methods We inoculated whole soybeans with EhV strain 86 (EhV-86) at a concentration of 1.80 × 10 8 virus/mL, which were then processed at a pilot solvent extraction facility to produce soybean hulls and meal. After processing, samples were evaluated for virus presence and viability using a previously validated viability qPCR (V-qPCR) method. Results No detection of EhV-86 occurred on environmental surfaces, air, and dust samples pre- or post-processing. Viable EhV-86 was detected in conditioned soybeans, dehulled soybeans, soybean hulls, soybean flakes, air-dried solvent extracted soybean flakes, post-desolventizer toaster soybean flakes, and soybean meal after reaching steady state during solvent extraction processing. Discussion It is important to note that 95% of viable virus was recovered (2.43 × 10 6 virus/g in replicate A and 2.61 × 10 6 virus/g in replicate B) in soybean meal, suggesting that longer retention times or application of chemical mitigants may be needed for more complete inactivation. The high concentration of viable viruses remaining on the soybean hulls after processing (1.98 × 10 7 virus/g in replicate A and 2.12 × 10 7 virus/g in replicate B) is a major concern for potential virus transmission in animal feed. These results demonstrate for the first time that ASFV-like NCLDVs can retain viability in soybean hulls, flakes, and meal during solvent extraction processing in a pilot facility and remain a hazard for virus transmission. Future risk assessments focused on the role of contaminated feed ingredients in transmission of viruses to swine farms must consider the ingredient composition of complete feeds delivered to farms and the initial concentration of viable viruses.

Multiple, diverse endogenous giant virus elements within the genome of a brown alga

Virus Evolution · 2025-01-01 · 7 citations

Abstract Endogenous viral elements (EVEs) have been found in diverse eukaryotic genomes. These elements are particularly frequent in the genomes of brown algae (Phaeophyceae) because these seaweeds are infected by viruses (Phaeovirus) of the phylum Nucleocytoviricota (NCV) that are capable of inserting into their host’s genome as part of their infective cycle. A search for inserted viral sequences in the genome of the freshwater brown alga Porterinema fluviatile identified seven large EVEs, including four complete or near-complete proviruses. The EVEs, which all appear to have been derived from independent insertion events, correspond to phylogenetically diverse members of the Phaeovirus genus and include members of both the A and B subgroups of this genus. This latter observation is surprising because the two subgroups were thought to have different evolutionary strategies and were therefore not expected to be found in the same host. The EVEs contain a number of novel genes including a H4 histone-like sequence but only one of the EVEs possesses a full set of NCV core genes, indicating that the other six probably correspond to nonfunctional, degenerated viral genomes. The majority of the genes within the EVEs were transcriptionally silent and most of the small number of genes that showed some transcriptional activity were of unknown function. However, the existence of some transcriptionally active genes and several genes containing introns in some EVEs suggests that these elements may be undergoing some degree of endogenization within the host genome over time.

Author Correction: Distinct virome compositions and lack of viral diversification indicate that viral spillover is a dead-end between the western honey bee and the common eastern bumblebee

Communications Biology · 2025-06-28

Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2

Virus Evolution · 2025-01-01 · 2 citations

Abstract Despite extensive use of vaccination, porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) continues to evolve, likely driven by escape from natural or vaccine-derived immunity. However, direct evidence of vaccine-induced evolutionary pressure remains limited. Here, we tracked the evolution of PRRSV-2 sublineage 1A strain IA/2014 (variant 1A-unclassified) genome from infection chains of sequentially infected pigs under different immune conditions. Weaned pigs were divided into three groups: a non-immunized control group and two groups vaccinated with different modified live virus (MLV) vaccines, namely Prevacent® PRRS MLV (variant 1D.2) and Ingelvac PRRS® MLV (variant 5A.1). Sixty-four days post-vaccination, the pigs were challenged with IA/2014 PRRSV-2. Virus infection chains (which used serum from pigs in batch n to infect batch n + 1) were maintained across six sequential batches of roughly seven pigs each, allowing for virus evolution to occur across the ~ 84 days of the infection chain. A total of 110 serum samples were successfully sequenced. Vaccinated groups exhibited over twice the genetic divergence from the original challenge virus (0.3%–0.4% mean nucleotide distance) compared to non-immunized group (0.15%). Variability was concentrated in ORF1a and ORF1b. Deep sequencing revealed more rapid shifts of viral quasispecies composition in vaccinated pigs, and more homogeneous viral populations over batches compared to non-immunized pigs. Selection pressure analyses indicated strong purifying selection in one vaccinated group, though without clear signals at known antigenic sites in all treatment groups. However, vaccinated pigs had significantly higher cycle threshold values (P<.001), indicating lower viral loads and suggesting potential fitness limitations for highly diverged viruses in immunized pigs. These findings demonstrate that MLV vaccination can exert substantial evolutionary pressure on PRRSV-2, driving genetic diversification and highlighting the need for continuous PRRS monitoring and adaptive control strategies.