John A. Lednicky

To date, no bovine viral diarrhea virus-2 (BVDV-2) coding-complete genomes are available from white-tailed deer (WTD) in Florida. We determined the coding-complete genome sequences of four BVDV-2 isolates from farmed WTD that were found dead in 2018. These belonged to BVDV-2 sub-genotype a.

1. AbstractThe Viable Virus Aerosol Sampler (VIVAS) enlarges microscale airborne virus particles via water vapor condensation, facilitating their efficient collection into a viability-conserving liquid medium. However, reliable prediction of its performance remains challenging across diverse environmental conditions. Field observations revealed that collection liquid levels, which significantly impact conservation of virus viability and VIVAS efficiency, fluctuate with ambient conditions and sampler settings. To address these issues, we built an extendable machine learning framework to identify optimal internal temperature settings for the VIVAS that maintain stable liquid volume under varying ambient conditions and to reliably predict the likelihood of achieving acceptable sampling performance. Using a regression pipeline trained on 292 experiments conducted in controlled laboratory environments, with 5-fold media-stratified cross-validation and Optuna hyperparameter tuning, the best-performing model was Support Vector Regression (SVR) with a Radial Basis Function (RBF) kernel, achieving root mean squared error (RMSE) of 0.2845, mean absolute error (MAE) of 0.2085, R2 = 0.8086, and mean absolute percentage error (MAPE) 12.45% in cross-validation. The model explained approximately 81% of liquid volume variability, representing the predictive performance for this complex thermodynamic system. The pipeline also retained flexibility to prioritize different performance metrics, including minimizing prediction error (RMSE or MAE) and maximizing variance explanation (R2), depending on the operational objectives of a given application. To facilitate practical implementation, a web application was developed to predict optimized VIVAS temperature settings needed to maintain the collection volume within its optimal range under varying ambient temperature, relative humidity, and particle concentration conditions.

Human Respiratory Syncytial Virus (HRSV) is a leading cause of respiratory infections in young children. HRSV cases declined dramatically in the initial stages of the COVID-19 pandemic, followed by a resurgence in 2022/2023. To investigate patterns of viral genetic diversity and evolutionary dynamics during this period, HRSV sequences were analyzed at national and global levels, including newly sequenced samples from pediatric patients at a major Florida medical center in Alachua County. Our Florida strains clustered within multiple clades, with no clear association between specific clades and clinical or epidemiologic characteristics. Phylodynamic analyses suggested post-pandemic changes in HRSV-A and HRSV-B population dynamics, while phylogeographic patterns were compatible with possible viral introductions from European countries. We also detected amino acid diversity in known G-protein epitope regions, indicating a genetic variation in antigenically relevant sites. These findings suggest that post-pandemic HRSV circulation was associated with changes in viral population dynamics and genetic diversity, emphasizing the value of continued genomic surveillance to monitor viral evolution and support future prevention strategies.

Background: Candidozyma auris, first recognized in 2009, has emerged as a pathogen of major global concern, particularly in association with healthcare-associated infections in long-term care facilities. Methods: In a study of infected and colonized patients conducted between 1/17/2023 and 11/30/2023 at our medical center in North-Central Florida, whole genome sequence data were obtained for 43 C. auris isolates from 36 patients. Results: Thirteen (30%) of the 43 isolates were from cultures collected as part of an investigation of a possible infection, with blood (seven isolates) being the most common source; eight (62%) of the 13 patients with clinical infections died. Isolates were within either a Clade I monophyletic subclade associated with European and Middle Eastern strains (n=27) or were from Florida subclades within C. auris Clade III (n=16). In seven instances multiple isolates with virtually identical genetic profiles were isolated from the same patient at time intervals that ranged from three weeks to seven months, with, in some instances, intervening negative cultures. All isolates were resistant to triazoles, albeit with resistance mutations at different nucleotide positions and within different genes for Clade I and Clade III isolates. One Clade I isolate was resistant to echinocandins. Conclusions: Data are consistent with a point-source C. auris outbreak involving a Clade I subclade of possible European origin, combined with multiple introductions and transmission of Clade III isolates from Florida. Strains were able to persist for extended periods of time in colonized/infected patients.

Trueperella pyogenes is a gram-positive, facultatively anaerobic bacterium known to cause infections in both domestic and wild animals, including white-tailed deer (WTD; Odocoileus virginianus ). However, limited studies have focused on its impact on farmed WTD. In this study, we aimed to explore the demographic features, antimicrobial resistance (AMR) profiles, and virulence factors of T. pyogenes isolated from farmed WTD in Florida. Between 2016 and 2023, we managed 831 deceased farmed WTD cases. Specimens from 715 animals were subjected to bacterial culture. T. pyogenes was isolated from 147 (20.6%) animals, ranking as the second most frequently isolated bacterial pathogen. All T. pyogenes -infected animals exhibited pneumonia. T. pyogenes infection cases were notably more prevalent during summer and fall. Between September 2020 and May 2022, all available T. pyogenes isolates ( n = 37) recovered from various specimen types from 30 diseased deer were included and analyzed using whole-genome sequencing and phylogenetic approaches. The results revealed substantial single-nucleotide polymorphism (SNP) diversity within the core genomes of the T. pyogenes strains. Antimicrobial resistance profiling showed that tetracycline resistance genes, particularly tetW , predominated, while genes associated with resistance to aminoglycosides, sulfonamides, and other tetracyclines were detected sporadically. Genes for several virulence factors were also identified, including pyolysin ( plo ), collagen-binding protein ( cbpA ), and various adhesion molecules. These findings highlight the importance of disease management strategies, including surveillance and targeted antimicrobial use, to mitigate T. pyogenes transmission in farmed WTD. Broader surveillance using non-postmortem clinical specimens and culture-independent approaches is needed to better understand its epidemiology. IMPORTANCE: Trueperella pyogenes is an opportunistic pathogen that has likely been underrecognized in its role in white-tailed deer health. Our demographic and genomic analysis of T. pyogenes isolated from deceased farmed white-tailed deer in Florida identified seasonal patterns, frequent association with pneumonia, and substantial genomic diversity among isolates. These findings highlight the need for enhanced surveillance, improved diagnostic approaches, and preventive measures to better understand and manage T. pyogenes infections in farmed and free-ranging cervid populations. By characterizing the demographic and genomic features of T. pyogenes in this understudied host system, this study provides a foundation for future research on pathogen ecology, disease surveillance, and cervid health management, including monitoring in settings where farmed deer may interact with surrounding wildlife.

Over the past three decades, cetacean morbilliviruses (CeMVs) have emerged as significant pathogens affecting cetacean populations worldwide. Here, we report the genome sequence of a new CeMV, designated Fraser’s dolphin morbillivirus (FDMV), isolated from a stranded Fraser’s dolphin (Lagenodelphis hosei) in Hawaiʻi in 2018. Next-generation sequencing facilitated recovery of the nearly complete FDMV genome (15,685 bp), and annotation indicated a genomic organization similar to that of other morbilliviruses, including six open reading frames. Genetic analysis of the FDMV RNA-dependent RNA polymerase gene sequence showed 87–89.6% nucleotide sequence identity compared with other CeMV strains. Phylogenetic analysis demonstrated that FDMV is a distinct member of the genus Morbillivirus, branching as the most basal member of the CeMV clade, which may represent a new species.

We report the isolation and coding complete genome sequences of a new CHeRI orbivirus from the spleen of a dead farmed white-tailed deer in Florida whose death was attributed to an infection by mule deerpox virus. Phylogenetic and genetic analyses support this new virus as the fifth strain of the CHeRI orbivirus 3 species, and we designated it CHeRI orbivirus 3–5. While our previous detections and isolations of CHeRI orbiviruses were from deer spleens that also contained epizootic hemorrhagic disease virus-2, or in one case, Hardee County ephemerovirus 1, no deerpox virus was isolated from the spleen of the animal in this report, marking the first time we have isolated a CHeRI orbivirus without a co-infecting agent.

Collection and identification of airborne viruses conventionally involve two separate processes: air sampling in the field and subsequent laboratory-based detection and analyses. They are time-consuming, which delays early warnings and hinders timely implementation of public health countermeasures. In-situ virus detection methods that enable preliminary identification at the sampling site can improve timeliness, eliminating the need for sample transport and allowing rapid decision-making. Herein, we developed and evaluated an integrated system that connects a water condensation-based aerosol collector called VIVAS with an in-situ detection platform known as VLEAD. We designed and fabricated an interface to serve both as the VIVAS’ collection chamber and as a conduit for fluid transfer into the VLEAD. The design achieved over 90% collection efficiency for particles ≥3 μm after computational fluid dynamics simulation optimization, and experimental testing confirmed a physical collection efficiency of approximately 95%. When exposed to lab-generated aerosols containing human coronavirus OC43 (HCoV-OC43), the system achieved a 100% detection rate for samples containing > 10³ genome equivalents (GE) of virus per sample (4–5 GE/μL, triplicates), verified by RT-qPCR. The integrated system replaced the standard Petri dish in the commercially available VIVAS and enabled seamless transfer for RT-LAMP-based detection. The limit of detection was comparable to the level at which viruses such as SARS-CoV-2 have been collected using the VIVAS during environmental sampling reported in other studies. That performance demonstrated strong potential for rapid, in-situ detection of airborne coronaviruses and potentially other viruses in field settings or public spaces during respiratory viral disease outbreaks.