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Pair Invariant Mass to Isolate Background in the Search for the Chiral Magnetic Effect in Au+Au Collisions at √sNN = 200 GeV
Quark interactions with topological gluon configurations can induce local chirality imbalance and parity violation in quantum chromodynamics, which can lead to the chiral magnetic effect (CME)-an electric charge separation along the strong magnetic field in relativistic heavy-ion collisions. The CME-sensitive azimuthal correlator observable (Delta gamma) is contaminated by background arising, in part, from resonance decays coupled with elliptic anisotropy (v(2)). We report here differential measurements of the correlator as a function of the pair invariant mass (m(inv)) in 20-50% centrality Au + Au collisions at root s(NN) = 200 GeV by the STAR experiment at the BNL Relativistic Heavy Ion Collider. Strong resonance background contributions to Delta gamma. are observed. At large m(inv) where this background is significantly reduced, the Delta gamma. value is found to be significantly smaller. An event-shape-engineering technique is deployed to determine the v(2) background shape as a function of m(inv). We extract a v(2)-independent and m(inv)-averaged signal Delta gamma(sig) = (0.03 +/- 0.06 +/- 0.08) x 10(-4), or (2 +/- 4 +/- 5)% of the inclusive Delta gamma (m(inv) > 0.4 GeV/c(2)) = (1.58 +/- 0.02 +/- 0.02) x 10(-4), within pion p(T) = 0.2-0.8 GeV/c and averaged over pseudorapidity ranges of -1 < eta < -0.05 and 0.05 < eta < 1. This represents an upper limit of 0.23 x 10(-4), or 15% of the inclusive result, at 95% confidence level for the m(inv)-integrated CME contribution.
Isolating and Quantifying Uncertainties in the Vibration Isolation Round-Robin Challenge
presentation slides
Mid-height seismic isolation of equipment in nuclear power plants: Numerical simulations and design recommendations
Seismic isolation can mitigate earthquake demands on safety-class equipment and is being considered for application to some advanced nuclear reactors. For tall, slender vessels that could represent an advanced reactor, a steam generator or a heat exchanger, mid-height seismic isolation has been shown to be beneficial and practical. Here, this paper focuses on numerical modeling of a mid-height isolated tall, slender vessel with two primary goals 1) investigate and quantify the benefits of mid-height seismic isolation for a range of support structure stiffnesses, isolation systems, and seismic inputs, and 2) provide analysis and design recommendations for isolation of safety-class equipment. Results of response-history analysis were in good agreement with experimental measurements and demonstrated that mid-height isolation can substantially reduce seismic demands on tall, slender vessels for a range of support structure stiffnesses, isolation systems, and seismic inputs. Importantly, the reductions in horizontal spectral accelerations in the mid-height isolated vessel from the non-isolated condition were not affected by the stiffness of the support structure. Recommendations are made for analysis and design of isolated equipment and testing of isolators used for equipment protection in nuclear facilities, which are also applicable to other industries.
Characterization of Pseudomonas aeruginosa and Acinetobacter calcoaceticus-baumannii complex traumatic wound isolates
Healing of traumatic wounds is complicated by infecting pathogens, with Pseudomonas aeruginosa and members of the Acinetobacter calcoaceticus-baumannii complex among the most common infectious agents. However, a full understanding of genotypic and phenotypic differences between circulating wound isolates is lacking. To address this, traumatic wounds were sampled at Emory University Hospital, and 24 isolates were characterized; we focused on P. aeruginosa and Acinetobacter due to their prevalence and tendency for antibiotic resistance. Even though these species are renowned for antibiotic resistance, only two of the tested isolates could be classified as multidrug resistant. Whole-genome sequencing and analysis revealed that isolates from different patients were genetically distinct; however, longitudinal isolates from the same patient were closely related and appeared to represent chronic colonization by the same strain. Phylogenetic analysis revealed that laboratory strains (PAO1 and AB5075) that were isolated decades previously and from different locations grouped closely to subsets of the recent wound isolates. Given the importance of biofilm formation in infection, the ability of the isolates to form biofilms was assessed; all isolates formed biofilms but showed temporal and magnitude differences. Analysis of a subset of isolates revealed that planktonic P. aeruginosa was resistant to human serum-mediated killing. While the same was true for the majority of Acinetobacter isolates, one showed planktonic sensitivity that was abrogated when grown in a biofilm. Taken together, these data reveal genotypic and phenotypic differences in circulating isolates of P. aeruginosa and A. baumannii.
Genomic and phenotypic characterization of multidrug-resistant Salmonella enterica serovar Reading isolates involved in a turkey-associated foodborne outbreak
Salmonella is a global bacterial foodborne pathogen associated with a variety of contaminated food products. Poultry products are a common source of Salmonella -associated foodborne illness, and an estimated 7% of human illnesses in the United States are attributed to turkey products. From November 2017 to March 2019, the Centers for Disease Control and Prevention reported a turkey-associated outbreak of multidrug-resistant (MDR; resistant to ≥3 antimicrobial classes) Salmonella enterica serovar Reading ( S . Reading) linked to 358 human infections in 42 US states and Canada. Since S . Reading was seldom linked to human illness prior to this outbreak, the current study compared genomic sequences of S . Reading isolates prior to the outbreak (pre-outbreak) to isolates identified during the outbreak period, focusing on genes that were different between the two groups but common within a group. Following whole-genome sequence analysis of five pre-outbreak and five outbreak-associated turkey/turkey product isolates of S . Reading, 37 genes located within two distinct chromosomal regions were identified only in the pre-outbreak isolates: (1) an ~5 kb region containing four protein-coding genes including uidA which encodes beta-glucuronidase, pgdA encoding peptidoglycan deacetylase, and two hypothetical proteins and (2) an ~28 kb region comprised of 32 phage-like genes and the xerC gene, which encodes tyrosine recombinase (frequently associated with phage genes). The five outbreak isolates also had a deletional event within the cirA gene, introducing a translational frame shift and premature stop codon. The cirA gene encodes a protein with dual receptor functions: a siderophore receptor for transport of dihydroxybenzoylserine as well as a colicin Ia/b receptor. Significant differences for the identified genetic variations were also detected in 75 S . Reading human isolates. Of the 41 S . Reading isolates collected before or in 2017, 81 and 90% of the isolates contained the uidA and pgdA genes, respectively, but only 24% of the isolates collected after 2017 harbored the uidA and pgdA genes. The truncation event within the cirA gene was also significantly higher in isolates collected after 2017 (74%) compared to before or in 2017 (5%). Phenotypic analysis of the S . Reading isolates for colicin and cefiderocol sensitivities (CirA) and β-methyl-D-glucuronic acid utilization (UidA and accessory proteins) supported the genomic data. Overall, a similar genome reduction pattern was generally observed in both the turkey and human isolates of S . Reading during the outbreak period, and the genetic differences were present in genes that could potentially promote pathogen dissemination due to variation in Salmonella colonization, fitness, and/or virulence.
Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis
We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named "pre-op" isolates) and then 6 days later from the anastomotic site (herein named "post-op" isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown.
Antimicrobial resistance and genomic characterization of Salmonella Dublin isolates in cattle from the United States
Salmonella enterica subspecies enterica serotype Dublin is a host-adapted serotype in cattle, associated with enteritis and systemic disease. The primary clinical manifestation of Salmonella Dublin infection in cattle, especially calves, is respiratory disease. While rare in humans, it can cause severe illness, including bacteremia, with hospitalization and death. In the United States, S . Dublin has become one of the most multidrug-resistant serotypes. The objective of this study was to characterize S . Dublin isolates from sick cattle by analyzing phenotypic and genotypic antimicrobial resistance (AMR) profiles, the presence of plasmids, and phylogenetic relationships. S . Dublin isolates (n = 140) were selected from submissions to the NVSL for Salmonella serotyping (2014–2017) from 21 states. Isolates were tested for susceptibility against 14 class-representative antimicrobial drugs. Resistance profiles were determined using the ABRicate with Resfinder and NCBI databases, AMRFinder and PointFinder. Plasmids were detected using ABRicate with PlasmidFinder. Phylogeny was determined using vSNP. We found 98% of the isolates were resistant to more than 4 antimicrobials. Only 1 isolate was pan-susceptible and had no predicted AMR genes. All S . Dublin isolates were susceptible to azithromycin and meropenem. They showed 96% resistance to sulfonamides, 97% to tetracyclines, 95% to aminoglycosides and 85% to beta-lactams. The most common AMR genes were: sulf2 and tetA (98.6%), aph(6)-Id (97.9%), aph(3’’)-Ib, (97.1%), floR (94.3%), and blaCMY-2 (85.7%). All quinolone resistant isolates presented mutations in gyr A. Ten plasmid types were identified among all isolates with IncA/C2, IncX1, and IncFII(S) being the most frequent. The S . Dublin isolates show low genomic genetic diversity. This study provided antimicrobial susceptibility and genomic insight into S . Dublin clinical isolates from cattle in the U.S. Further sequence analysis integrating food and human origin S . Dublin isolates may provide valuable insight on increased virulence observed in humans.
Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples
Candida tropicalis is a human pathogen that primarily infects the immunocompromised. Whereas the genome of one isolate, C. tropicalis MYA-3404, was originally sequenced in 2009, there have been no large-scale, multi-isolate studies of the genetic and phenotypic diversity of this species. Here, we used whole genome sequencing and phenotyping to characterize 77 isolates of C. tropicalis from clinical and environmental sources from a variety of locations. We show that most C. tropicalis isolates are diploids with approximately 2–6 heterozygous variants per kilobase. The genomes are relatively stable, with few aneuploidies. However, we identified one highly homozygous isolate and six isolates of C. tropicalis with much higher heterozygosity levels ranging from 36–49 heterozygous variants per kilobase. Our analyses show that the heterozygous isolates represent two different hybrid lineages, where the hybrids share one parent (A) with most other C. tropicalis isolates, but the second parent (B or C) differs by at least 4% at the genome level. Four of the sequenced isolates descend from an AB hybridization, and two from an AC hybridization. The hybrids are MTLa/α heterozygotes. Hybridization, or mating, between different parents is therefore common in the evolutionary history of C. tropicalis. The new hybrids were predominantly found in environmental niches, including from soil. Hybridization is therefore unlikely to be associated with virulence. In addition, we used genotype-phenotype correlation and CRISPR-Cas9 editing to identify a genome variant that results in the inability of one isolate to utilize certain branched-chain amino acids as a sole nitrogen source.
On component isolation of conceptual advanced reactors
Implementation of component isolation in nuclear industry is challenging due to gaps in research and the lack of specific guidelines. In this study, parameters affecting component-level isolation of advanced reactor vessels are identified based on a representative numerical model with explicit consideration of nonlinear soil-structure interaction (SSI). The objective of this study is to evaluate the effectiveness of, and to identify potential limitations of using conventional friction pendulum and lead-rubber bearings to seismically isolate vessels. It is found that slender vessels or components are particularly vulnerable to rotational accelerations at the isolation interface, which are caused by rotation of the sub-structure and by excitation of higher modes in the horizontal direction of the seismically isolated system. Component isolation is found to be more effective for relatively stiffer vessels and at sites with stiff soil properties. Considering that conventional isolators are deficient in resisting axial tension, it is observed that the optimum location for supporting a component to achieve seismic isolation, is at a cross-sectional plane passing through the center of mass of the vessel. These findings are corroborated by numerous simulations of the response of seismically isolated reactor vessels at different nuclear sites subject to a variety of ground motions.
Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives
The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C . geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C . geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C . geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C . geophilum , we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.
Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources
Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.
Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study
Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2"), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec 57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.
A structure-preserving machine learning framework for accurate prediction of structural dynamics for systems with isolated nonlinearities
The nonlinearities present in structural systems are often found in isolated regions within the structure, such as those containing joints or interfaces. However, despite the localized nature of these nonlinearities their presence serves to couple together the modes of the underlying linear system and significantly complicate the development of appropriate reduced-order models; the localized nonlinearities have a global effect on the dynamics of the system. Further, in the presence of evolving structural health the nonlinearities can arise from accumulating damage, with dynamics distinct from those observed in the healthy state. The present work develops a data-driven formulation to identify and include the contributions of the isolated nonlinearities on the dynamics of the underlying linear structure. A novel coordinate separation is developed that decomposes those nonlinearities restricted to the isolated subdomain from the known linear system defined over the entire domain, and the influence of the isolated nonlinearities is reintroduced as an appropriately identified traction at the boundary of the isolated subdomain, referred to as the deviatoric force. In the region exterior to the nonlinear subdomain the response of the ideal linear system recovers that of the original nonlinear system. In this work, the deviatoric force component is predicted using a structure-preserving multilayer perceptron, based only on measured responses at the boundary of the isolated subdomain. Therefore introduction of the perceptron is able to bypass the direct numerical simulation of the nonlinearities within the isolated subdomain. This approach is illustrated through a simple structural system in which an interior region contains cubic nonlinearities and hysteretic damping. Once trained, the machine learning system is able to accurately predict the deviatoric force so that the ideal system recovers the response of the original system in the region outside the isolated nonlinear subdomain. Moreover, the data-driven approach is able to accurately predict the response when the system is subject to differing initial conditions and external excitation without the need for retraining, so that the proposed approach provides a robust description of the structural dynamics of the overall system.
Revisiting the guidelines for ending isolation for COVID-19 patients
Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0–6.6%). However, this policy entails lengthy unnecessary isolations (4.8–8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.
Seismic isolation: A pathway to standardized advanced nuclear reactors
Standardizing advanced nuclear reactors is a pathway to substantially reducing their overnight capital cost and achieving parity with other power sources, including renewables and fossil fuels. The seismic load case has thwarted standardization of nuclear power plants because site-specific seismic hazard and local near-surface geology has triggered soil-structure-interaction analysis, design, equipment qualification, regulatory review, and licensing, ensuring that each build is different. To achieve standardized or site-independent certified advanced reactor designs, the impact of the seismic load case on the engineering and construction cost and time must be substantially mitigated. Seismic isolation is a mature technology that has been used for more than 30 years in non-nuclear sectors to substantially reduce earthquake demands in buildings and other infrastructure. In this paper, seismic isolation is used to enable standardization of advanced reactor designs, aimed at the complete re-use of a site-independent, certified design and repeated procurement of safety-class equipment. A pathway to standardized designs using seismic isolation is demonstrated for two fundamentally different advanced reactors: a molten salt reactor and a high temperature gas reactor. Each reactor building is equipped with three specialized pieces of safety-class equipment, namely, a reactor vessel, a steam generator, and a control rod drive mechanism housing that is attached to the reactor head. Analysis is performed per ASCE and ASME standards to design the buildings and the equipment for two base conditions: conventional (fixed base) and base isolated. The impact of the seismic load case is characterized for the reinforced concrete walls in the buildings and for the equipment, measured using vessel wall thickness and horizontal accelerations. Here the analysis results show that the fixed-base buildings, designed for a site of low seismic hazard (peak ground acceleration, PGA = 0.15 g) could be constructed at a site of much greater seismic hazard (PGA = 0.7 g) if seismic base isolation is employed. Importantly, the scope of the site-specific analysis, design, and qualification would be limited to the seismic isolators and the isolated substructure, drastically reducing plant-specific engineering, review, and licensing, and time to construction start. Regulatory challenges and opportunities with standardized reactor designs are identified.
BONCAT-Live for isolation and cultivation of active environmental bacteria
In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.
Dissecting Phenotype from Genotype with Clinical Isolates of SARS-CoV-2 First Wave Variants
The emergence and availability of closely related clinical isolates of SARS-CoV-2 offers a unique opportunity to identify novel nonsynonymous mutations that may impact phenotype. Global sequencing efforts show that SARS-CoV-2 variants have emerged and then been replaced since the beginning of the pandemic, yet we have limited information regarding the breadth of variant-specific host responses. Using primary cell cultures and the K18-hACE2 mouse, we investigated the replication, innate immune response, and pathology of closely related, clinical variants circulating during the first wave of the pandemic. Mathematical modeling of the lung viral replication of four clinical isolates showed a dichotomy between two B.1. isolates with significantly faster and slower infected cell clearance rates, respectively. While isolates induced several common immune host responses to infection, one B.1 isolate was unique in the promotion of eosinophil-associated proteins IL-5 and CCL11. Moreover, its mortality rate was significantly slower. Lung microscopic histopathology suggested further phenotypic divergence among the five isolates showing three distinct sets of phenotypes: (i) consolidation, alveolar hemorrhage, and inflammation, (ii) interstitial inflammation/septal thickening and peribronchiolar/perivascular lymphoid cells, and (iii) consolidation, alveolar involvement, and endothelial hypertrophy/margination. Together these findings show divergence in the phenotypic outcomes of these clinical isolates and reveal the potential importance of nonsynonymous mutations in nsp2 and ORF8.