Strain Evolution Research Articles

Startup flow with and without wall slip in a pipe plugged with weakly compressible complex fluids—A new insight

The present article explains the nontrivial synergetic effect of wall slip, compressibility, and thixotropy in a pressurized flow startup operation of various structured fluids. Opposite to intuition, experimental and numerical simulations suggest that the wall slip (adhesive failure) facilitates gel degradation (cohesive failure), revealing a new flow startup mechanism. The irreversible thixotropic rheological model, along with the static slip-based model, is utilized to describe the structural degradation kinetics in the bulk phenomenon and the near-wall phenomenon, respectively. The near-wall transient variations in axial velocity or strain evolution and the initial pressure propagation mechanism along the axis of the circular pipe explain the essence of the aforementioned synergy. Finally, a comparative study of the effect of wall slip on the pressure propagation mechanisms and startup flow of generalized Newtonian fluids, viscoelastic based thixotropic fluids, and viscoelastic solids is also performed. Wall slip can convert no-steady-state thixotropic elasto-viscoplastic flow cases into a steady-state fluid flow, whereas it causes viscoelastic solids to move with a slip velocity. Additionally, our study revealed that stick-slip phenomena occur at an acoustic time scale. It requires a compressive wave to travel with information of stick position to the outlet and again back to the inlet, concomitantly causing the release of additional fluid, thereby converting the stick to a slip regime. Conventionally, stick-slip phenomena were mainly associated with nonlinearity. Hence, our study opened a new direction. Finally, concomitant with the experimental observations, we found that stick-slip phenomena disappear when the fluid is uniformly compressed and a steady state is reached.

Raman Spectroscopy Investigation of Strain Evolution in Relaxed and Pseudomorphic Layers of Si0.4Ge0.6 Films Grown on (001) Si Substrates

Abstract In this study, the laminated strain of relaxed and the pseudomorphic layer in the Si0.4Ge0.6 films grown on (001) Si substrates are studied by Raman spectroscopy. With the SiGe films ranging from 20 nm to 1200 nm in thickness, biaxial strains are revealed through room-temperature Raman peak analysis. Notably, a highly strained layer named the pseudomorphic layer is observed in the 30-nm sample. The peak broadening induced by the scattering of phonons at the thickness of 30 nm suggests dense dislocations at the substrate-pseudomorphic layer interface. The study also finds that the relaxed layer has a much more dramatic relaxation compared to that of the pseudomorphic layer, while the pseudomorphic layer maintains a high degree of strain. These findings contribute to the understanding of the SiGe alloy growth, enhancing the fabrication of intricate SiGe-based devices with improved strain control and relaxation dynamics.

In Situ Neutron Diffraction Study of Strain Evolution and Load Partitioning During Elevated Temperature Tensile Test in HIP-Treated Electron Beam Powder Bed Fusion Manufactured Ti-6Al-4V

Abstract To manufacture almost fully dense components, electron beam powder bed fusion of Ti-6Al-4V is typically combined with post-heat treatment, such as hot isostatic pressing (HIP). The standard HIP treatment performed at 920°C and 100 MPa for 2 h results in coarsening of the microstructure and impacting the yield strength. A low-temperature HIP treatment performed at 800°C and 200 MPa for 2 h resulted in limited coarsening and comparable yield strength to as-built material. A coarser microstructure is detrimental to tensile properties. Tensile testing at different temperatures revealed that thermal activation of different slip systems could possibly affect the elongation behavior, demanding additional investigation. Performing in situ neutron time of flight diffraction during tensile testing provides data to analyze strain evolution and load partitioning in the crystal lattice, which includes the slip planes. A two-phase elastic–plastic self-consistent model has been used to analyze and compare the experimental results. The lattice strain evolution results indicated that the basal slip {0 0 0 2} was activated at 20°C while the pyramidal slip {1 0 $$\overline{1 }$$ 1 ¯ 1} was first activated during loading at 350°C. Load partitioning results showed that the β phase endures higher stresses than the α phase in the plastic regime.

Laboratory evolution of E. coli with a natural vitamin B12 analog reveals roles for cobamide uptake and adenosylation in methionine synthase-dependent growth.

Bacteria encounter chemically similar nutrients in their environment, which impact their growth in distinct ways. Among such nutrients are cobamides, the structurally diverse family of cofactors related to vitamin B12 (cobalamin), which function as cofactors for diverse metabolic processes. Given that different environments contain varying abundances of different cobamides, bacteria are likely to encounter cobamides that enable them to grow robustly and also those that do not function efficiently for their metabolism. To gain insights into how bacteria might respond under the latter conditions, we performed a laboratory evolution of a cobamide-dependent strain of Escherichia coli with pseudocobalamin (pCbl), a cobamide that E. coli uses less effectively than cobalamin for MetH-dependent methionine synthesis. Propagation and sequencing of nine independent lines identified potential genetic adaptations in cobamide-related genes that improved growth with less-preferred cobamides. We constructed targeted mutants to validate these findings and found that increasing the expression of the outer membrane cobamide transporter BtuB is beneficial during growth under cobamide-limiting conditions. Unexpectedly, we also found that overexpression of the cobamide adenosyltransferase BtuR confers a specific growth advantage with pCbl. Characterization of the latter phenotype revealed that BtuR and adenosylated cobamides contribute to optimal MetH-dependent growth. Together, these findings improve our understanding of how bacteria expand their cobamide-dependent metabolic potential.IMPORTANCEIn nature, bacteria commonly experience fluctuations in the availability of required nutrients. Thus, their environment often contains nutrients that are insufficient in quantity or that function poorly in their metabolism. Cobamides, the vitamin B12 family of cofactors, are ideal for investigating the influence of nutrient quality on bacterial growth. We performed a laboratory evolution experiment in E. coli with a less-preferred cobamide to examine whether and how bacteria can improve their growth with less ideal nutrients. We found that overexpression of genes for cobamide uptake and modification are genetic adaptations that improve growth under these conditions. Given that cobamides are key shared metabolites in microbial communities, our results reveal insights into bacterial interactions and competition for nutrients.

A Thermo‐Mechanical Localizing Gradient Damage Model With Modified Mazars Strain

ABSTRACTThis work establishes a thermo‐mechanical coupling model for thermally induced cracks in quasi‐brittle materials within the framework of localizing gradient damage theory. The constitutive relation considering the thermal expansion effect, and the heat conduction equation integrating the volumetric strain and damage evolution, are formulated based on the Clausius–Duhem inequality to ensure thermodynamic consistency. In particular, to accommodate the tension‐compression strength asymmetry across different quasi‐brittle materials, a modified Mazars strain is proposed as the driving force for the micro equivalent strain, where the first invariant of strain tensor and an adjustable ratio of compressive strength to tensile strength () are introduced. The numerical implementation employs the generalized‐α method for time domain discretization and the staggered scheme for decoupling. Numerical simulations demonstrate a nice feasibility of the modified Mazars strain in capturing both tensile and mixed‐mode failures, and the proposed model proves capable of characterizing complex crack behaviors under thermal loading in both quasi‐static and dynamic scenarios. The quenching test simulations of ceramic plates highlight the bidirectional coupling effects on crack patterns. Unidirectional coupling models that ignore the influence of volumetric strain and damage evolution on the temperature field would underestimate the temperature gradient, resulting in larger crack spacing and fewer cracks. In the thermal shock tests of cylindrical specimens, the transition in crack patterns from spiral shear bands to an annular damage zone with increasing compression‐tension strength ratio () is precisely captured, demonstrating the generality of the proposed model for various quasi‐brittle materials with tension‐compression strength asymmetry.

Antibacterials with Novel Chemical Scaffolds in Clinical Development.

The rise of antimicrobial resistance represents a significant global health threat, driven by the diminishing efficacy of existing antibiotics, a lack of novel antibacterials entering the market, and an over- or misuse of existing antibiotics, which accelerates the evolution of resistant bacterial strains. This review focuses on innovative therapies by highlighting 19 novel antibacterials in clinical development as of June 2024. These selected compounds are characterized by new chemical scaffolds, novel molecular targets, and/or unique mechanisms of action, which render their potential to break antimicrobial resistance particularly high. A detailed analysis of the scientific foundations behind each of these compounds is provided, including their pharmacodynamic profiles, current development state, and potential for overcoming existing limitations in antibiotic therapy. By presenting this subset of chemically novel antibacterials, the review highlights the ability to innovate in antibiotic drug development to counteract bacterial resistance and improve treatment outcomes.

Master Curve Evaluation Using the Fracture Toughness Data at Low Temperature of T-T0 < −50°C

Abstract The Master Curve methodology standardized by ASTM E1921 and JEAC4216 specifies an acceptable test temperature, T, to be selected within the range of ± 50°C from the evaluated reference temperature, T0. If small size specimens, such as 4mm thickness Mini-C(T) are used to measure fracture toughness, KJc, temperatures lower in this range should be selected to decrease the number of censored KJc due to plastic strain evolution that leads to specimen failure above the KJclimit. The combined constraints imposed by the T0 ± 50°C range and the KJclimit may cause difficulty in selecting an appropriate test temperature. The present study proposes a criterion based on Tave, the average of test temperature of uncensored valid KJc values in a data set, to judge whether a dataset including data obtained T-T0< −50°C can be used for estimation of T0. Analyses with synthetic KJc datasets demonstrated that if Tave-T0> = −50°C the resultant Master Curve reasonably represents the fracture toughness distribution even if the dataset includes data tested below T-T0 = −50°C. Analyses on recursively sampled datasets from an experimental fracture toughness dataset of over 200 values demonstrated that the concept of Tave reasonably works for T0 evaluation of such datasets even if a realistic limited number of specimens (e.g., 12-16) are tested. Allowing some data tested below T-T0 = −50 °C showed a higher percentage of valid T0 evaluations than can be achieved using the existing requirements of either ASTM E1921 or JEAC4216.

Thermo-viscoelastic analysis of a composite disk under parabolic temperature distribution using the Rayleigh-Ritz Method with Trigonometric Ritz Functions

The study focuses on the thermo-viscoelastic behavior of a composite disk subjected to a parabolic temperature distribution. The analysis employs the Rayleigh-Ritz method, combined with trigonometric Ritz functions, to model the dynamic response of the disk. The key objective is to investigate how temperature variations and viscoelastic material properties influence the radial and tangential stresses and strains in the disk. The thermo-viscoelastic problem is formulated by considering the time-dependent evolution of stresses and strains, incorporating both thermal expansion and viscoelastic relaxation effects. The radial stress and tangential stress are expressed as functions of time, governed by the relaxation functions, respectively. These functions describe the material's viscoelastic behavior, while the thermal expansion coefficients account for temperature-induced strain variations. The parabolic temperature distribution introduces a spatially varying thermal load, which is integrated into the thermo-viscoelastic equations. The Rayleigh-Ritz method is used to discretize the problem, with trigonometric Ritz functions chosen to represent the spatial variation of stresses and strains. This approach allows for efficient computation of the disk's response while capturing the anisotropic and viscoelastic nature of the composite material. The results highlight the interplay between thermal effects and viscoelastic behavior in determining the stress and strain distributions. The parabolic temperature distribution leads to non-uniform thermal expansion, which interacts with the viscoelastic relaxation processes to produce complex stress patterns. The analysis provides insights into the time-dependent evolution of stresses and strains, offering a comprehensive understanding of the thermo-viscoelastic response of the composite disk under thermal loading.

Effects of interfacial debonding of microspheres on mechanical properties of iron matrix syntactic foams: Roles of Ni coating

Effects of interfacial debonding of microspheres on mechanical properties of iron matrix syntactic foams were investigated through experimental and numerical analyses. Glass microspheres with and without Ni layers were used for dealing with different interfacial bonding states, where the layers increased strength 1.6 times higher than the non-layered syntactic foams. Numerical models estimated stress concentration and early evolution of plastic strain under tension, leading to greater degradation of properties by debonding compared to those under compression. Grain refinement and solid solution formation highly influenced strength, whereas thermal mismatch and load transfer effects were reduced by debonding.

Diversity in Thrips palmi: exploration of genetic and ecological heterogeneity.

Thrips palmi Karny (Thysanoptera: Thripidae), an impactful pest in Southeast and East Asia, spread to Africa, Oceania, and the Americas in the past decades. Besides being a principal pest of vegetables, legumes, fibre, and ornamental crops, T. palmi serves as the vector for several plant viruses that cause substantial economic losses. The impact of intraspecies heterogeneity in the evolution of pesticide-resistant, host-specific, and geo-ecological strains is known for several thrips species. The present study aims to explore the genetic basis of the intraspecies heterogeneity of T. palmi populations if any. The genetic diversity within T. palmi has been recognized by 35 microsatellite markers, sequencing mitochondrial cytochrome oxidase subunit I (mtCOI), and internal transcribed spacer 2 (ITS2) markers. A total of 93 populations were collected from diverse ecological niches of India. Out of which 20 populations were identified as T. palmi. A total of 286 mtCOI and 66 ITS2 sequences of T. palmi originating from different parts of the world including the sequences generated in this study were considered to ascertain the genetic diversity. All the collected Indian populations are clustered into two distinct ancestries in Structure analysis, with a predominant inclination towards Ancestry II. A high intraspecific diversity of global populations of T. palmi up to 19% based on mtCOI sequences and 15% in ITS2 sequences is indicative of the presence of cryptic species. Phylogenetic analyses and haplotype networking clustered the global population of T. palmi into five lineages. Restricted gene flow was anticipated among the major lineages of T. palmi. The results suggest the existence of reproductively isolated populations due to potential geographical barriers. Excess of rare alleles suggested a recent selective sweep or population expansion after a recent bottleneck that seeks a further evolutionary understanding of T. palmi population globally, and its introduction and ecesis in new areas. The study proposes that T. palmi populations across the globe represent a species complex with broader genetic boundaries and reproductive isolation that suggest further taxonomical appraisal.

A Constitutive Model for Anisotropic Sand Considering Fabric Evolution Under Proportional and Non‐Proportional Loadings

ABSTRACTA critical state plasticity model is proposed to describe the anisotropic sand behaviour under both proportional and non‐proportional loading conditions. An evolving fabric tensor is introduced into the model to reflect the influence of fabric anisotropy on the stress‐strain relation of sand. By employing a fabric‐dependent plastic flow direction, the non‐coaxial response can be simulated in a simple way. A non‐proportional loading mechanism is incorporated to consider the plastic deformation induced by the stress increment tangential to the yield surface. The influence of accumulative plastic strain on the dilatancy function and plastic modulus is properly considered, enabling the model to reasonably capture the evolutions of volumetric and deviatoric strains under both drained and undrained principal stress axes rotation. The model was validated based on the simulations of experimental results for monotonic loading and pure principal stress axes rotation tests covering a wide range of conditions.

Optimization of SARS-CoV-2 Mpro Inhibitors by a Structure-Based Multilevel Virtual Screening Method.

With the aim of developing novel anti-SARS-CoV-2 drugs to address the ongoing evolution and emergence of drug-resistant strains, the reported SARS-CoV-2 Mpro inhibitor WU-04 was selected as a lead to find novel, highly potent, and broad-spectrum inhibitors. Using a fragment-based multilevel virtual screening strategy, 15 hit compounds were identified and subsequently synthesized. Among them, A5 (IC50 = 1.05 μM), A6 (IC50 = 1.08 μM), and A9 (IC50 = 0.154 μM) demonstrated potent SARS-CoV-2 Mpro inhibition comparable to or slightly weaker than WU-04. Antiviral activity evaluations revealed that compound A9 exhibited the strongest antiviral activity with an EC50 value of 0.18 μM, quite comparable to the marketed drug Nirmatrelvir (EC50 = 0.123 μM) and inferior to WU-04 (EC50 = 0.042 μM). Molecular dynamics simulations elucidated the key interactions between compounds A5, A6, A9, and the binding pocket of SARS-CoV-2 Mpro, providing valuable insights into their mechanisms of action. These findings identify compound A9 as a promising lead for anti-SARS-CoV-2 drug development.

Study on Zonal Support Mechanism and the Surrounding Rock Control Technology of Rock Roadway Excavated by TBM in Coal Mine

ABSTRACTTunnel boring machine (TBM) has been increasingly used for excavating rock roadways in coal mines. However, the slower speed of support installation, compared to the cutterhead's fast rock‐breaking capability, limits the overall excavation speed of rock roadways. This study examines the construction of a gas drainage roadway in Shoushan No.1 coal mine using a double‐shield TBM. A mechanical model for TBM excavation was developed, considering the spatial effects of the excavation face. The study identified a zonal support mechanism for the surrounding rock in TBM excavation roadways, it also analyzed the effects of support reaction forces and virtual support forces on the surrounding rock of different zones. A zonal control technology for surrounding rock was proposed and successfully implemented in the field. The results indicate that the strain evolution of the surrounding rock behind the TBM excavation face displays distinct zonal features. Based on this, the study recommends timely support for critical areas of the roadway roof in rapidly deforming zones through localized active primary anchor bolting. In slower deforming zones, secondary active anchor bolting is recommended for the remaining parts of the roadway roof and the side supports. In stable zones, cables anchor bolting support are implemented. A phased control technology system for the zonal management of surrounding rock in TBM excavation roadway was developed, and optimal parameters were determined using numerical simulations. The phased and zonal control technology was successfully applied at Shoushan No. 1 coal mine, achieving a maximum excavation speed of 623 m per month. This study provides valuable insights into the application of rapid excavation technology by TBM under similar conditions.

Emergence of ceftriaxone-resistant Neisseria gonorrhoeae through horizontal gene transfer among Neisseria spp.

It has been suggested that the emergence of ceftriaxone-resistant strains of Neisseria gonorrhoeae involves the incorporation of the penA gene from commensal Neisseria spp. that are resistant to ceftriaxone. However, the mechanism of this mosaic penA generation is unknown. We obtained 10 strains of commensal Neisseria spp. showing ceftriaxone MIC >0.5 mg/L. The similarity of the penA gene region of these commensal Neisseria spp. strains and some ceftriaxone-resistant N. gonorrhoeae strains was investigated. To obtain transformants, commensal Neisseria spp., Neisseria lactamica, gDNA was used as donor DNA and a N. gonorrhoeae strain as the recipient. The sequence similarity in certain regions of penA-murE between some of the commensal Neisseria spp. strains and the N. gonorrhoeae FC428 strain was very high. The sequence of these regions was very similar among some ceftriaxone-resistant strains of Neisseria spp. The PenA of the transformants matched the full PenA 60 of the original FC428 strain. Furthermore, our findings indicated that the source of resistance could have been a penA fragment derived from Neisseria spp. that originally carried the same sequence. We suggest that FC428 developed ceftriaxone resistance by acquiring part of the penA-murE gene region from N. lactamica through horizontal gene transfer. The ceftriaxone-resistant N. lactamica shown here may also have emerged by acquiring part of penA from other Neisseria spp. From this work, our data provide insights into the understanding of the mechanism underlying the evolution of drug-resistant gonorrhea-causing strains.

Strain rebound and inhomogeneity in glass-to-metal seals: Radial vs axial strain evolution

Glass, as a widely used amorphous material, often undergoes pre-stressing during processing to enhance its stability, with glass-to-metal (GTM) seal being a prominent example. Despite extensive studies on residual stress/strain in sealing glass, critical gaps remain in decoupling directional strains and understanding their in situ evolution during the cooling process, especially with respect to their microstructural origins. This study employs advanced fiber Bragg grating (FBG) in situ monitoring to decouple and independently analyze radial and axial strain evolution, providing novel insights into the mechanical anisotropy of sealing glass. The results revealed significant directional strain inhomogeneity throughout the cooling process, with strain evolution characterized by five distinct phases: zero-strain, rapid strain increase, gradual strain increase, significant strain rebound, and strain stabilization. Notably, axial strain froze earlier than radial strain (590 °C vs 575 °C): a counterintuitive finding attributed to free volume (FV) dynamics within the glass. Both directions exhibited pronounced strain rebound at lower temperatures, driven by the accumulation of smaller rebound events, effectively explained by FV theory. Moreover, the mismatch in thermal expansion coefficients between the glass and the metal housing significantly amplified radial strain, resulting in marked directional differences in strain behavior. Finite element analysis further corroborated these findings, confirming more pronounced variations in axial strain compared to the more uniform behavior observed in radial strain. These results underscore the anisotropic mechanical response of sealing glass within GTM seals, emphasize the value of FBG in situ monitoring for understanding strain evolution, and provide insights into enhancing the reliability of GTM seals across various applications.

Synthesis of cationic N-acylated thiazolidine for selective activity against Gram-positive bacteria and evaluation of N-acylation's role in membrane-disrupting activity.

The evolution of antimicrobial-resistant strains jeopardizes the existing clinical drugs and demands new therapeutic interventions. Herein, we report the synthesis of cationic thiazolidine bearing a quaternary pyridinium group, in which thiazolidine was N-acylated with fatty acid to establish a hydrophilic-lipophilic balance that disrupts bacterial membranes. The bacterial growth inhibition assays and hemolytic activity against human red blood cells indicate that the N-acylated cationic thiazolidine (QPyNATh) inhibits Gram-positive bacteria at lower minimum inhibitory concentrations (MIC) and is selective for bacteria over mammalian cells. N-Acylation modulates MIC, and it is found that the N-palmitoylated compound, QPyN16Th, had the lowest MIC (1.95 μM) against Gram-positive, Enterococcus faecalis, Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA). In contrast, the N-myristoylated compound, QPyN14Th, showed the lowest MIC (31.25 μM) against Gram-negative, Escherichia coli, uropathogenic Escherichia coli, and Pseudomonas aeruginosa. At 1× MIC, QPyNATh permeabilizes the bacterial membrane, depolarizes the cytoplasmic membranes, and produces excess reactive oxygen species to kill the bacteria, as evidenced by live and dead staining. Interestingly, only QPyNATh containing a palmitoyl acyl chain demonstrated membrane-damaging activity at 2 μM concentrations, suggesting that the optimal hydrophilic-lipophilic balance enables QPyN16Th to selectively kill Gram-positive bacteria at lower doses. S. aureus develops resistance to ciprofloxacin quickly; however, no resistance to QPyN16Th is observed after several passages. As a proof of concept, the animal study revealed that QPyN16Th treatment reduced the bacterial burden in MRSA-infected zebrafish, allowing them to recover from infection and resume normal life. The results imply that lipidation and derivatizing thiazolidine with cationic charge offer an antimicrobial that is selective to treat Gram-positive bacterial infections, biocompatible, and less prone to develop resistance.

Microstructure evolution and dynamic recrystallization mechanism of tantalum-tungsten alloys under hot compression

Ta-W alloys exhibit outstanding comprehensive properties at high temperatures, allowing them to have great application prospects in the high-temperature field. High-temperature compression tests (1573~1873 K) were conducted to evaluate the high-temperature mechanical properties of Ta-12W alloy, and the strain-compensated Arrhenius-Type model and hot processing map were developed to predict the optimal processing window. The electron backscatter diffraction, Transmission electron microscope, and DEFORM-3D software were performed to investigate the microstructure evolution and distributions of strain. The results demonstrated that the flow stress of Ta-12W alloy presented apparent negative temperature sensitivity and positive strain rate sensitivity. Based on the thermal processing diagrams and EBSD analysis, the results show that the low deformation temperature and high strain rate introduce stress concentration and deformation instability in the Ta-12W alloy. The optimized processing temperature and strain rate are at 1800 ~1873 K/0.001 s-1~0.05 s-1, and the microstructure at 1873 K/0.001 s-1 is more uniform and exhibits a low residual stress level. As the temperature increases, dynamic recovery and dynamic recrystallization cause significant softening effects, and continuous dynamic recrystallization dominates the high-temperature deformation behavior. Moreover, multiple continuous dynamic recrystallizations occur simultaneously, including sub-grain nucleation inside large grains, sub-grain nucleation at grain boundaries, and grain fragmentation accompanied by grain rotation. This study revealed the mechanisms of microstructural evolution during hot deformation of Ta-12W alloy, providing important guidance for optimizing the thermomechanical processing parameters.

Virological Aspects of COVID-19 in Patients with Hematological Malignancies: Duration of Viral Shedding and Genetic Analysis.

Coronavirus disease 2019 (COVID-19) has been associated with a significant fatality rate and persistent evolution in immunocompromised patients. In this prospective study, we aimed to determine the duration of excretion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 37 Tunisian patients with hematological malignancies (40.5% with lymphoma and 37.8% with leukemia). In order to investigate the accumulation of viral mutations, we carried out genetic investigation on longitudinal nasopharyngeal samples using RT-PCR and whole-genome sequencing. Patients' samples were collected until the RT-PCR results became negative. SARS-CoV-2 infection was symptomatic in 48.6% of cases with fever, and cough was symptomatic in 61% of cases; the mortality rate was estimated to be 13.5%. The duration of viral RNA shedding ranged from 7 to 92 days after onset; it exceeded 18 days in 79.4% of cases. An intermittent PCR positivity was observed in two symptomatic patients. Persistent PCR positivity, defined as the presence of viral RNA for more than 30 days, was found in 51.4% of cases. No significant differences were observed for age, sex, type of hematological malignancy, or COVID-19 evolution between this group and a second one characterized by non-persistent PCR positivity. Lymphopenia was an independent predictor of prolonged SARS-CoV-2 RNA detection (p = 0.04). Three types of variants were detected; the most frequent was the Omicron. Globally, the mean intra-host variability in the SARS-CoV-2 genome was 1.31 × 10-3 mutations per site per year; it was 1.44 × 10-3 in the persistent group and 1.3 × 10-3 in the non-persistent group. Three types of mutations were detected; the most frequent were nucleotide substitutions in the spike (S) gene. No statistically significant difference was observed between the two groups as to the type and mean number of observed mutations in the whole genome and the S region (p = 0.650). Sequence analysis revealed the inclusion of one to eight amino acid-changing events in seventeen cases; it was characterized by genetic stability from the third to the twentieth day of evolution in six cases. For the two patients with intermittent PCR positivity, sequences obtained from samples before and after negative PCR were identical in the whole genome, confirming an intra-host evolution of the same viral strain. This study confirms the risk of persistent viral shedding in patients with hematological malignancies. However, persistence of PCR positivity seems to be correlated only with a continuous elimination of viral RNA debris. Additional studies based on cell culture analysis are needed to confirm these findings.

The Meq Genes of Nigerian Marek's Disease Virus (MDV) Field Isolates Contain Mutations Common to Both European and US High Virulence Strains.

Marek's disease (MD) is a pathology affecting chickens caused by Marek's disease virus (MDV), an acute transforming alphaherpesvirus of the genus Mardivirus. MD is characterized by paralysis, immune suppression, and the rapid formation of T-cell (primarily CD4+) lymphomas. Over the last 50 years, losses due to MDV infection have been controlled worldwide through vaccination; however, these live-attenuated vaccines are non-sterilizing and potentially contributed to the virulence evolution of MDV field strains. Mutations common to field strains that can overcome vaccine protection were identified in the C-terminal proline-rich repeats of the oncoprotein Meq (Marek's EcoRI-Q-encoded protein). These mutations in meq have been found to be distinct to their region of origin, with high virulence strains obtained in Europe differing from those having evolved in the US. The present work reports on meq mutations identified in MDV field strains in Nigeria, arising at farms employing different vaccination practices. DNA was isolated from FTA cards obtained at 12 farms affected by increased MD in the Plateau State, Nigeria. These sequences included partial whole genomes as well as targeted sequences of the meq oncogenes from these strains. Several of the meq genes were cloned for expression and their localization ability to interact with the chicken NF-IL3 protein, a putative Meq dimerization partner, were assessed. Sequence analysis of the meq genes from these Nigerian field strains revealed an RB1B-like lineage co-circulating with a European Polen5-like lineage, as well as recombinants harboring a combination of these mutations. In a number of these isolates, Meq mutations accumulated in both N-terminal and C-terminal domains. Our data, suggest a direct effect of the vaccine strategy on the selection of Meq mutations. Moreover, we posit the evolution of the next higher level of virulence MDVs, a very virulent plus plus pathotype (vv++).

Genome-Wide Genomic Analysis and Evolutionary Insights into Bovine Coronavirus Strains in Southwest China.

The global epidemic of bovine coronavirus (BCoV) has caused enormous economic losses. The characterisation and genetic composition of endemic strains in Southwest China remain elusive. This study aimed to fill this gap by isolating three BCoV strains from this region and sequencing their whole genomes. To elucidate the genetic evolution and characterisation of the prevalent strains, the results of BCoV sequences were compared in GenBank, with a focus on genetic evolution, mutation, and recombination patterns. The results showed close homology between strains NN190313 and NN230328, while strain NN221214 showed less similarity to these two strains but clustered with the French strain of the European branch. Intriguingly, NN190313 and NN230328 were grouped with goat-derived BCoV strains from Jiangsu Province in Eastern China in the Asian-American branch. In addition, recombination analyses revealed significant signals between NN230328 and either a Chinese goat-derived strain (XJCJ2301G) or a Shandong strain (ShX310). This study highlights the importance of monitoring cross-species transmission between cattle and goats, especially in the mountainous areas of Southwest China where mixed farming occurs, and thus, the monitoring of cross-species transmission between cattle and goats is important for preventing new public health challenges, providing important insights for research on cross-species transmission, early prevention, and control measures, with potential applications in vaccine development.