Distinct Genotypes Research Articles

Deciphering nitrogen dynamics in aeroponics: physio-biochemical and enzymatic responses influencing nitrogen use efficiency in contrasting potato genotypes

Excessive use of nitrogen (N) in crops, such as potatoes, can lead to economic and environmental repercussions. We hypothesized that potato genotypes with resilient root systems and high genetic capabilities for nitrogen-use efficiency (NUE) could effectively mitigate these challenges. Consequently, we investigated intraspecific variations and characteristics within six distinct potato genotypes exhibiting diverse NUEs in response to varying nitrogen levels in an aeroponic system. The morpho-physiological and biochemical properties showed significant genotypic variations, especially related to the N-assimilating enzyme levels and root characteristics. Notably, the root systems of all genotypes demonstrated greater responsiveness to low nitrogen levels, with genotype C17 showcasing the most substantial root system irrespective of nitrogen concentration. Root morphological traits displayed robust positive correlations with NUtE, primarily influenced by genotype rather than nitrogen concentration. Conversely, nitrogen levels, displaying positive correlations with NUpE, influenced growth and activities of N-assimilating enzymes. Based on their distinct root systems, metabolic activities, and NUE profiles, genotypes C17 and C11 were determined to be N-efficient and N-inefficient, respectively. This study provides novel insights into the physiological and biochemical mechanisms underlying nitrogen use efficiency in potato genotypes under aeroponic conditions, offering potential targets for breeding programs, optimizing fertilizer management and cultivation strategies to improve crop performance under nitrogen-deficient conditions. Future investigations, employing multi-omics approaches, will elucidate key genes and pathways in nitrogen metabolism, potentially offering avenues to enhance root architecture and improve NUE.

A Distinct Genotype, D/Ep6, Detected in Korean Female Patients: Chlamydia trachomatis Characterization from 2017 - 2018.

The objective of this study lies in identifying the dominant genotype of C. trachomatis isolated in Republic of Korea (ROK) between 2017 and 2018. A total of 504 clinical cervicovaginal swabs from patients were collected and inoculated on McCoy cell monolayers to isolate Chlamydial agents. C. trachomatis isolates were analyzed by sequencing of its ompA gene. A total of 54 C. trachomatis isolates were obtained. The constructed phylogenetic tree revealed the genotypes of isolates are D/Ep6 (48, 88.89%), D/Ep6-like (5, 9.26%), and Ja (1, 1.85%). The C. trachomatis D/Ep6-like have one single nucleotide polymorphism (SNP) compared to C. trachomatis D/Ep6, leading to E870K amino acid change. Phylogenetic analysis demonstrated globally rare C. trachomatis D/Ep6 was dominant in the ROK from 2017 to 2018. Findings in this study act as a keystone, bridging past and present molecular epidemiology of C. trachomatis in context of ROK.

The CaABCG14 transporter gene regulates the capsaicin accumulation in Pepper septum

Capsaicin (CAP), a crucial compound found in chili peppers, not only contributes to their spicy flavor but also possesses several industrial applications. CAP biosynthetic pathway is well known, while its transport mechanism remains elusive. Herein, we performed a comparative transcriptome analysis conducted on pepper fruit tissues at three different stages of development. Four important CAP transporter genes, including one MATE and three ABCs, were identified by differential expression and WGCNA analysis. Specifically, the expression patterns of three ABC genes were assessed in the septum of fruits from nine distinct genotypes of peppers with high capsaicin levels. Interestingly, CaABCG14 was associated with variations in CAP concentration and co-expressed with genes involved in CAP biosynthesis. Transient expression assay revealed that CaABCG14 is localized to the membrane and nucleus. Silencing of CaABCG14 resulted in a notable reduction in the levels of CAP contents and the expression of its biosynthetic genes in the septum of pepper. The overexpression of CaABCG14 greatly intensified the cytotoxic effects of CAP on the yeast cells. Taken together, we for the first time identified a new transporter gene CaABCG14, regulating the CAP accumulation in pepper septum. These findings offer a fresh molecular theoretical framework for CAP transport and accumulation.

Emergence of genetic diversity of Enterocytozoon bieneusi from snakes in China

Enterocytozoon bieneusi belongs to the phylum Microsporidia, a parasite reported to infect various domestic animals, wildlife and humans, thereby causing an intestinal disease characterized by severe or chronic diarrhea and malabsorption. The typical mode of transmission is contaminated water and food. Few studies on E. bieneusi infections have been reported in reptiles, however, our report focuses on the molecular characterization of E. bieneusi infection in snakes in China. We collected a total of 603 fecal samples from snakes in China. The samples were tested for the presence of E. bieneusi through PCR amplification of the internal transcribed spacer (ITS) locus. Our analysis showed E. bieneusi overall prevalence rate of 15.59 %, the highest prevalence was recorded in Eastern rat snake (21.99 %), followed by Corn snake (19.63 %) while the prevalence of 18.39 %, 15.79 %, 13.56 % were recorded in Common garter snake, Pine snake, Hognose snake respectively. Eastern kingsnake has the lowest infection rate of 5.71 %. Genotype analysis identified 26 distinct genotypes: 8 known and 18 novel. Phylogenetic analysis revealed that 25 genotypes belonged to Group 1, which includes isolates from various animal hosts and humans. However, genotype GX29 was classified under Group 9. Our study indicates that pet snakes are one of the potential sources of transmission of zoonotic microsporidiosis in China.

An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings.

Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A-J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both approaches have limitations. Whereas diagnostic sequencing, generally using the Sanger approach, tends to focus only on the S-gene and yields little or no information on intra-patient HBV genetic diversity, reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV diagnostic sequencing protocol suitable for clinical virology that yields both complete genome sequences and extensive intra-patient HBV diversity data. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit (Oxford nanopore Technologies, Oxford, OX4 4DQ, UK), ONT GridION sequencing, genotyping using genome detective software v1.132/1.133, a recombination analysis using jpHMM (26 October 2011 version) and RDP5.61 software, and drug resistance profiling using Geno2pheno v2.0 software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 residual diagnostic samples from HBV-infected patients in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.

Genetic diversity and molecular evolution of the internal transcribed spacer regions (ITS1–5.8S–ITS2) of Babesia vogeli

Canine babesiosis, a severe haemoparasitic disease caused by Babesia species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of B. vogeli on the basis of the internal transcribed spacer regions (ITS1–5.8S–ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (n = 62) exhibited 92.5–100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5–93.8 % between them. Notably, the newly generated Indian sequences (n = 21) demonstrated a high degree of homology, with 98.3–100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different B. vogeli populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2–25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The B. vogeli populations between Thailand and Tunisia exhibited the highest genetic differentiation (FST = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of B. vogeli indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-term molecular surveillance program. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of B. vogeli were observed on the basis of internal transcribed spacer regions (ITS1–5.8S–ITS2).

ELISA genotyping of hepatitis B virus in China with antibodies specific for genotypes B and C

Hepatitis B virus (HBV) causes hepatitis B (HB) and distinct HBV genotypes can lead to different prognoses. However, HBV genotyping is rarely done in clinics, because the traditional method by PCR-based DNA sequencing is impractical for clinical diagnosis with tedious process and low success rate. Herein, we have established an ELISA-based genotyping method to quickly determine the HBV genotypes of HB patients in China. First, two commercial antibodies, 16D12 and 6H3 specific for HBV genotypes B and C respectively, are chosen as capture antibodies, since these two genotypes dominate in China. Then two home-made genotype-specific antibodies, B19 and C04, are used as the detection antibodies for genotypes B and C in sandwiched ELISA. The ELISA kit shows high sensitivity (> 95%) and specificity (> 95%) in detecting genotypes B and C of Chinese HB patients. Moreover, the ELISA kit has demonstrated higher success rate (98.7%) than PCR-based DNA sequencing (93.5%) and a commercial PCR-based genotyping kit (92.2%) for sera with HBV DNA ≥ 1000 IU/mL and HBsAg ≥ 250 IU/mL. Such an advantage is more obvious for the sera with HBV DNA < 1000 IU/mL. The kappa analysis between the ELISA and PCR-based DNA sequencing results exhibits a kappa of 0.836, indicating a good correlation.

From landraces to haplotypes, exploiting a genomic and phenomic approach to identify heat tolerant genotypes within durum wheat landraces

Dry and hot climates severely impact wheat yields, necessitating the development of innovative solutions to accelerate the breeding and selection of more adaptable durum wheat genotypes. The aim of this study was to identify new wheat ecotypes that can bridge the gap between commercial varieties and adaptability to ongoing climate change. In this study, advanced genomic and phenomic techniques were combined to characterize a set of durum wheat landraces derived from single seed descent (SSD). This approach enabled the identification of novel variability in the TdHsp26-A1 and -B1 genes. As a result, 38 durum wheat genotypes were analyzed using targeted enrichment PCR, leading to the identification of 17 novel haplotype combinations with SNPs in the TdHsp26 genes. The response of these SSD haplotypes to heat stress was characterized at both the seedling and tillering growth stages. Phenotypic analysis of contrasting genotypes led to the selection of two distinct genotypes: SSD69 and SSD397. During heat stress, SSD69 exhibited altered accumulation of H2O2 and MDA content under both growth conditions, providing new insights into the oxidative response to heat stress. Additionally, this work identifies phenotypic traits that are suitable for detecting differences between variants. The geographic distribution of the different alleles aligned with the spread of durum wheat from its center of origin.

Gene expression analysis of Aquaporin genes in ruminants during growth phase in response to heat stress

Aquaporins (AQPs) are trans-membrane protein involved in water transport and different cellular functions such as cell adhesion, signalling and proliferation. These membrane proteins are essential for key physiological functions such as organ development, osmoregulation, tissue regeneration and metabolism. The regulation of AQP5 gene expression in ruminants during growth phase has not been analysed in-vivo. Therefore, the gene expression pattern was analysed in Jamunapari goats during 3 months to 12 month of age and adult age group in response to heat stress. The genotyping of the AQP5 gene was carried out by High-Resolution Melting (HRM) in four different goat breeds, which indicated four distinct genotypes in the population. The nucleotide diversity for the AQP5 gene ranged from 0.315 and 0.524 across the breeds. Additionally, a close evolutionary relationship between AQP5 and the HSP70 gene was observed, indicating a shared pathway for heat stress regulation. The m-RNA expression level of AQP5 at 3, 9, 12 month and adult age group exhibited 47.24, 1140, 43.17 and 12.55-fold higher expression than control. The m-RNA expression level of the AQP5 gene was up-regulated and significantly higher (P < 0.05) at 9-month age as compared to the other age groups. Heat stress phenotypes were classified based on respiration rate and heart rate, and the m-RNA expression of AQP5 was higher in heat stress-susceptible (HSS) individuals than heat stress-tolerant (HST) individuals at 3, 9, and 12 months of age. The AQP5 plays a significant role in thermoregulation during growth phases in response to heat stress in goats, however, it is required to understand the role of aquaporins at cellular level as well as to establish the association with production performance in ruminant system in-vivo.

Multiple-clone infections of Mpox: Insights from a single primary lesion

ObjectivesThe 2022 Mpox epidemic transitioned to human-to-human transmission through primary lesions, showing a higher rate of genomic mutations than typical for a DNA virus. While Orthopoxviruses are traditionally considered to cause monoclonal infections in a single patient, we explored whether Mpox virus (MPXV) exhibits genomic plasticity in primary lesions. MethodsFive clones, A3, A4, B3, C2, and C5, were isolated from a primary skin lesion of an adult male patient with Mpox and Human immunodeficiency virus on antiretroviral therapy who was not immunocompromised. Whole-genome sequencing was performed to analyze single nucleotide variations in each clone. The tissue culture infectious dose 50 (TCID50) and cytopathic effects (CPE) were measured at one, three, and six days post-infection as in vitro virus phenotypes. ResultsClones A4, C2, and C5 had dominantly identical sequences, while minor clones A3 and B3 had probable 3 and assured 1 additional unique mutation, respectively. Four mutations in A3 and B3 were located in the viral open reading frames, with A3 causing amino acid substitutions at two sites in B21R and B3 resulting in one amino acid change in I6L. Although there were no significant differences in TCID50 levels among the clones, B3 showed a greater CPE than the others at three and six days post-infection. ConclusionsThe coexistence of multiple clones with distinct genotypes and viral characteristics within a primary lesion suggests genomic plasticity in MPXV, indicating that genomic diversity may arise early in infection.

GenoTriplo: A SNP genotype calling method for triploids.

Triploidy is very useful in both aquaculture and some cultivated plants as the induced sterility helps to enhance growth and product quality, as well as acting as a barrier against the contamination of wild populations by escapees. To use genetic information from triploids for academic or breeding purposes, an efficient and robust method to genotype triploids is needed. We developed such a method for genotype calling from SNP arrays, and we implemented it in the R package named GenoTriplo. Our method requires no prior information on cluster positions and remains unaffected by shifted luminescence signals. The method relies on starting the clustering algorithm with an initial higher number of groups than expected from the ploidy level of the samples, followed by merging groups that are too close to each other to be considered as distinct genotypes. Accurate classification of SNPs is achieved through multiple thresholds of quality controls. We compared the performance of GenoTriplo with that of fitPoly, the only published method for triploid SNP genotyping with a free software access. This was assessed by comparing the genotypes generated by both methods for a dataset of 1232 triploid rainbow trout genotyped for 38,033 SNPs. The two methods were consistent for 89% of the genotypes, but for 26% of the SNPs, they exhibited a discrepancy in the number of different genotypes identified. For these SNPs, GenoTriplo had >95% concordance with fitPoly when fitPoly genotyped better. On the contrary, when GenoTriplo genotyped better, fitPoly had less than 50% concordance with GenoTriplo. GenoTriplo was more robust with less genotyping errors. It is also efficient at identifying low-frequency genotypes in the sample set. Finally, we assessed parentage assignment based on GenoTriplo genotyping and observed significant differences in mismatch rates between the best and second-best couples, indicating high confidence in the results. GenoTriplo could also be used to genotype diploids as well as individuals with higher ploidy level by adjusting a few input parameters.

Abstract C165: Interrogating the Tumor and Immune Microenvironment of Endometrial Cancers Among a Diverse Cohort of Cases

Abstract Endometrial cancer (EC) is the sixth most common gynecological malignancy, with an increasing incidence worldwide over the last two decades. African American women are more likely to be diagnosed with endometrial cancer than Caucasian women. Unfortunately, African American women are more frequently diagnosed with high-grade EC, which occurs 2-3 times more often compared to their white and Hispanic counterparts. Additionally, African American women have higher mortality rates from EC than Caucasian women, highlighting a significant cancer disparity among these patients. Uterine EC disparities are induced by complex ecosystems composed of cellular niches with distinct genotypes, phenotypes, and spatial transcriptomic landscapes. In estrogen-dependent EC tumorigenesis, the endometrium undergoes uncontrollable proliferation, progressing from normal to atypical hyperplasia and ultimately to carcinoma. The heterogeneity of EC tumors complicates therapeutic targeting, rendering EC a challenging disease to cure. This study aims to investigate the genetic and transcriptomic features found in the tumor microenvironment of African American patients with EC. Previous research has shown that the molecular classification of EC tumors can be categorized as estrogen-driven, hypermutant, microsatellite instable, or lacking a specific molecular profile. Current models do not adequately reflect the oncogenic origin and pathological progression in patients. The cohort of EC cases includes primary, metastatic, and normal tumor tissues classified as Uterine Endometrial Adenocarcinoma, along with two Serous Papillary cases with varying tumor grades (low to high grade). Spatial transcriptomics and whole exome sequencing were performed on these samples. Spatial transcriptomics will identify the alterations in gene expression and the spatial landscape of the cell neighborhoods driving tumor heterogeneity. Whole exome sequencing will provide insight into the germline and somatic variants present in EC, offering a deeper understanding of the potential genetic drivers in African American patients. The genes expressed across the EC tumor landscape are implicated in cell proliferation, epithelial- mesenchymal transition, DNA damage response, and immune response. The analysis will also show the transition of normal to malignant endometrium harboring high tumor mutational burden and microsatellite instability when comparing paired samples. This comprehensive approach aims to elucidate the genetic and transcriptomic underpinnings contributing to the disparities observed in African American patients with EC, ultimately informing better-targeted therapies and improving outcomes. Citation Format: Danyelle Paine, John Carpten. Interrogating the Tumor and Immune Microenvironment of Endometrial Cancers Among a Diverse Cohort of Cases [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C165.

Genetic resources of African mahogany in Brazil: genomic diversity and structure of forest plantations

BackgroundAfrican mahogany species (Khaya sp.) have been introduced to Brazil gaining increasing economic interest over the last years, as they produce high quality wood for industrial applications. To this date, however, the knowledge available on the genetic basis of African mahogany plantations in Brazil is limited, which has driven this study to examine the extent of genetic diversity and structure of three cultivated species (Khaya grandifoliola, Khaya senegalensis and Khaya ivorensis) and their prospects for forest breeding.ResultsIn total, 115 individuals were genotyped (48 of K. grandifoliola, 34 of K. senegalensis and 33 of K. ivorensis) for 3,330 filtered neutral loci obtained from genotyping-by-sequencing for the three species. The number of SNPs varied from 2,951 in K. ivorensis to 4,754 in K. senegalensis. Multiloci clustering, principal component analysis, Bayesian structure and network analyses showed a clear genetic separation among the three species. Structure analysis also showed internal structure within each species, highlighting genetic subgroups that could be sampled for selecting distinct genotypes for further breeding, although the genetic distances are moderate to low.ConclusionIn our study, SNP markers efficiently assessed the genomic diversity of African mahogany forest plantations in Brazil. Our genetic data clearly separated the three Khaya species. Moreover, pairwise estimates of genetic distances among individuals within each species showed considerable genetic divergence among individuals. By genotyping 115 pre-selected individuals with desirable growth traits, allowed us not only to recommend superior genotypes but also to identify genetically distinct individuals for use in breeding crosses.

Investigation of the α9-nicotinic receptor single nucleotide polymorphisms induced oncogenic properties and molecular mechanisms in breast cancer.

α9-nAChR, a subtype of nicotinic acetylcholine receptor, is significantly overexpressed in female breast cancer tumor tissues compared to normal tissues. Previous studies have proposed that specific single nucleotide polymorphisms (SNPs) in the CHRNA9 (α9-nAChR) gene are associated with an increased risk of breast cancer in interaction with smoking. The study conducted a breast cancer risk assessment of the α9-nAChR SNP rs10009228 (NM_017581.4:c.1325A > G) in the Taiwanese female population, including 308 breast cancer patients and 198 healthy controls revealed that individuals with the heterozygous A/G or A/A wild genotype have an increased susceptibility to developing breast cancer in the presence of smoking compared to carriers of the G/G variant genotype. Our investigation confirmed the presence of this missense variation, resulting in an alteration of the amino acid sequence from asparagine (N442) to serine (S442) to facilitate phosphorylation within the α9-nAchR protein. Additionally, overexpression of N442 (A/A) in breast cancer cells significantly enhanced cell survival, migration, and cancer stemness compared to S442 (G/G). Four-line triple-negative breast cancer patient-derived xenograft (TNBC-PDX) models with distinct α9-nAChR rs10009228 SNP genotypes (A/A, A/G, G/G) further demonstrated that chronic nicotine exposure accelerated tumor growth through sustained activation of the α9-nAChR downstream oncogenic AKT/ERK/STAT3 pathway, particularly in individuals with the A/G or A/A genotype. Collectively, our study established the links between genetic variations in α9-nAChR and smoking exposure in promoting breast tumor development. This emphasizes the need to consider gene-environment interactions carefully while developing effective breast cancer prevention and treatment strategies.

Single-cell detection of copy number changes reveals dynamic mechanisms of adaptation to antifungals in Candida albicans.

Genomic copy number changes are associated with antifungal drug resistance and virulence across diverse fungal pathogens, but the rate and dynamics of these genomic changes in the presence of antifungal drugs are unknown. Here we optimized a dual-fluorescent reporter system in the diploid pathogen Candida albicans to quantify haplotype-specific copy number variation (CNV) and loss of heterozygosity (LOH) at the single-cell level with flow cytometry. We followed the frequency and dynamics of CNV and LOH at two distinct genomic locations in the presence and absence of antifungal drugs in vitro and in a murine model of candidiasis. Copy number changes were rapid and dynamic during adaptation to fluconazole and frequently involved competing subpopulations with distinct genotypes. This study provides quantitative evidence for the rapid speed at which diverse genotypes arise and undergo dynamic population-level fluctuations during adaptation to antifungal drugs in vitro and in vivo.

Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection.

Accumulating evidence points to persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunocompromised individuals as a source of novel lineages. While intrahost evolution of the virus in chronically infected patients has previously been reported, existing knowledge is primarily based on samples from the nasopharynx. In this study, we investigate the intrahost evolution and genetic diversity that accumulated during a prolonged SARS-CoV-2 infection with the Omicron BF.7 sublineage, which is estimated to have persisted for >1 year in an immunosuppressed patient. Based on the sequencing of eight samples collected at six time points, we identified 87 intrahost single-nucleotide variants, 2 indels, and a 362-bp deletion. Our analysis revealed distinct viral genotypes in the nasopharyngeal (NP), endotracheal aspirate, and bronchoalveolar lavage samples. This suggests that NP samples may not offer a comprehensive representation of the overall intrahost viral diversity. Our findings not only demonstrate that the Omicron BF.7 sublineage can further diverge from its already exceptionally mutated state but also highlight that patients chronically infected with SARS-CoV-2 can develop genetically specific viral populations across distinct anatomic compartments. This provides novel insights into the intricate nature of viral diversity and evolution dynamics in persistent infections.

Avian Pathogenic Escherichia coli: An Overview of Infection Biology, Antimicrobial Resistance and Vaccination.

Avian Pathogenic Escherichia coli (APEC) is an extraintestinal pathotype of E. coli that leads to a range of clinical manifestations, including respiratory, systemic and reproductive infections of chickens in both egg and meat production. Unlike most E. coli pathotypes, APEC is not defined by specific virulence genes but rather is a collection of several distinct genotypes that can act as both primary and secondary pathogens leading to colibacillosis. Recent measures to reduce antimicrobials both as growth promoters and as flock-level therapeutics are considered to have led to increased numbers of animals affected. Nevertheless, antimicrobial resistance is a considerable problem in APEC, with resistance to third and fourth-generation cephalosporins via extended-spectrum beta-lactamases (ESBLs), fluoroquinolones and colistin seen as a particular concern. The need to control APEC without antimicrobial use at the flock level has seen an increased focus on vaccination. Currently, a few commercial vaccines are already available, and a range of approaches are being applied to develop new vaccines, and other controls, such as bacteriophage or probiotics, are attracting interest. The lack of a single defined APEC genotype presents challenges to these approaches.

In Vitro Synthetic Polyploidization in Medicinal and Aromatic Plants for Enhanced Phytochemical Efficacy—A Mini-Review

Medicinal and aromatic plants (MAPs) are well known for their valuable secondary metabolites and diverse phytochemicals responsible for a plethora of medicinal properties such as antimicrobial, antioxidant, anti-inflammatory, anticancerous, and analgesic activities, making them essential for various industries. Therefore, this significant market demand has led to the need to improve the quality and quantity of secondary metabolites and thus develop high-quality commercial products. In this context, polyploidization is considered a sound contemporary approach that produces new genotypes, leading to the overexpression of genes involved in biosynthesizing crucial metabolites. Enhanced natural metabolite production increases the biological activities of plant extracts along with enhanced tolerance against abiotic and biotic stresses to achieve homogeneity. This improvisation in the quality and quantity of plant secondary metabolites can maximize the medicinal value of the plants. Therefore, this mini-review aims to explore the importance of enhancing biological activity in medicinal plants, summarize the progress of synthetic polyploidization as a breeding tool in MAP species, and elucidate how this technique plays an important role in improving medicinal values. This breeding strategy could significantly advance future research and industrial applications by inducing superior genotypes with enhanced genomic complexity and improving traits like increased biomass, stress tolerance, and novel biochemical pathways. So, it can be concluded that in vitro synthetic polyploidization can be an effective tool for promoting the production of more distinctive genotypes with immense medicinal properties for a variety of commercial and pharmaceutical purposes.

Diversity in clinical isolates of Ictalurid herpesvirus 1 (IcHV1) from U.S. farm-raised catfish and virulence assessment in channel and channel × blue catfish hybrids.

Ictalurid herpesvirus 1 (IcHV1) is the most significant viral agent in U.S. catfish aquaculture. Little is known regarding the genetic stability and antigenic variability of IcHV1. Herein, the genetic and antigenic diversity of IcHV1 field isolates was assessed by restriction fragment length polymorphism (RFLP) analysis and serum neutralization assays. RFLP analysis identified two distinct genotypes (IcHV1A and IcHV1B), both discrete from blue catfish alloherpesvirus (BCAHV). Neutralization assays with anti-IcHV1 monoclonal antibody Mab-95 indicate shared antigenic determinants for IcHV1A and IcHV1B that are absent from BCAHV, which Mab-95 did not neutralize. Virulence assessments with representative isolates demonstrate significant differences between isolates within RFLP groups and pooled RFLP group data suggest IcHV1B (pooled survival [mean ± SE]: 58.3% ± 2.6) may be more virulent than IcHV1A (survival: 68.6% ± 2.4). Rechallenges with representative IcHV1A and IcHV1B isolates indicate a cross-protective effect, with fish surviving initial exposure to IcHV1A or IcHV1B showing robust protection when subsequently re-exposed to IcHV1A or IcHV1B. This work demonstrated significant differences in virulence between case isolates, identifying two discrete IcHV1 lineages, distinct from BCAHV, with similar virulence in channel and channel × blue catfish hybrids and a cross-protective effect in catfish surviving exposure to either lineage.

A Retrospective Analysis Reveals That the 2021 Outbreaks of African Swine Fever Virus in Ghana Were Caused by Two Distinct Genotypes.

African swine fever virus (ASFV) is the causative agent of African swine fever (ASF), a highly infectious and lethal disease of domesticated swine. Outbreaks of ASF have been mostly restricted to the continent of Africa. The outbreaks that have occurred outside of Africa were controlled by extensive depopulation of the domesticated pig population. However, in 2007, an outbreak occurred in the country of Georgia, where ASFV infected wild pigs and quickly spread across eastern Europe. Since the reintroduction of ASF into Europe, variants of the current pandemic strain, ASFV Georgia 2007/01 (ASFV-G), which is classified as Genotype 2 based on p72 sequencing, have been reported in countries within western Europe, Asia, and the island of Hispaniola. Additionally, isolates collected in 2020 confirmed the presence of variants of ASFV-G in Nigeria. Recently, we reported similar variants of ASFV-G collected from domestic pigs suspected of dying of ASF in Ghana in 2022. Here, we retroactively report, based on full-length sequencing, that similar variants were present in Ghana in 2021. The SNP analysis revealed derivatives of ASFV with distinct genetic markers. Furthermore, we identified three full-length ASFV genomes as Genotype 1, indicating that there were two genotypes circulating in proximity during the 2021 ASF outbreaks in Ghana.