Emerging infectious diseases (EIDs) pose an increasingly significant global burden, driven by urbanization, population explosion, global travel, changes in human behavior, and inadequate public health systems. The recent SARS-CoV-2 pandemic highlights the urgent need for innovative and robust technologies to effectively monitor newly emerging pathogens. Rapid identification, epidemiological surveillance, and transmission mitigation are crucial challenges for ensuring public health safety. Genomics has emerged as a pivotal tool in public health during pandemics, enabling the diagnosis, management, and prediction of infections, as well as the analysis and identification of cross-species interactions and the categorization of infectious agents. Recent advancements in high-throughput DNA sequencing tools have facilitated rapid and precise identification and characterization of emerging pathogens. This review article provides insights into the latest advances in various genomic techniques for pathogen detection and tracking and their applications in global outbreak surveillance. We assess methods that leverage pathogen sequences and explore the role of genomic analysis in understanding the epidemiology of newly emerged infectious diseases. Additionally, we address technical challenges and limitations, ethical and legal considerations, and highlight opportunities for integrating genomics with other surveillance approaches. By delving into the prospects and obstacles of genomics, we can gain valuable insights into its role in mitigating the threats posed by emerging pathogens and improving global preparedness in the face of future outbreaks.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), induced a global pandemic with a diverse array of clinical manifestations. While the acute phase of the pandemic may be waning, the intricacies of COVID-19′s impact on neurological health remain a crucial area of investigation. Early recognition of the spectrum of COVID-19 symptoms, ranging from mild fever and cough to life-threatening respiratory distress and multi-organ failure, underscored the significance of neurological complications, including anosmia, seizures, stroke, disorientation, encephalopathy, and paralysis. Notably, patients requiring intensive care unit (ICU) admission due to neurological challenges or due to them exhibiting neurological abnormalities in the ICU have shown increased mortality rates. COVID-19 can lead to a range of neurological complications such as anosmia, stroke, paralysis, cranial nerve deficits, encephalopathy, delirium, meningitis, seizures, etc., in affected patients. This review elucidates the burgeoning landscape of neurological sequelae associated with SARS-CoV-2 infection and explores the underlying neurobiological mechanisms driving these diverse manifestations. A meticulous examination of potential neuroinvasion routes by SARS-CoV-2 underscores the intricate interplay between the virus and the nervous system. Moreover, we dissect the diverse neurological manifestations emphasizing the necessity of a multifaceted approach to understanding the disease’s neurological footprint. In addition to elucidating the pathophysiological underpinnings, this review surveys current therapeutic modalities and delineates prospective avenues for neuro-COVID research. By integrating epidemiological, clinical, and diagnostic parameters, we endeavor to foster a comprehensive analysis of the nexus between COVID-19 and neurological health, thereby laying the groundwork for targeted therapeutic interventions and long-term management strategies.

A glioma is a solid brain tumor which originates in the brain or brain stem area. The diagnosis of gliomas based on standard-of-care (SOC) techniques includes karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), for detecting the pathogenic variants and chromosomal abnormalities. But these techniques do not reveal the complete picture of genetic complexity, thus requiring an alternative technology for better characterization of these tumors. The present study aimed to evaluate the clinical performance and feasibility of using optical genome mapping (OGM) for chromosomal characterization of gliomas. Herein, we evaluated 10 cases of gliomas that were previously characterized by CMA. OGM analysis showed concordance with the results of CMA in identifying the characterized Structural Variants (SVs) in these cases. More notably, it also revealed additional clinically relevant aberrations, demonstrating a higher resolution and sensitivity. These clinically relevant SVs included cryptic translocation, and SVs which are beyond the detection capabilities of CMA. Our analysis highlights the unique capability of OGM to detect all classes of SVs within a single assay, thereby unveiling clinically significant data with a shorter turnaround time. Adopting this diagnostic tool as a standard of care for solid tumors like gliomas shows potential for improving therapeutic management, potentially leading to more personalized and timely interventions for patients.

Circulating tumor cells (CTCs) are shed from the primary tumor into the bloodstream and represent dynamic molecular biomarkers for monitoring the progression of cancer. While profiling tumor tissues with over expression of cell surface markers, such as PD-L1 or HER2, is standard in guiding therapy, tissue samples are often inaccessible and inadequate, especially post-surgery or in cases of recurrence. Emerging clinical evidence indicates that CTC counts and biomarker surface expression can predict prognosis and therapeutic resistance more accurately than imaging or tissue-based approaches. Recent advancements in the CTC detection methods, based on physical properties or surface markers (e.g., EpCAM), coupled with next-generation sequencing (NGS) have enabled the isolation of these rare cells and their molecular characterization. Consequently, CTCs provide a real-time alternative, enabling repeated, longitudinal assessment of tumor phenotype and therapeutic response. This review emphasizes the translational potential of surface protein biomarkers on CTCs for profiling, namely PD-L1, HER2, and EGFR, as a clinically actionable approach to stratify patients, guide immunotherapy decisions, and monitor minimal residual disease (MRD), especially when longitudinal tissue biopsies are not feasible.

Background: Multidrug-resistant HIV strains challenge treatment efficacy and increase mortality rates. Next-generation sequencing (NGS) technology swiftly detects variants, facilitating personalized antiretroviral therapy. Aim: This study aimed to validate the Vela Diagnostics NGS platform for HIV drug resistance mutation analysis, rigorously assessed with clinical samples and CAP proficiency testing controls previously analyzed by Sanger sequencing. Method: The experimental approach involved the following: RNA extraction from clinical specimens, reverse transcription polymerase chain reaction (RT-PCR) utilizing the Sentosa SX 101 platform, library preparation with the Sentosa SQ HIV Genotyping Assay, template preparation, sequencing using the Sentosa SQ301 instrument, and subsequent data analysis employing the Sentosa SQ Suite and SQ Reporter software. Drug resistance profiles were interpreted using the Stanford HIV Drug Resistance Database (HIVdb) with the HXB2 reference sequence. Results: The Vela NGS system successfully identified a comprehensive array of drug resistance mutations across the tested samples: 28 nucleoside reverse transcriptase inhibitors (NRTI), 25 non-nucleoside reverse transcriptase inhibitors (NNRTI), 25 protease inhibitors (PI), and 10 integrase gene-specific variants. Dilution experiments further validated the system’s sensitivity, detecting drug resistance mutations even at viral loads lower than the recommended threshold (1000 copies/mL) set by Vela Diagnostics. Scope: This study underscores the validation and clinical applicability of the Vela NGS system, and its implementation may offer clinicians enhanced precision in therapeutic decision-making for individuals living with HIV.

The novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the most significant global health crises in recent history. The clinical characteristics of COVID-19 patients have revealed the possibility of immune activity changes contributing to disease severity. Nevertheless, limited information is available regarding the immune response in human lung tissue, which is the primary site of infection. In this study, we conducted an extensive analysis of lung tissue to screen for differentially expressed miRNAs and mRNAs in five individuals who died due to COVID-19 and underwent a rapid autopsy, as well as seven control individuals who died of other causes unrelated to COVID-19. To analyze the host response gene expression, miRNA microarray and Nanostring’s nCounter XT gene expression assay were performed. Our study identified 37 downregulated and 77 upregulated miRNAs in COVID-19 lung biopsy samples compared to the controls. A total of 653 mRNA transcripts were differentially expressed between the two sample types, with most transcripts (472) being downregulated in COVID-19-positive specimens. Hierarchical and PCA K-means clustering analysis showed distinct clustering between COVID-19 and control samples. Enrichment and network analyses revealed differentially expressed genes important for innate immunity and inflammatory response in COVID-19 lung biopsies. The interferon-signaling pathway was highly upregulated in COVID-19 specimens while genes involved in interleukin-17 signaling were downregulated. These findings shed light on the mechanisms of host cellular responses to COVID-19 infection in lung tissues and could help identify new targets for the prevention and treatment of COVID-19 infection.