Transcriptionally active nasopharyngeal commensals and opportunistic microbial dynamics define mild symptoms in the COVID 19 vaccination breakthroughs.

The development of COVID 19 vaccines as an effort to mitigate the outbreak, has saved millions of lives globally. However, vaccination breakthroughs have continuously challenged the vaccines' effectiveness and provided incentives to explore facets holding potential to alter vaccination-induced immunity and protection from subsequent infection, especially VOCs (Variants Of Concern). We explored the functional dynamics of nasopharyngeal transcriptionally active microbes (TAMs) between vaccination breakthroughs and unvaccinated SARS-CoV-2 infected individuals. Microbial taxonomic communities were differentially altered with skewed enrichment of bacterial class/genera of Firmicutes and Gammaproteobacteria with grossly reduced phylum Bacteroidetes in vaccination breakthrough individuals. The Bacillus genus was abundant in Firmicutes in vaccination breakthrough whereas Prevotella among Bacteroides dominated the unvaccinated. Also, Pseudomonas and Salmonella of Gammaproteobacteria were overrepresented in vaccination breakthrough, whilst unvaccinated showed presence of several genera, Achromobacter, Bordetella, Burkholderia, Neisseria, Hemophilus, Salmonella and Pseudomonas, belonging to Proteobacteria. At species level, the microbiota of vaccination breakthrough exhibited relatively higher abundance of unique commensals, in comparison to potential opportunistic microbes enrichment in unvaccinated patients' microbiota. Functional metabolic pathways like amino acid biosynthesis, sulphate assimilation, fatty acid and beta oxidation, associated with generation of SCFAs (short chain fatty acids), were enriched in vaccination breakthroughs. Majorly, metabolic pathways of LCFAs biosynthesis (long chain fatty acids; oleate, dodecenoate, palmitoleate, gondoate) were found associated with the unvaccinated. Our research highlights that vaccination decreases the microbial diversity in terms of depleting opportunistic pathogens and increasing the preponderance of commensals with respect to unvaccinated patients. Metabolic pathway analysis substantiates the shift in diversity to functionally modulate immune response generation, which may be related to mild clinical manifestations and faster recovery times during vaccination breakthroughs.

Preventing Risks of Infections and Medication Errors in IV therapy (PRIME): a patient safety initiative.

BACKGROUND: Two major avoidable reasons for adverse events in hospital are medication errors and intravenous therapy-induced infections or complications. Training for clinical staff and compliance to patient safety principles could address these. METHODS: Joint Commission International (JCI) consultants created a standardised, 6-month training programme for clinical staff in hospitals. Twenty-one tertiary care hospitals from across south-east Asia took part. JCI trained the clinical consultants, who trained hospital safety champions, who trained nursing staff. Compliance and knowledge were assessed, and monthly audits were conducted. RESULTS: There was an overall increase of 29% in compliance with parameters around medication preparation and vascular access device management. CONCLUSION: The programme improved safe practice around preparing medications management and managing vascular access devices. The approach could be employed as a continuous quality improvement initiative for the prevention of medication errors and infusion-associated complications.

Evaluation of ACS-NSQIP and CR-POSSUM risk calculators for the prediction of mortality after colorectal surgery: A retrospective cohort study.

Background: Several risk calculating tools have been introduced into clinical practice to provide patients and clinicians with objective, individualised estimates of procedure-related unfavourable outcomes. The currently available risk calculators (RCs) have been developed by well-endowed health systems in Europe and the USA. Applicability of these RCs in low-middle income country (LMIC) settings with wide disparities in patient population, surgical practice and healthcare infrastructure has not been adequately examined. Patients and Methods: Through this single tertiary care, LMIC-centre, retrospective cohort study, we investigated the accuracy of the two most widely validated RCs - American College of Surgeons-National Surgical Quality Improvement Program (ACS-NSQIP) RC and ColoRectal Physiological and Operative Severity Score for the Enumeration of Mortality and Morbidity (CR-POSSUM) - for the prediction of mortality in patients undergoing elective and emergency colorectal surgery (CRS) from March 2013 to March 2020. Online RCs were used to predict mortality and other outcomes. Accuracy was assessed by Brier score and C statistic. Results: Of 105 patients, 69 (65.71%) underwent elective and 36 (34.28%) underwent emergency CRS. The 30-day overall mortality was 12 - elective 1 (1.4%) and emergency 11 (30.5%). ACS-NSQIP RC performed better for the prediction of overall (C statistic 0.939, Brier score 0.065) and emergency (C statistic 0.840, Brier score 0.152) mortality. However, for elective CRS mortality, Brier scores were similar for both models (0.014), whereas C statistic (0.934 vs. 0.890) value was better for ACS-NSQIP. Conclusions: Both ACS-NSQIP and CR-POSSUM were accurate for the prediction of CRS mortality. However, compared to CR-POSSUM, ACS-NSQIP performed better. The overall performance of both models is indicative of their wider applicability in LMIC centres also.

Effectiveness of convalescent plasma in Indian patients with COVID-19.

BACKGROUND: Convalescent plasma (CP) is being used as a treatment option in hospitalized patients with COVID-19. Till date, there is conflicting evidence on efficacy of CP in reducing COVID-19 related mortality. OBJECTIVE: To evaluate the effect of CP on 28-day mortality reduction in patients with COVID-19. METHODS: We did a multi-centre, retrospective case control observational study from 1st May 2020 to 31st August 2020. A total of 1079 adult patients with moderate and severe COVID-19 requiring oxygen, were reviewed. Of these, 694 patients were admitted to ICU. Out of these, 333 were given CP along with best supportive care and remaining 361 received best supportive care only. RESULTS: In the overall group of 1079 patients, mortality in plasma vs no plasma group was statistically not significant (22.4% vs 18.5%; p = 0.125; OR = 1.27, 95% CI: 0.94--1.72). However, in patients with COVID-19 admitted to ICU, mortality was significantly lower in plasma group (25.5% vs 33.2%; p = 0.026; OR = 0.69, 95%CI: 0.50-0.96). This benefit of reduced mortality was most seen in age group 60 to 74 years (26.7% vs 43.0%; p = 0.004; OR = 0.48, 95% CI: 0.29-0.80), driven mostly by females of this age group (23.1% vs 53.5%; p = 0.013; OR = 0.26, 95% CI: 0.09-0.78). Significant difference in mortality was observed in patients with one comorbidity (22.3% vs 36.5%; p = 0.004; OR = 0.50, 95% CI: 0.31-0.80). Moreover, patients on ventilator had significantly lower mortality in the plasma arm (37.2% vs 49.3%; p = 0.009; OR = 0.61, 95% CI: 0.42-0.89); particularly so for patients on invasive mechanical ventilation (63.9% vs 82.9%; p = 0.014; OR = 0.37, 95% CI: 0.16-0.83). CONCLUSION: The use of CP was associated with reduced mortality in COVID-19 elderly patients admitted in ICU, above 60 years of age, particularly females, those with comorbidities and especially those who required some form of ventilation.

Identification of predictors and model for predicting prolonged length of stay in dengue patients.

PURPOSE: Our objective is to identify the predictive factors and predict hospital length of stay (LOS) in dengue patients, for efficient utilization of hospital resources. METHODS: We collected 1360 medical patient records of confirmed dengue infection from 2012 to 2017 at Max group of hospitals in India. We applied two different data mining algorithms, logistic regression (LR) with elastic-net, and random forest to extract predictive factors and predict the LOS. We used an area under the curve (AUC), sensitivity, and specificity to evaluate the performance of the classifiers. RESULTS: The classifiers performed well, with logistic regression (LR) with elastic-net providing an AUC score of 0.75 and random forest providing a score of 0.72. Out of 1148 patients, 364 (32%) patients had prolonged length of stay (LOS) (> 5 days) and overall hospitalization mean was 4.03 ± 2.44 days (median ± IQR). The highest number of dengue cases belonged to the age group of 10-20 years (21.1%) with a male predominance. Moreover, the study showed that blood transfusion, emergency admission, assisted ventilation, low haemoglobin, high total leucocyte count (TLC), low or high haematocrit, and low lymphocytes have a significant correlation with prolonged LOS. CONCLUSION: Our findings demonstrated that the logistic regression with elastic-net was the best fit with an AUC of 0.75 and there is a significant association between LOS greater than five days and identified patient-specific variables. This method can identify the patients at highest risks and help focus time and resources.

Prevalence of Flu-like Symptoms and COVID-19 in Healthcare Workers from India.

BACKGROUND: The current COVID-19 pandemic is unprecedented. As the numbers expand exponentially, a paucity of data regarding health care workers (HCWs), who are at the forefront of this disaster, exists. Hence we decided to conduct a study amongst the HCWs to determine the prevalence and risk factor stratification. METHODS: This was an online questionnaire-based survey of healthcare workers conducted at Max Super Speciality Hospital, Saket, New Delhi, India from 23rd March to 30th April 2020. Data on flu-like symptoms, travel history, posting in high-risk or low risk zones, and prophylactic drugs was collected. RESULTS: Out of the 18000 HCWs who were approached 4403 responded and adequate data of 3667 was available for analysis. 14.7% had flu-like symptoms. 1.8% (20/1113) of the participants tested were positive for the virus. HCWs posted in the high-risk zones had more symptoms than those working in low-risk zones (169/539, 31.4% vs 679/3128, 21.7%), p<0.001; but no difference in COVID-19 positivity rates (p=0.849). Symptomatic HCWs had higher positivity (10/193, 5.2%) than the asymptomatic ones (10/920, 1.1%), p=0.001. HCQ was taken by 755/1113 (67.8%) people and 14 (1.9%) of these reported positive for the virus. CONCLUSION: This is the first study on healthcare workers from India to the best of our knowledge. Our findings suggest that posting in a high-risk zone with adequate PPE does not pose higher risk to the HCWs. Moreover, HCQ as a prophylactic has no use. CLINICALTRIALS.GOV IDENTIFIER: NCT04339608.

Outcomes of Emergency Laparotomy (EL) Care Protocol at Tertiary Care Center from Low-Middle-Income Country (LMIC).

BACKGROUND: Emergency laparotomy mortality ranges between 10 and 20% in best of Western healthcare systems and is currently a major focus for quality improvement programs. In contrast, emergency surgery scenario in LMIC is largely undefined, often neglected and complex (large burden of diseases but only limited capacity for adequate treatment). We evaluated the efficacy of 'EL care protocol' aimed at cost-effective optimal utilization of best available local expertise and infrastructure. METHODS: One hundred and two consecutive adult patients (≥16 years) who underwent EL from December 2012-December 2015 at a private tertiary hospital were retrospectively analyzed. The patients who underwent emergency laparoscopic procedures were excluded from the analysis. The EL care protocol included. (1) Admission to surgical intensive care unit for pre- and postoperative optimization. (2) Preferred radiologic investigation: abdominal computed tomography (CT) scan. (3) Surgery and critical care by senior surgical gastroenterologists and internists/anesthesiologists, respectively. Outcome measures were procedure-related complications (Clavien-Dindo classification), readmissions and costs. RESULTS: Of the 102 patients, there were 62 males and 40 females with median age of 60 (range 16-93) years. There were no complications in 22 (21.6%) patients, while Clavien-Dindo complications grade I or II occurred in 48 (47%) patients. Grade V Clavien-Dindo complications and the 30-day mortality were similar of 19 (18.6%). The readmission rate was 8 (7.8%). The expected mortality for the study group by P-POSSUM score was 31.2 (30.6%). The ratio (O/E) of observed to expected mortality was 0.61. The all inclusive median cost of treatment was INR 379,255 ($5590). CONCLUSIONS: LMIC centers should develop their own center-specific EL care protocols to improve outcomes of EL.

TCR repertoire dynamics and their responses underscores dengue severity.

Despite recognizing the immune response's role in dengue progression, the intricate dynamics of T cell receptor (TCR) variations across DENV infection severities remain elusive. This study addresses this gap by analyzing in-house generated RNA-seq data from 112 dengue patients with varying disease severities. Our findings reveal that severe dengue patients exhibit pronounced clinical manifestations including leukopenia, thrombocytopenia, and elevated lymphocyte levels, Intriguingly, these patients also showed increased diversity in γ and δ TCR chains, unique TRGV and TRBV segment usage, and extended δ-CDR3 sequences, suggesting specialized inflammatory functions. Furthermore, mutations in the NS5 and 3'UTR regions of the dengue genome correlated with increased TRDV and TRGV chains, indicating a significant role for these mutations in the prevalence of specific TCR chains during severe infections. Overall, the study highlights the complex role of TCR repertoire in dengue pathogenesis, enhancing our understanding of TCR dynamics for future infectious diseases.

RNA editing in host lncRNAs as potential modulator in SARS-CoV-2 variants-host immune response dynamics.

Both host and viral RNA editing plays a crucial role in host's response to infection, yet our understanding of host RNA editing remains limited. In this study of in-house generated RNA sequencing (RNA-seq) data of 211 hospitalized COVID-19 patients with PreVOC, Delta, and Omicron variants, we observed a significant differential editing frequency and patterns in long non-coding RNAs (lncRNAs), with Delta group displaying lower RNA editing compared to PreVOC/Omicron patients. Notably, multiple transcripts of UGDH-AS1 and NEAT1 exhibited high editing frequencies. Expression of ADAR1/APOBEC3A/APOBEC3G and differential abundance of repeats were possible modulators of differential editing across patient groups. We observed a shift in crucial infection-related pathways wherein the pathways were downregulated in Delta compared to PreVOC and Omicron. Our genomics-based evidence suggests that lncRNA editing influences stability, miRNA binding, and expression of both lncRNA and target genes. Overall, the study highlights the role of lncRNAs and how editing within host lncRNAs modulates the disease severity.

Metatranscriptomic insights into the dengue patient blood microbiome: Enhanced microbial diversity and metabolic activity in severe patients.

BACKGROUND: Dengue is the most re-emergent infection, with approximately 100 million new cases reported annually, yet no effective treatment or vaccine exists. Here, we aim to define the microbial community structure and their functional profiles in the dengue positive patients with varying disease severity. METHODOLOGY/PRINCIPAL FINDINGS: Hospital admitted 112 dengue-positive patients blood samples were analyzed by dual RNA-sequencing to simultaneously identify the transcriptionally active microbes (TAMs), their expressed genes and associated pathways. Results highlight that patients with severe dengue exhibited increased microbial diversity and presence of opportunistic species (unique and core) which includes Bacillus cereus, Burkholderia pseudomallei, Streptococcus suis, and Serratia marcescens. The functional profile analysis revealed enriched metabolic pathways such as protein degradation, nucleotide biosynthesis, ion transport, cell shape integrity, and ATP formation in severe cases, indicating the high energy demands and adaptability of these microbes. CONCLUSION: Our metatranscriptomic approach provides a species-level characterization of blood microbiome composition and reveals a heightened diversity of TAMs in patients with severe dengue, underscoring the need for further research into the role of blood microbiota in disease progression. Comparing the microbial signatures across the severity classes early in the disease offers unique potential for convenient and early diagnosis of dengue infection.

Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing.

Dengue fever, a neglected tropical arboviral disease, has emerged as a global health concern in the past decade. Necessitating a nuanced comprehension of the intricate dynamics of host-virus interactions influencing disease severity, we analysed transcriptomic patterns using bulk RNA-seq from 112 age- and gender-matched NS1 antigen-confirmed hospital-admitted dengue patients with varying severity. Severe cases exhibited reduced platelet count, increased lymphocytosis, and neutropenia, indicating a dysregulated immune response. Using bulk RNA-seq, our analysis revealed a minimal overlap between the differentially expressed gene and transcript isoform, with a distinct expression pattern across the disease severity. Severe patients showed enrichment in retained intron and nonsense-mediated decay transcript biotypes, suggesting altered splicing efficiency. Furthermore, an up-regulated programmed cell death, a haemolytic response, and an impaired interferon and antiviral response at the transcript level were observed. We also identified the potential involvement of the RBM39 gene among others in the innate immune response during dengue viral pathogenesis, warranting further investigation. These findings provide valuable insights into potential therapeutic targets, underscoring the importance of exploring transcriptomic landscapes between different disease sub-phenotypes in infectious diseases.

Machine-learning prediction models for any blood component transfusion in hospitalized dengue patients.

BACKGROUND: Blood component transfusions are a common and often necessary medical practice during the epidemics of dengue. Transfusions are required for patients when they developed severe dengue fever or thrombocytopenia of 10×109/L or less. This study therefore investigated the risk factors, performance and effectiveness of eight different machine-learning algorithms to predict blood component transfusion requirements in confirmed dengue cases admitted to hospital. The objective was to study the risk factors that can help to predict blood component transfusion needs. METHODS: Eight predictive models were developed based on retrospective data from a private group of hospitals in India. A python package SHAP (SHapley Additive exPlanations) was used to explain the output of the "XGBoost" model. RESULTS: Sixteen vital variables were finally selected as having the most significant effects on blood component transfusion prediction. The XGBoost model presented significantly better predictive performance (area under the curve: 0.793; 95 % confidence interval: 0.699-0.795) than the other models. CONCLUSION: Predictive modelling techniques can be utilized to streamline blood component preparation procedures and can help in the triage of high-risk patients and readiness of caregivers to provide blood component transfusions when required. This study demonstrates the potential of multilayer algorithms to reasonably predict any blood component transfusion needs which may help healthcare providers make more informed decisions regarding patient care.

SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing.

Like single-stranded RNA viruses, SARS-CoV-2 hijacks the host transcriptional machinery for its own replication. Numerous traditional differential gene expression-based investigations have examined the diverse clinical symptoms caused by SARS-CoV-2 infection. The virus, on the other hand, also affects the host splicing machinery, causing host transcriptional dysregulation, which can lead to diverse clinical outcomes. Hence, in this study, we performed host transcriptome sequencing of 125 hospital-admitted COVID-19 patients to understand the transcriptomic differences between the severity sub-phenotypes of mild, moderate, severe, and mortality. We performed transcript-level differential expression analysis, investigated differential isoform usage, looked at the splicing patterns within the differentially expressed transcripts (DET), and elucidated the possible genome regulatory features. Our DTE analysis showed evidence of diminished transcript length and diversity as well as altered promoter site usage in the differentially expressed protein-coding transcripts in the COVID-19 mortality patients. We also investigated the potential mechanisms driving the alternate splicing and discovered a compelling differential enrichment of repeats in the promoter region and a specific enrichment of SINE (Alu) near the splicing sites of differentially expressed transcripts. These findings suggested a repeat-mediated plausible regulation of alternative splicing as a potential modulator of COVID-19 disease severity. In this work, we emphasize the role of scarcely elucidated functional role of alternative splicing in influencing COVID-19 disease severity sub-phenotypes, clinical outcomes, and its putative mechanism. IMPORTANCE The wide range of clinical symptoms reported during the COVID-19 pandemic inherently highlights the numerous factors that influence the progression and prognosis of SARS-CoV-2 infection. While several studies have investigated the host response and discovered immunological dysregulation during severe infection, most of them have the common theme of focusing only up to the gene level. Viruses, especially RNA viruses, are renowned for hijacking the host splicing machinery for their own proliferation, which inadvertently puts pressure on the host transcriptome, exposing another side of the host response to the pathogen challenge. Therefore, in this study, we examine host response at the transcript-level to discover a transcriptional difference that culminates in differential gene-level expression. Importantly, this study highlights diminished transcript diversity and possible regulation of transcription by differentially abundant repeat elements near the promoter region and splicing sites in COVID-19 mortality patients, which together with differentially expressed isoforms hold the potential to elaborate disease severity and outcome.

Intertwined Dysregulation of Ribosomal Proteins and Immune Response Delineates SARS-CoV-2 Vaccination Breakthroughs.

Globally, COVID-19 vaccines have emerged as a boon, especially during the severe pandemic phases to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, saving millions of lives. However, mixed responses to vaccination with breakthrough challenges provided a rationale to explore the immune responses generated postvaccination, which plausibly alter the subsequent course of infection. In this regard, we comprehensively profiled the nasopharyngeal transcriptomic signature of double-dose-vaccinated individuals with breakthrough infections in comparison to unvaccinated infected persons. The vaccinated individuals demonstrated a gross downregulation of ribosomal proteins along with immune response genes and transcription/translational machinery that methodically modulated the entire innate immune landscape toward immune tolerance, a feature of innate immune memory. This coordinated response was orchestrated through 17 transcription factors captured as differentially expressed in the vaccination breakthroughs, including epigenetic modulators of CHD1 and LMNB1 and several immune response effectors, with ELF1 emerging as one of the important transcriptional regulators of the antiviral innate immune response. Deconvolution algorithm using bulk gene expression data revealed decreased T-cell populations with higher expression of memory B cells in the vaccination breakthroughs. Thus, vaccination might synergize the innate immune response with humoral and T-cell correlates of protection to more rapidly clear SARS-CoV-2 infections and reduce symptoms within a shorter span of time. An important feature invariably noted after secondary vaccination is downregulation of ribosomal proteins, which might plausibly be an important factor arising from epigenetic reprogramming leading to innate immune tolerance. IMPORTANCE The development of multiple vaccines against SARS-CoV-2 infection is an unprecedented milestone achieved globally. Immunization of the mass population is a rigorous process for getting the pandemic under control, yet continuous challenges are being faced, one of them being breakthrough infections. This is the first study wherein the vaccination breakthrough cases of COVD-19 relative to unvaccinated infected individuals have been explored. In the context of vaccination, how do innate and adaptive immune responses correspond to SARS-CoV-2 infection? How do these responses culminate in a milder observable phenotype with shorter hospital stay in vaccination breakthrough cases compared with the unvaccinated? We identified a subdued transcriptional landscape in vaccination breakthroughs with decreased expression of a large set of immune and ribosomal proteins genes. We propose a module of innate immune memory, i.e., immune tolerance, which plausibly helps to explain the observed mild phenotype and fast recovery in vaccination breakthroughs.

Longitudinal study across SARS-CoV-2 variants identifies transcriptionally active microbes (TAMs) associated with Delta severity.

Emergence of new SARS-CoV-2 VOCs jeopardize global vaccine and herd immunity safeguards. VOCs interactions with host microbiota might affect clinical course and outcome. This longitudinal investigation involving Pre-VOC and VOCs (Delta & Omicron) holo-transcriptome based nasopharyngeal microbiome at taxonomic levels followed by metabolic pathway analysis and integrative host-microbiome interaction. VOCs showed enrichment of Proteobacteria with dominance of Pseudomonas. Interestingly, Proteobacteria with superiority of Pseudomonas and Acinetobacter, were highlights of Delta VOC rather than Omicron. Common species comprising the core microbiome across all variants, reiterated the significance of Klebsiella pneumoniae in Delta, and its association with metabolic pathways enhancing inflammation in patients. Microbe-host gene correlation network revealed Acinetobacter baumannii, Pseudomonas stutzeri, and Pseudomonas aeuroginosa modulating immune pathways, which might augment clinical severity in Delta. Importantly, opportunistic species of Acinetobacter, Enterococcus, Prevotella, and Streptococcus were abundant in Delta-mortality. The study establishes a functional association between elevated nasal pathobionts and dysregulated host response, particularly for Delta.

Dual RNA-Seq reveals transcriptionally active microbes (TAMs) dynamics in the serum of dengue patients associated with disease severity.

Introduction: Dengue virus (DENV) is a flavivirus that has emerged as a global health threat, characterized by either asymptomatic or mild self-limiting febrile illness, but a subset of DENV outbreaks have been associated with severe disease. Studies have looked into the host immune response and dengue viral load during infection. However, it remains unknown how the active microbial isolates modulate the dengue viral infection. In this study, we demonstrate the significance of in-depth analysis of microbiota composition in the serum samples of dengue-infected patients. Materials and methods: RNA was extracted from the serum samples collected from 24 dengue positive patients. The human mapped reads generated through RNA-Sequencing (RNA-Seq) were removed, while the unmapped (non-human) reads were employed for microbial taxonomic classification using Kraken2 and Bracken2. Further, we assessed the initial blood parameters analyzing the complete blood count (CBC) profile of the patients. Results: Findings revealed differential abundance of commensals and pathogenic microbes in the early febrile period of hospitalized dengue patients, segregated into, High Viral Reads (HVR) and Low Viral Reads (LVR). The Campylobacter genus was abundant in the HVR whereas Lactobacillus dominated the LVR patients. At species level, the microbiota of HVR exhibited higher abundance of unique potential opportunistic microbes, compared to the commensal microbes' enrichment in the LVR patients'. We hypothesize that the DENV might alter the microbiota composition as observed by the increase in preponderance of opportunistic pathogens and an absence of commensals in the HVR. The presence of commensals in the LVR might explain, i) overall lower dengue viral reads compared to the HVR, and ii) shift in lymphocytes (high) and neutrophils (low) counts; resulting in a comparatively milder clinical manifestation in this group. Our findings may help in understanding the co-infection aspect that will be important to develop dengue therapeutics and vaccines. Discussion: This study highlights the potential of the unexplored roles of the TAMs in modulating the dengue disease severity using the metatranscriptomic sequencing. This study serves to enhance our understanding of the distinctive microbial and hematologic signatures in the early infection stage that differentiate patients with high viral reads patients from those with low dengue viral reads.

Co-evolution of SARS-CoV-2 variants and host immune response trajectories underlie COVID-19 pandemic to epidemic transition.

COVID-19 pandemic saw emergence of multiple SAR-CoV-2 variants. Exacerbated risk of severe outcome and hospital admissions led us to comprehend differential host-immune kinetics associated with SARS-CoV-2 variants. Longitudinal investigation was conducted through different time periods of Pre-VOC and VOCs (Delta & Omicron) mapping host transcriptome features. Robust antiviral type-1 interferon response marked Omicron infection, which was largely missing during Pre-VOC and Delta waves. SARS-CoV-2-host protein-protein interactions and docking complexes highlighted N protein to interact with HNRNPA1 in Pre-VOC, demonstrating its functional role for enhanced viral replication. Omicron revealed enhanced binding efficiency of LARP1 to N protein, probably potentiating antiviral effects of LARP1. Differential expression of zinc finger protein genes, especially in Omicron, mechanistically support induction of strong IFN (Interferon) response, thereby strengthening early viral clearance. Study highlights eventual adaptation of host to immune activation patterns that interrupt virus evolution with enhanced immune-evasion mutations and counteraction mechanisms, delimiting the next phase of COVID-19 pandemic.

Early transcriptomic host response signatures in the serum of dengue patients provides insights into clinical pathogenesis and disease severity.

Dengue virus (DENV), known to cause viral infection, belongs to the family Flaviviridae, having four serotypes (DENV1-4) that spreads by the bite of the Aedes aegypti mosquito. India has been suffering from dengue outbreaks annually with widespread epidemics by prevalence of all the four DENV serotypes. The diverse spectrum of clinical manifestations in dengue infection, mild to severe forms, makes the need of timely diagnosis and prompt treatment an essence. The identification of a dengue host response signature in serum can increase the understanding of dengue pathogenesis since most dengue NS1 Ag tests have been developed and evaluated in serum samples. Here, to understand the same, we undertook a dual RNA-sequencing (RNA-Seq) based approach from the serum samples of dengue-infected patients. The results thus yield the early transcriptional signatures that discriminated the high viral reads patients from patients who had low dengue viral reads. We identified a significant upregulation of two sets of genes, key antiviral (IFIT3, RSAD2, SAT1) and vascular dysfunction (TNFS10, CXCL8) related genes in the high viral reads group. Deeper delving of this gene profile revealed a unique two-way response, where the antiviral genes can mediate the disease course to mild, contrarily the increased expression of the other gene set might act as pointers of severe disease course. Further, we explored the hematologic parameters from the complete blood count (CBC), which suggests that lymphocytes (low) and neutrophils (high) might serve as an early predictor of prognosis in dengue infection. Collectively, our findings give insights into the foundation for further investigation of the early host response using the RNA isolated from dengue patients' serum samples and opens the door for careful monitoring of the early clinical and transcriptome profiles for management of the dengue patients.

Transcriptomic study reveals lncRNA-mediated downregulation of innate immune and inflammatory response in the SARS-CoV-2 vaccination breakthrough infections.

Introduction: The emergence of multiple variants of concerns (VOCs) with higher number of Spike mutations have led to enhanced immune escape by the SARS-CoV-2. With the increasing number of vaccination breakthrough (VBT) infections, it is important to understand the possible reason/s of the breakthrough infections. Methods: We performed transcriptome sequencing of 57 VBT and unvaccinated COVID-19 patients, followed by differential expression and co-expression analysis of the lncRNAs and the mRNAs. The regulatory mechanism was highlighted by analysis towards repeat element distribution within the co-expressed lncRNAs, followed by repeats driven homologous interaction between the lncRNAs and the promoter regions of genes from the same topologically associated domains (TAD). Results: We identified 727 differentially expressed lncRNAs (153 upregulated and 574 downregulated) and 338 mRNAs (34 up- and 334 downregulated) in the VBT patients. This includes LUCAT1, MALAT1, ROR1-AS1, UGDH-AS1 and LINC00273 mediated modulation of immune response, whereas MALAT1, NEAT1 and GAS5 regulated inflammatory response in the VBT. LncRNA-mRNA co-expression analysis highlighted 34 lncRNAs interacting with 267 mRNAs. We also observed a higher abundance of Alu, LINE1 and LTRs within the interacting lncRNAs of the VBT patients. These interacting lncRNAs have higher interaction with the promoter region of the genes from the same TAD, compared to the non-interacting lncRNAs with the enrichment of Alu and LINE1 in the gene promoter. Discussion: Significant downregulation and GSEA of the TAD gene suggest Alu and LINE1 driven homologous interaction between the lncRNAs and the TAD genes as a possible mechanism of lncRNA-mediated suppression of innate immune/inflammatory responses and activation of adaptive immune response. The lncRNA-mediated suppression of innate immune/inflammatory responses and activation of adaptive immune response might explain the SARS-CoV-2 breakthrough infections with milder symptoms in the VBT. Besides, the study also highlights repeat element mediated regulation of genes in 3D as another possible way of lncRNA-mediated immune-regulation modulating vaccination breakthroughs milder disease phenotype and shorter hospital stay.