BACKGROUND: Leptospirosis presents with highly variable clinical manifestations affecting different organ systems in different individuals. The presentation ranges from an asymptomatic or mild disease to a severe disease associated with multiorgan failure and higher mortality. Leptospirosis is highly underreported due to a lack of diagnostic modalities and less suspicion among clinicians. METHODOLOGY: We present this single-center retrospective case series of 12 cases, which include various common and uncommon scenarios by which the disease can present and can be missed due to lack of suspicion. The study contains individual patient characteristics including demographic, laboratory, clinical, and treatment data. The association between these variables and mortality was analyzed using p-values and results were described. A p-value of<0.05 was considered statistically significant. RESULTS: A total of 12 cases were included in the study. The male-to-female ratio was 3:1. The mean age was higher (37.75±9.81 years) in cases who died than those who recovered (34.25±14.09). Factors like history of alcoholism, presence of chronic liver disease (CLD), jaundice, acute renal failure, requirement of dialysis, and requirement of intensive care were significantly associated with increased risk of death (odds ratio >1, p-value <0.05). The most common symptom of presentation was fever in 11 (91.66%) cases. Jaundice and renal failure were significantly associated with death (odds ratio 1.2, p-value 0.04). The requirement of intensive care treatment (odds ratio 2.1, p-value 0.05) and dialysis (odds ratio 39.66, p-value 0.03) were also significantly associated with death. The percentage of death was lower in the group of patients who received combination antibiotic therapy. CONCLUSION: Leptospirosis has varied presentations in different individuals and the diagnosis can be missed due to lack of specific signs and symptoms. Severe diseases involving multiple organs and preexisting comorbidities are associated with higher mortality rates. Timely diagnosis and treatment are necessary to reduce mortality and increase survival.
Tuberculous meningitis is the most serious complication of tuberculosis. Early diagnosis is crucial to start relevant treatment to prevent death and disability. Electronic databases PubMed, Google Scholar, and Cochrane Library were used to find relevant articles from January 1980 to June 2022. The random-effect model in terms of pooled sensitivity, specificity, and diagnostic odds ratio (DOR) with 95% confidence interval was adopted to derive the diagnostic efficacy of cerebrospinal fluid (CSF) adenosine deaminase (ADA) for the diagnosis of tuberculous meningitis (TBM) in adult patients. A total of 22 studies (20 prospective and two retrospective data) have been included in this meta-analysis, having 1927 participants. We perceived acceptable pooled sensitivity, specificity, summary receiver operating characteristics (SROCs), and diagnostic odds ratio (DOR) of 0.85 (95% CI: 0.77-0.90), 0.90 (95% CI: 0.85-0.93), 0.94 (95% CI: 0.91-0.96) and 48 (95% CI: 26-86), respectively, for CSF-ADA for differentiating TBM from non-TBM in adult patients. To ascertain the certainty of evidence for CSF-ADA as a diagnostic marker for TBM, Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) analysis was used. CSF-ADA is an auspicious diagnostic test with a high degree of specificity and acceptable sensitivity for the diagnosis of tuberculous meningitis, however, with very low certainty of evidence.
Validation of a risk factor in a multifactorial disease like ischemic stroke is necessary to practice precision medicine. Many risk factors have been attributed to causing ischemic stroke but contribute very little to it. There are many risk factors that need to be validated, and fibrinogen is one such risk factor. Using a meta-analysis technique, we investigated fibrinogen as a risk factor for ischemic stroke. We searched the computerized databases such as PubMed, Google Scholar, and Cochrane to explore articles on ischemic stroke. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using a random effects model. A total of 10 case-control studies with 6877 cases and 7219 controls were included in the study that match inclusion and exclusion criteria. The Asiatic population was portrayed in four studies, whereas the Caucasian population was portrayed in six studies. Under the recessive model, an elevated level of serum fibrinogen is linked to an increased risk of ischemic stroke as shown by pooled odds ratio (OR: 1.47, 95% CI: 1.19-1.76, I2 = 78.3%, P = 0.000). Our meta-analysis concluded that a high level of fibrinogen is associated with an increased risk of ischemic stroke.
X-linked agammaglobulinemia (XLA) is an X-linked recessive primary immunodeficiency disorder caused due to a pathogenic variant in the Bruton tyrosine (BTK) gene with an incidence of 1:379,000 live births and 1:190,000 male births. Patients affected with XLA present with recurrent infections of the gastrointestinal and respiratory tracts. Here we report the first case series of 17 XLA patients of 10 South Indian families with a wide spectrum of clinical and genetic features. In our cohort, patients presented mainly with recurrent pneumonia, gastrointestinal infection, otitis media, pyoderma, abscesses, empyema, arthritis, and osteomyelitis. Using next-generation and Sanger sequencing we have identified 10 unique pathogenic and likely pathogenic variants in 17 patients. This encompasses three nonsynonymous, two stop-gain, two frameshifts, two structural, and one splicing variant, out of which two of them are novel. Based on the type of variant, patients had variable clinical features and treatment responses. We have also evaluated Btk protein expression for six patients in comparison to the healthy individuals and determined mosaic Btk expression patterns in four mothers. We have also performed family screening in 6 families using Sanger sequencing and identified 19 carriers for the variant. The diagnosis for the patients led to the proper treatment i.e. 15 patients were on intravenous immunoglobulin (IVIG) and the other two had successful hematopoietic stem cell transplantation (HSCT). Unfortunately, two of our patients died due to sepsis, while on IVIG. We envision the present study could help in better understanding of patients with XLA and help in family screening and prenatal diagnosis. To the best of our knowledge, this is the largest case series of patients affected with XLA from South India.
Agammaglobulinemia , Genetic Diseases, X-Linked , Agammaglobulinaemia Tyrosine Kinase/genetics , Agammaglobulinemia/diagnosis , Agammaglobulinemia/genetics , Child , Genetic Diseases, X-Linked/diagnosis , Genetic Diseases, X-Linked/genetics , Genetic Diseases, X-Linked/therapy , Humans , Immunoglobulins, Intravenous/therapeutic use , Male , Mutation
Delhi, the national capital of India, has experienced multiple SARS-CoV-2 outbreaks in 2020 and reached a population seropositivity of over 50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant B.1.617.2 (Delta) replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and partial reduction of immunity elicited by prior infection (median estimates; x1.5-fold, 20% reduction). Seropositivity of an employee and family cohort increased from 42% to 86% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi. One-Sentence SummaryDelhi experienced an overwhelming surge of COVID-19 cases and fatalities peaking in May 2021 as the highly transmissible and immune evasive Delta variant replaced the Alpha variant.
Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
Many antibody and immune escape variants in SARS-CoV-2 are now documented in literature. The availability of SARS-CoV-2 genome sequences enabled us to investigate the occurrence and genetic epidemiology of the variants globally. Our analysis suggests that a number of genetic variants associated with immune escape have emerged in global populations.
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying Variants Of Concern (VOC). Besides, viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host Single Nucleotide Variations (iSNVs). Analysing 1, 347 samples collected till June 2020, we recorded 18, 146 iSNV sites throughout the SARS-CoV-2 genome. Both, mutations in RdRp as well as APOBEC and ADAR mediated RNA editing seem to contribute to the differential prevalence of iSNVs in hosts. Noteworthy, 41% of all unique iSNVs were reported as SNVs by 30th September 2020 in samples submitted to GISAID, which increased to [~]80% by 30th June 2021. Following this, analysis of another set of 1, 798 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) variations appeared as iSNVs before getting fixed in the population. We also observe hyper-editing events at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/417519v3_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@12b6ac2org.highwire.dtl.DTLVardef@16df897org.highwire.dtl.DTLVardef@dbbec2org.highwire.dtl.DTLVardef@c8de14_HPS_FORMAT_FIGEXP M_FIG C_FIG
Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.
The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.
Lichens, symbiotic organisms with special features, are able to synthesize exclusive secondary metabolites that are attracting increasing interest in their pharmacological activities. Present study aimed to perform an initial screening of the antioxidant capacities of 29 lichens from Parmeliaceae family, and the cytoprotective potential of the most promising species in a model of central nervous system-like cells. Also, another goal was to determine the main chemical constituents of the promising lichens. After molecular identification of all lichen specimens by PCR techniques regarding the molecular marker ITS rDNA, antioxidant activity was measured in terms of free radical scavenging properties through ORAC assay. Methanol extracts of the three species with highest ORAC values (Cetrelia braunsiana (Cb), Parmotrema saccatilobum (Ps) and Usnea ghattensis (Ug)) were analyzed for phytochemical characterization through TLC and HPLC methods. We identified alectoronic acid as major metabolite in Cb, protocetraric acid in Ps and usnic, stictic and constictic acids in Ug. Concerning cytoprotective properties, their extracts were tested on human neuroblastoma cell line SH-SY5Y. Protection against H2O2- induced oxidative stress in such neuron- like model was assessed by cell viability assays, thus determining their optimal concentrations. Then, their effect on oxidative stress markers, such as intracellular ROS formation, glutathione levels and caspase-3 activity, were evaluated. In general, lichens extracts were able to reverse the oxidative damage caused by H2O2, and promoted neurons survival. Results obtained in this study imply that these lichen species might be used as promising sources for natural compounds with potential neuroprotective activity, suggesting future research avenues
Los líquenes son organismos simbióticos de especiales características capaces de sintetizar metabolitos secundarios únicos, con un creciente interés por sus propiedades farmacológicas. El presente estudio persiguió realizar un cribado de la actividad antioxidante de 29 especies liquénicas de la familia Parmeliaceae, y el potencial citoprotector de los más interesantes en un modelo neuronal. Otro objetivo consistió en derminar los principales constituyentes de dichas especies. Tras la identificación molecular de todos los especímenes por técnicas de PCR, la actividad antioxidante se evaluó por la capacidad captadora de radicales libres en el ensayo ORAC. Se analizaron por TLC y HPLC los extractos metanólicos de las tres especies con mayor valor ORAC (Cetrelia braunsiana (Cb), Parmotrema saccatilobum (Ps) and Usnea ghattensis (Ug)) y se identificaron como principales metabolitos el ácido alectorónico en Cb, el ácido protocetrárico en Ps y los ácidos úsnico, estíctico y constíctico en Ug. Estos tres extractos se probaron en células de neuroblastoma humano (línea celular SH- SY5Y). Se testó la citoprotección contra el estrés oxidativo inducido por H2O2 mediante ensayos de viabilidad celular, estableciendo las concentraciones óptimas. Posteriormente, se valoraron sus efectos en marcadores de estrés oxidativo, como la formación intracelular de especies reactivas de oxígeno, los niveles de glutatión y la actividad de la enzima caspasa-3. En general, los extractos liquénicos revirtieron el daño oxidativo causado por H2O2, promoviendo la supervivencia neuronal. Los resultados obtenidos de este estudio apuntan que las especies estudiadas pueden ser prometedoras fuentes de productos naturales con potencial actividad neuroprotecora, sugiriendo futuras líneas de investigación
In Vitro Techniques/classification , In Vitro Techniques/methods , In Vitro Techniques/trends , Antioxidants/administration & dosage , Antioxidants/pharmacology , Antioxidants/therapeutic use , Intracellular Space , In Vitro Techniques/instrumentation , Antioxidants/physiology , Methanol/pharmacology
