Common laboratory organic solvents are better medium for molecular detection of RNA viruses using PCR.

PURPOSE: The unavailability of recommended viral transport medium during epidemics of respiratory viral infections is a substantial healthcare concern. It may prompt the use of alternatives, which may give rise to results with questionable validity. The present study was carried out to assess and validate the utility of commonly available solvents in the hospital/healthcare set-ups which may be used as ready and economical alternatives to commercial VTMs. METHODS: To evaluate the readily available solvents as an alternative to VTM, cell culture supernatant of pH1N1 2009 isolate with HA titres of 1:4 and extracted viral RNA of SARS-CoV-2 were spiked in a 1:10 ratio in ethanol, acetone, methanol and were compared to commercially available VTM for detection of influenza virus by real time RT-PCR (qRT-PCR). The tubes were kept at room temperature 24 h, 48 h and 72 h. Ct values of the various solvents at different time points were compared and statistical analysis was performed using Python. RESULTS: The Ct values of the Influenza and SARS-CoV2 viral genes in each solvent were maintained for 3 days at room temperatures, suggesting viral samples were stably preserved in the solvent for 3 days. CONCLUSION: Methanol was found to be the most promising solvent for increasing the stability of viral RNA thereby enhancing the molecular diagnosis of the concerned pathogen.

Canine-inspired Unidirectional Flows for Improving Memory Effects in Machine Olfaction.

A dog's nose differs from a human's in that air does not change direction but flows in a unidirectional path from inlet to outlet. Previous simulations showed that unidirectional flow through a dog's complex nasal passageways creates stagnant zones of trapped air. We hypothesize that these zones give the dog a "physical memory," which it may use to compare recent odors to past ones. In this study, we conducted experiments with our previously built Gaseous Recognition Oscillatory Machine Integrating Technology (GROMIT) and performed corresponding simulations in two dimensions. We compared three settings: a control setting that mimics the bidirectional flow of the human nose; a short-circuit setting where odors exit before reaching the sensors; and a unidirectional configuration using a dedicated inlet and outlet that mimics the dog's nose. After exposure to odors, the sensors in the unidirectional setting showed the slowest return to their baseline level, indicative of memory effects. Simulations showed that both short-circuit and unidirectional flows created trapped recirculation zones, which slowed the release of odors from the chamber. In the future, memory effects such as the ones found here may improve the sensitivity and utility of electronic noses.

Antiviral Activity of Rosmarinic Acid Against Four Serotypes of Dengue Virus.

The present study was undertaken to evaluate the putative antiviral activity of Rosmarinic acid (RA) against four serotypes of dengue virus (DENV). Our previous in silico binding analysis revealed that RA binds strongly to the envelope domain III (EDIII) protein of all four DENV serotypes. We employed an in vitro Biolayer Interferometry-based OCTET™ platform to study the binding interaction of RA with EDIII protein of the four DENV serotypes. Additionally, a functional plaque assay was developed to investigate the potential inhibition of infection of the four DENV serotypes. Using OCTET™, the binding interaction of RA to DENV-EDIII protein of the four DENV serotypes demonstrates interaction which can be arranged in the following order: EDIII-DENV1 (Koff value of 1.05 s-1) > EDIII-DENV2 (Koff value of 5.63 × 10-01 s-1) > EDIII-DENV3 (Koff value of 4.63 × 10-02 s-1) > EDIII-DENV4 (Koff value of 3.53 × 10-02 s-1). Subsequently, the inhibiting ability of RA using plaque assay confirmed reduction in the number of plaques for all four serotypes, indicating the ability of RA not only to bind, but also to inhibit the infection of four serotypes in cell culture, while being non-toxic at the concentrations used in the study. However, the effect of RA was variable on different serotypes, demonstrating highest effect on DENV1 (EC50 = 13.73 µg/mL, SI ≥ 728) followed by DENV2 (EC50 = 77.74 µg/mL, SI ≥ 129), DENV3 (EC50 = 244 µg/mL, SI ≥ 41) and DENV4 (EC50 = 280 µg/mL, SI ≥ 36).

Towards Integrated Management of Dengue in Mumbai.

With increasing urbanisation, the dengue disease burden is on the rise in India, especially in large cities such as Mumbai. Current dengue surveillance in Mumbai includes municipal corporation carrying out specific activities to reduce mosquito breeding sites and the use of insecticides to suppress the adult mosquito populations. Clinical cases remain either underreported or misreported due to the restriction to government clinics, missing the large private health care sector. There is a need for an integrated approach to manage dengue outbreaks in Mumbai. There are various novel strategies available for use that can be utilised to improve disease detection, mosquito surveillance, and control of mosquito-borne diseases. These novel technologies are discussed in this manuscript. Given the complex ecosystem of mosquito-borne diseases in Mumbai, integrating data obtained from these technologies would support the ongoing mosquito control measures in Mumbai.

Evolutionary analysis of rabies virus using the partial Nucleoprotein and Glycoprotein gene in Mumbai region of India.

Nearly 1.7 million cases of dog bites are reported every year in India and many cases of animal rabies are left unattended and undiagnosed. Therefore, a mere diagnosis of rabies is not sufficient to understand the epidemiology and the spread of the rabies virus (RV) in animals. There is a paucity of information about the evolutionary dynamics of RV in dogs and its biodiversity patterns in India. In total, 50 dog-brain samples suspected of rabies were screened by the nucleoprotein- (N) and glycoprotein- (G) gene PCR. The N and G genes were subsequently sequenced to understand the molecular evolution in these genes. The phylogenetic analysis of the N gene revealed that six isolates in the Mumbai region belonged to a single Arctic lineage. Time-scaled phylogeny by Bayesian coalescent analysis of the partial N gene revealed that the time to the most recent common ancestor (TMRCA) for the sequences belonged to the cluster from 2006.68 with a highest posterior density of 95 % betweeen 2005-2008, which is assigned to Indian lineage I. Migration pattern revealed a strong Bayes factor between Mumbai to Delhi, Panji to Hyderabad, Delhi to Chennai, and Chennai to Chandigarh. Phylogenetic analysis of the G gene revealed that the RVs circulating in the Mumbai region are divided into three lineages. Time-scaled phylogeny by the Bayesian coalescent analysis method estimated that the TMRCA for sequences under study was from 1993 and Indian clusters was from 1962. In conclusion, the phylogenetic analysis of the N gene revealed that six isolates belonged to single Arctic lineages along with other Indian isolates and they were clustered into a single lineage but divided into three clades based on the G-gene sequences. The present study highlights and enhances the current molecular epidemiology and evolution of RV and revealed strong location bias and geographical clustering within Indian isolates on the basis of N and G genes.

In silico binding analysis of lutein and rosmarinic acid against envelope domain III protein of dengue virus.

OBJECTIVE: The study was performed to evaluate in silico binding ability of lutein and rosmarinic acid (RA) with the envelope domain III (EDIII) proteins of the four serotypes of dengue virus (DENV), enlightening potential antiviral activity of the two compounds. MATERIALS AND METHODS: EDIII protein structures for the four DENV serotypes were retrieved from RCSB Protein data bank (PDB) and used as receptors. Four ligands of lutein and four of RA were selected from the ZINC database and used for computational molecular docking and ligand interaction analysis with the four receptors using bioinformatics tools like AutoDock Vina and Molecular Operating Environment (MOE) software. RESULTS: The EDIII of the four serotypes demonstrated significant interaction with ligands of lutein and RA. RA ligand ZINC899870, particularly presented best-binding energy values of 6.4, -7.0, and 6.9 kcal/mol with EDIII of serotype DENV-1, DENV-2, and DENV-4 respectively. Whereas, lutein ligand, ZINC14879959 presented best-binding energy value of 7.9 kcal/mol for EDIII of serotype DENV-3. From the results predicted by MOE, the hydroxyl (OH) of 3, 4-dihydroxyphenyl group of RA ligand ZINC899870 is actively involved in interaction with all four serotypes. CONCLUSION: RA is a competent candidate for further evaluation of potential in vitro antiviral activity that can be effective in conferring protection against the four serotypes of DENV.

Preparation of Coronavirus nosodes sourced from a clinical sample of SARS-Cov-2 positive patient, inactivated strain, and spike glycoprotein

IntroductionNosodes, the homeopathicpreparationssourcedfrom biological materials including clinical samples, cultures of organisms, and diseased tissues have been in use against the source-specific infections as well as other diseases. The nosodes have demonstrated some efficacy in managing epidemics, such as influenza, dengue, and leptospirosis.This article presents the need and process of development ofnosodes from the SARS-CoV-2 to explore its prophylactic and therapeutic potentials against certain related viral diseases.Materials and methodsA clinical sample of SARS-Cov-2 positive patient,based on the cycle threshold (CT) value of the qRT-PCR, heat-inactivated SARS-CoV-2, and spike glycoprotein all were processed for making nosodesas per the method described in Homoeopathy Pharmacopoeia of India.Molecular tests, such as qRT-PCR and sterility tests were performed to establish the live organisms, RNA material, and the absence of contamination.ResultsThree variants of CoronavirusNosodewere developed using a clinical sample,heat-inactivatedSARS-CoV-2, and spike glycoprotein.In potencies 3c and above, no detectableSARS-CoV-2 RNA material was found by PCR.The analytical results for nosodes were reported as compliant for sterility testing as per the IP.ConclusionThree variants of Coronavirus nosodes were preparedwhich need to be evaluated further through pre-clinical and clinical studies.(AU)

Optimization of Ex Vivo Murine Bone Marrow Derived Immature Dendritic Cells: A Comparative Analysis of Flask Culture Method and Mouse CD11c Positive Selection Kit Method.

12-14 days of culturing of bone marrow (BM) cells containing various growth factors is widely used method for generating dendritic cells (DCs) from suspended cell population. Here we compared flask culture method and commercially available CD11c Positive Selection kit method. Immature BMDCs' purity of adherent as well as suspended cell population was generated in the decreasing concentration of recombinant-murine granulocyte-macrophage colony-stimulating factor (rmGM-CSF) in nontreated tissue culture flasks. The expression of CD11c, MHCII, CD40, and CD86 was measured by flow cytometry. We found significant difference (P < 0.05) between the two methods in the adherent cells population but no significant difference was observed between the suspended cell populations with respect to CD11c+ count. However, CD11c+ was significantly higher in both adhered and suspended cell population by culture method but kit method gave more CD11c+ from suspended cells population only. On the other hand, using both methods, immature DC expressed moderate level of MHC class II molecules as well as low levels of CD40 and CD86. Our findings suggest that widely used culture method gives the best results in terms of yield, viability, and purity of BMDCs from both adherent and suspended cell population whereas kit method works well for suspended cell population.

Assessment of In vivo Antiviral Potential of Datura metel Linn. Extracts against Rabies Virus.

OBJECTIVE: The soxhlet, cold, and ayurvedic extracts of Datura metel Linn. were evaluated for in vivo antirabies activity. MATERIALS AND METHODS: Soxhlet and cold extraction method were used to extract Datura (fruit and seed) extracts, and ayurvedic extraction of Datura was prepared. In vivo toxicity assay was performed as per the OECD 420. LD50 dose was calculated by Reed and Muench method. The in vivo antirabies activity was screened in Swiss albino mice with the virus challenge dose of 10 LD50 (intracerebrally) in both preexposure (PE) and postexposure treatment with oral administration of Datura extracts in Swiss albino mice and observed for 21 days. The virus load in the mice brain was evaluated by TCID50 titration method. RESULTS: Datura (ayurvedic preparation) was found to be nontoxic up to 2000 mg/kg in Swiss albino mice, i.e., 60 mg/30 g of mice, when administered (0.5 ml) orally and observed till 21 days. Up to 20% survival rate on the test group (PE of Datura extracts) up to 14 days postinfection as compared to the virus control group (10 LD50) was observed. No survival rate was observed in the postexposure group of Datura extract; however, the survival time was increased by 4 days as compared to the virus control group. Viral load of the infected mice brain sample was estimated in vero cell line, and 3 log reduction in the virus titer was observed in text group as compared to the virus control, suggesting that Datura extract has an in vivo antirabies activity. CONCLUSION: To the best of our knowledge, this is the first study of in vivo antiviral activity of an ayurvedic preparation of D. metel Linn. against rabies virus. Datura extracts have a potential in vivo antirabies activity. SUMMARY: In the present study, Datura metel Linn. (ayurvedic preparation) extract exhibited survival (20%) in the preexposure (PE) of the virus and the survival time was increased in the postexposure treatment where the disease was established. The mortality was observed, and the viral load was determined by titration method. Abbreviation Used: TCID50: tissue culture infectious dose 50; LD50: lethal dose 50; RV CVS: Rabies virus challenge virus standard; PE: Pre exposure; IC: intracerebral; PI: post infection; FITC: Fluorescein isothiocyanate.

Oxidative Stress Markers in Tuberculosis and HIV/TB Co-Infection.

INTRODUCTION: Dysfunction of redox homeostasis has been implicated in many pathological conditions. An imbalance of pro- and anti-oxidants have been observed in Tuberculosis (TB) and its co-morbidities especially HIV/AIDS. The pro inflammatory milieu in either condition aggravates the physiological balance of the redox mechanisms. The present study therefore focuses on assessing the redox status of patients suffering from TB and HIV-TB co-infection. AIM: To assess the oxidative stress markers in the HIV-TB and TB study cohort. MATERIALS AND METHODS: The current prospective study was conducted in Haffkine Institute, Parel, Maharashtra, India, during January 2013 to December 2015. Blood samples from 50 patients each suffering from active TB and HIV-TB co-infection were collected from Seth G.S.Medical College and KEM Hospital Mumbai and Group of Tuberculosis Hospital, Sewree Mumbai. Samples were processed and the experiments were carried out at the Department of Biochemistry, Haffkine Institute. Samples from 50 healthy volunteers were used as controls. Serum was assessed for pro-oxidant markers such as Nitric Oxide (NO), Thiobarbituric Acid Reactive Species (TBARS), C-Reactive Protein (CRP), superoxide anion. Antioxidant markers such as catalase and Superoxide Dismutase (SOD) were assessed. Total serum protein, was also assessed. RESULTS: Among the pro-oxidants, serum NO levels were decreased in TB group while no change was seen in HIV-TB group. TBARS and CRP levels showed significant increase in both groups; superoxide anion increased significantly in HIV-TB group. Catalase levels showed decreased activities in TB group. SOD activity significantly increased in HIV-TB but not in TB group. The total serum proteins were significantly increased in HIV-TB and TB groups. The values of Control cohort were with the normal reference ranges. CONCLUSION: In the present study, we found the presence of oxidative stress to be profound in the TB and HIV-TB co-infection population.

Expression of domain III of the envelope protein from GP-78: a Japanese encephalitis virus.

Acute encephalitis caused by the Japanese encephalitis virus (JEV) represents a growing epidemic and is a cause for concern in Southeast Asia. JEV is transmitted to humans through the bite of the Culicine mosquito species. The virus genome comprising of an RNA strand also encodes the envelope protein (E) which surrounds the virus. The E protein aids in fusion of virus with the cellular membrane of the host cell with the help of three structurally distinct domains (DI, DII, DIII) that are connected by flexible hinge regions. Of these domains, DIII (JEV-DIII) has been reported to interact with the cellular membrane, aid viral entry and viral replication. Hence JEV-DIII has the potential to be an antigen that can provide immune protection to a JEV infection. In this study, we describe the cloning and expression of DIII of GP-78, a virulent strain of JEV prevalent in India. Our data clearly shows that JEV-DIII expressed from pVAC1 in HEK293T cells is membrane targeted. To our knowledge, this is the first demonstration of a recombinant construct that may block JEV entry into the cells and/or evoke specific antibodies against JEV. Future studies will reveal if our construct will elicit significant immune responses which will alleviate or ameliorate the pro-inflammatory responses induced by JEV.

Evaluation of In vitro Antiviral Activity of Datura metel Linn. Against Rabies Virus.

OBJECTIVE: The soxhlet and cold extracts of Datura metel Linn. were evaluated for in vitro antirabies activity. MATERIALS AND METHODS: Soxhlet and cold extraction method were used to extract Datura (fruit and seed) extracts. In vitro cytotoxicity assay was performed by 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide assay. Based on the CC50 range, the in vitro antirabies activity of the extracts was screened by rapid fluorescent focus inhibition test and molecular method. RESULTS: The Datura (fruit and seed) extracts were not cytotoxic below 5 mg/ml (CC50). Titer of 10-4 rabies virus challenge virus standard (RV CVS) (1 50% tissue culture infective dose [1 TCID50]) was obtained by RFFT method and the challenge dose of 10 TCID50 was used for antirabies assay. Datura fruit and seed (soxhlet and cold) extracts showed 50% inhibition of RV CVS at 2.5 mg/ml and 1.25 mg/ml (inhibitory concentration 50% [IC50]), respectively. The tested extracts showed selectivity index (CC50/IC50) ranging from 2 to 4. The viral RNA was extracted and real-time reverse transcription-polymerase chain reaction was performed which also revealed a 2-fold reduction of viral load at 1.25 mg/ml of the Datura seed (soxhlet methanolic and cold aqueous) extracts. CONCLUSION: To the best of our knowledge, this is the first study of in vitro antiviral activity of D. metel Linn. against rabies virus. Datura seed extracts have a potential in vitro antirabies activity and, in future, can be further screened for in vivo activity against rabies virus in murine model. SUMMARY: In the present study, Datura metel. Linn showed and in-vitro anti rabies activity in Vero cell line which was determined by RFFIT method and PCR method.

Pathway Analysis of Proteomics Profiles in Rabies Infection: Towards Future Biomarkers?

Rabies is a zoonotic viral disease that invariably leads to fatal encephalitis, which can be prevented provided post-exposure prophylaxis is initiated timely. Ante-mortem diagnostic tests are inconclusive, and rabies is nontreatable once the clinical signs appear. A large number of host factors are responsible for the altered neuronal functions observed in rabies; however their precise role remains uninvestigated. We therefore used two-dimensional electrophoresis and mass spectrometry analysis to identify differentially expressed host proteins in an experimental murine model of rabies. We identified 143 proteins corresponding to 45 differentially expressed spots (p < 0.05) in neuronal tissues of Swiss albino mice in response to infection with neurovirulent rabies strains. Time series analyses revealed that a majority of the alterations occur at 4 to 6 days post infection, in particular affecting the host's cytoskeletal architecture. Extensive pathway analysis and protein interaction studies using the bioinformatic tools such as Ingenuity Pathway Analysis and STRING revealed novel pathways and molecules (e.g., protein ubiquitination) unexplored hitherto. Further activation/inhibition studies of these pathway molecular leads would be relevant to identify novel biomarkers and mechanism-based therapeutics for rabies, a disease that continues to severely impact global health.

Differential proteomic analysis of respiratory samples from patients suffering from influenza.

The exact molecular pathways involved in the pathogenesis of influenza are yet unclear. In the present study we investigated the upper respiratory proteome in influenza patients. 200 nasal and throat swab samples were collected from patients suffering from acute respiratory illness. These samples were confirmed for influenza pandemic A/H1N1/2009 and influenza type B using qRT-PCR. 10 similar swabs were collected from healthy individuals and were used as controls. Proteins were extracted from the cell pellets and were subjected to 2-D gel electrophoresis. The differentially expressed proteins were identified using MALDI-TOF. Identified proteins were classified into different functional groups based on functions reported in the databases. 25 % of these proteins were involved in cytoskeletal formation, whereas 14 % were involved in signal transduction. Proteins involved in anti-viral responses, Ca-signaling, transport, and tumor suppression constituted 10 % each, where as 5 % of proteins each belong to Nicotinic acetylcholine receptor, Protein Synthesis and anti-bacterial proteins. 10 % of the proteins have not been described previously. This is the first report on respiratory proteome profile in Influenza patients. The study emphasizes the role of such profiling studies using multiple platforms for bio-marker discoveries, especially non-invasive diagnostic marker in Influenza and other infectious diseases.

Bacillus Calmette-Guérin Confers Neuroprotection in a Murine Model of Japanese Encephalitis.

OBJECTIVE: Japanese encephalitis (JE) is a debilitating disease caused by infection with the JE virus (JEV; family: Flaviviridae), which leaves neurological sequelae in survivors but more often leads to mortality. Neurodegeneration caused by inflammation is the primary pathology behind the clinical manifestation of encephalitis caused by JEV. Bacillus Calmette-Guérin (BCG) has been used in immunoprophylaxis for tuberculosis and in the adjuvant therapy of many malignancies, and has exhibited neuroprotective activities in experimental models of Parkinson and Alzheimer disease. This study aimed at assessing the neuroprotective role of BCG in a murine model of JE. METHODS: Suckling mice were inoculated with 106 CFU of BCG and at 18 days postinoculation were challenged with 100 LD50 of JEV. PBS-inoculated mice were used as controls. Mice were sacrificed on days 2, 4, 6, and 8. Brain tissue was homogenized for RNA extraction. One-step real-time RT-PCR was performed to assess the relative gene expressions of TNF-α, IL-6, and iNOS. RESULTS: The BCG-inoculated (BCG+JEV) group exhibited a significant delay in the presentation of neuropathological symptoms, longer survival, and a downregulation in the expression of TNF-α, IL-6, and iNOS on days 2, 4, and 6 post-JEV challenge compared to the JEV group. CONCLUSION: These findings indicate that the administration of BCG offers neuroprotection in the murine model of JE. BCG should therefore be further investigated as an adjuvant in the management of JE. BCG is an accepted vaccine for tuberculosis in many countries that are endemic for JEV. This approach may have a significant impact on the public health burden in these countries.

Evaluation of neuroimmunomodulatory activity of recombinant human interferon α.

OBJECTIVE: Recombinant human interferon (rhIFN)-α is a potent immunoregulator having a wide range of therapeutic applications. In the present study, rhIFN-α was evaluated for its neuroimmunomodulatory activity. METHOD: Dose-dependent gene expression of cytokines and chemokines in the brain of rhIFN-administered mice was studied using real-time SYBR green PCR. RESULTS: Statistically significant increase in expression levels of tumor necrosis factor-α, interleukin (IL)-6, IL-1ß and IFN-γ were observed. CONCLUSION: The findings indicate that rhIFN-α may be used at an optimized dose to cause appropriate neuromodulation of cytokine/chemokine secretion that can aid in the development of therapeutic approaches for many infectious diseases of the central nervous system for which therapies are lacking.

Characterization of influenza virus among influenza like illness cases in Mumbai, India.

The present study was carried out to monitor influenza viruses by identifying the virus and studying the seasonal variation during 2007-2009 in Mumbai. A total of 193 clinical respiratory samples (nasal and throat swab) were collected from patients having influenza like illness in Mumbai region. One-step real-time reverse-transcriptase PCR (rRTPCR) was used to detect Influenza type A (H1 and H3) and Influenza type B virus. Isolation of the virus was carried out using in vitro system which was further confirmed and typed by hemagglutination assay and hemagglutination inhibition assay. Out of 193 samples 24 (12.4 3%) samples tested positive for influenza virus, of which 13 (6.73 %) were influenza type A virus and 10 (5.18 %) were influenza type B virus, while 1 sample (0.51 %) was positive for both. By culture methods, 3 (1.55 %) viral isolates were obtained. All the three isolates were found to be Influenza type B/Malaysia (Victoria lineage) by Hemagglutination Inhibition Assay. The data generated from the present study reveals that both Influenza type A and B are prevalent in Mumbai with considerable activity. The peak activity was observed during monsoon season.