Early Trends to Show the Efficacy of Cordyceps militaris in Mild to Moderate COVID Inflammation.

Background/objective Cordyceps enhances animal survival against influenza by boosting the immune system. In animal studies, it also had anti-inflammatory and preventive properties. Cordyceps stimulates the immune system by increasing the activity and production of various immune cells. Some studies have shown the role of Cordyceps in the novel SARS-CoV-2 virus responsible for the COVID-19 pandemic, in addition to other respiratory diseases caused by the Picorna viruses, SARS-CoV, MERS-CoV, and Influenza viruses. However, it remains unknown whether this food supplement is safe and has anti-inflammatory effects in patients with COVID-19. Therefore, the objectives of this study were to evaluate the use and efficacy of Cordyceps capsules as an adjunct to standard treatment in patients with mild (symptomatic) to moderate COVID-19 infection. Methods A randomised, double-blind, placebo-controlled study was conducted to evaluate the efficacy and safety of Cordyceps capsules (a food supplement) 500 mg as adjuvant therapy in patients with COVID-19. The rationale for dose selection was as per the existing evidence from toxicity studies. The inclusion criteria were patients with either a mild or moderate COVID-19 infection. Clinical features suggestive of dyspnoea or hypoxia, fever, and cough, including SpO2 <94% (range 90-94%) on room air and a respiratory rate ≥24 per minute, were also included. Results Sixty-five patients were recruited for the study, with 33 in the Cordyceps group and 32 in the placebo group. Out of 58 evaluable patients, 33 recovered on day 5, 49 on day 10, and 58 on days 16 and 30. The recovery of patients steadily increased from 56.9% on day 5 to 100% on day 30. The time to clinical recovery was shorter in the Cordyceps group than in the placebo group (mean 6.6 vs. 7.3 days; p > 0.05) overall and for mild disease. However, there was no difference in the time to recovery (time from day 1 to the resolution of all symptoms) for moderate disease. A lower frequency of normal chest X-rays on day 1 and a higher number on day 16 in the treatment group than in the placebo group suggest an improvement in the number of normal chest X-rays with Cordyceps. Significant changes were seen in biomarkers MCPIP, CxCL10, and IL-1ß for overall (both mild and moderate patients) on days 5 and 10 as compared to baseline, and in biomarkers CRP and CxCL10 in moderate category patients on days 5 and 10, respectively. There were no statistically significant changes in IL-6, ferritin, lactate dehydrogenase (LDH), C-reactive protein (CRP), or D-dimer levels between baseline and day 5/10 in patients taking Cordyceps capsules and also between the treatment and placebo groups. Conclusion Cordyceps capsules administered at a dose of 500 mg three times a day along with supportive treatment showed effectiveness in patients with mild to moderate COVID-19 infection, as evidenced by the proportionately higher number of recoveries on day 5, the relatively shorter time for improvement of clinical symptoms, and the proportionately higher number of patients showing negative RT-PCR tests on day 10. Thus, Cordyceps appears to be a safe immunological adjuvant for the treatment of patients with mild-to-moderate COVID-19. Future studies with a larger sample size would shed more light on the evidence, as there are limitations in the generalizability of the results from the present study due to the small sample size.

Evaluation of Xpert MTB/RIF Assay on Stool Samples for the Diagnosis of Pulmonary Tuberculosis among the Pediatric Population.

Objective Microbiological confirmation of tuberculosis (TB) in pediatric cases is challenging due to its paucibacillary nature and difficulty in specimen collection. This study aimed to validate stool as an alternative sample for the diagnosis of pediatric pulmonary TB via Xpert MTB/RIF (Xpert) assay. Materials and Methods This cross-sectional study included 75 pediatric patients up to 10 years of age with signs and symptoms suggestive of TB. From each recruited patient, pulmonary and stool samples were collected in a sterile container. The collected samples were subjected to Ziehl-Neelsen staining, BACTEC MGIT 960 culture (MGIT), Xpert, and in-house multiplex polymerase chain reaction for TB diagnosis. Results About 13.33% (10/75) of the pulmonary samples and, of them, 50% (5/75) of the stool samples were positive by Xpert assay. The sensitivity and specificity of Xpert assay with stool and pulmonary samples were 50 (95% confidence interval [CI]: 18.71-81.29%) and 100% (95% CI: 94.48-100%), respectively. Conclusion The Xpert assay on stool samples showed limited sensitivity and good specificity in the diagnosis of pulmonary TB. Therefore, it can be proposed as an alternative screening sample to diagnose TB in pediatric cases for which getting a respiratory sample is extremely difficult. However, further studies with greater number of samples and multiple baseline variables are required to support our findings. Strategies to optimize stool Xpert assay should be performed to enhance the sensitivity of this method to detect Mycobacterium tuberculosis in children.

Microsporidia in HIV-Positive and HIV-Negative Pediatric Patients with Diarrhea at a Tertiary Care Hospital.

Background Human microsporidiosis presents as an important and rapidly emerging opportunistic infection. However, the exact burden of this infection especially in the pediatric population of Northern India remains unknown. In this study, we investigated the prevalence of microsporidia among human immunodeficiency virus (HIV)-positive and HIV-negative pediatric patients who presented with diarrhea. Methods A total of 263 children were recruited consisting of 98 HIV seropositive with diarrhea and 165 HIV seronegative but with diarrhea. Morning stool samples were collected and both direct and formol ether concentrated samples were examined for the presence of intestinal parasites. The modified acid-fast staining was done for coccidian parasites and trichrome stain for microsporidia detection. Further, the species were detected using a real-time polymerase chain reaction (PCR) targeting a conserved region of the small ribosomal subunit rRNA gene of Enterocytozoon bieneusi , Encephalitozoon hellem , Encephalitozoon intestinalis , and Encephalitozoon cuniculi . Results Overall, one or more parasites were detected in 52.04% (51/98) of HIV seropositive and 53.33% (88/165) of seronegative children ( p = 0.8391). However, coccidian parasites were detected in a significantly huge number of HIV seropositive children (21.43% [21/98]) as compared with HIV seronegative children (4.24% [7/165]). Microsporidial DNA could be detected in HIV seropositive with diarrhea children (17.35% [17/98]) by PCR. A significant correlation between low CD4 count (≤ 200/µL) and intestinal parasite positivity could be established. Conclusion Microsporidia is a significant cause of diarrhea in HIV seropositive pediatric patients and should be kept in mind as one of the differential diagnoses in such patients.

Molecular Identification of Non-tuberculous Mycobacteria in Suspected Tuberculosis Cases in Central India.

Introduction Mycobacterium tuberculosis complex (MTBC), the primary cause of tuberculosis (TB), must be accurately identified to implement effective patient management and control strategies. Non-tuberculous mycobacteria (NTM) in suspected TB cases can result in erroneous diagnoses and needless treatment. Objective The study aimed to identify NTM in patients suspected of TB at a tertiary care hospital in central India using molecular methods. Methods This prospective study enrolled 400 suspected pulmonary and extra-pulmonary TB patients. Patients between the age of two to 90 years, of either gender, new and previously treated cases, Culture positive, patients with immune-compromised status, patients not responding to ATT, HIV positive and negative, and willing to give consent were included in the study. Liquid culture via the Mycobacterial growth indicator tube (MGIT) system was used to culture mycobacteria from clinical samples. The SD Bioline Ag MPT64 Test (Standard Diagnostics, South Korea) and in-house multiplex-PCR (mPCR) were used to differentiate between Mycobacterium tuberculosis complex and NTM species for the molecular identification of NTM GenoType® Mycobacterium Common Mycobacteria (CM) assay kit (HAIN Life Science, Nehren, Germany) was used following the manufacturer's protocol. Results Only 59/400 (14.7%) of the samples produced a positive result in MGIT culture, indicating the presence of mycobacteria, and 85.25% of the remaining 341 samples were negative for mycobacterial growth. Further investigation of these 59 cultures with mPCR and SD Bioline Ag MPT64 test showed that 12 (20.33%) cultures were determined to be NTM, while the remaining 47 (79.67%) were identified as MTBC. Genotype characterization with GenoType® mycobacterium CM assay kit revealed that five of the 12 NTM isolates (41.67%) showed patterns that were consistent with Mycobacterium (M.) fortuitum, three (25%) showed patterns that were consistent with M. abscessus, and four (33.33%) showed patterns that were consistent with M. tuberculosis. Conclusion These results emphasize the value of molecular methods for precisely identifying mycobacterial species, particularly in suspected TB cases. The high prevalence of NTM in positive cultures emphasizes the significance of differentiating between MTBC and NTM to prevent misdiagnosis and ensure proper care. Understanding the epidemiology and clinical significance of these organisms in central India is made possible by the identification of particular NTM species.

Diagnosis of tuberculous pleural effusion in a tertiary care hospital of central India: The role of xpert Mycobacterium tuberculosis/rifampicin.

Background: In India, 15%-20% of tuberculosis (TB) cases are categorized as extra-pulmonary TB, and tuberculous pleural effusion (TPE) is the second-most common type after tuberculous lymphadenitis. However, the paucibacillary nature of TPE makes its diagnosis challenging. As a result, relying on empirical anti-TB treatment (ATT) based on clinical diagnosis becomes necessary for achieving the best possible diagnostic outcome. The study aims to determine the diagnostic utility of Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) for the detection of TB in TPE in high incidence setting of Central India. Methods: The study enrolled 321 patients who had exudative pleural effusion detected through radiological testing and were suspected of having TB. The medical procedure of thoracentesis was conducted to collect the pleural fluid, which was then subjected to both the Ziehl-Neelsen staining and Xpert MTB/RIF test. The patients who showed improvement after receiving anti-tuberculosis treatment (ATT) were considered the composite reference standard. Results: The sensitivity of smear microscopy was found to be 10.19%, while that of the Xpert MTB/RIF method was 25.93% when compared to the composite reference standard. The accuracy of clinical diagnosis was measured using receiver operating characteristics based on clinical symptoms, and it was found to be 0.858 (area under the curve). Conclusions: The study shows that Xpert MTB/RIF has significant value in diagnosing TPE, despite its low sensitivity of 25.93%. Clinical diagnosis based on symptoms was relatively accurate, but relying on symptoms alone is not enough. Using multiple diagnostic tools, including Xpert MTB/RIF, is crucial for accurate diagnosis. Xpert MTB/RIF has excellent specificity and can detect RIF resistance. Its quick results make it useful in situations where a rapid diagnosis is necessary. While it should not be the only diagnostic tool, it has a valuable role in diagnosing TPE.

Diagnostic Performance of Multiplex PCR for Detection of Mycobacterium tuberculosis Complex in Presumptive Pulmonary Tuberculosis Patients and Its Utility in Smear Negative Specimens.

Objective The primary objective of this study was to assess the diagnostic performance of multiplex polymerase chain reaction (mPCR) for the detection of Mycobacterium tuberculosis complex (MTBC) in presumptive pulmonary TB patients, in the setting of a tertiary level teaching hospital in central India, in comparison to liquid culture using BACTEC mycobacteria growth indicator tubes (MGIT) 960 TB system as the gold standard. The secondary objective was to assess the performance of mPCR for Ziehl Neelsen smear negative samples and ascertain the utility of this assay in smear negative samples. Materials and Methods Sputum or bronchoalveolar lavage samples were collected from patients who were adults, aged 18 years or older, presenting with presumptive pulmonary TB, and subjected to three microbiological investigations, that is, Ziehl Neelsen staining, mycobacterial culture using mycobacterial growth indicator tubes in the BD BACTEC MGIT 960 instrument, and the mPCR. Statistical Analysis For statistical analysis, 2 × 2 contingency tables were prepared and analyzed separately for all samples and for smear-negative samples using GraphPad and MedCalc tools. Sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of mPCR were calculated by taking MGIT culture as the reference standard. Results For all samples ( n = 114), sensitivity of mPCR for the detection of (MTBC) was 93.48% (95% confidence interval [CI]: 82.10-98.63%), specificity was 95.59% (95% CI: 87.64-99.08%), positive predictive value (PPV) was 93.48% (95% CI: 82.54-97.75%), and NPV was 95.59% (95% CI: 87.87-98.48%). For smear negative samples ( n = 80), sensitivity was 80.00% (95% CI: 51.91-95.67%), specificity was 98.46% (95% CI: 91.72-99.96%), PPV was 92.31% (95% CI: 62.80-98.84%), and NPV was 95.52% (95% CI: 88.57-98.33%). Conclusion In this study, we were able to demonstrate the good performance characteristics of the mPCR for the detection of MTBC from clinical samples of patients with presumptive pulmonary tuberculosis, with MGIT liquid culture as the reference standard. It may be concluded that mPCR can be considered equivalent to MGIT culture in terms of clinical decision making and yield of positivity, owing to the good sensitivity and specificity for the detection of MTBC.

A comparative analysis of molecular genotypes of Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative patients.

Setting: Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi. Objectives: We aimed to identify the distribution of various genotypes of M. tuberculosis among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital. Patients and methods: Genotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed. Results: A total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of Mycobacterium tuberculosis (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 M. tuberculosis isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance. Conclusion: The Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.

Infant BCG vaccination and risk of pulmonary and extrapulmonary tuberculosis throughout the life course: a systematic review and individual participant data meta-analysis.

BACKGROUND: BCG vaccines are given to more than 100 million children every year, but there is considerable debate regarding the effectiveness of BCG vaccination in preventing tuberculosis and death, particularly among older children and adults. We therefore aimed to investigate the age-specific impact of infant BCG vaccination on tuberculosis (pulmonary and extrapulmonary) development and mortality. METHODS: In this systematic review and individual participant data meta-analysis, we searched MEDLINE, Web of Science, BIOSIS, and Embase without language restrictions for case-contact cohort studies of tuberculosis contacts published between Jan 1, 1998, and April 7, 2018. Search terms included "mycobacterium tuberculosis", "TB", "tuberculosis", and "contact". We excluded cohort studies that did not provide information on BCG vaccination or were done in countries that did not recommend BCG vaccination at birth. Individual-level participant data for a prespecified list of variables, including the characteristics of the exposed participant (contact), the index case, and the environment, were requested from authors of all eligible studies. Our primary outcome was a composite of prevalent (diagnosed at or within 90 days of baseline) and incident (diagnosed more than 90 days after baseline) tuberculosis in contacts exposed to tuberculosis. Secondary outcomes were pulmonary tuberculosis, extrapulmonary tuberculosis, and mortality. We derived adjusted odds ratios (aORs) using mixed-effects, binary, multivariable logistic regression analyses with study-level random effects, adjusting for the variable of interest, baseline age, sex, previous tuberculosis, and whether data were collected prospectively or retrospectively. We stratified our results by contact age and Mycobacterium tuberculosis infection status. This study is registered with PROSPERO, CRD42020180512. FINDINGS: We identified 14 927 original records from our database searches. We included participant-level data from 26 cohort studies done in 17 countries in our meta-analysis. Among 68 552 participants, 1782 (2·6%) developed tuberculosis (1309 [2·6%] of 49 686 BCG-vaccinated participants vs 473 [2·5%] of 18 866 unvaccinated participants). The overall effectiveness of BCG vaccination against all tuberculosis was 18% (aOR 0·82, 95% CI 0·74-0·91). When stratified by age, BCG vaccination only significantly protected against all tuberculosis in children younger than 5 years (aOR 0·63, 95% CI 0·49-0·81). Among contacts with a positive tuberculin skin test or IFNγ release assay, BCG vaccination significantly protected against tuberculosis among all participants (aOR 0·81, 95% CI 0·69-0·96), participants younger than 5 years (0·68, 0·47-0·97), and participants aged 5-9 years (0·62, 0·38-0·99). There was no protective effect among those with negative tests, unless they were younger than 5 years (0·54, 0·32-0·90). 14 cohorts reported on whether tuberculosis was pulmonary or extrapulmonary (n=57 421). BCG vaccination significantly protected against pulmonary tuberculosis among all participants (916 [2·2%] in 41 119 vaccinated participants vs 334 [2·1%] in 16 161 unvaccinated participants; aOR 0·81, 0·70-0·94) but not against extrapulmonary tuberculosis (106 [0·3%] in 40 318 vaccinated participants vs 38 [0·2%] in 15 865 unvaccinated participants; 0·96, 0·65-1·41). In the four studies with mortality data, BCG vaccination was significantly protective against death (0·25, 0·13-0·49). INTERPRETATION: Our results suggest that BCG vaccination at birth is effective at preventing tuberculosis in young children but is ineffective in adolescents and adults. Immunoprotection therefore needs to be boosted in older populations. FUNDING: National Institutes of Health.

Organ Involvement in COVID-19: A Molecular Investigation of Autopsied Patients.

Precise reasons for severe manifestation of SARS-CoV-2 remain unanswered, and efforts have been focused on respiratory system management. Demonstration of unequivocal presence of SARS-CoV-2 in vital body organs by cadaver autopsy was the only way to prove multi-organ involvement. Hence, the primary objective of the study was to determine presence of the SARS-CoV-2 in various organs of patients succumbing to SARS-CoV-2 infection. A total of 246 samples from different organs of 21 patients who died due to severe COVID-19 illness were investigated by qRT-PCR, and SARS-CoV-2 was detected in 181 (73.57%) samples and highest positivity of SARS-CoV-2 being (expectedly) found in nasopharynx (90.4%) followed by bilateral lungs (87.30%), peritoneal fluid (80%), pancreas (72.72%), bilateral kidneys (68.42%), liver (65%) and even in brain (47.2%). The deceased patients were categorized to three subgroups based upon the extent of organs in which SARS-CoV-2 was detected by qRT-PCR (high intensity ≥80%, intermediate intensity = 65-80% and low intensity ≤65% organs involvement). It was conclusively established that SARS-CoV-2 has the property of invasion beyond lungs and even crosses the blood-brain barrier, resulting in multi-system disease; this is probably the reason behind cytokine storm, though it is not clear whether organ damage is due to direct injury caused by the virus or result of inflammatory assault. Significant inverse correlation was found between the Ct value of lung samples and number of organs involved, implying that higher viral load in lungs is directly proportionate to involvement of extrapulmonary organs and patients with higher viral load in respiratory secretions should be monitored more closely for any warning signs and the treatment strategies should also address involvement of other organs for better outcome, because lungs, though the primary site of infection, are not the only organ system responsible for pathogenesis of systemic illness.

Clinical, Virological, and Pathological Profile of Patients Who Died of COVID-19: An Autopsy-Based Study From India.

Background and objective Ever since its emergence in December 2019, coronavirus disease 2019 (COVID-19) has affected more than 220 million people worldwide, resulting in more than 45 million deaths. The present autopsy-based study was undertaken to understand the pathophysiology of the disease and correlate the histopathological and virological findings with the antemortem clinical and biochemical determinants. Methods In this prospective observational study, autopsies were carried out on 21 reverse transcription-polymerase chain reaction (RT-PCR)-proven COVID-19 patients who had died of the disease. The histopathological findings of tissue samples from lungs, liver, and kidneys collected during the autopsy were graded based on their presence or absence; if present, they were graded as either focal or diffuse. The findings were correlated with antemortem clinical and biochemical findings. Postmortem tissue RT-PCR analysis was conducted, and findings were compared with postmortem histopathological findings. Results There was multisystem involvement with the COVID-19 cases. The involvement of lungs was observed in most of the cases (90.4%). The presence of viral RNA was observed in all the organs including the liver (57.1%) and kidney (66.6%). An association was observed between antemortem biochemical parameters [aspartate aminotransferase (AST), alanine aminotransferase (ALT)] and the histopathological features in the liver. No correlation between the Sequential Organ Failure Assessment (SOFA) score recorded clinically and lung histopathology was observed; nor was there any correlation between blood urea-creatinine levels and kidney histopathology. Conclusions Our study shows that COVID-19 is a multisystemic disease and the mortality associated with it is likely to be multifactorial. Despite the presence of amplifiable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various organs, no association could be established between the clinical and histopathology findings. Neither the duration of hospitalization nor the duration of mechanical ventilation showed any correlation with the severity of histopathological findings in the lungs at autopsy.

Assessment of Risk Factors and Outcome of Early Versus Late Cytomegalovirus Infection Infection in Living-related D+/R + Renal Allograft Recipients.

Introduction: Cytomegalovirus infection (CMV) in a kidney transplant recipient (KTR) is a serious complication resulting in increased morbidity, mortality and reduced graft survival. There is limited data on early (within 3 months posttransplant) CMV infection (ECMVI) vs. late CMV infection (LCMVI) in patients not receiving CMV prophylaxis. In India, majority of kidney transplants are D + R + combination. This study aimed to compare the risk factors and outcome of ECMVI vs. LCMVI in living related post-KTR. Methods: This was a single-center ambispective study of adult KTR from living donor between January 2001 and December 2015 who had CMV infection. This study had two cohorts: retrospective and prospective. Retrospective cohort included all KTR from January 2001 to September 2014. Prospective cohort included KTR who received transplants from October 2014 to December 2015. Of both cohorts, patients with early and late CMV infection were included. All patients received triple-drug immunosuppression. CMV infection was diagnosed when KTR had detectable CMV copies > 500/mL. In the prospective cohort, CMV PCR was done at 45 days, 3, 6, 9 and 12 months in all patients. Patients with CMV were treated on conventional lines. All patients were followed up till June 2016. Results: Of 2175 retrospective cohort, 97 and of the 155 prospective cohorts 75 had CMV infection, total being 172 CMV infections. Of these, 90 patients had ECNVI and 82 LCMVI. Induction was used in 48.8% in ECMVI group vs. 35.3% in LCMVI group (p = 0.02). CNI toxicity was present prior to CMV infection in 15 (17.4%) in ECMVI as compared to 14 (17.9%) in LCMVI (P = 0.93). In the ECMVI, 6 (6.6%) had acute rejection as compared to 13 (15.8%) in the LCMVI (P = 0.05). While asymptomatic CMV infection was more common in early (63.3% vs 37.8%, P = 0.001), symptomatic CMV without tissue diagnosis was more common in late (54.8% vs. 31.1%, P = 0.002). Total duration of post-transplant follow-up was 22.8 ± 22.1 months in ECMVI as compared to 49.7 + 40.9 months in the LCMVI (P < 0.001). The serum creatinine at last follow-up was 1.9 ± 1.6 mg/dL in ECMVI group and 2.4 ± 2.0 mg/dL in LCMVI (P = 0.02). Conclusion: In D+/R + living renal transplant recipients, without routine CMV prophylaxis, late CMV infection had more tissue invasive disease and is associated with inferior graft function on long-term follow-up.

Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China.

Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.

Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide.

The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is responsible for the COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. A novel reverse epitomics approach, 'overlapping-epitope-clusters-to-patches' method is utilized to identify the antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are named as 'Ag-Patch or Ag-Patches', for Antigenic Patch or Patches. The identification of Ag-Patches is based on the clusters of overlapping epitopes rising from SARS-CoV-2 proteins. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel method for the vaccine design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs. We identified 73 CTL (Cytotoxic T-Lymphocyte) and 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 overlapping epitopes targeting 55 different HLA alleles leading to 99.98% of world human population coverage. The MPVs and Toll-Like Receptor ectodomain complex shows stable complex formation tendency. Further, the cDNA analysis favors high expression of the MPVs constructs in a human cell line. We identified highly immunogenic novel Ag-Patches from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach and utilized them to design MPVs. We conclude that the novel MPVs could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide. Communicated by Ramaswamy H. Sarma.

Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India.

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the "bridging variant" between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

The World Health Organization Collaborating Center for Emergency and Trauma (WHO-CCET) in South East Asia, The World Academic Council of Emergency Medicine (WACEM), and The American College of Academic International Medicine (ACAIM) 2021 Framework for using Telemedicine Technology at Healthcare Institutions.

The coronavirus disease 2019 crisis has forced the world to integrate telemedicine into health delivery systems in an unprecedented way. To deliver essential care, lawmakers, physicians, patients, payers, and health systems have all adopted telemedicine and redesigned delivery processes with accelerated speed and coordination in a fragmented way without a long-term vision or uniformed standards. There is an opportunity to learn from the experiences gained by this pandemic to help shape a better health-care system that standardizes telemedicine to optimize the overall efficiency of remote health-care delivery. This collaboration focuses on four pillars of telemedicine that will serve as a framework to enable a uniformed, standardized process that allows for remote data capture and quality, aiming to improve ongoing management outside the hospital. In this collaboration, we recommend learning from this experience by proposing a telemedicine framework built on the following four pillars-patient safety and confidentiality; metrics, analytics, and reform; recording of audio-visual data as a health record; and reimbursement and accountability.

Profiles of Volatile Biomarkers Detect Tuberculosis from Skin.

Tuberculosis (TB) is an infectious disease that threatens >10 million people annually. Despite advances in TB diagnostics, patients continue to receive an insufficient diagnosis as TB symptoms are not specific. Many existing biodiagnostic tests are slow, have low clinical performance, and can be unsuitable for resource-limited settings. According to the World Health Organization (WHO), a rapid, sputum-free, and cost-effective triage test for real-time detection of TB is urgently needed. This article reports on a new diagnostic pathway enabling a noninvasive, fast, and highly accurate way of detecting TB. The approach relies on TB-specific volatile organic compounds (VOCs) that are detected and quantified from the skin headspace. A specifically designed nanomaterial-based sensors array translates these findings into a point-of-care diagnosis by discriminating between active pulmonary TB patients and controls with sensitivity above 90%. This fulfills the WHO's triage test requirements and poses the potential to become a TB triage test.

Heterogeneous patterns of COVID-19 transmission in an Urban set up - sero-epidemiological survey data from Ujjain, Madhya Pradesh (a central Indian city).

In the wake of rising number of SARS-CoV-2 cases, the Government of India had placed mass-quarantine measures, termed as "lockdown" measures from end-March 2020. The subsequent phase-wise relaxation from July 2020 led to a surge in the number of cases. This necessitated an understanding of the true burden of SARS-CoV-2 in the community. Consequently, a sero-epidemiological survey was carried out in the central Indian city of Ujjain, Madhya Pradesh. This article details the processes of data acquisition, compilation, handling, and information derivation from the survey. Information on socio-demographic and serological variables were collected from 4,883 participants using a multi-stage stratified random sampling method. Appropriate weightage was calculated for each participant as sampling fraction derived from Primary Sampling Unit (PSU), Secondary Sampling Unit (SSU) and Tertiary Sampling Unit (TSU). The weightage was then applied to the data to adjust the findings at population level. The comprehensive and robust methodology employed here may act as a model for similar future endeavours. At the same time, the dataset can also be relevant for researchers in fields such as data science, epidemiology, virology and earth modelling.