A T cell-targeted multi-antigen vaccine generates robust cellular and humoral immunity against SARS-CoV-2 infection.

SARS-CoV-2, the etiological agent behind the coronavirus disease 2019 (COVID-19) pandemic, has continued to mutate and create new variants with increased resistance against the WHO-approved spike-based vaccines. With a significant portion of the worldwide population still unvaccinated and with waning immunity against newly emerging variants, there is a pressing need to develop novel vaccines that provide broader and longer-lasting protection. To generate broader protective immunity against COVID-19, we developed our second-generation vaccinia virus-based COVID-19 vaccine, TOH-VAC-2, encoded with modified versions of the spike (S) and nucleocapsid (N) proteins as well as a unique poly-epitope antigen that contains immunodominant T cell epitopes from seven different SARS-CoV-2 proteins. We show that the poly-epitope antigen restimulates T cells from the PBMCs of individuals formerly infected with SARS-CoV-2. In mice, TOH-VAC-2 vaccination produces high titers of S- and N-specific antibodies and generates robust T cell immunity against S, N, and poly-epitope antigens. The immunity generated from TOH-VAC-2 is also capable of protecting mice from heterologous challenge with recombinant VSV viruses that express the same SARS-CoV-2 antigens. Altogether, these findings demonstrate the effectiveness of our versatile vaccine platform as an alternative or complementary approach to current vaccines.

Comparison of the Risk of Crohn's Disease Postoperative Recurrence Between Modified Rutgeerts Score i2a and i2b Categories: An Individual Patient Data Meta-analysis.

BACKGROUND: The modified Rutgeerts' score [RS] differentiates i2a-lesions confined to the anastomosis-and i2b-more than five aphthous ulcers in the neoterminal ileum with normal intervening mucosa, with or without anastomotic lesions-categories. Its relevance for the therapeutic management of Crohn's disease [CD] patients after ileocolic resection is still debated. Our objective was to compare the postoperative recurrence risk in patients with an i2a or i2b score, using an individual patient data meta-analysis. METHODS: We conducted a systematic literature search until July 2020, to identify all relevant studies reporting the i2a/i2b status in the year following ileocolic resection and clinical and/or surgical postoperative CD recurrence in their follow-up. Individual patient-level data were obtained from the corresponding authors. The association between the modified RS and time-to-event was evaluated using a mixed Cox model with the centre as the random effect. RESULTS: Seven studies published between 2008 and 2019 were included, corresponding to 400 patients: 189 [47%] i2a and 211 [53%] i2b. Median [interquartile range, IQR] time from ileocolic resection to ileocolonoscopy was 6.2 [5.5, 7.9] months and median [IQR] follow-up time after ileocolonoscopy was 4.5 [2.9, 7.3] years. The risk of clinical postoperative recurrence at 1 and 3 years was 11% [6-15%], and 25% [18-32%] in the i2a group versus 9% [5-13%] and 33% [26-41%] in the i2b group [p = 0.63 and p = 0.12, respectively]. No significant difference was observed in terms of time to clinical postoperative recurrence [p = 0.16] or surgical postoperative recurrence [p = 0.87]. Results did not change after excluding patients having initiated an immunosuppressant or a biologic in the 3 months after endoscopy [remaining cohort, n = 361]. CONCLUSIONS: In this individual patient data meta-analysis, no difference was observed between i2a and i2b subcategories with regards to clinical or surgical postoperative recurrence. As we wait for prospective trials, the same treatment strategy could be applied to all patients classified as i2 on the Rutgeerts score.

Covid-19 pneumonia: An unusual radiological presentation.

A 26 year old female presented with complaints of high grade fever and cough for 10 days. Nasopharyngeal swab tested for COVID-19 RT-PCR at admission was negative. Clinical examination suggested a patch of bronchial breathing in left infrascapular region and bilateral diffuse rhonchi. Chest X-ray was suggestive of left lower zone consolidation. HRCT showed a large patch of consolidation with GGO along with a cavitary lesion involving left lower lobe. Sputum for RT-PCR COVID 19 was positive. Patient was managed as per covid-19 protocol, subsequently showing clinical and radiological improvement.

A discrepancy between CT angiography and transesophageal echocardiographic measurements of the annular size affect long-term survival following trans-catheter aortic valve replacement.

Introduction: Accurate measurement of the aortic valve annulus is critical for proper valve sizing for the transcatheter aortic valve replacement (TAVR) procedure. While computed tomography angiography (CTA) is the widely-accepted standard, two-dimensional (2D) and three-dimensional(3D) transesophageal echocardiography (TEE) is commonly performed to measure the size of the aortic valve and to verify appropriate seating of prostheses. Methods: Patients undergoing TAVR between 2013-2015 were examined. 2D- and 3D-TEEmeasurements were compared to CTA taken as standard. Patients were followed for at least one year. The presence and effect of discrepancy (defined as a difference of more than 10%) between CTA and TEE measurements on survival were examined. Results: One hundred eighty-five patients (70 men) were included. 2D- and 3D-TEE measurements underestimated the annulus size by -1.49 and -1.32 mm, respectively. Discrepancies > 10% between TEE and CTA methods in estimating the aortic annulus size were associated with a decrease in post implant survival. The peak pressure gradient across the aortic prosthesis measured one year after the implant was higher in patients with an initial discrepancy between 3D-TEE and CTA measurements. In a multivariate cox-regression model, the discrepancy between CTA and 2D-TEE readings and the smaller size of the aortic annular area were the predictors of long-term survival. Conclusion: Both 2D and 3D-TEE underestimate the aortic annulus measurements compared to CTA, with 2D-TEE being relatively more precise than 3D-TEE technology. The presence of a discrepancy between echocardiographic and CTA measurements of the aortic annulus is associated with a lower survival rate.

No Benefit of Concomitant Immunomodulator Therapy on Efficacy of Biologics That Are Not Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases: A Meta-analysis.

BACKGROUND & AIMS: There is debate over whether patients with inflammatory bowel diseases (IBD) treated with biologics that are not tumor necrosis factor antagonists (such as vedolizumab or ustekinumab) should receive concomitant treatment with immunomodulators. We conducted a meta-analysis to compare the efficacy and safety of concomitant immunomodulator therapy vs vedolizumab or ustekinumab monotherapy. METHODS: In a systematic search of publications, through July 31, 2019, we identified 33 studies (6 randomized controlled trials and 27 cohort studies) of patients with IBD treated with vedolizumab or ustekinumab. The primary outcome was clinical benefit, including clinical remission, clinical response, or physician global assessment in patients who did vs did not receive combination therapy with an immunomodulator. Secondary outcomes were endoscopic improvement and safety. We performed random-effects meta-analysis and estimated odds ratio (OR) and 95% CIs. RESULTS: Overall, combination therapy was not associated with better clinical outcomes in patients receiving vedolizumab (16 studies: OR, 0.84; 95% CI, 0.68-1.05; I2=13.9%; Q test P = .17) or ustekinumab (15 studies: OR, 1.1; 95% CI, 0.87-1.38; I2 = 11%; Q test P = .28). Results were consistent in subgroup analyses, with no difference in clinical remission or response in induction vs maintenance studies or in patients with Crohn's disease vs ulcerative colitis in studies of vedolizumab. Combination therapy was not associated with better endoscopic outcomes in patients receiving vedolizumab (3 studies: OR, 1.13; 95% CI, 0.48-2.68; I2 = 0; Q test P=.96) or ustekinumab (2 studies: OR, 0.58; 95% CI, 0.21-1.16; I2 = 47%; Q test P = .17). Combination therapy was not associated with an increase in adverse events during vedolizumab therapy (4 studies: OR, 1.17; 95% CI, 0.75-1.84; I2 = 0; Q test P = .110). CONCLUSIONS: In a meta-analysis of data from studies of patients with IBD, we found that combining vedolizumab or ustekinumab with an immunomodulator is no more effective than monotherapy in induction or maintenance of remission.

Change in MRI-PDFF and Histologic Response in Patients With Nonalcoholic Steatohepatitis: A Systematic Review and Meta-Analysis.

BACKGROUND & AIMS: Magnetic resonance imaging proton density fat fraction (MRI-PDFF) offers promise as a non-invasive biomarker of treatment response in early-phase nonalcoholic steatohepatitis (NASH) trials. We performed a systematic review to quantify the association between a ≥ 30% reduction in MRI-PDFF and histologic response in NASH. METHODS: We searched the Cochrane Library, Embase, Medline and trial registries through May 2020 for early-phase clinical trials that incorporated MRI-PDFF and examined histologic response following intervention in adults with NASH. Subjects were classified as MRI-PDFF responders (relative decline in liver fat ≥30%) or non-responders (relative decline in liver fat <30%). MRI-PDFF responders versus non-responders were compared. Primary outcome was histologic response defined as a 2-point improvement in NAFLD Activity Score with at least 1-point improvement in lobular inflammation or ballooning. Secondary outcome was NASH resolution. Proportions and random effects odds ratios (OR) with corresponding 95% confidence intervals (CI) were calculated. RESULTS: Seven studies met inclusion criteria, comprising 346 subjects (median age 51 years; 59% female; 46% with diabetes). MRI-PDFF responders were significantly more likely to have a histologic response (51% vs 14%, P < .001; OR 6.98, 95% CI 2.38-20.43, P < .001) and NASH resolution (41% vs 7%, P < .001; OR 5.45, 95% CI 1.53-19.46, P = .009) compared to non-responders. CONCLUSIONS: This meta-analysis demonstrates that a ≥30% relative decline in MRI-PDFF is associated with higher odds of histologic response and NASH resolution. These results support the use of MRI-PDFF in non-invasive monitoring of treatment response in early-phase NASH clinical trials and provide helpful data for sample-size estimation for histology-based assessment.

Premedication as primary prophylaxis does not influence the risk of acute infliximab infusion reactions in immune-mediated inflammatory diseases: A systematic review and meta-analysis.

INTRODUCTION: Up to 25% of patients treated with infliximab experience hypersensitivity reactions. Prophylactic premedication prior to infliximab infusion, comprising corticosteroids and/or antihistamines, is widely used in clinical practice but its efficacy has recently been called into question due to the lack of pathophysiological rationale and validation by controlled trials. MATERIALS AND METHODS: We conducted a comprehensive literature search of multiple electronic databases from inception to June 2017 to identify studies reporting the impact of corticosteroid and/or antihistamine premedication on the risk of acute (<24 h) hypersensitivity reaction to infliximab in immune-mediated inflammatory diseases (IMIDs). Random-effects meta-analysis was performed. RESULTS: Ten studies, eight observational studies and two randomized control trials, were identified including a total of 3892 patients with IMIDs, and 1,385 patients with IBD. Corticosteroid premedication was not associated with a decreased risk of hypersensitivity reaction in either IMIDs (7 studies; OR, 1.07, 95%CI, 0.64-1.78; I2 = 57.5%) or IBD (3 studies; OR, 1.04, 95% CI, 0.52-2.07; I2 = 57%). Antihistamine premedication was not associated with a decreased risk of hypersensitivity reaction in IMIDs (3 studies: OR, 1.39, 95% CI, 0.70-2.73; I2 = 85%). The combination of corticosteroids and antihistamines did not decrease the risk of acute infliximab infusion reaction in IMIDs (6 studies; OR, 2.12, 95% CI, 0.61-7.35; I2 = 94%), but was associated with an increased risk in IBD (4 studies, OR, 4.17, 95% CI, 1.61-10.78; I2 = 77%). CONCLUSION: Corticosteroid and/or antihistamine premedication is not associated with a decreased risk of acute hypersensitivity reactions to infliximab in patients with IMIDs. We believe that these premedications should no longer be part of standard protocols.

Efficacy and Safety of Ashwagandha Root Extract in Subclinical Hypothyroid Patients: A Double-Blind, Randomized Placebo-Controlled Trial.

BACKGROUND: Subclinical hypothyroidism, a thyroid disorder without obvious symptoms of thyroid deficiency, occurs in 3%-8% of the global population. Ashwagandha [Withania somnifera (L.) Dunal], a traditional medicine in Ayurveda, is often prescribed for thyroid dysfunctions. OBJECTIVE: This pilot study was designed to evaluate the efficacy and safety of ashwagandha root extract in subclinical hypothyroid patients. DESIGN, SETTING, AND PARTICIPANTS: A prospective, randomized, double-blind, single-center placebo-controlled study was performed at Sudbhawana Hospital, Varanasi, India between May 2016 and September 2016. Fifty subjects with elevated serum thyroid stimulating hormone (TSH) levels (4.5-10 µIU/L) aged between 18 and 50 were randomized in either treatment (n = 25) or placebo (n = 25) groups for an 8-week treatment period. INTERVENTIONS: Ashwagandha root extract (600 mg daily) or starch as placebo. Efficacy Variables: Serum TSH, serum triiodothyronine (T3), and thyroxine (T4) levels. RESULTS: A total of four subjects (two from each group) withdrew their consent before the second visit. Eight weeks of treatment with ashwagandha improved serum TSH (p < 0.001), T3 (p = 0.0031), and T4 (p = 0.0096) levels significantly compared to placebo. Ashwagandha treatment effectively normalized the serum thyroid indices during the 8-week treatment period in a significant manner (time-effects: TSH [p < 0.001], T3 [p < 0.001], and T4 [p < 0.001]). Four subjects (8%) (ashwagandha: 1[4%]; Placebo: 3[12%]) out of 50 reported few mild and temporary adverse effects during this study. CONCLUSION: Treatment with ashwagandha may be beneficial for normalizing thyroid indices in subclinical hypothyroid patients.

Indica rice genome assembly, annotation and mining of blast disease resistance genes.

BACKGROUND: Rice is a major staple food crop in the world. Over 80% of rice cultivation area is under indica rice. Currently, genomic resources are lacking for indica as compared to japonica rice. In this study, we generated deep-sequencing data (Illumina and Pacific Biosciences sequencing) for one of the indica rice cultivars, HR-12 from India. RESULTS: We assembled over 86% (389 Mb) of rice genome and annotated 56,284 protein-coding genes from HR-12 genome using Illumina and PacBio sequencing. Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels. To mine disease resistance genes, we sequenced few indica rice cultivars that are reported to be highly resistant (Tetep and Tadukan) and susceptible (HR-12 and Co-39) against blast fungal isolates in many countries including India. Whole genome sequencing of rice genotypes revealed high rate of mutations in defense related genes (NB-ARC, LRR and PK domains) in resistant cultivars as compared to susceptible. This study has identified R-genes Pi-ta and Pi54 from durable indica resistant cultivars; Tetep and Tadukan, which can be used in marker assisted selection in rice breeding program. CONCLUSIONS: This is the first report of whole genome sequencing approach to characterize Indian rice germplasm. The genomic resources from our work will have a greater impact in understanding global rice diversity, genetics and molecular breeding.

Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis.

Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant and accounts for most of the clinical disease worldwide. However, there are no publically available, closed ST2 genomes and pathogenesis studies have not focused on these strains. We report the complete genome and methylome of BPH0662, a multidrug-resistant, hospital-adapted, ST2 S. epidermidis, and describe the correlation between resistome and phenotype, as well as demonstrate its relationship to publically available, international ST2 isolates. Furthermore, we delineate the methylome determined by the two type I restriction modification systems present in BPH0662 through heterologous expression in Escherichia coli, allowing the assignment of each system to its corresponding target recognition motif. As the first, to our knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable reference for future genomic studies of this clinically relevant lineage. Defining the methylome and the construction of these E. coli hosts provides the foundation for the development of molecular tools to bypass restriction modification systems in this lineage that has hitherto proven intractable.

The complete methylome of Helicobacter pylori UM032.

BACKGROUND: The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome). RESULTS: The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning. CONCLUSION: Consistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori.

Multiple Genome Sequences of Helicobacter pylori Strains of Diverse Disease and Antibiotic Resistance Backgrounds from Malaysia.

Helicobacter pylori causes human gastroduodenal diseases, including chronic gastritis and peptic ulcer disease. It is also a major microbial risk factor for the development of gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. Twenty-one strains with different ethnicity, disease, and antimicrobial susceptibility backgrounds were sequenced by use of Illumina HiSeq and PacBio RS platforms.

Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives.

BACKGROUND: Helicobacter pylori is a Gram-negative bacterium that persistently infects the human stomach inducing chronic inflammation. The exact mechanisms of pathogenesis are still not completely understood. Although not a natural host for H. pylori, mouse infection models play an important role in establishing the immunology and pathogenicity of H. pylori. In this study, for the first time, the genome sequences of clinical H. pylori strain UM032 and mice-adapted derivatives, 298 and 299, were sequenced using the PacBio Single Molecule, Real-Time (SMRT) technology. RESULT: Here, we described the single contig which was achieved for UM032 (1,599,441 bp), 298 (1,604,216 bp) and 299 (1,601,149 bp). Preliminary analysis suggested that methylation of H. pylori genome through its restriction modification system may be determinative of its host specificity and adaptation. CONCLUSION: Availability of these genomic sequences will aid in enhancing our current level of understanding the host specificity of H. pylori.

Cytoplasmic histidine kinase (HP0244)-regulated assembly of urease with UreI, a channel for urea and its metabolites, CO2, NH3, and NH4(+), is necessary for acid survival of Helicobacter pylori.

Helicobacter pylori colonizes the normal human stomach by maintaining both periplasmic and cytoplasmic pH close to neutral in the presence of gastric acidity. Urease activity, urea flux through the pH-gated urea channel, UreI, and periplasmic alpha-carbonic anhydrase are essential for colonization. Exposure to pH 4.5 for up to 180 min activates total bacterial urease threefold. Within 30 min at pH 4.5, the urease structural subunits, UreA and UreB, and the Ni(2+) insertion protein, UreE, are recruited to UreI at the inner membrane. Formation of this complex and urease activation depend on expression of the cytoplasmic sensor histidine kinase, HP0244. Its deletion abolishes urease activation and assembly, impairs cytoplasmic and periplasmic pH homeostasis, and depolarizes the cells, with an approximately 7-log loss of survival at pH 2.5, even in 10 mM urea. Associated with this assembly, UreI is able to transport NH(3), NH(4)(+), and CO(2), as shown by changes in cytoplasmic pH following exposure to NH(4)Cl or CO(2). To be able to colonize cells in the presence of the highly variable pH of the stomach, the organism expresses two pH-sensor histidine kinases, one, HP0165, responding to a moderate fall in periplasmic pH and the other, HP0244, responding to cytoplasmic acidification at a more acidic medium pH. Assembly of a pH-regulatory complex of active urease with UreI provides an advantage for periplasmic buffering.

Size selective sampling using mobile, 3D nanoporous membranes.

We describe the fabrication of 3D membranes with precisely patterned surface nanoporosity and their utilization in size selective sampling. The membranes were self-assembled as porous cubes from lithographically fabricated 2D templates (Leong et al., Langmuir 23:8747-8751, 2007) with face dimensions of 200 microm, volumes of 8 nL, and monodisperse pores ranging in size from approximately 10 microm to 100 nm. As opposed to conventional sampling and filtration schemes where fluid is moved across a static membrane, we demonstrate sampling by instead moving the 3D nanoporous membrane through the fluid. This new scheme allows for straightforward sampling in small volumes, with little to no loss. Membranes with five porous faces and one open face were moved through fluids to sample and retain nanoscale beads and cells based on pore size. Additionally, cells retained within the membranes were subsequently cultured and multiplied using standard cell culture protocols upon retrieval.