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Background and Objectives: Rapid clinical manifestation/progression of the meningococcal meningitis and lacunae in conventional bacteriological test often encourages indiscriminate use of antibiotics much before the etiology is established. This study was planned to evaluate ctrA PCR for rapid molecular detection. In addition, multiplex PCR and sequencing was done for serogroup prediction to provide essential epidemiological and laboratory evidence for decision makers of health department of the country for choosing appropriate vaccine and phylogenetic analysis to establish lineage. Materials and Methods: 73 CSF samples, collected from equal number of suspected cases, were investigated by both bacteriological (microscopy, culture, LA and drug sensitivity testing) as well as molecular tests i.e. PCR targeting conserved ctrA gene, multiplex PCR for serogroup characterization and DNA sequencing. Results: ctrA PCR revealed sensitivity, specificity, positive predictive value and negative predictive values of 93.15%, 100%,100%, and 88.23% respectively. Multiplex PCR based genogrouping followed by DNA sequencing, BLAST and phylogenetic analysis revealed complete homology with earlier submitted Neisseria meningitidis serogroup A strain Z2491 to suggest the sole involvement of only serogroup A in the outbreak. Two strains showed resistance to cefuroxime, ciprofloxacin, nalidixic acid. Only one strain showed resistance to ciprofloxacin, emphasizing the need for a constant surveillance system. Conclusion: These diagnostic molecular tools are of paramount importance in establishing etiology, serogrouping, and epidemiological surveillance especially in developing countries like India.

Inspired by natural metallopeptides, our work focuses on engineering self-assembling nanostructures of C 2 -symmetric metallopeptide conjugates (MPC) from a pyridine-bis-tripeptide bioprobe that uniquely detects lead (Pb 2+ ) ions by emitting a fluorescence signal at 450 nm, which is further intensified in the presence of DAPI ( λ em = 458 nm), enhancing the bioimaging quality. This study enables precise lead quantification by modulating the ionic conformation and morphology. Experimental and theoretical insights elucidate the nanostructure formation mechanism, laying the groundwork for materials encapsulation and advancing lead detoxification. Our proof-of-principle experiment, demonstrating actin filament recovery in lead-treated cells, signifies therapeutic potential for intracellular lead aggregation and introduces novel avenues in biotechnological applications within biomaterials science.

Innovations in protein engineering can help redesign allergenic proteins to reduce adverse reactions in sensitive individuals. To accomplish this aim, a better knowledge of the molecular properties of allergenic proteins and the molecular features that make a protein allergenic is needed. We present a novel AI-based tool, AllergenAI, to quantify the allergenic potential of a given protein. Our approach is solely based on protein sequences, differentiating it from previous tools that use some knowledge of the allergens' physicochemical and other properties in addition to sequence homology. We used the collected data on protein sequences of allergenic proteins as archived in the three well-established databases, SDAP 2.0, COMPARE, and AlgPred 2, to train a convolutional neural network and assessed its prediction performance by cross-validation. We then used Allergen AI to find novel potential proteins of the cupin family in date palm, spinach, maize, and red clover plants with a high allergenicity score that might have an adverse allergenic effect on sensitive individuals. By analyzing the feature importance scores (FIS) of vicilins, we identified a proline-alanine-rich (P-A) motif in the top 50% of FIS regions that overlapped with known IgE epitope regions of vicilin allergens. Furthermore, using∼ 1600 allergen structures in our SDAP database, we showed the potential to incorporate 3D information in a CNN model. Future, incorporating 3D information in training data should enhance the accuracy. AllergenAI is a novel foundation for identifying the critical features that distinguish allergenic proteins.

Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) cases are more prone to Influenza and SARS-CoV-2 infection. Accordingly, we genetically characterized Influenza and SARS-CoV-2 in 633 ILI and SARI cases by rRT-PCR and WGS. ILI and SARI cases showed H1N1pdm09 prevalence of 20.9% and 23.2% respectively. 135 (21.3%) H1N1pdm09 and 23 (3.6%) H3N2 and 5 coinfection (0.78%) of H1N1pdm09 and SARS-CoV-2 were detected. Phylogenetic analysis revealed H1N1pdm09 resemblance to clade 6B.1A.5a.2 and their genetic relatedness to InfA/Perth/34/2020, InfA/Victoria/88/2020 and InfA/Victoria/2570/2019. Pan 24 HA and 26 NA nonsynonymous mutations and novel HA (G6D, Y7F, Y78H, P212L, G339R, T508K and S523T) and NA (S229A) mutations were observed. S74R, N129D, N156K, S162N, K163Q and S164T alter HA Cb and Sa antibody recognizing site. Similarly, M19T, V13T substitution and multiple mutations in transmembrane and NA head domain drive antigenic drift. SARS-CoV-2 strains genetically characterized to Omicron BA.2.75 lineage containing thirty nonsynonymous spike mutations exhibited enhanced virulence and transmission rates. Coinfection although detected very minimal, the mutational changes in H1N1pdm09 and SARS-CoV-2 virus infected individuals could alter antibody receptor binding sites, allowing the viruses to escape immune response resulting in better adaptability and transmission. Thus continuous genomic surveillance is required to tackle any future outbreak., (© 2024. The Author(s).)

Aim: To determine the role of geminin as a tool for differentiating various types of cervical intraepithelial neoplasia (CIN) and cervical carcinoma (CC)., Methods: Seventy women newly diagnosed with CIN or CC undergoing cervical biopsy were included; their clinical profile, human papilloma virus (HPV) positivity, and colposcopy findings were noted, and biopsy tissue was analyzed for geminin content., Results: On geminin immunohistochemistry, 100% of women with CIN3 and 96.29% of women with CC had geminin two plus or more. When analyzed as ordinal variables, there was a significant correlation (spearman's rho 0.35, p 0.01) between geminin and biopsy results (CIN1, CIN2, CIN3, and CC)., Conclusions: Screening tests for cervical cancer, like conventional pap smears, liquid-based pap smears, and triaging with HPV, have limitations. It is important to be able to differentiate between high-grade lesions, invasive cancer, and low-grade lesions. The detection of geminin in these cells may aid in the confirmation of the diagnosis and ensure adequate treatment. Cervical intraepithelial lesions and carcinoma cervix demonstrated a correlation between increased geminin expression in CIN1 vs. CC and CIN2 vs. CC. Geminin may be a potential surrogate marker for higher-grade cervical lesions, and further research is needed to corroborate evidence in this direction., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2024, Bagde et al.)

SARS-CoV-2 has expressively changed its sequences during the COVID-19 pandemic situation by encompassing persistent evolutionary mutational changes resulting in the emergence of many clades and lineages. Evolution of these SARS-CoV-2 variants have significantly imparted fitness advantage to the virus, enhanced its transmissibility and severity of the disease. These new variants are a potential threat to the vaccine efficacy as well. It is therefore pertinent to monitor the evolution of these variants and their epidemiological and clinical impact, in a geographic setting. This study has thus looked into the geographic distribution and genetic diversity of SARS-CoV-2 variants and the evolutionary circulation of different clades in Chhattisgarh (CG) state from March 2020 to July 2023. A total of 3018 sequences were retrieved from the GISAID database, in which 558 were submitted by us. The demographic data revealed male preponderance of 56.45% versus 43.54% females, with the overall mean age of 36.5 years. SARS-CoV-2 sequences represented many variants viz., Delta (55%), Omicron (22%) and others (15%) with a small proportion of recombinant (5%), Kappa (2%), and Alpha (1%). The viral clades G was found predominant for a year from initial days of pandemic in March, 2020 to January, 2021 which then subsequently evoluted to subclade GK (Delta B.1.617.2) and remained in circulation in CG till November, 2021. From December 2021, the GRA (Omicron B.1.1.529) variant had replaced GK to become the dominant strain and continues to predominate in present time. GRA clade is however continuously encompassing new recombinant strains, having various non-synonymous mutations especially in spike protein. The non-synonymous mutation P314L in ORF1b, S84L in ORF8 and D614G in spike protein were found as the pan mutation carried over from clade G to GRA. The continuous evolution in SARS-CoV2 warrants periodical geographic genomic surveillance monitoring to timely detect any new variants having the potential of causing future outbreak., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem., (© 2023 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.)

Scope: The unstructured region of Ara h 2, referred to as epitope 3, contains a repeated motif, DYPSh (h = hydroxyproline) that is important for IgE binding., Methods and Results: IgE binding assays to 20mer and shorter peptides of epitope 3, defines a 16mer core sequence containing one copy of the DPYSh motif, DEDSYERDPYShSQDP. This study performs alanine scanning of this and a related 12mer mimotope, LLDPYAhRAWTK. IgE binding, using a pool of 10 sera and with individual sera, is greatly reduced when alanine is substituted for aspartate at position 8 (D8; p < 0.01), tyrosine at position 10 (Y10; p < 0.01), and hydroxyproline at position 12 (h12; p < 0.001). IgE binding to alanine-substituted peptides of a mimotope containing the DPY&#95;h motif confirm the critical importance of Y (p < 0.01) and h (p < 0.01), but not D. Molecular modeling of the core and mimotope suggests an h-dependent conformational basis for the recognition of these sequences by polyclonal IgE., Conclusions: IgE from pooled sera and individual sera differentially bound amino acids throughout the sequences of Epitope 3 and its mimotope, with Y10 and h12 being most important for all sera. These results are highly significant for designing hypoallergenic forms of Ara h 2., (© 2023 Wiley-VCH GmbH.)

H 2 production via water-gas shift reaction (WGS) is an important process and applied widely. Cobalt-modified CeO 2 are promising catalysts for WGS reaction. Herein, a series of Co/Nb-CeO 2 catalysts were prepared by varying the rate of precipitant addition during the coprecipitation method and examined for hydrogen generation through WGS reaction. The rates of precipitant addition were 1, 5, 15, and 25 mL/min. We obtained ceria supported cobalt catalysts with different sizes and morphology such as 3, 8 nm nanoclusters, 30 nm cubic nanoparticles, and 50 nm hexagonal nanoparticles. The well dispersed small cobalt particles in Co/Nb-CeO 2 that was prepared at 5 mL/min titration rate exhibit strong interaction between cobalt oxide and CeO 2 that retards the reduction of CoO x producing Co-CoO x pairs. In contrast, 1-Co/Nb-CeO 2 and 25-Co/Nb-CeO 2 result in bigger and aggregated Co particles, resulting in fewer interfaces with CeO 2 . The Co 0 , Co δ+ , Ce 3+ , and O v species are responsible for improved reducibility in Co/Nb-CeO 2 catalysts and were quantitively measured using XPS, XAS, and Raman spectroscopy. The Co-CoO x interface assists dissociation of the H 2 O molecule; CO oxidation requires low activation energy and realizes a high turnover frequency of 9.8 s -1 . The 5-Co/Nb-CeO 2 catalyst achieved thermodynamic equilibrium equivalent CO conversion with efficient H 2 production during WGS reaction at a gas hourly space velocity of 315,282 h -1 . Successively, the 5-Co/Nb-CeO 2 catalyst exhibited stable performance for straight 168 h attributed to stable CO-Co δ+ intermediate formation, achieving efficient inhibition of typical CO chemistry over the Co metal, suitable for hydrogen generation from waste derived synthesis gas.

Background: Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2., Methods: In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022., Findings: Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8  years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement., Interpretation: The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Potdar, Vijay, Mukhopadhyay, Aggarwal, Bhardwaj, Choudhary, Gupta, Kaur, Narayan, Kumar, Singh, Abdulkader, Murhekar, Mishra, Thangavel, Nagamani, Dhodapkar, Fomda, Varshney, Majumdar, Dutta, Vijayachari, Turuk, Majumdar, Sahoo, Pandey, Bhargava, Negi, Khatri, Kalawat, Biswas, Khandelwal, Borkakoty, Manjushree, Singh, Iravane, Kaveri, Shantala, Brijwal, Choudhary, Dar, Malhotra, Jain and ILI-SARI Surveillance Team.)

Background: Allergenic proteins can cause IgE-mediated adverse reactions in sensitized individuals. Although the sequences of many allergenic proteins have been identified, bioinformatics data analysis with advanced computational methods and modeling is needed to identify the basis for IgE binding and cross-reactivity., Objective: We aim to present the features and use of the updated Structural Database of Allergenic Proteins 2.0 (SDAP 2.0) webserver, a unique, publicly available resource to compare allergens using specially designed computational tools and new high-quality 3-D models for most known allergens., Methods: Previously developed and novel software tools for identifying cross-reactive allergens using sequence and structure similarity are implemented in SDAP 2.0. A comprehensive set of high-quality 3-D models of most allergens was generated with the state-of-the-art AlphaFold 2 software. A graphics tool enables the interactive visualization of IgE epitopes on experimentally determined and modeled 3-D structures., Results: A user can search for allergens similar to a given input sequence with the FASTA algorithm or the window-based World Health Organization/International Union of Immunological Societies (WHO/IUIS) guidelines on safety concerns of novel food products. Peptides similar to known IgE epitopes can be identified with the property distance tool and conformational epitopes by the Cross-React method. The updated database contains 1657 manually curated sequences including all allergens from the IUIS database, 334 experimentally determined X-ray or NMR structures, and 1565 3-D models. Each allergen/isoallergen is classified according to its protein family., Conclusions: SDAP provides access to the steadily increasing information on allergenic structures and epitopes with integrated bioinformatics tools to identify and analyze their similarities. In addition to serving the research and regulatory community, it provides clinicians with tools to identify potential coallergies in a sensitive patient and can help companies to design hypoallergenic foods and immunotherapies., (© 2023 The Author(s).)

Introduction: The emergence of the Omicron SARS-CoV-2 variant from various states of India in early 2022 has caused fear of its rapid spread. The lack of such reports from Chhattisgarh (CG), a central state in India, has prompted us to identify the Omicron circulating lineages and their mutational dynamics., Materials and Methods: Whole-genome sequencing (WGS) of SARS-CoV-2 was performed in 108 SARS-CoV-2 positive combined samples of nasopharyngeal and oropharyngeal swabs obtained from an equal number of patients., Results: All 108 SARS-CoV-2 sequences belonged to Omicron of clade 21L (84%), 22B (11%), and 22D (5%). BA.2 and its sub-lineages were predominantly found in 93.5% of patients, BA.5.2 and its sub-lineage BA.5.2.1 in 4.6% of patients, and B.1.1.529 in 2% of patients. Various BA.2 sub-lineages identified were BA.2 (38%), BA.2.38 (32%), BA.2.75 (9.25%), BA.2.56, BA.2.76, and BA.5.2.1 (5% each), BA.2.74 (4.6%), BA.5.2.1 (3.7%), BA.2.43 and B.1.1.529 (1.8% each), and BA.5.2 (0.9%). Maximum mutations were noticed in the spike (46), followed by the nucleocapsid (5), membrane (3), and envelope (2) genes. Mutations detected in the spike gene of different Omicron variants were BA.1.1.529 (32), BA.2 (44), BA.2.38 (37), BA.2.43 (38), BA.2.56 (30), BA.2.74 (31), BA.2.75 (37), BA.2.76 (32), BA.5.2, and BA.5.2.1 (38 similar mutations). The spike gene showed the signature mutations of T19I and V213G in the N-terminal domain (NTD), S373P, S375F, T376A, and D405N in receptor-binding domain (RBD), D614G, H655Y, N679K, and P681H at the furin cleavage site, N764K and D796K in fusion peptide, and Q954H and N969K in heptapeptide repeat sequence (HR)1. Notably, BA.2.43 exhibited a novel mutation of E1202Q in the C terminal. Other sites included ORF1a harboring 13 mutations followed by ORF1b (6), ORF3a (2), and ORF6 and ORF8 (1 mutation each)., Conclusion: BA.2 followed by BA.2.38 was the predominant Omicron lineage circulating in Chhattisgarh. BA.2.75 could supersede other Omicron due to its mutational consortium advantage. The periodical genomic monitoring of Omicron variants is thus required for real-time assessment of circulating strains and their mutational-induced severity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Singh, Sharma, Shaw, Bhargava and Negi.)

Human Coronaviruses (hCoVs) belongs to the enormous and dissimilar family of positive-sense, non-segmented, single-stranded RNA viruses. The RNA viruses are prone to high rates of mutational recombination resulting in emergence of evolutionary variant to alter various features including transmissibility and severity. The evolutionary changes affect the immune escape and reduce effectiveness of diagnostic and therapeutic measures by becoming undetectable by the currently available diagnostics and refractory to therapeutics and vaccines. Whole genome sequencing studies from various countries have adequately reported mosaic recombination between different lineage strain of SARS-CoV-2 whereby RNA dependent RNA polymerase (RdRp) gene reconnects with a homologous RNA strand at diverse position. This all lead to evolutionary emergence of new variant/ lineage as evident with the emergence of XBB in India at the time of writing this review. The continuous periodical genomic surveillance is utmost required for understanding the various lineages involved in recombination to emerge into hybrid variant. This may further help in assessing virus transmission dynamics, virulence and severity factor to help health authorities take appropriate timely action for prevention and control of any future COVID-19 outbreak., Competing Interests: Conflict of interestThe authors have no conflict of interest regarding the publication of this article., (© The Author(s), under exclusive licence to Association of Clinical Biochemists of India 2022, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Purpose: Scrub typhus, caused by Orientia tsutsugamushi (O. tsutsugamushi) present nonspecific clinical features during manifestation of acute undifferentiated febrile illness (AUFI) to render its early diagnosis difficult. Accordingly, this study was undertaken to assess an in-house groEL PCR versus IgM ELISA for the diagnosis of scrub typhus and to genotypically characterise the randomly selected scrub typhus positive cases., Methods: Blood samples, collected from two hundred twenty one (221) AUFI cases were subjected to groEL PCR and IgM ELISA for diagnosis of scrub typhus. Eleven randomly selected PCR positive cases were processed for DNA sequencing to determine the genetic diversity of O. tsutsugamushi in Chhattisgarh., Results: Scrub typhus prevalence of 35.2% were detected among AUFI cases using both in-house groEL PCR and IgM ELISA. PCR alone showed sensitivity, specificity, positive and negative predictive values of 66.6% (CI: 55.08-76.94), 100% (CI: 90 to 100),100% (CI: 93.15 to 100) and 57.37% (CI: 44.05 to 69.96) while for IgM ELISA, these parameters were 62.8% (CI: 51.13-73.50), 100% (CI: 90 to 100), 100% (CI: 92.75 to 100) and 54.68% (CI: 41.75 to 67.18) respectively. PCR and ELISA could detect scrub typhus in 37.2% and 33.3% cases, when tested alone. groEL PCR detected the O. tsutsugamushi throughout the course of infection. Phylogenetic analysis depicted 5 of 11 positive cases belonged to Kuroki, Japan strain of O. tsutsugamushi, followed by Gilliam and Karp strain in 4 and 2 cases respectively., Conclusion: Scrub typhus should be considered in differential diagnosis of AUFI. groEL PCR may aid on to IgM ELISA test for optimum laboratory diagnosis of scrub typhus by its implementation especially in seronegative cases. Predominance of Kuroki-like strain followed by Gillian and Karp strains of O. tsutsugamushi in Chhattisgarh confirm variable geographical distribution of O. tsutsugamushi and provide the baseline epidemiological data which will eventually be used to help the researchers for developing better diagnostic tests and vaccine covering the predominant genotypes., (Copyright © 2022 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Background: Omicron was detected in South Africa for the first time at the month of November 2021, from then it expanded swiftly over the world, outcompeting other SARS-CoV-2 variants such as Delta. The toxicity, resistance to antiviral medicines, transmissibility, and vaccine-induced immunity of newly developed SARS-CoV-2 variants are major worldwide health concerns., Aim of Study: This study investigates the comprehensive explanation of all mutations and their evolutionary linkages between the Omicron variant and recently discovered SARS-CoV-2 variants., Method: On Illumina MiniSeq Machine, 31 RNA isolates from clinical specimens were sequenced utilizing next-generation sequencing technique. Different bioinformatics tools have been used to analyze the mutations in omicron variant. A phylogenetic tree was constructed to determine Omicron's evolutionary relationships with other variants., Results: In our investigation, we discovered 79 distinct types of mutations in 31 fully vaccinated COVID-19 positive samples. Mostly mutations were found in non-spike region. According to the NJ approach of phylogenetic tree revels, the nearest variants were in the order listed, based on sequence identity: Omicron, Gamma, Alpha, Delta, Mu and Beta. On the other hand as per UPGMA approach, the Omicron variation creates a novel monophyletic clade that is distinct from previous SARS-CoV-2 variants., Conclusion: Despite the fact that some of the mutations are prevalent in Omicron and other VOCs, there are several unique mutations that have been connected to the virus's transmissibility and immune evasion, indicating a substantial shift in SARS-CoV-2 evolution., (Copyright © 2022 Instituto Mexicano del Seguro Social (IMSS). Published by Elsevier Inc. All rights reserved.)

Background There is a scarcity of reports of comparative analysis between the first and second waves of the pandemic from any part of India. This article aims to comprehensively investigate the epidemiology of coronavirus disease 2019 (COVID-19) during the course of the pandemic in the state of Chhattisgarh, central India. Methodology A comparative epidemiological analysis of the first and second waves of COVID-19 across Chhattisgarh was conducted on the vital parameters of total tests performed, cases diagnosed, age and gender distribution, case fatality ratio (CFR), and mitigation strategy reported by the state and central government health agencies using the data from Indian Council of Medical Research and National Informatics Centre portals. Results The second wave was shorter than the first wave but the absolute number of cases increased by 2.4 times and deaths by 2.7 times. There was a significant increase in cases per million, deaths per million, and test positivity rate. The hospitalization rate and test per case ratio dropped in the second wave from 33 to 20 and from 12.6 to 7.2, respectively. Both infection and deaths were higher among males in both the waves (p < 0.001). CFR increased from 1.2% in the first wave to 1.4% in the second wave (p < 0.001; odds ratio = 1.14 (1.1-1.19)). Increased mortality was seen in all ages except the young (≤20 years) and the old (>60 years). Conclusions The significantly high number of cases and deaths during the second wave provides evidence to undertake preparedness measures for mitigating any future waves. Regular surveillance, monitoring, and analysis of epidemiological data are pertinent for continued situational awareness., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2022, Agarwala et al.)

The introduction of plant extracts to mitigate the symptoms of "hay fever", about a century ago, led to discoveries beginning sixty years ago on determining the sequences and eventually structures of allergenic proteins. As more proteins were cloned, there was a need to rapidly identify and categorize those with significant similarity to known allergens. The Structural Database of Allergenic Proteins (SDAP) was created at the beginning of the 21st century as the first cross-referenced website to allow rapid overview of the structures and sequences of allergenic proteins. SDAP provides a way to identify sequence and functional similarities between these proteins, despite the complex nomenclature system based on the Latin names of their different sources. A rapid FASTA search simplifies grouping allergens from the same structural or functional family. SDAP also provides an overview of the rapidly expanding literature on the sequence, structure and epitopes of allergenic proteins and a way to estimate the potential allergenicity of novel proteins based on rules provided by the IUIS. Twenty years and a pandemic later, the list of allergenic proteins and their attributes continues to grow. SDAP is expanding and improving to allow rapid access to all this information., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Schein, Negi and Braun.)

COVID-19 pandemic 2nd wave catastrophic effect in the state of Chhattisgarh, India, from where no exclusive genomic data yet published, has prompted us to undertake this study to unearth the causative variant. Whole-genome sequencing of SARS-CoV-2 isolated from COVID-19 infected nine vaccinated healthcare workers (HCW), thirty mild/moderate, seventeen severe, and twenty-seven deceased patients, was performed. The significant predominance of the SARS-CoV-2 variant of concern (VOC), Delta (lineage B.1.617.2) identified in sixty-four (77.1%) cases in contrast to B.1 and its sublineage in eleven (13.2%), variant under monitoring (VUM), Kappa (lineage B.1.617.1) in five (6.0%) and another VOC Alpha (lineage B.1.1.7) in three (3.6%) cases respectively (p < 0.05, χ 2  = 162.49). 88.8% vaccine breakthrough, 60% mild/moderate, 94.4% severe and 81.5% dead patients were infected by Delta. Kappa presents exclusively in mild/moderate, Alpha in vaccine breakthrough, mild/moderate, and dead patient and B.1 and its sublineages in mild, severe, and dead patient categories. Delta variant spike mutation of T19R, G142D, E156G, L452R, and deletion (F157 and R158) helps in escaping antibody response, T478K and D614G enhance viral affinity with ACE2 receptor while P681R and D950N result in higher replication and transmissibility by cleaving S1/S2 at furin site. We conclude that Delta variant predominant role along with co-occurrence of Kappa, Alpha, and B.1 variant during COVID-19 2nd wave pandemic in Chhattisgarh may pose a potential threat of future outbreak through hybrid variant evolution. Thus, intensive genomic surveillance for monitoring variant evolution and a more efficacious vaccine against the Delta and Alpha variants are required., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

SARS-CoV-2 has steadily mutated during its spread to > 300 million people throughout the world. The WHO has designated strains with certain mutations, "variants of concern" (VOC), as they may have higher infectivity and/or resist neutralization by antibodies in sera of vaccinated individuals and convalescent patients. Methods to detect regionally emerging VOC are needed to guide treatment and vaccine design. Cluster and network analysis was applied to over 1.2 million sequences of the SARS-CoV-2 spike protein from 36 countries in the GISAID database. While some mutations rapidly spread throughout the world, regionally specific groups of variants were identified. Strains circulating in each country contained different sets of high frequency mutations, many of which were known VOCs. Mutations within clusters increased in frequency simultaneously. Low frequency, but highly correlated mutations detected by the method could signal emerging VOCs, especially if they occur at higher frequency in other regions. An automated version of our method to find high frequency mutations in a set of SARS-COV-2 spike sequences is available online at http://curie.utmb.edu/SAR.html ., (© 2022. The Author(s).)

Purpose: Since ancient era leprosy is existing across the world. India, Indonesia and Brazil still harbour major proportion of global cases. Child leprosy and Grade II disability indicate delayed diagnosis and persistence of transmission in community. So, this study was conducted with aim to evaluate the diagnostic efficacy of PCR in comparison to SSS (Slit Skin Smear) microscopy for detection of leprosy in early stages in both cases and carriers (contacts)., Methods: A cross sectional observational study was conducted on 100 subjects including 50 clinically diagnosed new cases of leprosy and their 50 contacts. Each group was subjected to SSS (Slit Skin Smear) microscopy and PCR using RLEP gene as target., Results: The overall male: female ratio was 2.44. The Slit Skin smear (SSS) microscopy positivity was 34% (n = 17/50) among cases while it was 0% (n = 0/50) among contacts. The overall positivity for PCR was 42% (n = 42/100) being 66% (n = 33/50) in cases and 18% (n = 9/50) in contacts. About 30% (n = 25/83) of all the microscopically negative subjects were found to be positive by PCR., Conclusions: PCR was found to be a better diagnostic tool both among cases and their contacts. It should be used for screening contacts for early diagnosis and treatment and thus preventing transmission in community., Key Message: To diagnose case and contacts of leprosy in early stages even in very low bacterial density using PCR., (Copyright © 2021 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

About half of the US population is sensitized to one or more allergens, as found by a National Health and Nutrition Examination Survey (NHANES). The most common treatment for seasonal allergic responses is the daily use of oral antihistamines, which can control some of the symptoms, but are not effective for nasal congestion, and can be debilitating in many patients. Peptide immunotherapy is a promising new approach to treat allergic airway diseases. The small size of the immunogens cannot lead to an unwanted allergic reaction in sensitized patients, and the production of peptides with sufficient amounts for immunotherapy is time- and cost-effective. However, it is not known what peptides are the most effective for an immunotherapy of allergens. We previously produced a unique monoclonal antibody (mAb) E58, which can inhibit the binding of multiple groups of mAbs and human IgEs from patients affected by the major group 1 allergens of ragweed (Amb a 1) and conifer pollens (Jun a 1, Cup s 1, and Cry j 1). Here, we demonstrated that a combined approach, starting from two linear E58 epitopes of the tree pollen allergen Jun a 1 and the ragweed pollen allergen Amb a 1, and residue modifications suggested by molecular docking calculations and peptide design could identify a large number of high affinity binding peptides. We propose that this combined experimental and computational approach by structural analysis of linear IgE epitopes and peptide design, can lead to potential new candidates for peptide immunotherapy., (Copyright © 2021 Elsevier Inc. All rights reserved.)

There is an urgent need for inexpensive, rapid and specific antigen-based assays to test for vaccine efficacy and detect infection with SARS-CoV-2 and its variants. We have identified a small, synthetic protein (JS7), representing a region of maximum variability within the receptor binding domain (RBD), which binds antibodies in sera from nine patients with PCR-verified COVID-19 of varying severity. Antibodies binding to either JS7 or the SARS-CoV-2 recombinant RBD, as well as those that disrupt binding between a fragment of the ACE2 receptor and the RBD, are proportional to disease severity and clinical outcome. Binding to JS7 was inhibited by linear peptides from the RBD interface with ACE2. Variants of JS7, such as E484K or N501Y, can be quickly synthesized in pure form in large quantities by automated methods. JS7 and related synthetic antigens can provide a basis for specific diagnostics for SARS-CoV-2 infections., (Copyright © 2021. Published by Elsevier Inc.)