Inferring B-cell derived T-cell receptor induced multi-epitope-based vaccine candidate against enterovirus 71: a reverse vaccinology approach.

Purpose: Enterovirus 71, a pathogen that causes hand-foot and mouth disease (HFMD) is currently regarded as an increasing neurotropic virus in Asia and can cause severe complications in pediatric patients with blister-like sores or rashes on the hand, feet, and mouth. Notwithstanding the significant burden of the disease, no authorized vaccine is available. Previously identified attenuated and inactivated vaccines are worthless over time owing to changes in the viral genome. Materials and Methods: A novel vaccine construct using B-cell derived T-cell epitopes from the virulent polyprotein found the induction of possible immune response. In order to boost the immune system, a beta-defensin 1 preproprotein adjuvant with EAAAK linker was added at the N-terminal end of the vaccine sequence. Results: The immunogenicity of the designed, refined, and verified prospective three-dimensional-structure of the multi-epitope vaccine was found to be quite high, exhibiting non-allergenic and antigenic properties. The vaccine candidates bound to toll-like receptor 3 in a molecular docking analysis, and the efficacy of the potential vaccine to generate a strong immune response was assessed through in silico immunological simulation. Conclusion: Computational analysis has shown that the proposed multi-epitope vaccine is possibly safe for use in humans and can elicit an immune response.

Insights into genome plasticity and gene regulation in Orientia tsutsugamushi through genome-wide mining of microsatellite markers.

Microsatellite markers are being used for molecular identification and characterization as well as estimation of evolution patterns due to their highly polymorphic nature. The repeats hold 40% of the entire genome of Orientia tsutsugamushi (OT), but not yet been characterized. Thus, we investigated the genome-wide presence of microsatellites within nine complete genomes of OT and analyzed their distribution pattern, composition, and complexity. The in-silico study revealed that the genome of OT enriched with microsatellites having a total of 126,187 SSRs and 10,374 cSSRs throughout the genome, of which 70% and 30% are represented within the coding and non-coding regions, respectively. The relative density (RD) and relative abundance (RA) of SSRs were 42-44.43/kb and 6.25-6.59/kb, while for cSSRs this value ranged from 7.06 to 8.1/kb and 0.50 to 0.55/kb, respectively. However, RA and RD were weakly correlated with genome size and incidence of microsatellites. The mononucleotide repeats (54.55%) were prevalent over di- (33.22%), tri- (11.88%), tetra- (0.27%), penta- (0.02%), hexanucleotide (0.04%) repeats, with poly (A/T) richness over poly (G/C). The motif composition of cSSRs revealed that maximum cSSRs were made up of two microsatellites having unique duplication patterns such as AT-x-AT and CG-x-CG. To our knowledge, this is the first study of microsatellites in the OT genome, where characterization of such variations in repeat sequences would be important in deciphering the origin, rate of mutation, and role of repeat sequences in the genome. More numbers of microsatellites represented within the coding region provide an insight into the genome plasticity that may interfere with gene regulation to mitigate host-pathogen interaction and evolution of the species.

Role of South Asian outflow on the oxidative potential of marine aerosols over the Indian Ocean.

Oxidative potential (OP) of fine marine aerosols (PM2.5) over the northern Indian Ocean (N_IO) and equatorial Indian Ocean (E_IO) were studied using shipborne measurements conducted as part of the Integrated Campaign for Aerosols, gases and Radiation Budget (ICARB-2018). During the study, an enhanced concentration of PM2.5 was found over N_IO (27.22 ± 14.29 µg.m-3) compared with E_IO (15.91 ± 2.58 µg.m-3), as N_IO experiences continental outflow from anthropogenically dominated South Asian region. However, E_IO received pristine air masses from the middle of the Arabian Sea, implying a reduced concentration. The OP of PM2.5 was evaluated using a dithiothreitol (DTT) assay. The mass (DTTm or intrinsic OP) and volume (DTTv or extrinsic OP) normalized DTT exhibited a significant spatial variation over the Indian Ocean (IO). Intrinsic OP showed ∼2 times higher values over N_IO than E_IO, indicating aging of aerosols during long-range transport impacts OP of marine aerosol. Similarly, increased concentrations of anthropogenic species such as non-sea sulfate (nssSO42-), nitrate (NO3-), ammonium (NH4+), non-sea potassium ion (nssK+), water-soluble transition metals (Fe, Ti, Zn, Cu, Mn, Cr), elemental carbon (EC), organic carbon (OC), water-soluble organic carbon (WSOC), were also observed over N_IO compared with E_IO. Pearson correlation and multiple linear regression (MLR) analysis revealed that combustion sources, chemical processing and co-transportation of anthropogenic species during long-range transport are the main drivers of intrinsic OP in the outflow region.

Activation of Host Cellular Signaling and Mechanism of Enterovirus 71 Viral Proteins Associated with Hand, Foot and Mouth Disease.

Enteroviruses are members of the Picornaviridae family consisting of human enterovirus groups A, B, C, and D as well as nonhuman enteroviruses. Human enterovirus type 71 (EV71) has emerged as a major cause of viral encephalitis, known as hand, foot, and mouth disease (HFMD), in children worldwide, especially in the Asia-Pacific region. EV71 and coxsackievirus A16 are the two viruses responsible for HFMD which are members of group A enteroviruses. The identified EV71 receptors provide useful information for understanding viral replication and tissue tropism. Host factors interact with the internal ribosome entry site (IRES) of EV71 to regulate viral translation. However, the specific molecular features of the respective viral genome that determine virulence remain unclear. Although a vaccine is currently approved, there is no effective therapy for treating EV71-infected patients. Therefore, understanding the host-pathogen interaction could provide knowledge in viral pathogenesis and further benefits to anti-viral therapy development. The aim of this study was to investigate the latest findings about the interaction of viral ligands with the host receptors as well as the activation of immunerelated signaling pathways for innate immunity and the involvement of different cytokines and chemokines during host-pathogen interaction. The study also examined the roles of viral proteins, mainly 2A and 3C protease, interferons production and their inhibitory effects.

Gene expression and involvement of signaling pathways during host-pathogen interplay in Orientia tsutsugamushi infection.

Scrub typhus is a neglected tropical disease that affects one-third of the world's population. The disease is caused by Orientia tsutsugamushi (OT), an obligate intracellular Gram-negative bacterium. OT efficiently escapes from the endosomal pathway after entering the host cell and replicates inside cytosol. OT infection promotes cellular autophagy, the autonomous defense mechanism unlike other bacteria. This study has discussed the bacterial invasion process through the extracellular matrix and the immune response activated by the bacterium within the hosts. Furthermore, we have emphasized the importance of extracellular matrix and their cross-talk with the immune cells, such as, macrophages, neutrophils, and dendritic cells followed by their inflammatory response. We have also put an insight into the host factors associated with signaling pathways during scrub typhus disease with a special focus on the OT-induced stress response, autophagy, apoptosis, and innate immunity. Multiple cytokines and chemokines play a significant role in activating different immune-related signaling pathways. Due to the presence of high antigenic diversity among strains, the signaling pathways during the host-pathogen interplay of OT with its host is very complicated. Thus, it hinders to mitigate the severity of the pandemic occurred by the respective pathogen. Our investigation will provide a useful guide to better understand the virulence and physiology of this intracellular pathogen which will lead towards a better therapeutic diagnosis and vaccine development.

Molecular characterization and evolutionary analysis of Orientia tsutsugamushi in eastern Indian population.

Scrub typhus is a bacterial zoonotic acute febrile illness (AFI) caused by the obligate intracellular bacterium Orientia tsutsugamushi, which is an antigenically diverse strain frequently observed in the tropical region of Southeast Asian countries. The recent investigation was conducted to delineate the genotype identification of Orientia tsutsugamushi predominating in the eastern zone of India such as Odisha to decipher its strain type, and evaluate its diversity as well as evolutionary pattern based on the nucleotide analysis of the immune dominant 56 KDa gene. During this study, we have investigated 100 clinical samples (2014-2018), out of which 28 were positive for scrub typhus followed by its molecular characterization and phylogenetic analysis utilizing 56 KDa partial genes. Population genetic parameters showed the presence of 287 polymorphic sites within the analyzed 56 KDa gene. The gene diversity (Hd) and sequence diversity (π) was estimated 0.638 and 0.280, respectively. Selection pressure analysis (θ = dN/dS) having the value 0.222 suggests that the gene lied under purifying selection. The present study suggested a high rate of genetic diversity within the isolates. This research study sheds light on the hereditary and evolutionary relationships of Orientia strains found in the eastern Indian population. Understanding regional genetic variation is critical for vaccine development and sero-diagnostics methods. A significant level of genetic variability was observed during this study. This information has a way to understand more about antigen diversity that leads to develop an effective vaccine candidate for this pathogen.

Evaluating the filtration efficiency of commercial facemasks' materials against respiratory aerosol droplets.

Respiratory droplets serve as a viable transmission mechanism for many viruses and other pathogens. Facemasks are commonly used to minimize the risk of this transmission. However, information on the size-resolved filtration efficiency of commonly available commercial facemasks is not readily available in the literature. To fill this gap, the current study performs aerosolized chamber experiments to evaluate the filtration efficiencies of commonly available commercial facemasks' materials in a size range of 0.3-10 µm. Results rank the performance of filtration through commercial facemasks' materials as follows (values in brackets indicate the average filtration efficiencies across 0.3-10 µm): 6-Layer N95 mask (0.918) > N95 mask - without valve (0.88) > KN95 mask (0.84) > N95 mask -with valve (0.834) > Heavy knitted cotton mask (0.808) > Surgical mask (0.778) > Cotton mask-2 layers (0.744) > Nylon fabric mask-2 layers (0.740) > T-shirt fabric mask-2 layers (0.708) > T-shirt fabric mask-1 layer (0.648). The size-resolved filtration efficiencies through the material across the evaluated commercial facemasks ranged from 38-83% in the size range of 0.3-0.5 µm, 55-88% in the size range of 0.5-1 µm, 69-93% in the size range of 1-2.5 µm, 76-96% in the size range of 2.5-5 µm, and 86-99% in the size range of 5-10 µm. Subsequently, the filtration efficiencies of materials post washing (with detergent in warm water and allowing to dry completely) were also evaluated. The average reduction in filtration efficiencies post washing are as follows: 6-Layer N95 mask: 3%, N95 mask - without valve: 2%, KN95 mask: 4%, N95 mask -with valve: 3%, Heavy knitted cotton mask: 4%, Surgical mask: 18%, Cotton mask-2 layers: 11%, Nylon fabric mask-2 layers: 6%, T-shirt fabric mask-2 layers: 6%, T-shirt fabric mask-1 layer: 8%. This decrease in the filtration efficiency was more pronounced for the sub-micron particles than the super-micron ones.Implications: Facemasks are commonly used to minimize the risk of pathogens through ambient air transmission. However, information on the size-resolved filtration efficiency of commonly available commercial facemasks materials is not readily available in the literature. To fill this gap, the current study performs aerosolized chamber experiments to evaluate the filtration efficiencies of commonly available commercial facemasks materials in a size range of 0.3-10 µm. The performance of the commercial facemasks materials as follows in the order of (values in brackets indicate the average filtration efficiencies across 0.3-10 µm): 6-Layer N95 mask (0.918) > N95 mask - without valve (0.88) > KN95 mask (0.84) > N95 mask -with valve (0.834) > Heavy knitted cotton mask (0.808) > Surgical mask (0.778) > Cotton mask-2 layers (0.744) > Nylon fabric mask-2 layers (0.740) > T-shirt fabric mask-2 layers (0.708) > T-shirt fabric mask-1 layer (0.648). The choice of facemask is greatly driven by the size of viable respiratory droplets that need to be eliminated. If droplets with particle size less than 0.5 µm are required to be filtered, N95 masks without the valve or more layers are preferred. If the primary objective is to filter particles between 0.5-1 µm, then N95 (both with or without valves) or KN95 masks are recommended. Surgical masks and heavy knitted cotton masks may also be used for this purpose, but with caution.

A study on variation of atmospheric pollutants over Bhubaneswar during imposition of nationwide lockdown in India for the COVID-19 pandemic.

The nationwide lockdown in India to flatten the pandemic COVID-19 curve has resulted in the reduction of anthropogenic emission sources to a great extent. This study reports change in air quality and its impact on the environment during the unique lockdown scenario at Bhubaneswar, a coastal smart city in east India. The urban air shows a remarkable reduction in the mean pollutant levels influenced by traffic emission viz. NOx (~ 67 %) and BC (~ 47 %) during lockdown over the pre-lockdown. Comparatively, a lower reduction of CO (~ 14 %) is attributed to the dominance of natural atmospheric chemical regulation and biogenic sources in addition to anthropogenic contributions. In addition to the lockdown, frequent rain events due to depression in the Bay of Bengal (BoB) also had a significant role in the reduction of the primary pollutants over the study site. An enhancement of secondary pollutant viz. O3 (~ 3%) with a distinct diurnal pattern was observed during the first phase of lockdown over the pre-lockdown period. An anti-correlation between O3 and NOx during pre-lockdown points to a higher O3 production potential with decreasing NOx. While a reduction in the titration of O3 due to suppression of fresh NO emissions led to accumulation of O3 in the first phase of lockdown, inhibited photochemistry due to cloudy skies as well as reduction in precursors led to lower O3 values during the later phases of lockdown.