Genomic characterization of Influenza A (H1N1)pdm09 and SARS-CoV-2 from Influenza Like Illness (ILI) and Severe Acute Respiratory Illness (SARI) cases reported between July-December, 2022.

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.

An Overview of SARS-CoV-2 Potential Targets, Inhibitors, and Computational Insights to Enrich the Promising Treatment Strategies.

The rapid spread of the SARS-CoV-2 virus has emphasized the urgent need for effective therapies to combat COVID-19. Investigating the potential targets, inhibitors, and in silico approaches pertinent to COVID-19 are of utmost need to develop novel therapeutic agents and reprofiling of existing FDA-approved drugs. This article reviews the viral enzymes and their counter receptors involved in the entry of SARS-CoV-2 into host cells, replication of genomic RNA, and controlling the host cell physiology. In addition, the study provides an overview of the computational techniques such as docking simulations, molecular dynamics, QSAR modeling, and homology modeling that have been used to find the FDA-approved drugs and other inhibitors against SARS-CoV-2. Furthermore, a comprehensive overview of virus-based and host-based druggable targets from a structural point of view, together with the reported therapeutic compounds against SARS-CoV-2 have also been presented. The current study offers future perspectives for research in the field of network pharmacology investigating the large unexplored molecular libraries. Overall, the present in-depth review aims to expedite the process of identifying and repurposing drugs for researchers involved in the field of COVID-19 drug discovery.

Polyethylene terephthalate waste derived nanomaterials (WDNMs) and its utilization in electrochemical devices.

Plastics are a vital component of our daily lives in the contemporary globalization period; they are present in all facets of modern life. Because the bulk of synthetic plastics utilized in the market are non-biodegradable by nature, the issues associated with their contamination are unavoidable in an era dominated by polymers. Polyethylene terephthalate (PET), which is extensively used in industries such as automotive, packaging, textile, food, and beverages production represents a major share of these non-biodegradable polymer productions. Given its extensive application across various sectors, PET usage results in a considerable amount of post-consumer waste, majority of which require disposal after a certain period. However, the recycling of polymeric waste materials has emerged as a prominent topic in research, driven by growing environmental consciousness. Numerous studies indicate that products derived from polymeric waste can be converted into a new polymeric resource in diverse sectors, including organic coatings and regenerative medicine. This review aims to consolidate significant scientific literatures on the recycling PET waste for electrochemical device applications. It also highlights the current challenges in scaling up these processes for industrial application.

A comprehensive profile of SARS-CoV-2 variants spreading during the COVID-19 pandemic: a genomic characterization study from Chhattisgarh State, India.

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.

Time-dependent plastic behavior of bacteria leading to rupture.

A study of the mechanical response of bacteria is essential in designing an antibacterial surface for implants and food packaging applications. This research evaluated the mechanical response of Escherichia coli under different loading conditions. Indentation and prolonged creep tests were performed to understand their viscoelastic-plastic response. The results indicate that varying loading rates from 1 µm/s to 5 µm/s show an increase in modulus of 182% and 90%, calculated in the loading and unloading cycles, respectively, and a decrease in adhesion force by 42%. However, on varying loads from 5 nN to 25 nN, nominal change is observed in both modulus and adhesion force. The rupture curve at 100 nN load shows elastic and a small plastic deformation accompanied by a sharp peak indicating the cell wall rupture. The rupture force at the peak was found to be 34.38 ± 5.15 nN, irrespective of the loading rate, making it a failure criterion for bacteria rupture. The creep response of bacteria increases (for 6 s) and then remains constant (for 15 s) with time, indicating that a standard linear solid (SLS) model applies to this behavior. This work attempts to evaluate the mechanical properties of E. coli bacteria focusing on its rupture by contact killing mechanism.

Amelioration of the physio-biochemical responses to salinity stress and computing the primary germination index components in cauliflower on seed priming.

The significant horticultural crop, cauliflower (Brassica oleracea L. var. botrytis) is vulnerable to the excessive salt concentration in the soil, which contributes to its scaled-down growth and productivity, among other indices. The current study examines the efficacy of hydropriming, halopriming, and osmopriming on the physio-biochemical attributes and tolerance to salinity (100 mM NaCl) in cauliflower under controlled conditions. The results showed that the salinity (100 mM NaCl) has significant deleterious impacts on cauliflower seed germination, seedling growth, and photosynthetic attributes, and provoked the production of reactive oxygen species. In contrast, different priming approaches proved beneficial in mitigating the negative effects of salinity and boosted the germination, vigor indices, seedling growth, and physio-biochemical attributes like photosynthetic pigments, protein, and proline content while suppressing oxidative damage and MDA content in cauliflower seedlings in treatment- and dose-dependent manner. PCA revealed 61% (PC1) and 15% (PC2) of the total variance with substantial positive relationships and high loading conditions on all germination attributes on PC1 with greater PC1 scores for PEG treatments showing the increased germination indices in PEG-treated seeds among all the priming treatments tested. All 13 distinct priming treatments tried clustered into three groups as per Ward's approach of systematic categorization, clustering the third group showing relatively poor germination performances. Most germination traits exhibited statistically significant associations at the p < 0.01 level. Overall, the results established the usefulness of the different priming approaches facilitating better germination, survival, and resistance against salinity in the cauliflower to be used further before sowing in the salt-affected agro-ecosystems.

An innate pathogen sensing strategy involving ubiquitination of bacterial surface proteins.

Sensing of pathogens by ubiquitination is a critical arm of cellular immunity. However, universal ubiquitination targets on microbes remain unidentified. Here, using in vitro, ex vivo, and in vivo studies, we identify the first protein-based ubiquitination substrates on phylogenetically diverse bacteria by unveiling a strategy that uses recognition of degron-like motifs. Such motifs form a new class of intra-cytosolic pathogen-associated molecular patterns (PAMPs). Their incorporation enabled recognition of nonubiquitin targets by host ubiquitin ligases. We find that SCFFBW7 E3 ligase, supported by the regulatory kinase, glycogen synthase kinase 3ß, is crucial for effective pathogen detection and clearance. This provides a mechanistic explanation for enhanced risk of infections in patients with chronic lymphocytic leukemia bearing mutations in F-box and WD repeat domain containing 7 protein. We conclude that exploitation of this generic pathogen sensing strategy allows conservation of host resources and boosts antimicrobial immunity.

Identification of a promising inhibitor from Illicium verum (star anise) against the main protease of SARS-CoV-2: insights from the computational study.

SARS-CoV-2, the causing agent of coronavirus disease (COVID-19), first broke out in Wuhan and rapidly spread worldwide, resulting in a global health emergency. The lack of specific drugs against the coronavirus has made its spread challenging to control. The main protease (Mpro) is a key enzyme of SARS-CoV-2 used as a key target in drug discovery against the coronavirus. Medicines derived from plant phytoconstituents have been widely exploited to treat various diseases. The present study has evaluated the potential of Illicium verum (star anise) phytoconstituents against Mpro by implementing a computational approach. We performed molecular docking and molecular dynamics simulation study with a set of 60 compounds to identify their potential to inhibit the main protease (Mpro) of SARS-CoV-2. DFT study and post dynamics free energy calculations were also performed to strengthen the findings. The identified four compounds by docking study exhibited the highest potential compared to other selected phytoconstituents. Further, density functional theory (DFT) calculation, molecular dynamics simulation and post dynamics MM-GBSA energy calculation predicted Verimol-G as a potential compound, which formed stable interactions through the catalytic dyad residues. The HOMO orbital energy (-0.250038) from DFT and the post dynamics binding free energy calculation (-73.33 Kcal/mol) correlate, suggesting Verimol-G is the best inhibitor compared to the other phytoconstituents. This compound also complies with the ADME properties of drug likeliness. Thus, based on a computational study, we suggest that Verimol G may be developed as a potential inhibitor against the main protease to combat COVID-19.Communicated by Ramaswamy H. Sarma.

Mosaic Recombination Inflicted Various SARS-CoV-2 Lineages to Emerge into Novel Virus Variants: a Review Update.

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.

Evaluation of an in-house PCR for diagnosing scrub typhus along with a preliminary study of genotypic characterization of Orientia tsutshugamushi circulating in Chhattisgarh: A prospective clinico-microbiological study.

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.

Comparison of Antero-Posterior Lip Position in Most Favored Facial Profile of Jaipur Population.

Background The enhancement of facial esthetics is one of the essential goals of orthodontic treatment. The concept of an excellent facial profile can differ between two individuals of the same population. Esthetics is a very vital component in Orthodontic diagnosis and treatment planning. Orthodontic treatment aims to achieve facial harmony by stabilizing the occlusion and pleasing facial and dental esthetics. Therefore, the characteristics of a pleasing, well-balanced face and a functioning occlusion should be evaluated. Aim This study aimed to determine preferable Antero-posterior lip positions in the Jaipur population and determine the range of anteroposterior lip positions as evaluated by orthodontists, patients, and professionals from a series of different lip positions in facial silhouettes, and compare their assessments. Materials and Methods The sample comprised 50 subjects (25 males & 25 females) from Jaipur. All angular and linear measurements were recorded for both males and females separately. The mean value of those readings was placed in NEMOTECH cephalometric software, and an average profile construction was done. This average profile will determine the lip fullness/ facial profile of males and females of the Jaipur (Rajasthan) population. A series of 7 profile silhouettes for males and seven profile silhouettes for females was developed by altering the lip positions (protrusion & retrusion in 2mm increments till 6 mm from the average profile) parallel to Frankfort horizontal plane (F-H) plane. Constructed facial silhouettes (seven male and female) were evaluated by (50) Orthodontists, (50) oral surgeons, general dentists (50), and non-specialists population (100). Evaluators were asked for the best profile in each gender from 1 to 7 in order of their preference. Result On calculating the standard deviation values, the profile selected as most favored for females is 2.33 by orthodontists, on the contrary, the standard deviation for Oral Surgeons, General Dentists & Non-specialists is 2.04, 2.14, and 2.12 respectively. It was found that profile retruded -2mm for males was the most favored, and profile retruded -4mm for males was second most favored. Average Profile /the profile without retrusion or protrusion was selected by orthodontists as the most favored profile. Profile retruded -2mm was the most favored profile for males clinically significant. It was found that profile retruded -2mm for females was the most favored, and profile retruded -4mm for females was second most favored. Profile retruded -2mm was the most favored profile for females by Orthodontists, General Dentists & non-specialists. Profile retruded -4mm was the most favored for females by Oral Surgeons. overall made insignificant. Conclusion The most favored facial profile is -2mm (profile 1) retruded lip posture in both males and females. According to Orthodontists most favored facial profile is 0mm (profile 6) average profile in males and -2mm (profile 1) retruded lip position in females. According to non-specialists most favored facial profile is -2mm (profile 1) retruded lip position in both males and females.

Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives.

Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N2 ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N2 ) accessible and bioavailable in the form of ammonium (NH4 + ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.

Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India.

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, χ2 = 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.

Mutational characterization of Omicron SARS-CoV-2 lineages circulating in Chhattisgarh, a central state of India.

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.

Genetic analysis of human papilloma virus 16 E6/E7 variants obtained from cervical cancer cases in Chhattisgarh, a central state of India.

Human papilloma virus genotype 16 (HPV-16), a predominant etiological cause of cervical cancer (CC) vary in inflicting oncogenicity according to their geographical distribution and mutational changes. With no published data from central India, the present study aimed to genetically analyze HPV-16 E6/E7 variant obtained from CC women of Chhattisgarh. In twenty one CC patients, PCR amplified E6/E7 genes were decoded by DNA sequencing to study phylogenetic relatedness, mutational changes and their in-silico effect on protein structure. E6 analysis revealed nineteen sequences exhibited intratypic variation. L83V mutation was observed in 76.2% sequences followed by S71C seen in 28.6% sequences. Mutations of E41G, A46G, F47V, R77S, L99V and Q107K were observed in three sequences each. C140 Stop codon mutation has caused early truncation of E6 in three sequences to produce the conformational structural change. In contrast, E7 was relatively more conserved showing D4E (4.7%), G88R (23.8%), I93T (9.5%) and C94S (9.5%) mutations. Other than L83V and S71C, E6 and E7 mutations were reported for the first time from India. E6/E7 nonsynonmous mutations have a spectrum of biological effect in progression of CC. Phylogenetic analysis revealed ten sequence belonged to Asian while eleven to European sublineage to show CC cases in Chhattisgarh are a mix of Asian and European lineage. Asian sequences showing higher frequency of L83V mutations and exclusive presence of S71C and C140 Stop codon mutations may be linked with higher oncogenicity. Various E6/E7 mutational data may prove useful for development of better diagnostic and vaccine for the region of Chhattisgarh.

Correction: Comparative analysis of various clinical specimens in detection of SARS-CoV-2 using rRT-PCR in new and follow up cases of COVID-19 infection: Quest for the best choice.

[This corrects the article DOI: 10.1371/journal.pone.0249408.].

Comparative analysis of various clinical specimens in detection of SARS-CoV-2 using rRT-PCR in new and follow up cases of COVID-19 infection: Quest for the best choice.

BACKGROUND: An appropriate specimen is of paramount importance in Real Time reverse transcription-polymerase chain reaction (rRT-PCR) based diagnosis of novel coronavirus (nCoV) disease (COVID-19). Thus, it's pertinent to evaluate various diversified clinical specimens' diagnostic utility in both diagnosis and follow-up of COVID-19. METHODS: A total of 924 initial specimens from 130 COVID-19 symptomatic cases before initiation of treatment and 665 follow up specimens from 15 randomly selected cases comprising of equal number of nasopharyngeal swab (NPS), oropharyngeal swab (OPS), combined NPS and OPS (Combined swab), sputum, plasma, serum and urine were evaluated by rRT-PCR. RESULTS: Demographic analysis showed males (86) twice more affected by COVID-19 than females (44) (p = 0.00001). Combined swabs showed a positivity rate of 100% followed by NPS (91.5%), OPS (72.3%), sputum (63%), while nCoV was found undetected in urine, plasma and serum specimens. The lowest cycle threshold (Ct) values of targeted genes E, ORF1b and RdRP are 10.56, 10.14 and 12.26 respectively and their lowest average Ct values were found in combined swab which indicates high viral load in combined swab among all other specimen types. Analysis of 665 follow-up multi-varied specimens also showed combined swab as the last specimen among all specimen types to become negative, after an average 6.6 (range 4-10) days post-treatment, having lowest (15.48) and average (29.96) Ct values of ORF1b respectively indicating posterior nasopharyngeal tract as primary nCoV afflicted site with high viral load. CONCLUSION: The combined swab may be recommended as a more appropriate specimen for both diagnosis and monitoring of COVID-19 treatment by rRT-PCR for assessing virus clearance to help physicians in taking evidence-based decision before discharging patients. Implementing combined swabs globally will definitely help in management and control of the pandemic, as it is the need of the hour.

A highly efficient bilayer graphene/ZnO/silicon nanowire based heterojunction photodetector with broadband spectral response.

This paper presents three self-powered photodetectors namely, p+-bilayer graphene (BLG)/n+-ZnO nanowires (NWs), p+-BLG/n+-Si NWs/p--Si and p+-BLG/n+-ZnO NWs/p--Si. The Silvaco Atlas TCAD software is utilized to characterize the optoelectronic properties of all the devices and is validated by analytical modeling. The proposed dual-junction photodetectors cover broadband spectral response varying from ultraviolet to near-infrared wavelengths. The dual-heterojunction broadband photodetector exhibits photocurrent switching with the rise and fall time of 1.48 and 1.27 ns, respectively. At -0.5 V bias, the highest external quantum efficiency, photocurrent responsivity, specific detectivity, and the lowest noise equivalent power of 71%, 0.28 A W-1, 4.2 × 1012 cmHz1/2 W-1, and 2.59 × 10-17 W, respectively, are found for the dual-heterojunction device with a wavelength of 480 nm at 300 K. The proposed nanowires based photodetectors offer great potential to be utilized as next-generation optoelectronic devices.

Molecular Dynamics Simulation of Amorphous SiO2, B2O3, Na2O-SiO2, Na2O-B2O3, and Na2O-B2O3-SiO2 Glasses with Variable Compositions and with Cs2O and SrO Dopants.

Selection of suitable glass composition for vitrification of high-level radioactive wastes (HLWs) is one of the major challenges in nuclear waste reprocessing. Atomic and molecular level understanding of various structural, thermodynamical, and dynamical properties of a glass matrix can help in preliminary screening and thus reduce the dependency to some extent on tedious experimental procedures. In that context, extensive molecular dynamics (MD) simulations have been performed to calculate various microscopic properties of the glass matrix. The present article demonstrates that the "Buckingham potential-included long-ranged Coulomb interaction" can be utilized to simulate the glasses of varied compositions. The proposed simulation model has been validated for a wide range of glass compositions: pure glass matrix-SiO2 and B2O3; binary glass mixtures-SiO2-B2O3, Na2O-SiO2, and Na2O-B2O3; ternary glass-Na2O-SiO2-B2O3; and also the Cs2O- and SrO-doped matrix of sodium borosilicate. Most importantly, the MD results have been validated with those of in-house synthesized glasses. The effect of alkali addition on the density and network connectivity of the glass matrix has been explored. The results capture well the boron anomalies for varied concentrations of network formers and network modifiers. The intermediate structural ordering in glasses has been explored by calculating the partial and total structure factors. Further, the characteristic vibration density of states of constituent atoms in the glass matrix is determined. In addition, the glass structures with the addition of dopant oxides Cs2O and SrO have been examined as they are known to be prime heat-generating agents in HLWs. The results establish the structure and dynamics of the doped glass matrix to be a complex nature of the dopant's mass, concentration, charge, and ionic radius. The present MD results might be of great academic and technological significance for further studies in the field of vitrification and prediction of effects associated with the dopant's nature and concentration.

Bilayer graphene/HgCdTe based very long infrared photodetector with superior external quantum efficiency, responsivity, and detectivity.

We present a high-performance bilayer graphene (BLG) and mercury cadmium telluride (Hg1-x Cd x=0.1867Te) heterojunction based very long wavelength infrared (VLWIR) conductive photodetector. The unique absorption properties of graphene enable a long carrier lifetime of charge carriers contributing to the carrier-multiplication due to impact ionization and, hence, large photocurrent and high quantum efficiency. The proposed p+-BLG/n-Hg0.8133Cd0.1867Te photodetector is characterized and analyzed in terms of different electrical and optical characteristic parameters using computer simulations. The obtained results are further validated by developing an analytical model based on drift-diffusion, tunneling and Chu's methods. The photodetector has demonstrated a superior performance including improved dark current density (∼1.75 × 10-14 µA cm-2), photocurrent density (∼8.33 µA cm-2), internal quantum efficiency (QEint ∼ 99.49%), external quantum efficiency (QEext ∼ 89%), internal photocurrent responsivity (∼13.26 A W-1), external photocurrent responsivity (∼9.1 A W-1), noise equivalent power (∼8.3 × 10-18 W), total noise current (∼1.06 fA), signal to noise ratio (∼156.18 dB), 3 dB cut-off frequency (∼36.16 GHz), and response time of 9.4 ps at 77 K. Furthermore, the effects of different external biasing, light power intensity, and temperature are evaluated, suggesting a high QEext of 3337.70% with a bias of -0.5 V near room temperature.