Cross-reactivity of SARS-CoV-2 with other pathogens, especially dengue virus: A historical perspective.

Dengue is a vector-borne viral disease caused by a Flavivirus whereas the COVID-19 pandemic was caused by a highly contagious virus, SARS-CoV-2 belonging to the family Coronaviridae. However, COVID-19 severity was observably less in dengue-endemic countries and vice versa especially during the active years of the pandemic (2019-2021). We observed that dengue virus (DENV) antibodies (Abs) could cross-react with SARS-CoV-2 spike antigen. This resulted in SARS-CoV-2 false positivity by rapid Ab test kits. DENV Abs binding to SARS-CoV-2 receptor-binding domain (and the reverse scenario), as revealed by docking studies further validated DENV and SARS-CoV-2 cross-reactivity. Finally, SARS-CoV-2 Abs were found to cross-neutralize DENV1 and DENV2 in virus neutralization test (VNT). Abs to other pathogens like Plasmodium were also cross-reactive but non-neutralizing for SARS-CoV-2. Here, we analyze the existing data on SARS-CoV-2 cross-reactivity with other pathogens, especially dengue to assess its impact on health (cross-protection?) and differential sero-diagnosis/surveillance.

Erratum: Author affiliation addition: "Hepatitis B virus detected in paper currencies in a densely populated city of India: A plausible source of horizontal transmission?"

[This corrects the article on p. 775 in vol. 12, PMID: 33200016.].

Detection of Leptomonas seymouri narna-like virus in serum samples of visceral leishmaniasis patients and its possible role in disease pathogenesis.

Kala-azar/Visceral Leishmaniasis (VL) caused by Leishmania donovani (LD) is often associated with Leptomonas seymouri (LS) co-infection in India. Leptomonas seymouri narna-like virus 1 (Lepsey NLV1) has been reported in multi-passaged laboratory isolates of VL samples which showed LD-LS co-infection. A pertinent question was whether this virus of LS is detectable in direct clinical samples. DNA from the serum of twenty-eight LD diagnosed patients was subjected to LD-specific and LS-specific PCR to reconfirm the presence of LD parasites and to detect LD-LS co-infections. RNA extracted from same samples was subjected to RT-PCR, qRT-PCR and sequencing using virus-specific primers to detect/identify and quantify the virus. The presence of the virus was confirmed in thirteen of eighteen (72%) recently collected VL and PKDL samples. Cytokine profiling showed significantly elevated IL-18 in only LD infected patients compared to the virus-positive LD and control samples. IL-18 is crucial for Th1 and macrophage activation which eventually clears the parasite. The Lepsey NLV1 interaction with the immune system results in reduced IL-18 which favors LD survival and increased parasitic burden. The study emphasizes the need to revisit LD pathogenesis in the light of the association and persistence of a protozoan virus in kala-azar and PKDL patients.

COVID-19 serum can be cross-reactive and neutralizing against the dengue virus, as observed by the dengue virus neutralization test.

OBJECTIVES: Observing the serological cross-reactivity between SARS-CoV-2 and dengue virus (DV), we aimed to elucidate its effect on dengue serodiagnosis and infectivity in a highly dengue-endemic city in India. METHODS: A total of 52 COVID-19 (reverse transcription-polymerase chain reaction [RT-PCR] positive) serum samples were tested in rapid lateral flow immunoassays and DV immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) to detect DV or SARS-CoV-2 IgG/immunoglobulin M. The COVID-19 antibody (Ab) positive samples were subjected to a virus neutralization test (Huh7 cells) using DV type 1 (DV1) clinical isolate. RESULTS: Most (93%) of the SARS-CoV-2 Ab-positive serum samples cross-reacted with DV in rapid or ELISA tests. All were DV RNA and nonstructural protein 1 (NS1) antigen-negative. COVID-19 serum samples that were DV cross-reactive neutralized DV1. Of these, 57% had no evidence of DV pre-exposure (DV NS1 Ab-negative). The computational study also supported potential interactions between SARS-CoV-2 Ab and DV1. CONCLUSION: DV serodiagnosis will be inconclusive in areas co-endemic for both viruses. The COVID-19 pandemic appears to impart a protective response against DV in DV-endemic populations.

Lattice dynamics of Ge1-xSnx alloy nanowires.

Alloying group IV semiconductors offers an effective way to engineer their electronic properties and lattice dynamics. The incorporation of Sn in Ge permits a transition from an indirect to a direct bandgap semiconductor. Here, by combining polarization, laser power-dependent and temperature-dependent micro-Raman spectroscopy we explore the full lattice dynamics of Ge1-xSnx (x = 0.01, 0.06 and 0.08) alloy nanowires. In the high Sn content samples (x ≥ 0.06), a low-frequency tail and a high-frequency shoulder are observed which are associated with the F2g optical phonon mode of Ge (Ge-Ge mode). The new modes are assigned to the stretching of Ge-Ge bonds due to Sn-induced lattice relaxation and compression, respectively. The symmetry of the observed Raman modes has been studied by polarization-dependent Raman scattering. Nonlinear fitting of the laser power-dependent intensity of the high-frequency Ge-Ge mode in the Ge1-xSnx alloy nanowires with x = 0.06 and 0.08 suggests the activation of a third-order stimulated Raman scattering process, due to the high intensity localized electric field surrounding the Sn clusters. Finally, from the temperature-dependent Raman study, we have estimated the isobaric Grüneisen parameters for all the observed modes.

Non-structural protein 1 (NS1) variants from dengue virus clinical samples revealed mutations that influence NS1 production and secretion.

Dengue diagnosis primarily relies on NS1 ELISA and serological (IgG/IgM) tests. There are reports of low and variable sensitivity of the widely used NS1 ELISA tests. Poor sensitivity has been attributed to patient's infection status, prevalent serotypes, and the geographical origin of the samples. We investigated whether NS1 mutations directly have any impact on NS1 ELISA-based dengue virus (DENV) detection in clinical samples. Fifty-eight serum samples were collected from dengue-endemic area during 2015-2017 and tested with three commonly used NS1 ELISA kits. The samples were subjected to diagnostic RT-PCR and sequencing of structural gene(s). Sequencing of NS1 gene revealed amino acid changes which were transferred to respective wild type NS1 backbone to determine their effects on NS1 production and secretion in Huh-7, Vero, and A549 cells. Eighty-seven percent samples were virus RNA-positive but 65% of these were NS1 ELISA-positive. NS1-gene mutations like Val236➔Ala (DENV2) or Trp68➔stop codon in DENV3 were associated with decreased NS1 production and secretion. These mutations were originally identified in NS1 ELISA-negative clinical isolates. All DENV1 and > 80% DENV2 were NS1 ELISA-positive. The three NS1 ELISA could not detect recently circulating DENV3 single infections despite being RNA-positive. Among serotypes 1-3, wild-type NS1 production was highest for DENV1 and lowest for DENV3 in all cell lines tested. Mutations in circulating DENV directly correlated with NS1 production and secretion and, hence, ELISA-based NS1 detection. Further studies to define more NS1 mutations in clinical samples are needed to optimize ELISA kits for more sensitive dengue diagnosis.

One-Step Grown Carbonaceous Germanium Nanowires and Their Application as Highly Efficient Lithium-Ion Battery Anodes.

Developing a simple, cheap, and scalable synthetic method for the fabrication of functional nanomaterials is crucial. Carbon-based nanowire nanocomposites could play a key role in integrating group IV semiconducting nanomaterials as anodes into Li-ion batteries. Here, we report a very simple, one-pot solvothermal-like growth of carbonaceous germanium (C-Ge) nanowires in a supercritical solvent. C-Ge nanowires are grown just by heating (380-490 °C) a commercially sourced Ge precursor, diphenylgermane (DPG), in supercritical toluene, without any external catalysts or surfactants. The self-seeded nanowires are highly crystalline and very thin, with an average diameter between 11 and 19 nm. The amorphous carbonaceous layer coating on Ge nanowires is formed from the polymerization and condensation of light carbon compounds generated from the decomposition of DPG during the growth process. These carbonaceous Ge nanowires demonstrate impressive electrochemical performance as an anode material for Li-ion batteries with high specific charge values (>1200 mAh g-1 after 500 cycles), greater than most of the previously reported for other "binder-free" Ge nanowire anode materials, and exceptionally stable capacity retention. The high specific charge values and impressively stable capacity are due to the unique morphology and composition of the nanowires.

Non-cytopathic herpes simplex virus type-1 isolated from acyclovir-treated patients with recurrent infections.

Herpes simplex virus (HSV) usually produces cytopathic effect (CPE) within 24-72 h post-infection (P.I.). Clinical isolates from recurrent HSV infections in patients on Acyclovir therapy were collected between 2016 and 2019 and tested in cell cultures for cytopathic effects and further in-depth characterization. Fourteen such isolates did not show any CPE in A549 or Vero cell lines even at 120 h P.I. However, these cultures remained positive for HSV-DNA after several passages. Sequence analysis revealed that the non-CPE isolates were all HSV-1. Analysis of the thymidine kinase gene from the isolates revealed several previously reported and two novel ACV-resistant mutations. Immunofluorescence and Western blot data revealed a low-level expression of the immediate early protein, ICP4. Late proteins like ICP5 or capsid protein, VP16 were almost undetectable in these isolates. AFM imaging revealed that the non-CPE viruses had structural deformities compared to wild-type HSV-1. Our findings suggest that these strains are manifesting an unusual phenomenon of being non-CPE herpesviruses with low level of virus protein expressions over several passages. Probably these HSV-1 isolates are evolving towards a more "cryptic" form to establish chronic infection in the host thereby unraveling yet another strategy of herpesviruses to evade the host immune system.

Growth and analysis of the tetragonal (ST12) germanium nanowires.

New semiconducting materials, such as state-of-the-art alloys, engineered composites and allotropes of well-established materials can demonstrate unique physical properties and generate wide possibilities for a vast range of applications. Here we demonstrate, for the first time, the fabrication of a metastable allotrope of Ge, tetragonal germanium (ST12-Ge), in nanowire form. Nanowires were grown in a solvothermal-like single-pot method using supercritical toluene as a solvent, at moderate temperatures (290-330 °C) and a pressure of ∼48 bar. One-dimensional (1D) nanostructures of ST12-Ge were achieved via a self-seeded vapour-liquid-solid (VLS)-like paradigm, with the aid of an in situ formed amorphous carbonaceous layer. The ST12 phase of Ge nanowires is governed by the formation of this carbonaceous structure on the surface of the nanowires and the creation of Ge-C bonds. The crystalline phase and structure of the ST12-Ge nanowires were confirmed by X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM) and Raman spectroscopy. The nanowires produced displayed a high aspect ratio, with a very narrow mean diameter of 9.0 ± 1.4 nm, and lengths beyond 4 µm. The ST12-Ge nanowire allotrope was found to have a profound effect on the intensity of the light emission and the directness of the bandgap, as confirmed by a temperature-dependent photoluminescence study.

Solution phase growth and analysis of super-thin zigzag tin selenide nanoribbons.

Tin selenide (SnSe), a highly promising layered material, has been garnering particular interest in recent times due to its significant promise for future energy devices. Herein we report a simple solution-phase approach for growing highly crystalline layered SnSe nanoribbons. Polyvinylpyrrolidone (PVP) was used as a templating agent to selectively passivates the (100) and (001) facets of the SnSe nanoribbons resulting in the unique growth of nanoribbons along theirb-axis with a defined zigzag edge state along the sidewalls. The SnSe nanoribbons are few layers thick (∼20 layers), with mean widths of ∼40 nm, and achievable length of >1µm. Nanoribbons could be produced in relatively high quantities (>150 mg) in a single batch experiment. The PVP coating also offers some resistance to oxidation, with the removal of the PVP seen to lead to the formation of a SnSe/SnOxcore-shell structure. The use of non-toxic PVP to replace toxic amines that are typically employed for other 1D forms of SnSe is a significant advantage for sustainable and environmentally friendly applications. Heat transport properties of the SnSe nanoribbons, derived from power-dependent Raman spectroscopy, demonstrate the potential of SnSe nanoribbons as thermoelectric material.

A Rapid and Easy-to-Perform Method of Nucleic-Acid Based Dengue Virus Diagnosis Using Fluorescence-Based Molecular Beacons.

Detecting dengue virus (DENV) infection in patients as early as possible makes the disease management convenient. Conventionally, DENV infection is diagnosed by ELISA-based methods, but sensitivity and specificity are major concerns. Reverse-transcription-PCR (RT-PCR)-based detection confirms the presence of DENV RNA; however, it is expensive, time-consuming, and skilled personnel are required. A fluorescence-based detection system that detects DENV RNA in patient's serum directly, without any nucleic acid amplification step, has been developed. The method uses target-specific complementary sequence in the molecular beacon, which would specifically bind to the DENV RNA. The molecular beacons are approximately 40 bases long hairpin structures, with a fluorophore-quencher system attached at the terminal ends of the stem. These probes are biotinylated in the stem region, so that they can be immobilized on the streptavidin-tagged magnetic beads. These magnetic beads, coupled with biotinylated molecular beacons, are used for the detection of the target RNA in the serum by incubating the mixture. After incubation, beads are separated and re-suspended in a buffer. The measurement of fluorescence is taken in fluorometer after 15 min incubation at 50 °C. The whole work is carried out in a single tube. This rapid method can precisely detect dengue RNA within two hours, confirming ongoing DENV replication in the patient.

A Review of Self-Seeded Germanium Nanowires: Synthesis, Growth Mechanisms and Potential Applications.

Ge nanowires are playing a big role in the development of new functional microelectronic modules, such as gate-all-around field-effect transistor devices, on-chip lasers and photodetectors. The widely used three-phase bottom-up growth method utilising a foreign catalyst metal or metalloid is by far the most popular for Ge nanowire growth. However, to fully utilise the potential of Ge nanowires, it is important to explore and understand alternative and functional growth paradigms such as self-seeded nanowire growth, where nanowire growth is usually directed by the in situ-formed catalysts of the growth material, i.e., Ge in this case. Additionally, it is important to understand how the self-seeded nanowires can benefit the device application of nanomaterials as the additional metal seeding can influence electron and phonon transport, and the electronic band structure in the nanomaterials. Here, we review recent advances in the growth and application of self-seeded Ge and Ge-based binary alloy (GeSn) nanowires. Different fabrication methods for growing self-seeded Ge nanowires are delineated and correlated with metal seeded growth. This review also highlights the requirement and advantage of self-seeded growth approach for Ge nanomaterials in the potential applications in energy storage and nanoelectronic devices.

Archived dengue serum samples produced false-positive results in SARS-CoV-2 lateral flow-based rapid antibody tests.

Co-endemicity of SARS-CoV-2 and dengue virus (DV) infection is becoming a matter of serious concern as it has been already reported that antibodies (Ab) elicited by SARS-CoV-2 infection can produce false-positive results in dengue IgG and IgM rapid tests and vice versa. Here we communicate that five of thirteen DV antibody-positive serum samples from Kolkata, archived in 2017 (predating the COVID-19 outbreak), produced false-positive results in SARS-CoV-2 IgG/IgM lateral flow-based rapid tests. Our results emphasize the importance of implementing tests with higher specificity to conduct sero-surveillance for accurate estimation of SARS-CoV-2/DV prevalence in regions where both viruses now co-exist.

Stretching the Equilibrium Limit of Sn in Ge1-x Sn x Nanowires: Implications for Field Effect Transistors.

Ge1-x Sn x nanowires incorporating a large amount of Sn would be useful for mobility enhancement in nanoelectronic devices, a definitive transition to a direct bandgap for application in optoelectronic devices and to increase the efficiency of the GeSn-based photonic devices. Here we report the catalytic bottom-up fabrication of Ge1-x Sn x nanowires with very high Sn incorporation (x > 0.3). These nanowires are grown in supercritical toluene under high pressure (21 MPa). The introduction of high pressure in the vapor-liquid-solid (VLS) like growth regime resulted in a substantial increase of Sn incorporation in the nanowires, with a Sn content ranging between 10 and 35 atom %. The incorporation of Sn in the nanowires was found to be inversely related to nanowire diameter; a high Sn content of 35 atom % was achieved in very thin Ge1-x Sn x nanowires with diameters close to 20 nm. Sn was found to be homogeneously distributed throughout the body of the nanowires, without apparent clustering or segregation. The large inclusion of Sn in the nanowires could be attributed to the nanowire growth kinetics and small nanowire diameters, resulting in increased solubility of Sn in Ge at the metastable liquid-solid interface under high pressure. Electrical investigation of the Ge1-x Sn x (x = 0.10) nanowires synthesized by the supercritical fluid approach revealed their potential in nanoelectronics and sensor-based applications.

Structural Evolution of Nanophase Separated Block Copolymer Patterns in Supercritical CO2.

Nanopatterns can readily be formed by annealing block copolymers (BCPs) in organic solvents at moderate or high temperatures. However, this approach can be challenging from an environmental and industrial point of view. Herein, we describe a simple and environmentally friendly alternative to achieve periodically ordered nanoscale phase separated BCP structures. Asymmetric polystyrene-b-poly(ethylene oxide) (PS-b-PEO) thin film patterns of different molecular weight were achieved by annealing in supercritical carbon dioxide (sc-CO2). Microphase separation of PS-b-PEO (16,000-5000) film patterns were achieved by annealing in scCO2 at a relatively low temperature was previously reported by our group. The effects of annealing temperature, time and depressurisation rates for the polymer system were also discussed. In this article, we have expanded this study to create new knowledge on the structural and dimensional evolution of nanohole and line/space surface periodicity of four other different molecular weights PS-b-PEO systems. Periodic, well defined, hexagonally ordered films of line and hole patterns were obtained at low CO2 temperatures (35-40 °C) and pressures (1200-1300 psi). Further, the changes in morphology, ordering and feature sizes for a new PS-b-PEO system (42,000-11,500) are discussed in detail upon changing the scCO2 annealing parameters (temperature, film thickness, depressurization rates, etc.). In relation to our previous reports, the broad annealing temperature and depressurisation rate were explored together for different film thicknesses. In addition, the effects of SCF annealing for three other BCP systems (PEO-b-PS, PS-b-PDMS, PS-b-PLA) is also investigated with similar processing conditions. The patterns were also generated on a graphoepitaxial substrate for device application.

Computational modelling supports that dengue virus envelope antibodies can bind to SARS-CoV-2 receptor binding sites: Is pre-exposure to dengue virus protective against COVID-19 severity?

The world is going through the scourge of the COVID-19 pandemic since January 2020. However, the pandemic appears to be less severe in highly dengue endemic countries. In this connection, several studies reported that sero-diagnostic tests for dengue virus (DV) yielded considerable false-positive results for SARS-CoV-2 and vice versa in dengue endemic regions, thereby indicating towards potential cross-reactivity between these two viruses. We anticipated that SARS-CoV-2 and DV might share antigenic similarity and performed computational docking studies to test this hypothesis. Our results predicted with high confidence that human DV antibodies can indeed, bind to RBD of SARS-CoV-2 Spike protein. Some of these interactions can also potentially intercept human ACE2 receptor binding to RBM. Dengue serum samples predating the COVID-19, had been found to cross-react with SARS-CoV-2 Spike and this provides direct experimental validation of our predictions. Our analysis also showed that m396 and 80R antibodies (against SARS-CoV-1) did not dock with RBM of SARS-CoV-2, a fact already proven experimentally. This confirmed reliability and robustness of our approach. So, it is highly probable that immunological memory/antibodies to DV in endemic countries may reduce the severity and spread of COVID-19. It is not known whether SARS-CoV-2 antibodies will hinder DV infections by binding to DV particles and reduce dengue incidences in the future or, augment DV infection and severity by deploying antibody-dependent enhancement.

Hepatitis B virus detected in paper currencies in a densely populated city of India: A plausible source of horizontal transmission?

BACKGROUND: The recent rise in the incidence of hepatitis B virus (HBV) infections in a densely populated city of eastern India ("mixing vessel" of people of varied socio-economic and immune status) prompted this study. Applying saliva on fingers for enumerating bank notes is a common practice in the Indian subcontinent. Paper notes may be a potential source of "horizontal" transmission of this virus, especially if there are cuts/bruises on the oral mucous membrane or skin. AIM: To investigate whether paper currencies could be a plausible mode of horizontal transmission of HBV infection. METHODS: Polymerase chain reactions (PCR) followed by nucleotide sequencing was done for the detection of HBV. Hepatitis B virus surface antigen enzyme-linked immunosorbent assay(HBsAg ELISA) was performed on all HBV deoxyribonucleic acid-positive samples to check the detectability of the virus. Atomic force microscopy (AFM) was carried out for visual confirmation of HBV particles in ultracentrifuged/immunoprecipitated samples from currency paper washings. RESULTS: HBV-specific PCRs on pellets obtained after ultracentrifugation/ immunoprecipitation of the currency paper washings detected potentially intact/viable HBV (genotype D2) in 7.14% of samples (n = 70). AFM gave the visual confirmation of HBV particles in ultracentrifuged/immunoprecipitated samples from currency paper washings. However, HBV isolates from the currency notes could not be detected by HBsAg ELISA. CONCLUSION: It is a common practice in the Indian subcontinent to count paper currencies by applying saliva on fingertips. Paper notes may be a potential source of "horizontal" transmission of this virus, especially if there are cuts/bruises on the oral mucous membrane or skin, but it was practically not possible to demonstrate experimentally such transmission. Detection of potentially intact/viable and "occult" HBV from currency poses potential risk of silent transmission of this virus among the general population.

Probing dipole and quadrupole resonance mode in non-plasmonic nanowire using Raman spectroscopy.

Electric field enhancement in semiconductor nanostructures offers a possibility to find an alternative to the metallic particles which is well known for tuning the light-matter interaction due to its strong polarizability and size-dependent surface plasmon resonance energy. Raman spectroscopy is a powerful technique to monitor the electric field as its scattering depends on the electromagnetic eigenmode of the particle. Here, we observe enhanced polarized Raman scattering from germanium nanowires of different diameters. The incident electromagnetic radiation creates a distribution of the internal electric field inside the naowires which can be enhanced by manipulating the nanowire diameter, the incident electric field and its polarization. Our estimation of the enhancement factor, including its dependence on nanowire diameter, agrees well with the Mie theory for an infinite cylinder. Furthermore, depending on diameter of nanowire and wavelength of incident radiation, polarized Raman study shows dipolar (antenna effect) and quadrupolar resonances, which has never been observed in germanium nanowire. We attempt to understand this polarized Raman behavior using COMSOL Multiphysics simulation, which suggests that the pattern observed is due to photon confinement within the nanowires. Thus, the light scattering direction can be toggled by tuning the polarization of incident excitation and diameter of non plasmonic nanowire.

Germanium tin alloy nanowires as anode materials for high performance Li-ion batteries.

The combination of two active Li-ion materials (Ge and Sn) can result in improved conduction paths and higher capacity retention. Here we report for the first time, the implementation of Ge1-x Sn x alloy nanowires as anode materials for Li-ion batteries. Ge1-x Sn x alloy nanowires have been successfully grown via vapor-liquid-solid technique directly on stainless steel current collectors. Ge1-x Sn x (x = 0.048) nanowires were predominantly seeded from the Au0.80Ag0.20 catalysts with negligible amount of growth was also directly catalyzed from stainless steel substrate. The electrochemical performance of the the Ge1-x Sn x nanowires as an anode material for Li-ion batteries was investigated via galvanostatic cycling and detailed analysis of differential capacity plots (DCPs). The nanowire electrodes demonstrated an exceptional capacity retention of 93.4% from the 2nd to the 100th charge at a C/5 rate, while maintaining a specific capacity value of ∼921 mAh g-1 after 100 cycles. Voltage profiles and DCPs revealed that the Ge1-x Sn x nanowires behave as an alloying mode anode material, as reduction/oxidation peaks for both Ge and Sn were observed, however it is clear that the reversible lithiation of Ge is responsible for the majority of the charge stored.