Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants.

BACKGROUND: Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic following its initial emergence in China. SARS-CoV-2 has a positive-sense single-stranded RNA virus genome of around 30Kb. Using next-generation sequencing technologies, a large number of SARS-CoV-2 genomes are being sequenced at an unprecedented rate and being deposited in public repositories. For the de novo assembly of the SARS-CoV-2 genomes, a myriad of assemblers is being used, although their impact on the assembly quality has not been characterized for this virus. In this study, we aim to understand the variabilities on assembly qualities due to the choice of the assemblers. RESULTS: We performed 6648 de novo assemblies of 416 SARS-CoV-2 samples using eight different assemblers with different k-mer lengths. We used Illumina paired-end sequencing reads and compared the assembly quality of those assemblers. We showed that the choice of assembler plays a significant role in reconstructing the SARS-CoV-2 genome. Two metagenomic assemblers, e.g. MEGAHIT and metaSPAdes, performed better compared with others in most of the assembly quality metrics including, recovery of a larger fraction of the genome, constructing larger contigs and higher N50, NA50 values, etc. We showed that at least 09% (259/2873) of the variants present in the assemblies between MEGAHIT and metaSPAdes are unique to one of the assembly methods. CONCLUSION: Our analyses indicate the critical role of assembly methods for assembling SARS-CoV-2 genome using short reads and their impact on variant characterization. This study could help guide future studies to determine the best-suited assembler for the de novo assembly of virus genomes.

Black Phosphorus Mid-Infrared Photodetectors with High Gain.

Recently, black phosphorus (BP) has joined the two-dimensional material family as a promising candidate for photonic applications due to its moderate bandgap, high carrier mobility, and compatibility with a diverse range of substrates. Photodetectors are probably the most explored BP photonic devices, however, their unique potential compared with other layered materials in the mid-infrared wavelength range has not been revealed. Here, we demonstrate BP mid-infrared detectors at 3.39 µm with high internal gain, resulting in an external responsivity of 82 A/W. Noise measurements show that such BP photodetectors are capable of sensing mid-infrared light in the picowatt range. Moreover, the high photoresponse remains effective at kilohertz modulation frequencies, because of the fast carrier dynamics arising from BP's moderate bandgap. The high photoresponse at mid-infrared wavelengths and the large dynamic bandwidth, together with its unique polarization dependent response induced by low crystalline symmetry, can be coalesced to promise photonic applications such as chip-scale mid-infrared sensing and imaging at low light levels.

Use of whole blood and dried blood spot for detection of HIV-1 nucleic acids using reverse transcription loop-mediated isothermal amplification.

For monitoring viral load (VL) or Early Infant Diagnosis (EID) of HIV-1, real-time Polymerase Chain Reaction (qPCR) is used to perform on plasma or Dried Blood Spot (DBS) sample. The qPCR method is expensive and requires sophisticated equipment. Therefore, there is a requirement for newer and cheaper technology for VL measurement or EID. In this analytical study, a Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) assay was optimized and applied for amplification of HIV nucleic acids (NA) extracted from plasma, heat-treated plasma, heat-treated whole blood and lysis buffer-treated dried blood spot (DBS). The amplified product of RT-LAMP assay was detected by color change of Hydroxy naphthol blue (HNB) dye, step ladder pattern band on agarose gel after electrophoresis and sigmoid-shaped curve in the real-time thermal cycler. Comparing the results from RT-LAMP testing of all conditions with the results obtained by RT-qPCR results, viewed as the gold standard; a relative analytical sensitivity and specificity of RT-LAMP was calculated as 100 % and 90 % respectively. The corresponding positive predictive value (PPV) and negative predictive value (NPV) were 93.75 % and 100 %, respectively. The percentage of agreement between the RT-LAMP and RT-qPCR was 88.46% and Cohen's kappa value was 0.75 shows a substantial agreement between the two tests. This study suggests that whole blood or DBS may be useful specimens for analysis by HIV-1 specific RT-LAMP, to provide a cost effective alternative to RT-qPCR for the detection of HIV-1 nucleic acid at the point of care, or in early infant diagnoses.

Synthesis of Crystalline Black Phosphorus Thin Film on Sapphire.

Black phosphorus (BP) has recently attracted significant attention due to its exceptional physical properties. Currently, high-quality few-layer and thin-film BP are produced primarily by mechanical exfoliation, limiting their potential in future applications. Here, the synthesis of highly crystalline thin-film BP on 5 mm sapphire substrates by conversion from red to black phosphorus at 700 °C and 1.5 GPa is demonstrated. The synthesized ≈50 nm thick BP thin films are polycrystalline with a crystal domain size ranging from 40 to 70 µm long, as indicated by Raman mapping and infrared extinction spectroscopy. At room temperature, field-effect mobility of the synthesized BP thin film is found to be around 160 cm2 V-1 s-1 along armchair direction and reaches up to about 200 cm2 V-1 s-1 at around 90 K. Moreover, red phosphorus (RP) covered by exfoliated hexagonal boron nitride (hBN) before conversion shows atomically sharp hBN/BP interface and perfectly layered BP after the conversion. This demonstration represents a critical step toward the future realization of large scale, high-quality BP devices and circuits.

Nanostructured Thin Film Silicon Anodes for Li-Ion Microbatteries.

Thin film microbatteries require electrode materials with high areal specific capacities and good cyclability. Use of vapor-deposited silicon thin films as anodes in Li-ion microbatteries offers the advantage of high capacity as well as compatibility with other processes used for microsystem fabrication. Unfortunately, monolithic silicon films greater than 200 nm in thickness pulverize during lithiation and delithiation. We have used metal-assisted-chemical-etching of sputter-deposited amorphous silicon films to make nanoporous silicon layers and arrays of silicon nanopillars as a means of achieving anodes with high areal capacity and good cyclability. We have compared the performance of these nanostructured layers with the performance of monolithic silicon films in Li half-cells. A reduced first cycle coulombic efficiency was observed in all cases and was attributed to the irreversible formation of Li2O due to the presence of oxygen in the sputter-deposited silicon films. This was controlled through modifications of the sputtering conditions. As expected, monolithic films thicker than 200 nm showed poor cycling performance due to pulverization of the film. Nanoporous silicon showed good initial cycling performance but the performance degraded due to porosity collapse and delamination. Arrays of silicon nanopillars made from 750 nm silicon films exhibited good cycling, rate performance and an areal capacity (0.20 mA h cm(-2)) 1.6 times higher than what could be obtained with monolithic Si films with similar cyclability.