Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device.

Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.

Comparison of Anti-Dengue and Anti-Zika IgG on a Plasmonic Gold Platform with Neutralization Testing.

Antibody cross-reactivity confounds testing for dengue virus (DENV) and Zika virus (ZIKV). We evaluated anti-DENV and anti-ZIKV IgG detection using a multiplex serological platform (the pGOLD assay, Nirmidas, Palo Alto, CA) in patients from the Asunción metropolitan area in Paraguay, which experiences annual DENV outbreaks but has reported few autochthonous ZIKV infections. Acute-phase sera were tested from 77 patients who presented with a suspected arboviral illness from January to May 2018. Samples were tested for DENV and ZIKV RNA by real-time reverse transcription-PCR, and for DENV nonstructural protein 1 with a lateral-flow immunochromatographic test. Forty-one patients (51.2%) had acute dengue; no acute ZIKV infections were detected. Sixty-five patients (84.4%) had anti-DENV-neutralizing antibodies by focus reduction neutralization testing (FRNT50). Qualitative detection with the pGOLD assay demonstrated good agreement with FRNT50 (kappa = 0.74), and quantitative results were highly correlated between methods (P < 0.001). Only three patients had anti-ZIKV-neutralizing antibodies at titers of 1:55-1:80, and all three had corresponding DENV-neutralizing titers > 1:4,000. Hospitalized dengue cases had significantly higher anti-DENV IgG levels (P < 0.001). Anti-DENV IgG results from the pGOLD assay correlate well with FRNT, and quantitative results may inform patient risk stratification.

Quantification of antibody avidities and accurate detection of SARS-CoV-2 antibodies in serum and saliva on plasmonic substrates.

Accurate assays for the detection of antibodies to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) are essential for the control of the COVID-19 (coronavirus disease 2019) pandemic. Here, we report antibody and antibody-avidity assays, relying on near-infrared-fluorescence amplification by nanostructured plasmonic gold substrates, for the simultaneous detection of antibodies to the S1 subunit of the spike protein and to the receptor binding domain of SARS-CoV-2 in human serum and saliva, and for quantifying immunoglobulin avidities against coronavirus antigens from SARS-CoV-2, SARS-CoV-1 and the common-cold viruses OC43, HKU1, NL63 and 229E. The antibody assay detected immunoglobulin M in 87% (52 of 60) COVID-19-positive serum samples collected 6 or more days after symptom onset (and the immunoglobulins M and G in all 33 samples collected at least 15 days after symptom onset), and correctly classified 456 out of the 457 COVID-19-negative serum samples tested (424 of them collected before the pandemic, including 73 that were positive for other viruses). We used the antibody-avidity assay to study antibody-maturation patterns, anamnestic responses, and cross-immunity to the common-cold coronaviruses.

Diagnosis of Zika virus infection on a nanotechnology platform.

We developed a multiplexed assay on a plasmonic-gold platform for measuring IgG and IgA antibodies and IgG avidity against both Zika virus (ZIKV) and dengue virus (DENV) infections. In contrast to IgM cross-reactivity, IgG and IgA antibodies against ZIKV nonstructural protein 1 (NS1) antigen were specific to ZIKV infection, and IgG avidity revealed recent ZIKV infection and past DENV-2 infection in patients in dengue-endemic regions. This assay could enable specific diagnosis of ZIKV infection over other flaviviral infections.

Validation of IgG, IgM multiplex plasmonic gold platform in French clinical cohorts for the serodiagnosis and follow-up of Toxoplasma gondii infection.

We report the use of the multiplexed T. gondii IgG, IgM test on plasmonic gold (pGOLD) platform in the setting of T. gondii infection by analyzing 244 sera from Nice, France (seroconversion, chronically infected, non-infected and newborns serum samples). Results were compared with commercial tests for the detection of IgG and IgM and their overall clinical final interpretation of a complete serological profile. The IgG and IgM test results on the platform were in agreement in, respectively, 95% and 93% with the commercial kits. When comparing with the overall clinical interpretation of the serological profile, the agreement reached 99.5% and 97.7% for IgG and IgM, respectively. This innovative pGOLD platform allows detection of both IgG and IgM simultaneously with only ~1 microliter of serum. The multiplexed IgG/IgM test on pGOLD platform is a strong candidate for its use in the massive screening programs for toxoplasmosis during pregnancy.

Dislocation multi-junctions and strain hardening.

At the microscopic scale, the strength of a crystal derives from the motion, multiplication and interaction of distinctive line defects called dislocations. First proposed theoretically in 1934 (refs 1-3) to explain low magnitudes of crystal strength observed experimentally, the existence of dislocations was confirmed two decades later. Much of the research in dislocation physics has since focused on dislocation interactions and their role in strain hardening, a common phenomenon in which continued deformation increases a crystal's strength. The existing theory relates strain hardening to pair-wise dislocation reactions in which two intersecting dislocations form junctions that tie the dislocations together. Here we report that interactions among three dislocations result in the formation of unusual elements of dislocation network topology, termed 'multi-junctions'. We first predict the existence of multi-junctions using dislocation dynamics and atomistic simulations and then confirm their existence by transmission electron microscopy experiments in single-crystal molybdenum. In large-scale dislocation dynamics simulations, multi-junctions present very strong, nearly indestructible, obstacles to dislocation motion and furnish new sources for dislocation multiplication, thereby playing an essential role in the evolution of dislocation microstructure and strength of deforming crystals. Simulation analyses conclude that multi-junctions are responsible for the strong orientation dependence of strain hardening in body-centred cubic crystals.