Transmitted drug resistance and transmission clusters among ART-naïve HIV-1-infected individuals from 2019 to 2021 in Nanjing, China.

Background: Transmitted drug resistance (TDR) is an increasingly prevalent problem worldwide, which will significantly compromise the effectiveness of HIV treatments. However, in Nanjing, China, there is still a dearth of research on the prevalence and transmission of TDR among ART-naïve HIV-1-infected individuals. This study aimed to understand the prevalence and transmission of TDR in Nanjing. Methods: A total of 1,393 participants who were newly diagnosed with HIV-1 and had not received ART between January 2019 and December 2021 were enrolled in this study. HIV-1 pol gene sequence was obtained by viral RNA extraction and nested PCR amplification. Genotypes, TDR and transmission cluster analyses were conducted using phylogenetic tree, Stanford HIV database algorithm and HIV-TRACE, respectively. Univariate and multivariate logistic regression analyses were performed to identify the factors associated with TDR. Results: A total of 1,161 sequences were successfully sequenced, of which CRF07_BC (40.6%), CRF01_AE (38.4%) and CRF105_0107 (6.3%) were the main HIV-1 genotypes. The overall prevalence of TDR was 7.8%, with 2.0% to PIs, 1.0% to NRTIs, and 4.8% to NNRTIs. No sequence showed double-class resistance. Multivariate logistic regression analysis revealed that compared with CRF01_AE, subtype B (OR = 2.869, 95%CI: 1.093-7.420) and female (OR = 2.359, 95%CI: 1.182-4.707) were risk factors for TDR. Q58E was the most prevalent detected protease inhibitor (PI) -associated mutation, and V179E was the most frequently detected non-nucleoside reverse transcriptase inhibitor (NNRTI) -associated mutation. A total of 613 (52.8%) sequences were segregated into 137 clusters, ranging from 2 to 74 sequences. Among 44 individuals with TDR (48.4%) within 21 clusters, K103N/KN was the most frequent TDR-associated mutation (31.8%), followed by Q58E/QE (20.5%) and G190A (15.9%). Individuals with the same TDR-associated mutations were usually cross-linked in transmission clusters. Moreover, we identified 9 clusters in which there was a transmission relationship between drug-resistant individuals, and 4 clusters in which drug-resistant cases increased during the study period. Conclusion: The overall prevalence of TDR in Nanjing was at a moderate level during the past 3 years. However, nearly half of TDR individuals were included in the transmission clusters, and some drug-resistant individuals have transmitted in the clusters. Therefore, HIV drug-resistance prevention, monitoring and response efforts should be sustained and expanded to reduce the prevalence and transmission of TDR in Nanjing.

Impact of inactivated COVID-19 vaccines on lung injury in B.1.617.2 (Delta) variant-infected patients.

BACKGROUND: Chest computerized tomography (CT) scan is an important strategy that quantifies the severity of COVID-19 pneumonia. To what extent inactivated COVID-19 vaccines could impact the COVID-19 pneumonia on chest CT is not clear. METHODS: This study recruited 357 SARS-COV-2 B.1.617.2 (Delta) variant-infected patients admitted to the Second Hospital of Nanjing from July to August 2021. An artificial intelligence-assisted CT imaging system was used to quantify the severity of COVID-19 pneumonia. We compared the volume of infection (VOI), percentage of infection (POI) and chest CT scores among patients with different vaccination statuses. RESULTS: Of the 357 Delta variant-infected patients included for analysis, 105 were unvaccinated, 72 were partially vaccinated and 180 were fully vaccinated. Fully vaccination had the least lung injuries when quantified by VOI (median VOI of 222.4 cm3, 126.6 cm3 and 39.9 cm3 in unvaccinated, partially vaccinated and fully vaccinated, respectively; p < 0.001), POI (median POI of 7.60%, 3.55% and 1.20% in unvaccinated, partially vaccinated and fully vaccinated, respectively; p < 0.001) and chest CT scores (median CT score of 8.00, 6.00 and 4.00 in unvaccinated, partially vaccinated and fully vaccinated, respectively; p < 0.001). After adjustment for age, sex, comorbidity, time from illness onset to hospitalization and viral load, fully vaccination but not partial vaccination was significantly associated with less lung injuries quantified by VOI {adjust coefficient[95%CI] for "full vaccination": - 106.10(- 167.30,44.89); p < 0.001}, POI {adjust coefficient[95%CI] for "full vaccination": - 3.88(- 5.96, - 1.79); p = 0.001} and chest CT scores {adjust coefficient[95%CI] for "full vaccination": - 1.81(- 2.72, - 0.91); p < 0.001}. The extent of reduction of pulmonary injuries was more profound in fully vaccinated patients with older age, having underlying diseases, and being female sex, as demonstrated by relatively larger absolute values of adjusted coefficients. Finally, even within the non-severe COVID-19 population, fully vaccinated patients were found to have less lung injuries. CONCLUSION: Fully vaccination but not partially vaccination could significantly protect lung injury manifested on chest CT. Our study provides additional evidence to encourage a full course of vaccination.

Metagenomic Next-Generation Sequencing vs. Traditional Microbiological Tests for Diagnosing Varicella-Zoster Virus Central Nervous System Infection.

BACKGROUND: Unbiased metagenomic next-generation sequencing (mNGS) detects pathogens in a target-independent manner. It is not well-understood whether mNGS has comparable sensitivity to target-dependent nucleic acid test for pathogen identification. METHODS: This study included 31 patients with chickenpox and neurological symptoms for screening of possible varicella-zoster virus (VZV) central nervous system (CNS) infection. Microbiological diagnosing of VZV cerebrospinal fluid (CSF) infection was performed on stored CSF samples using mNGS, quantitative and qualitative VZV-specific PCR assays, and VZV IgM antibodies test. RESULTS: The median age was 30.0 [interquartile range (IQR), 24.3-33.3] years. 51.6% of the patients were men. About 80.6% of the patients had normal CSF white blood cell counts (≤ 5 × 106/L). VZV IgM antibodies presented in 16.1% of the CSF samples, and nucleic acids were detectable in 16.1 and 9.7% using two different VZV-specific real-time PCR protocols. Intriguingly, maximal identification of VZV elements was achieved by CSF mNGS (p = 0.001 and p = 007; compared with qualitative PCR and VZV IgM antibody test, respectively), with sequence reads of VZV being reported in 51.6% (16/31) of the CSF samples. All VZV PCR positive samples were positive when analyzed by mNGS. Of note, human betaherpesvirus 6A with clinical significance was unexpectedly detected in one CSF sample. CONCLUSIONS: Our study suggests that CSF mNGS may have higher sensitivity for VZV detection than CSF VZV PCR and antibody tests, and has the advantage of identifying unexpected pathogens.

Materials Properties and Solvated Electron Dynamics of Isolated Nanoparticles and Nanodroplets Probed with Ultrafast Extreme Ultraviolet Beams.

We present ultrafast photoemission measurements of isolated nanoparticles in vacuum using extreme ultraviolet (EUV) light produced through high harmonic generation. Surface-selective static EUV photoemission measurements were performed on nanoparticles with a wide array of compositions, ranging from ionic crystals to nanodroplets of organic material. We find that the total photoelectron yield varies greatly with nanoparticle composition and provides insight into material properties such as the electron mean free path and effective mass. Additionally, we conduct time-resolved photoelectron yield measurements of isolated oleylamine nanodroplets, observing that EUV photons can create solvated electrons in liquid nanodroplets. Using photoemission from a time-delayed 790 nm pulse, we observe that a solvated electron is produced in an excited state and subsequently relaxes to its ground state with a lifetime of 151 ± 31 fs. This work demonstrates that femotosecond EUV photoemission is a versatile surface-sensitive probe of the properties and ultrafast dynamics of isolated nanoparticles.

Mapping nanoscale absorption of femtosecond laser pulses using plasma explosion imaging.

We make direct observations of localized light absorption in a single nanostructure irradiated by a strong femtosecond laser field, by developing and applying a technique that we refer to as plasma explosion imaging. By imaging the photoion momentum distribution resulting from plasma formation in a laser-irradiated nanostructure, we map the spatial location of the highly localized plasma and thereby image the nanoscale light absorption. Our method probes individual, isolated nanoparticles in vacuum, which allows us to observe how small variations in the composition, shape, and orientation of the nanostructures lead to vastly different light absorption. Here, we study four different nanoparticle samples with overall dimensions of ∼100 nm and find that each sample exhibits distinct light absorption mechanisms despite their similar size. Specifically, we observe subwavelength focusing in single NaCl crystals, symmetric absorption in TiO2 aggregates, surface enhancement in dielectric particles containing a single gold nanoparticle, and interparticle hot spots in dielectric particles containing multiple smaller gold nanoparticles. These observations demonstrate how plasma explosion imaging directly reveals the diverse ways in which nanoparticles respond to strong laser fields, a process that is notoriously challenging to model because of the rapid evolution of materials properties that takes place on the femtosecond time scale as a solid nanostructure is transformed into a dense plasma.

Observation and control of shock waves in individual nanoplasmas.

Using an apparatus that images the momentum distribution of individual, isolated 100-nm-scale plasmas, we make the first experimental observation of shock waves in nanoplasmas. We demonstrate that the introduction of a heating pulse prior to the main laser pulse increases the intensity of the shock wave, producing a strong burst of quasimonoenergetic ions with an energy spread of less than 15%. Numerical hydrodynamic calculations confirm the appearance of accelerating shock waves and provide a mechanism for the generation and control of these shock waves. This observation of distinct shock waves in dense plasmas enables the control, study, and exploitation of nanoscale shock phenomena with tabletop-scale lasers.

High flux coherent super-continuum soft X-ray source driven by a single-stage, 10mJ, Ti:sapphire amplifier-pumped OPA.

We demonstrate the highest flux tabletop source of coherent soft X-rays to date, driven by a single-stage 10 mJ Ti:sapphire regenerative amplifier at 1 kHz. We first down-convert the laser to 1.3 µm using a parametric amplifier, before up-converting it to soft X-rays using high harmonic generation in a high-pressure, phase matched, hollow waveguide geometry. The resulting optimally phase matched broadband spectrum extends to 200 eV, with a soft X-ray photon flux of > 10(6) photons/pulse/1% bandwidth at 1 kHz, corresponding to > 10(9) photons/s/1% bandwidth, or approximately a three order-of-magnitude increase compared with past work. Finally, using this broad bandwidth X-ray source, we demonstrate X-ray absorption spectroscopy of multiple elements and transitions in molecules in a single spectrum, with a spectral resolution of 0.25 eV, and with the ability to resolve the near edge fine structure.

Photoelectron spectroscopy of CdSe nanocrystals in the gas phase: a direct measure of the evanescent electron wave function of quantum dots.

We present the first photoelectron spectroscopy measurements of quantum dots (semiconductor nanocrystals) in the gas phase. By coupling a nanoparticle aerosol source to a femtosecond velocity map imaging photoelectron spectrometer, we apply robust gas-phase photoelectron spectroscopy techniques to colloidal quantum dots, which typically must be studied in a liquid solvent or while bound to a surface. Working with a flowing aerosol of quantum dots offers the additional advantages of providing fresh nanoparticles for each laser shot and removing perturbations from bonding with a surface or interactions with the solvent. In this work, we perform a two-photon photoionization experiment to show that the photoelectron yield per exciton depends on the physical size of the quantum dot, increasing for smaller dots. Next, using effective mass modeling we show that the extent to which the electron wave function of the exciton extends from the quantum dot, the so-called "evanescent electron wavefunction", increases as the size of the quantum dot decreases. We show that the photoelectron yield is dominated by the evanescent electron density due to quantum confinement effects, the difference in the density of states inside and outside of the quantum dots, and the angle-dependent transmission probability of electrons through the surface of the quantum dot. Therefore, the photoelectron yield directly reflects the fraction of evanescent electron wave function that extends outside of the quantum dot. This work shows that gas-phase photoelectron spectroscopy is a robust and general probe of the electronic structure of quantum dots, enabling the first direct measurements of the evanescent exciton wave function.

Direct visualization of laser-driven electron multiple scattering and tunneling distance in strong-field ionization.

Using a simple model of strong-field ionization of atoms that generalizes the well-known 3-step model from 1D to 3D, we show that the experimental photoelectron angular distributions resulting from laser ionization of xenon and argon display prominent structures that correspond to electrons that pass by their parent ion more than once before strongly scattering. The shape of these structures can be associated with the specific number of times the electron is driven past its parent ion in the laser field before scattering. Furthermore, a careful analysis of the cutoff energy of the structures allows us to experimentally measure the distance between the electron and ion at the moment of tunnel ionization. This work provides new physical insight into how atoms ionize in strong laser fields and has implications for further efforts to extract atomic and molecular dynamics from strong-field physics.