RAIN: machine learning-based identification for HIV-1 bNAbs.

Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infections. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoires is still lacking. Here, we develop a straightforward computational method for the Rapid Automatic Identification of bNAbs (RAIN) based on machine learning methods. In contrast to other approaches, which use one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for the accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained and sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of distinct HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using an in vitro neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.

Incidence and Impact of Ventilator Associated Multidrug Resistant Pneumonia in Patients with SARS-COV2.

Introduction: Ventilator Associated Pneumonia (VAP) is associated with significant cost, morbidity, and mortality. There is limited data on the incidence of VAP, appropriate antibiotic timing, and the impact of multidrug resistant VAP in intubated Coronavirus disease-19 (COVID-19) patients. Methods: A retrospective study was conducted at 2 tertiary urban academic centers involving 132 COVID-19 patients requiring invasive mechanical ventilation (IMV). The epidemiology of VAP, the impact of prior empiric antibiotic administration on the development of Multidrug Resistant Organism (MDRO) infections, and the impact of VAP on patient outcomes were studied. Results: The average age of the patients was 60.58% were males, 70% were African-Americans and two-thirds of patients had diabetes, hypertension, or heart disease. The average Body Mass Index (BMI) was 32.9. Forty-one patients (27%) developed VAP. Patients with VAP had a significantly higher Sequential Organ Failure Assessment (SOFA) score prior to Intensive Care Unit (ICU) admission. Sixty percent received empiric antibiotics before initiation of IMV, mostly on hospital admission, and 81% received empiric antibiotics at the time of intubation. The administration of empiric antibiotics was not associated with a higher prevalence of VAP. The prevalence of VAP was 22 per 1000 days on ventilation. No difference in mortality was seen between VAP and non-VAP groups at 49% and 57% respectively (p = 0.4). VAP was associated with increased ICU length of stay (LOS), 30 vs. 16 days (p < 0.001), and longer hospital LOS 35 vs. 17 days (p < 0.001). 40% of VAPs were caused by MDROs. The most common organism was Staphylococcus aureus (28%), with almost half (48%) being methicillin resistant Staphylococcus aureus (MRSA). Conclusion: VAP was a common complication of patients intubated for COVID-19 pneumonia. Most patients received empiric antibiotics upon the hospital and/or ICU admission. There was a 40% incidence of multidrug resistant pneumonia. Patients who developed VAP had almost twice as long hospital and ICU LOS.

Active PD-L1 incorporation within HIV virions functionally impairs T follicular helper cells.

The limited development of broadly neutralizing antibodies (BnAbs) during HIV infection is classically attributed to an inadequate B-cell help brought by functionally impaired T follicular helper (Tfh) cells. However, the determinants of Tfh-cell functional impairment and the signals contributing to this condition remain elusive. In the present study, we showed that PD-L1 is incorporated within HIV virions through an active mechanism involving p17 HIV matrix protein. We subsequently showed that in vitro produced PD-L1high but not PD-L1low HIV virions, significantly reduced Tfh-cell proliferation and IL-21 production, ultimately leading to a decreased of IgG1 secretion from GC B cells. Interestingly, Tfh-cell functions were fully restored in presence of anti-PD-L1/2 blocking mAbs treatment, demonstrating that the incorporated PD-L1 proteins were functionally active. Taken together, the present study unveils an immunovirological mechanism by which HIV specifically exploits the regulatory potential of PD-L1 to suppress the immune system during the course of HIV infection.

Structural basis for HCMV Pentamer receptor recognition and antibody neutralization.

Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial and endothelial cells. Upon infection, Pentamer elicits the most potent neutralizing response against HCMV, representing a key vaccine candidate. Despite its relevance, the structural basis for Pentamer receptor recognition and antibody neutralization is largely unknown. Here, we determine the structures of Pentamer bound to neuropilin 2 (NRP2) and a set of potent neutralizing antibodies against HCMV. Moreover, we identify thrombomodulin (THBD) as a functional HCMV receptor and determine the structures of the Pentamer-THBD complex. Unexpectedly, both NRP2 and THBD also promote dimerization of Pentamer. Our results provide a framework for understanding HCMV receptor engagement, cell entry, antibody neutralization, and outline strategies for antiviral therapies against HCMV.