Host proteins are essential for entry and replication of HIV and provide important non-viral therapeutic targets. Large-scale RNAi-based screens have identified nearly a thousand candidate host factors, but with little agreement among studies and few validated factors. Here, we demonstrate that a genome-wide CRISPR-based screen identifies bona fide host factors in a physiologically relevant cell system. We identify five factors, including CD4 and CCR5, that are required for HIV infection yet dispensable for cellular proliferation and viability. TPST2 and SLC35B2 act in a common pathway to sulfate CCR5 on extracellular tyrosine residues, facilitating recognition by HIV envelope. ALCAM mediates cell aggregation, which is required for cell-to-cell HIV transmission. We validate these pathways in primary human CD4+ T cells through Cas9-mediated knockout and antibody blockade. Our findings indicate that HIV infection and replication rely on a limited set of host-dispensable genes and suggest focusing on these pathways for therapeutic intervention.

The emergence of SARS-CoV-2 variants that escape convalescent and vaccine-induced antibody responses has renewed focus on the development of broadly protective T cell-based vaccines. Here we apply structure-based network analysis and assessments of HLA class I-peptide stability to define mutationally constrained CD8 + T cell epitopes across the SARS-CoV-2 proteome. Highly networked residues are conserved temporally among circulating variants and across the Sarbecovirus subgenus, and disproportionately impair Spike pseudotyped lentivirus infectivity when mutated. Evaluation of HLA class I stabilizing activity for 18 globally prevalent alleles identifies CD8 + T cell epitopes within highly networked regions with limited mutational frequencies in circulating SARS-CoV-2 variants and deep-sequenced primary isolates. Moreover, these epitopes elicit demonstrable CD8 + T cell reactivity in convalescent individuals but reduced recognition in mRNA-based vaccine recipients. These data thereby elucidate key mutationally constrained regions and immunogenic epitopes in the SARS-CoV-2 proteome for a global T cell-based vaccine against emerging variants and sarbecoviruses.

Defining factors that govern CD8 + T cell immunodominance is critical for the rational design of vaccines for viral pathogens. Here, we assess the contribution of human leukocyte antigen (HLA) class-I-peptide stability for 186 optimal HIV epitopes across 18 HLA alleles using transporter associated with antigen processing (TAP)-deficient mono-allelic HLA-expressing cell lines. We find that immunodominant HIV epitopes increase surface stabilization of HLA class-I molecules in comparison to subdominant epitopes. HLA class-I-peptide stability is also strongly correlated with overall immunodominance hierarchies, particularly for epitopes from high-abundance proteins (e.g., Gag). Moreover, HLA alleles associated with HIV protection are preferentially stabilized by epitopes derived from topologically important viral regions at a greater frequency than neutral and risk alleles. These findings indicate that relative stabilization of HLA class-I is a key factor for CD8 + T cell epitope immunodominance hierarchies, with implications for HIV control and the design of T-cell-based vaccines.

Hospitals often seek to improve the effectiveness and experience of care through new building construction. However, the association between the built hospital environment, patient outcomes, and patient experience remains unclear. This retrospective matched cohort study leveraged natural experimental conditions to characterize major clinical outcomes and patient experience in medicine patients admitted to a new hospital building incorporating evidence-based design features compared with controls admitted to legacy buildings. Among patients discharged between June 1, 2019, and March 1, 2020, there were no significant differences in intensive care unit transfer, inpatient mortality, 30-day readmission, 30-day mortality, or length of stay. However, discharge from the new hospital building was associated with a higher percentage of top box scores on the Hospital Consumer Assessment of Healthcare Providers and Systems overall hospital rating item (60% vs 76%, P = 0.02). Further studies are needed to identify specific hospital design features that influence patient experience and clinical outcomes.