SARS-CoV-2 Omicron lineage XBB spike structures, conformations, antigenicity, and receptor recognition (preprint)

A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryo-EM structures of XBB.1.5, XBB.1.16 and EG.5 spike (S) ectodomains to reveal enhanced occupancy of the receptor inaccessible closed state. Interprotomer receptor binding domain (RBD) interactions previously observed in BA.1 and BA.2 were retained to reinforce the 3-RBD-down state. Improved stability of XBB.1.5 and XBB.1.16 RBD compensated for loss of stability caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. Long-range impacts of S1 subunit mutations affected conformation and epitope presentation in the S2 subunit. Taken together, our results feature a theme of iterative optimization of S protein stability as Omicron continues to evolve, while maintaining high affinity receptor binding and bolstering immune evasion.

ENGAGING THE DISENGAGED: HCV SELF TESTING AND LINKAGE TO CARE FOR DTS CLIENTS DURING COVID

Introduction Home self-testing has been validated for HIV with evidence for increased uptake, comparable linkage to care and an absence of harm in those at risk. However, there are limited data on this strategy for people at risk of HCV infection (WHO 2021). Surrey HCV ODN Drug and Alcohol services (iAccess & Inclusion) provide a range of interventions including structured treatment for people with a history of alcohol or substance misuse. During COVID most clinics moved to telephone consultations, reducing BBV screening opportunities. This project targeted service users with > 12 months follow up for reengagement with HCV testing through supported home self-testing for HCV with rapid linkage to care through the ODN. Methods Interrogation of the EPR at the DTS (iAccess and Inclusion) identified a target population of older clients (>45years) who had not previously engaged with the offer of HCV testing. Exclusion criteria: previous positive HCVAb result, prior HCV treatment, negative DBS test within 6 months. Initial telephone contact from the hepatology CNS, Hep C Trust peer or Drug service recovery worker to was used to explain the project in detail and gain consent for participation. Participants received a postal testing pack including bespoke patient information leaflet and Oraquick® point of care test. The team used a dedicated phone number to discuss results and deliver support. Positive HCV Ab tests triggered an urgent assessment by the hepatology CNS supported by Hep C Trust peers. Results Preliminary results are available for the first six months (completion planned May 2022). Across the network 210 people agreed to participate and received home HCV self-test kits. 92 reported test results (44% of postal tests dispatched). Six HCVAb+ 80 HCVAb-, six test failures. 6.5% of completed tests detected HCV Ab. Of the six HCVAb+ identified to date five have attended for confirmatory PCR in the ODN. Two of five were PCR negative (spontaneous clearance), two PCR positive patients have commenced treatment and one awaits additional diagnostics. The strength of the ODN linkage to care processes is reflected in the client pathway, including two patients who were subsequently incarcerated and followed up by the ODN prison in reach team. Conclusions Postal testing for HCV using a rapid point of care test is feasible and provides an opportunity to engage at risk individuals for HCV testing. Once engaged linkage to care was effective utilizing the ODN network. This approach has also provided a useful avenue for HCV diagnosis and the care cascade during the pandemic when many clinic assessments have been managed remotely.

Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sub-lineage has gained in proportion relative to BA.1. Because spike (S) protein variations may underlie differences in their pathobiology, here we determine cryoelectron microscopy (cryo-EM) structures of the BA.2 S ectodomain and compare these with previously determined BA.1 S structures. BA.2 receptor-binding domain (RBD) mutations induce remodeling of the RBD structure, resulting in tighter packing and improved thermostability. Interprotomer RBD interactions are enhanced in the closed (or 3-RBD-down) BA.2 S, while the fusion peptide is less accessible to antibodies than in BA.1. Binding and pseudovirus neutralization assays reveal extensive immune evasion while defining epitopes of two outer RBD face-binding antibodies, DH1044 and DH1193, that neutralize both BA.1 and BA.2. Taken together, our results indicate that stabilization of the closed state through interprotomer RBD-RBD packing is a hallmark of the Omicron variant and show differences in key functional regions in the BA.1 and BA.2 S proteins.

mRNA-encoded HIV-1 Env trimer ferritin nanoparticles induce monoclonal antibodies that neutralize heterologous HIV-1 isolates in mice.

The success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared with trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here, we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next-generation sequencing demonstrates acquisition of critical mutations, and monoclonal antibodies that neutralize heterologous HIV-1 isolates are isolated. Thus, mRNA-LNP can encode complex immunogens and may be of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.

Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.