Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features

In the Antibody Mediated Prevention (AMP) trials (HVTN 704/HPTN 085 and HVTN 703/HPTN 081), prevention efficacy (PE) of the monoclonal broadly neutralizing antibody (bnAb) VRC01 (vs. placebo) against HIV-1 acquisition diagnosis varied according to the HIV-1 Envelope (Env) neutralization sensitivity to VRC01, as measured by 80% inhibitory concentration (IC80). Here, we performed a genotypic sieve analysis, a complementary approach to gaining insight into correlates of protection that assesses how PE varies with HIV-1 sequence features. We analyzed HIV-1 Env amino acid (AA) sequences from the earliest available HIV-1 RNA-positive plasma samples from AMP participants diagnosed with HIV-1 and identified Env sequence features that associated with PE. The strongest Env AA sequence correlate in both trials was VRC01 epitope distance that quantifies the divergence of the VRC01 epitope in an acquired HIV-1 isolate from the VRC01 epitope of reference HIV-1 strains that were most sensitive to VRC01-mediated neutralization. In HVTN 704/HPTN 085, the Env sequence-based predicted probability that VRC01 IC80 against the acquired isolate exceeded 1 µg/mL also significantly associated with PE. In HVTN 703/HPTN 081, a physicochemical-weighted Hamming distance across 50 VRC01 binding-associated Env AA positions of the acquired isolate from the most VRC01-sensitive HIV-1 strain significantly associated with PE. These results suggest that incorporating mutation scoring by BLOSUM62 and weighting by the strength of interactions at AA positions in the epitope:VRC01 interface can optimize performance of an Env sequence-based biomarker of VRC01 prevention efficacy. Future work could determine whether these results extend to other bnAbs and bnAb combinations.

Evaluation of Archival HIV DNA in Brain and Lymphoid Tissues

HIV reservoirs persist in anatomic compartments despite antiretroviral therapy (ART). Characterizing archival HIV DNA in the central nervous system (CNS) and other tissues is crucial to inform cure strategies. We evaluated paired autopsy brain-frontal cortex (FC), occipital cortex (OCC), and basal ganglia (BG)-and peripheral lymphoid tissues from 63 people with HIV. Participants passed away while virally suppressed on ART at the last visit and without evidence of CNS opportunistic disease. We quantified total HIV DNA in all participants and obtained full-length HIV-envelope (FL HIV-env) sequences from a subset of 14 participants. We detected HIV DNA (gag) in most brain (65.1%) and all lymphoid tissues. Lymphoid tissues had higher HIV DNA levels than the brain (P < 0.01). Levels of HIV gag between BG and FC were similar (P > 0.2), while OCC had the lowest levels (P = 0.01). Females had higher HIV DNA levels in tissues than males (gag, P = 0.03; 2-LTR, P = 0.05), suggesting possible sex-associated mechanisms for HIV reservoir persistence. Most FL HIV-env sequences (n = 143) were intact, while 42 were defective. Clonal sequences were found in 8 out of 14 participants, and 1 participant had clonal defective sequences in the brain and spleen, suggestive of cell migration. From 10 donors with paired brain and lymphoid sequences, we observed evidence of compartmentalized sequences in 2 donors. Our data further the idea that the brain is a site for archival HIV DNA during ART where compartmentalized provirus may occur in a subset of people. Future studies assessing FL HIV-provirus and replication competence are needed to further evaluate the HIV reservoirs in tissues. IMPORTANCE HIV infection of the brain is associated with adverse neuropsychiatric outcomes, despite efficient antiretroviral treatment. HIV may persist in reservoirs in the brain and other tissues, which can seed virus replication if treatment is interrupted, representing a major challenge to cure HIV. We evaluated reservoirs and genetic features in postmortem brain and lymphoid tissues from people with HIV who passed away during suppressed HIV replication. We found a differential distribution of HIV reservoirs across brain regions which was lower than that in lymphoid tissues. We observed that most HIV reservoirs in tissues had intact envelope sequences, suggesting they could potentially generate replicative viruses. We found that women had higher HIV reservoir levels in brain and lymphoid tissues than men, suggesting possible sex-based mechanisms of maintenance of HIV reservoirs in tissues, warranting further investigation. Characterizing the archival HIV DNA in tissues is important to inform future HIV cure strategies.

Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations - application to HIV-1 quasispecies

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies.

POS1551-HPR MEDICAL EXPERT KNOWLEDGE MEETS AI: HOW EXPERT KNOWLEDGE CAN IMPROVE SYMPTOM ASSESSMENT APPS - A NEW APPROACH IN RARE DISEASES

Background

By definition, rare diseases occur in fewer than 5 in 10,000 people. However, in Germany alone, there are approximately 4 million people affected (1). Due to their rarity, rare diseases are often overlooked by general practitioners with limited knowledge about them. There are often only a handful of specialized experts for each condition. Yet, those experts are frequently not evenly distributed across the healthcare system, and often, patients lack access. Therefore, the time to diagnosis is often long and poses many challenges. Artificial intelligence (AI) approaches, such as those used in symptom assessment apps can potentially help to detect disease and thus, shorten the time to diagnosis (2).

The general approach underlying the AI of symptom assessment apps is to gather medical knowledge from data (e.g. electronic health record or literature searches). However, for rare diseases, there is only limited research available. In this study we used a new approach: to abstract medical expert knowledge by conducting guided interviews and transforming them into clinical vignettes.

Objectives

There are two objectives. First, we aimed to integrate expert knowledge on the lysosomal storage diseases (LSDs) Fabry, Gaucher and Pompe into the Ada symptom assessment application and use this expert knowledge to optimize Ada’s LSD condition models. LSDs are of particular importance as they represent import differential diagnoses to rheumatic diseases.

Second, we will conduct questionnaires with patients and LSD experts, comparing the optimized to the previous condition models’ performance. We will investigate whether the novel approach of guided interviews, in combination with literature research, results in a better performance than literature research alone.

Methods

Our novel approach is to curate expert medical knowledge from guided interviews with medical experts. The interviews aim to gather knowledge on the symptom constellations with which patients typically present to their physicians. This knowledge is subsequently used to create prototype clinical cases and transform them into structured case vignettes. The rare disease structured case vignettes can be readily transcribed into Ada’s knowledge base.

Results

We conducted guided interviews with clinical experts from the Medizinische Hochschule Hannover (MHH) to create clinical vignettes for the LSDs Fabry, Gaucher and Pompe disease. We conducted interviews with four medical experts and created a total of 11 clinical vignettes: five vignettes for Fabry disease, four for Gaucher disease and two for Pompe disease. Figure 1 demonstrates the vignette creation process. Then, in combination with systematic literature searches, the vignettes were used to update Ada’s existing condition models for Fabry and Gaucher disease and to add Pompe disease.

Figure 1.

The novel medical model creation approach uses guided expert interviews to create prototypic clinical vignettes, which can be readily transcribed in a medical modeling language to create individual disease models

Conclusion

Participants will complete two assessments: an Ada version with the old knowledge base and an Ada version with the updated models. The study plans to enroll 15 LSD patients - five per condition - and nine LSD experts. For the conditions Fabry and Gaucher disease, we will ask the participants to rate both Ada versions. For Pompe disease, we will ask participants to rate the latest Ada version with the updated knowledge base. This novel approach has various clinical implications, including potentially shortening the ‘time to diagnosis’ for rare diseases, thus giving patients faster access to the treatments they need.

References

[1]National Organization for Rare Diseases, Globel genes Project

[2]Ronicke, S., Hirsch, M. C., Türk, E., Larionov, K., Tientcheu, D., & Wagner, A. D. (2019). Can a decision support system accelerate rare disease diagnosis? Evaluating the potential impact of Ada DX in a retrospective study. Orphanet journal of rare diseases, 14(1), 1-12.

Disclosure of Interests

Anne Pankow Grant/research support from: The study originates from a collaboration project between Ada Health, Charité and Sanofi. However Sanofi was neither directly nor indirectly involved in the concept, conduction or interpretation of the study (results)., Nico Meißner Grant/research support from: The study originates from a collaboration project between Ada Health, Charité and Sanofi. However Sanofi was neither directly nor indirectly involved in the concept, conduction or interpretation of the study (results)., Laura Fouquette: None declared, Ewelina Türk: None declared, Stephen Gilbert: None declared, Thilo Tübler: None declared, Anhib Das: None declared, Christoph Terkamp: None declared, Jessica Kaufeld: None declared, Gerd Rüdiger Burmester: None declared, Annette D. Wagner: None declared

POS0359-PARE YouTube AS A SOURCE OF INFORMATION ON AUTOINFLAMMATORY DISEASES

Background

Getting access to specialists for autoinflammatory diseases (AIDs) is challenging. Therefore, an increasing number of patients and healthcare professionals are seeking information on this topic via the internet, e.g., on the video platform YouTube, which has attracted a huge audience in recent years (1). However, not much is known about the quality of videos pertaining on AIDs.

Objectives

To assess videos about AIDs uploaded on YouTube and to evaluate the quality and usefulness of available information from both the patient’s and professional healthcarer´s perspective.

Methods

A YouTube.com search was conducted in January 2022: Selected keywords were “autoinflammatory diseases” (AID), “periodic fever syndrome” (PFS), “familial mediterranean fever” (FMF), “cryopyrin associated periodic syndrome” (CAPS), “tumor necrosis factor associated periodic syndrome” (TRAPS), “adult onset of still´s disease” (AOSD) and “systemic juvenile idiopathic arthritis”(sJIA). For every keyword, the top 20 videos in their order of relevance were included. Video duration, number of views, likes, dislikes, comments and uploading source were extracted. The quality of a video´s information was evaluated independently by two physicians based on the modified global quality scale (GQS) (2). Subgroup analyses were performed classifying healthcare professionals and patients as target group.

Results

In total 140 videos were screened. We excluded 5 videos due to language other than English, 7 duplicates and 23 not suitable ones. 105 videos met the inclusion criteria for further analysis. Video characteristics are presented in Table 1. Based on the GQS, overall quality of videos for patients was found to be low in 64,8%, intermediate in 27,6%, and high in 7,6% of videos. The quality of videos for professionals was similar: 54,3% were judged to be of low, 23,8% of intermediate, and 21,9% of high quality (Figure 1). Subgroup analyses focusing on videos for professionals found sJIA videos to achieve the highest scores (31,6% with high quality) whereas videos regarding CAPS were rated the least useful ones (15,4% with high quality). In videos for patients, sJIA videos also ranked highest (42,1% with high quality) whereas no high quality videos could be identified for TRAPS. Videos are more often aimed at specialists such as doctors or medical students (65.7%) and less often at affected patients or relatives (34.3%). Video duration was significantly longer in videos targeting a professional audience (p < 0.001). In videos for professionals, length was significantly correlated with higher quality (p < 0.001).

Table 1.

Video Characteristics

Figure 1.

Quality Scale

Conclusion

YouTube as a source of information could have great potential for rare diseases. However, this study demonstrates that the majority of videos regarding AIDs is of limited quality and available videos more often adress users with a professional medical background. Only a small proportion of existing videos provide understandable and useful information for AID patients.

References

[1]Madathil KC, Rivera-Rodriguez AJ, Greenstein JS, Gramo- padhye AK (2015) Healthcare information on YouTube: a sys- tematic review. Health Inform J 21(3):173–194. https://doi. org/10.1177/1460458213512220

[2]Bernard A, Langille M, Hughes S, Rose C, Leddin D,Veldhuyzen Van Zanten S (2007). A systematic review of patient inflammatory bowel disease information resourceson the World Wide Web.Am J Gastroenterol102: 2070–2077

Disclosure of Interests

None declared

Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study

Background

The SARS-CoV-2 omicron (B.1.1.529) variant, which was first identified in November, 2021, spread rapidly in many countries, with a spike protein highly diverged from previously known variants, and raised concerns that this variant might evade neutralising antibody responses. We therefore aimed to characterise the sensitivity of the omicron variant to neutralisation.

Methods

For this cross-sectional study, we cloned the sequence encoding the omicron spike protein from a diagnostic sample to establish an omicron pseudotyped virus neutralisation assay. We quantified the neutralising antibody ID₅₀ (the reciprocal dilution that produces 50% inhibition) against the omicron spike protein, and the fold-change in ID₅₀ relative to the spike of wild-type SARS-CoV-2 (ie, the pandemic founder variant), for one convalescent reference plasma pool (WHO International Standard for anti-SARS-CoV-2 immunoglobulin [20/136]), three reference serum pools from vaccinated individuals, and two cohorts from Stockholm, Sweden: one comprising previously infected hospital workers (17 sampled in November, 2021, after vaccine rollout and nine in June or July, 2020, before vaccination) and one comprising serum from 40 randomly sampled blood donors donated during week 48 (Nov 29–Dec 5) of 2021. Furthermore, we assessed the neutralisation of omicron by five clinically relevant monoclonal antibodies (mAbs).

Findings

Neutralising antibody responses in reference sample pools sampled shortly after infection or vaccination were substantially less potent against the omicron variant than against wild-type SARS-CoV-2 (seven-fold to 42-fold reduction in ID₅₀ titres). Similarly, for sera obtained before vaccination in 2020 from a cohort of convalescent hospital workers, neutralisation of the omicron variant was low to undetectable (all ID₅₀ titres <20). However, in serum samples obtained in 2021 from two cohorts in Stockholm, substantial cross-neutralisation of the omicron variant was observed. Sera from 17 hospital workers after infection and subsequent vaccination had a reduction in average potency of only five-fold relative to wild-type SARS-CoV-2 (geometric mean ID₅₀ titre 495 vs 105), and two donors had no reduction in potency. A similar pattern was observed in randomly sampled blood donors (n=40), who had an eight-fold reduction in average potency against the omicron variant compared with wild-type SARS-CoV-2 (geometric mean ID₅₀ titre 369 vs 45). We found that the omicron variant was resistant to neutralisation (50% inhibitory concentration [IC₅₀] >10 μg/mL) by mAbs casirivimab (REGN-10933), imdevimab (REGN-10987), etesevimab (Ly-CoV016), and bamlanivimab (Ly-CoV555), which form part of antibody combinations used in the clinic to treat COVID-19. However, S309, the parent of sotrovimab, retained most of its activity, with only an approximately two-fold reduction in potency against the omicron variant compared with ancestral D614G SARS-CoV-2 (IC₅₀ 0·1–0·2 μg/mL).

Interpretation

These data highlight the extensive, but incomplete, evasion of neutralising antibody responses by the omicron variant, and suggest that boosting with licensed vaccines might be sufficient to raise neutralising antibody titres to protective levels.

Funding

European Union Horizon 2020 research and innovation programme, European and Developing Countries Clinical Trials Partnership, SciLifeLab, and the Erling-Persson Foundation.

Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies

Conventional approaches to isolate and characterize nanobodies are laborious. We combine phage display, multivariate enrichment, next-generation sequencing, and a streamlined screening strategy to identify numerous anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nanobodies. We characterize their potency and specificity using neutralization assays and hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most potent nanobodies bind to the receptor binding motif of the receptor binding domain (RBD), and we identify two exceptionally potent members of this category (with monomeric half-maximal inhibitory concentrations around 13 and 16 ng/ml). Other nanobodies bind to a more conserved epitope on the side of the RBD and are able to potently neutralize the SARS-CoV-2 founder virus (42 ng/ml), the Beta variant (B.1.351/501Y.V2) (35 ng/ml), and also cross-neutralize the more distantly related SARS-CoV-1 (0.46 μg/ml). The approach presented here is well suited for the screening of phage libraries to identify functional nanobodies for various biomedical and biochemical applications.

A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.

A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.

Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) with resistance to neutralizing antibodies are threatening to undermine vaccine efficacy. Vaccination and infection have led to widespread humoral immunity against the pandemic founder (Wu-Hu-1). Against this background, it is critical to assess the outcomes of subsequent immunization with variant antigens. It is not yet clear whether heterotypic boosts would be compromised by original antigenic sin, where pre-existing responses to a prior variant dampen responses to a new one, or whether the memory B cell repertoire would bridge the gap between Wu-Hu-1 and VOCs. We show, in macaques immunized with Wu-Hu-1 spike, that a single dose of adjuvanted beta variant receptor binding domain (RBD) protein broadens neutralizing antibody responses to heterologous VOCs. Passive transfer of plasma sampled after Wu-Hu-1 spike immunization only partially protects K18-hACE2 mice from lethal challenge with a beta variant isolate, whereas plasma sampled following heterotypic RBD boost protects completely against disease.

Black carbon and other light-absorbing impurities in snow in the Chilean Andes

Vertical profiles of black carbon (BC) and other light-absorbing impurities were measured in seasonal snow and permanent snowfields in the Chilean Andes during Austral winters 2015 and 2016, at 22 sites between latitudes 18°S and 41°S. The samples were analyzed for spectrally-resolved visible light absorption. For surface snow, the average mass mixing ratio of BC was 15 ng/g in northern Chile (18-33°S), 28 ng/g near Santiago (a major city near latitude 33°S, where urban pollution plays a significant role), and 13 ng/g in southern Chile (33-41°S). The regional average vertically-integrated loading of BC was 207 µg/m² in the north, 780 µg/m² near Santiago, and 2500 µg/m² in the south, where the snow season was longer and the snow was deeper. For samples collected at locations where there had been no new snowfall for a week or more, the BC concentration in surface snow was high (~10-100 ng/g) and the sub-surface snow was comparatively clean, indicating the dominance of dry deposition of BC. Mean albedo reductions due to light-absorbing impurities were 0.0150, 0.0160, and 0.0077 for snow grain radii of 100 µm for northern Chile, the region near Santiago, and southern Chile; respective mean radiative forcings for the winter months were 2.8, 1.4, and 0.6 W/m². In northern Chile, our measurements indicate that light-absorption by impurities in snow was dominated by dust rather than BC.