CORDIS - EU research results

Nanobodies and antibodies against 2019-nCoV

Periodic Reporting for period 2 - CoroNAb (Nanobodies and antibodies against 2019-nCoV)

Reporting period: 2021-04-01 to 2022-03-31

As foreseen at the outset of this project, SARS-CoV-2 has caused a devastating loss of life, freedom, and economic activity around the globe, and continues to do so. In early 2020, there were no vaccines and no therapies to fight against SARS-CoV-2.

Antibodies form the basis of adaptive immunity and can be elicited by vaccination or delivered as therapeutics. Nanobodies are antibody fragments derived from camelid heavy chain-only antibodies. They are small and can be rapidly isolated, making them highly suitable as rapid-response antivirals.

CoroNAb’s overall objectives can be summarized as:
To investigate protein subunit immunization strategies that elicit antibodies that neutralize SARS-CoV-2.
To identify and study, in detail, the antibodies that are elicited by such immunization strategies.
To identify and characterize alpaca single-domain antibodies that can bind to and neutralize SARS-CoV-2.
To model pandemic dynamics and the potential effects of interventions.

The CoroNAb consortium consists of specialists across 4 different countries:
3 neighbouring labs at Karolinska Institutet (Murrell, Karlsson Hedestam, McInerney) working on immunization and nanobody/antibody identification.
Sai Reddy’s lab at ETH Zurich, focusing on therapeutic antibody identification and optimization using cutting edge technologies.
The lab of the Head of Adjuvant Research at Statens Serum Institut, Copenhagen, Gabriel Kristian Pedersen.
A phylodynamics epidemic modeling lab led by Erik Volz from Imperial College London.
CoroNAb consortium has made substantial progress towards its overall objectives. PIs McInerney and Murrell at Karolinska Institutet immunized alpacas and generated nanobody libraries, eventually yielded one early neutralizing nanobody (“Ty1”), and many second-generation nanobodies with cross-variant neutralizing breadth and novel modes of neutralization.

Other members of the CoroNAb consortium at Karolinska, led by PIs Karlsson Hedestam and Murrell, have been focused on neutralizing antibody responses and comparing immunogens via serological readouts in both mice and rhesus macaques. Mouse immunization studies compared prefusion-stabilized spike to Receptor Binding Domain (RBD), with the former showing far greater immunogenicity. Later, it was shown that a Beta variant RBD elicited potent cross-neutralization when used as a booster immunogen.

Our pseudovirus neutralization assay, which was itself a distinct aim, has been used across the spectrum of CoroNAb activities, profiling both serum and identified nanobodies, as well as engaging as a key partner in collaborations. Notably, we disseminated the first pseudovirus neutralization results for Omicron, demonstrating that in cohorts with multiple antigenic exposures, the loss of neutralization was not as extreme as initially feared.

CoroNAb consortium member at ETH Zurich, PI Reddy, focused on development and use of a mammalian display platform for the antibody screening and optimization. In the early stages of this project, these approaches were to investigate whether SARS-CoV-1 mAbs can be broadened to neutralize SARS-CoV-2, and subsequently mAb discovery and optimization using a single-cell RNAseq platform, and to discover new antibodies from plasma cell populations.

At Statens Serum Institut, under PI Pedersen, work was focused on the comparison of adjuvants. Using spike protein from KI, multiple adjuvant formulations were characterized by various methods. A mouse immunization study was conducted to examine immune responses from spike immunization with each of these adjuvants. Ultimately, the immunogenicity and safety of the three different adjuvant systems were tested in mice. The studies demonstrated that the SARS-CoV-2 spike protein administered with various adjuvants boosted immune responses to the spike protein after a single immunization.

At Imperial College London, PI Volz led work involving the development of methodological approaches for tracking the epidemic from genomic data, and building models to infer key parameters that characterize the epidemic, applied initially to genomes sampled from the UK and subsequently in a global comparative analysis using genomes deposited in GISAID. These models have been applied to two research questions: 1) the transmissibility of genetic variants; and 2) phylodynamic models to estimate intervention effect.
The “state of the art” is hard to define in a field that is moving as quickly as SARS-CoV-2 research. However, key CoroNAb developments can be highlighted.

As far as we are aware, we were the first to isolate a neutralizing nanobody from an animal immunized with SARS-CoV-2 antigens. This generated substantial public interest, and was followed by a plethora of work identifying progressively more potent nanobodies.

Pandemic modeling work, to which CoroNAb investigators contributed, was key to understanding the effects on transmissibility and pathogenicity of one of the earliest notable SARS-CoV-2 mutations: D614G. Models developed under CoroNAb were subsequently important for the initial detection and characterisation of the B.1.1.7 lineage in England.

Also on the topic of variants, CoroNAb investigators were the first to report results with an immunogen derived from a Variant of Concern (in this study, we focused on 501Y.V2 first identified in South Africa). This also included the challenge study using a 501Y.V2 viral isolate to assess protection, showing that immunization with the wild-type spike fails to protect against 501Y.V2 whereas boosting with a 501Y.V2 derived immunogen can protect against infection with this new variant.

CoroNAb researchers were the first to release results for an Omicron-adapted pseudovirus neutralization assay, characterizing the loss of neutralization potency against Omicron in two Swedish cohorts, which formed part of the argument that additional immunizations with existing vaccines might suffice for the near future.
Images from various CoroNAb publications, reproduced with permission from the authors.