A minimally-edited mouse model for infection with multiple SARS-CoV-2 strains

Nakandakari-Higa, Sandra; Parsa, Roham; Reis, Bernardo Sgarbi; Carvalho, Roberto Gameiro de; Mesin, Luka; Hoffmann, Hans-Heinrich; Bortolatto, Juliana; Muramatsu, Hiromi; Lin, Paulo J.C.; Bilate, Angelina M.; Rice, Charles M.; Pardi, Norbert; Mucida, Daniel; Victora, Gabriel D.; Canesso, Maria Cecília Campos

doi:10.3389/fimmu.2022.1007080

“…The hybrid human/mouse ACE2 knock-in model introduced herein contributes substantially to the extant limited array of mouse models capable of physiological ACE2 expression under the regulation of endogenous Ace2 promoter elements, which are susceptible to multiple SARS-CoV-2 variants. This model exhibits distinct attributes concerning the number and localization of substituted amino acids and the iterations of CRISPR–Cas9-mediated editing, setting it apart from previously established models 41 – 44 . Subsequent comparative studies are imperative for a rigorous assessment of infection susceptibility and disease progression across these disparate models.…”

Section: Discussionmentioning

confidence: 99%

Antibody-independent protection against heterologous SARS-CoV-2 challenge conferred by prior infection or vaccination

Fumagalli,

Ravà,

Marotta

et al. 2024

Nat Immunol

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Vaccines have reduced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) morbidity and mortality, yet emerging variants challenge their effectiveness. The prevailing approach to updating vaccines targets the antibody response, operating under the presumption that it is the primary defense mechanism following vaccination or infection. This perspective, however, can overlook the role of T cells, particularly when antibody levels are low or absent. Here we show, through studies in mouse models lacking antibodies but maintaining functional B cells and lymphoid organs, that immunity conferred by prior infection or mRNA vaccination can protect against SARS-CoV-2 challenge independently of antibodies. Our findings, using three distinct models inclusive of a novel human/mouse ACE2 hybrid, highlight that CD8+ T cells are essential for combating severe infections, whereas CD4+ T cells contribute to managing milder cases, with interferon-γ having an important function in this antibody-independent defense. These findings highlight the importance of T cell responses in vaccine development, urging a broader perspective on protective immunity beyond just antibodies.

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“…Infection of murine ACE2 (M.musculus) is possible with the N501Y substitution in spike [16-18], and we indeed observed increased infection with the Alpha, as well as the other N501Y encoding RBDs from Beta, Gamma, and BA1 spikes (Fig 7B). Previous studies have shown that Asn501 is largely incompatible with rodent ACE2 His353, as murine ACE2 with a H353K mutation can restore infection with virus encoding Asn501 RBD [19]. Human ACE2 with a K353H substitution reduces infectivity with Asn501 RBD virus [20], and the N501Y change circumvents these incompatibilities.…”

Section: Plos Pathogensmentioning

confidence: 97%

Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage

Shukla,

Roelle,

Snell

et al. 2024

PLoS Pathog

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Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike’s interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.

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“…Infection of murine ACE2 ( M.musculus ) is possible with the N501Y substitution in spike [16–18], and we indeed observed increased infection with the Alpha, as well as the other N501Y encoding RBDs from Beta, Gamma, and BA1 spikes ( Fig 7B ). Previous studies have shown that Asn501 is largely incompatible with rodent ACE2 His353, as murine ACE2 with a H353K mutation can restore infection with virus encoding Asn501 RBD [19]. Human ACE2 with a K353H substitution reduces infectivity with Asn501 RBD virus [20], and the N501Y change circumvents these incompatibilities.…”

Section: Sars-cov-2 Variant Infectivity With Ace2 Orthologsmentioning

confidence: 99%

Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage

Shukla,

Roelle,

Snell

et al. 2024

Preprint

0

View full text Add to dashboard Cite

Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike’s interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.

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A minimally-edited mouse model for infection with multiple SARS-CoV-2 strains

Cited by 7 publications

References 43 publications

Antibody-independent protection against heterologous SARS-CoV-2 challenge conferred by prior infection or vaccination

Antibody-independent protection against heterologous SARS-CoV-2 challenge conferred by prior infection or vaccination

Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage

Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage

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