SARS-CoV-2 biology and host interactions – Nature.com

Gorbalenya, A. E. et al. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5, 536544 (2020).

Article Google Scholar

Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270273 (2020).

Article CAS PubMed PubMed Central Google Scholar

Zhu, N. et al. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727733 (2020).

Article CAS PubMed PubMed Central Google Scholar

Coronavirus (COVID-19) Dashboard. WHO https://covid19.who.int/ (2022).

Telenti, A., Hodcroft, E. B. & Robertson, D. L. The evolution and biology of SARS-CoV-2 variants. Cold Spring Harb. Persp. Med. 12, a041390 (2022).

Article CAS Google Scholar

Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 19, 409424 (2021).

Article CAS PubMed PubMed Central Google Scholar

Grant, R. et al. When to update COVID-19 vaccine composition. Nat. Med. 29, 776780 (2023).

Article CAS PubMed Google Scholar

Jungreis, I., Sealfon, R. & Kellis, M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nat. Commun. 12, 2642 (2021).

Article CAS PubMed PubMed Central Google Scholar

Jungreis, I. et al. Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: a homology-based resolution. Virology 558, 145151 (2021).

Article CAS PubMed Google Scholar

Finkel, Y. et al. The coding capacity of SARS-CoV-2. Nature 589, 125130 (2020).

Article PubMed Google Scholar

Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459468 (2020).

Article CAS PubMed PubMed Central Google Scholar

Kim, D. et al. The architecture of SARS-CoV-2 transcriptome. Cell 181, 914921.e10 (2020).

Article CAS PubMed PubMed Central Google Scholar

Huston, N. C. et al. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Mol. Cell 81, 584598.e5 (2021).

Article CAS PubMed PubMed Central Google Scholar

Lan, T. C. T. et al. Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nat. Commun. 13, 1128 (2022).

Article CAS PubMed PubMed Central Google Scholar

Ziv, O. et al. The short- and long-range RNARNA interactome of SARS-CoV-2. Mol. Cell 80, 10671077.e5 (2020).

Article CAS PubMed PubMed Central Google Scholar

Madhugiri, R., Fricke, M., Marz, M. & Ziebuhr, J. Coronavirus cis-acting RNA elements. Adv. Virus Res. 96, 127163 (2016).

Article CAS PubMed PubMed Central Google Scholar

Tidu, A. et al. The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation. RNA 27, 253264 (2021). This publication demonstrated that SARS-CoV-2 relies on stem loop 1 in the 5 UTR to evade the nsp1-induced translational shutoff of its own genes.

Article CAS PubMed Central Google Scholar

Bujanic, L. et al. The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression. RNA 28, 766779 (2022).

Article CAS PubMed PubMed Central Google Scholar

Iserman, C. et al. Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid. Mol. Cell 80, 10781091.e6 (2020).

Article CAS PubMed PubMed Central Google Scholar

Bhatt, P. R. et al. Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science 372, 13061313 (2021). In-depth structural and biochemical analysis into the mechanism of the programmed ribosomal frameshift for SARS-CoV-2.

Article CAS PubMed PubMed Central Google Scholar

Sun, L. et al. In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs. Cell 184, 18651883.e20 (2021).

Article CAS PubMed PubMed Central Google Scholar

Jackson, C. B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry into cells. Nat. Rev. Mol. Cell Biol. 23, 320 (2021). Comprehensive review on SARS-CoV-2 entry mechanism.

Article PubMed PubMed Central Google Scholar

Hoffmann, M., Kleine-Weber, H. & Phlmann, S. A multibasic cleavage site in the spike protein of SARS-CoV-2 is essential for infection of human lung cells. Mol. Cell 78, 779784.e5 (2020). This article highlights the presence of a multibasic S1/S2 cleavage site in the SARS-CoV-2 spike protein that can be cut by furin and is a prerequisite for viral entry into lung cells.

Article CAS PubMed PubMed Central Google Scholar

Hansen, J. et al. Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science 369, 10101014 (2020).

Article CAS PubMed PubMed Central Google Scholar

Robbiani, D. F. et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature 584, 437442 (2020).

Article CAS PubMed PubMed Central Google Scholar

Pinto, D. et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290295 (2020).

Article CAS PubMed Google Scholar

Yuan, M. et al. A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science 368, 630633 (2020).

Article CAS PubMed PubMed Central Google Scholar

Liu, L. et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature 584, 450456 (2020). This is one of the first publications to report the receptor-binding domain (RBD) and N-terminal domain (NTD) epitopes as the two main neutralization targets on the SARS-CoV-2 spike protein.

Article CAS PubMed Google Scholar

Chi, X. et al. A neutralizing human antibody binds to the N-terminal domain of the spike protein of SARS-CoV-2. Science 369, 650655 (2020).

Article CAS PubMed PubMed Central Google Scholar

Meng, B. et al. SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity. Cell Rep. 40, 111220 (2022). Here, it was shown that the SARS-CoV-2 spike proteins NTD can modulate S1/S2 cleavage and influence TMPRSS2 usage and fusogenicity.

Article CAS PubMed PubMed Central Google Scholar

Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271280.e8 (2020). The first publication to confirm that, similar to SARS-CoV, the processing of the SARS-CoV-2 spike protein is mediated by TMPRSS2.

Article CAS PubMed PubMed Central Google Scholar

Zhao, M. M. et al. Cathepsin L plays a key role in SARS-CoV-2 infection in humans and humanized mice and is a promising target for new drug development. Signal. Transduct. Target. Ther. 6, 134 (2021).

Article CAS PubMed PubMed Central Google Scholar

Ziegler, C. G. K. et al. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. Cell 181, 10161035.e19 (2020).

Article CAS PubMed PubMed Central Google Scholar

Su, M. C. et al. An atypical RNA pseudoknot stimulator and an upstream attenuation signal for 1 ribosomal frameshifting of SARS coronavirus. Nucleic Acids Res. 33, 42654275 (2005).

Article CAS PubMed PubMed Central Google Scholar

Zhang, K. et al. Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Nat. Struct. Mol. Biol. 28, 747754 (2021).

Article CAS PubMed PubMed Central Google Scholar

Brierley, I., Digard, P. & Inglis, S. C. Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot. Cell 57, 537547 (1989).

Article CAS PubMed PubMed Central Google Scholar

Sun, Y. et al. Restriction of SARS-CoV-2 replication by targeting programmed 1 ribosomal frameshifting. Proc. Natl Acad. Sci. USA 118, e2023051118 (2021).

Article CAS PubMed PubMed Central Google Scholar

Osipiuk, J. et al. Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat. Commun. 12, 743 (2021).

Article CAS PubMed PubMed Central Google Scholar

Jin, Z. et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582, 289293 (2020).

Article CAS PubMed Google Scholar

Ziebuhr, J., Snijder, E. J. & Gorbalenya, A. E. Virus-encoded proteinases and proteolytic processing in the Nidovirales. J. Gen. Virol. 81, 853879 (2000).

Article CAS PubMed Google Scholar

Thoms, M. et al. Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science 369, 12491256 (2020). Thoms et al. (2020) and Schubert et al. (2020) elucidate the binding of SARS-CoV-2 nsp1 to the ribosome and cause translational shutdown.

Article CAS PubMed PubMed Central Google Scholar

Schubert, K. et al. SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat. Struct. Mol. Biol. 27, 959966 (2020).

Article CAS PubMed Google Scholar

Fisher, T. et al. Parsing the role of NSP1 in SARS-CoV-2 infection. Cell Rep. 39, 110954 (2022).

Article CAS PubMed PubMed Central Google Scholar

Snijder, E. J., Decroly, E. & Ziebuhr, J. The nonstructural proteins directing coronavirus RNA synthesis and processing. In Advances in Virus Research Vol. 96 (ed. Ziebuhr, J.) 59126 (Academic Press, 2016).

Cortese, M. et al. Integrative imaging reveals SARS-CoV-2-induced reshaping of subcellular morphologies. Cell Host Microbe 28, 853866.e5 (2020).

Article CAS PubMed PubMed Central Google Scholar

Snijder, E. J. et al. A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis. PLoS Biol. 18, e3000715 (2020).

Article CAS PubMed PubMed Central Google Scholar

Wolff, G., Melia, C. E., Snijder, E. J. & Brcena, M. Double-membrane vesicles as platforms for viral replication. Trends Microbiol. 28, 10221033 (2020).

Article CAS PubMed PubMed Central Google Scholar

Klein, S. et al. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat. Commun. 11, 5885 (2020).

Article CAS PubMed PubMed Central Google Scholar

Ricciardi, S. et al. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Nature 606, 761768 (2022).

Article CAS PubMed PubMed Central Google Scholar

Twu, W. I. et al. Contribution of autophagy machinery factors to HCV and SARS-CoV-2 replication organelle formation. Cell Rep. 37, 110049 (2021).

Article CAS PubMed PubMed Central Google Scholar

Tabata, K. et al. Convergent use of phosphatidic acid for hepatitis C virus and SARS-CoV-2 replication organelle formation. Nat. Commun. 12, 7276 (2021).

Article CAS PubMed PubMed Central Google Scholar

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SARS-CoV-2 biology and host interactions - Nature.com

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