Like other scientific communities all across the globe, the Single Cell Community is committed to contribute with its research to help win the fight against the COVID-19 pandemic. Please find below recent (single cell) publications and other useful resources for COVID-19 research within the Single Cell community.
Publications
Jansen, J., Reimer, K. C., Nagai, J. S., Varghese, F. S., Overheul, G. J., de Beer, M., Roverts, R., Daviran, D., Fermin, L., Willemsen, B., Beukenboom, M., Djudjaj, S., von Stillfried, S., van Eijk, L. E., Mastik, M., Bulthuis, M., Dunnen, W. D., van Goor, H., Hillebrands, J. L., Triana, S. H., … Kramann, R. (2021). SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell stem cell, 29(2), 217–231.e8. Advance online publication. https://doi.org/10.1016/j.stem.2021.12.010
Georg, P., Astaburuaga-García, R., Bonaguro, L., Brumhard, S., Michalick, L., Lippert, L. J., Kostevc, T., Gäbel, C., Schneider, M., Streitz, M., Demichev, V., Gemünd, I., Barone, M., Tober-Lau, P., Helbig, E. T., Hillus, D., Petrov, L., Stein, J., Dey, H. P., Paclik, D., … PA-COVID-19 Study Group (2021). Complement activation induces excessive T cell cytotoxicity in severe COVID-19. Cell, 185(3), 493–512.e25. Advance online publication. https://doi.org/10.1016/j.cell.2021.12.040
Interlandi, M., Kerl, K., & Dugas, M. (2022). InterCellar enables interactive analysis and exploration of cell-cell communication in single-cell transcriptomic data. Communications biology, 5(1), 21. https://doi.org/10.1038/s42003-021-02986-2
Wendisch, D., Dietrich, O., Mari, T., von Stillfried, S., Ibarra, I. L., Mittermaier, M., Mache, C., Chua, R. L., Knoll, R., Timm, S., Brumhard, S., Krammer, T., Zauber, H., Hiller, A. L., Pascual-Reguant, A., Mothes, R., Bülow, R. D., Schulze, J., Leipold, A. M., Djudjaj, S., … Sander, L. E. (2021). SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis. Cell, 184(26), 6243–6261.e27. https://doi.org/10.1016/j.cell.2021.11.033
Krämer, B., Knoll, R., Bonaguro, L., ToVinh, M., Raabe, J., Astaburuaga-García, R., Schulte-Schrepping, J., Kaiser, K. M., Rieke, G. J., Bischoff, J., Monin, M. B., Hoffmeister, C., Schlabe, S., De Domenico, E., Reusch, N., Händler, K., Reynolds, G., Blüthgen, N., Hack, G., Finnemann, C., … Nattermann, J. (2021). Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. Immunity, S1074-7613(21)00365-4. Advance online publication. https://doi.org/10.1016/j.immuni.2021.09.002
Lotfollahi, M., Naghipourfar, M., Luecken, M. D., Khajavi, M., Büttner, M., Wagenstetter, M., Avsec, Ž., Gayoso, A., Yosef, N., Interlandi, M., Rybakov, S., Misharin, A. V., & Theis, F. J. (2021). Mapping single-cell data to reference atlases by transfer learning. Nature biotechnology, 10.1038/s41587-021-01001-7. Advance online publication. https://doi.org/10.1038/s41587-021-01001-7
Masoodi, M., Peschka, M., Schmiedel, S., Haddad, M., Frye, M., Maas, C., Lohse, A., Huber, S., Kirchhof, P., Nofer, J. R., & Renné, T. (2022). Disturbed lipid and amino acid metabolisms in COVID-19 patients. Journal of molecular medicine (Berlin, Germany), 1–14. Advance online publication. https://doi.org/10.1007/s00109-022-02177-4
Krasemann, S., Haferkamp, U., Pfefferle, S., Woo, M. S., Heinrich, F., Schweizer, M., Appelt-Menzel, A., Cubukova, A., Barenberg, J., Leu, J., Hartmann, K., Thies, E., Littau, J. L., Sepulveda-Falla, D., Zhang, L., Ton, K., Liang, Y., Matschke, J., Ricklefs, F., Sauvigny, T., … Pless, O. (2022). The blood-brain barrier is dysregulated in COVID-19 and serves as a CNS entry route for SARS-CoV-2. Stem cell reports, S2213-6711(21)00650-0. Advance online publication. https://doi.org/10.1016/j.stemcr.2021.12.011
Neufeldt, C. J., Cerikan, B., Cortese, M., Frankish, J., Lee, J. Y., Plociennikowska, A., Heigwer, F., Prasad, V., Joecks, S., Burkart, S. S., Zander, D. Y., Subramanian, B., Gimi, R., Padmanabhan, S., Iyer, R., Gendarme, M., El Debs, B., Halama, N., Merle, U., Boutros, M., … Bartenschlager, R. (2022). SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB. Communications biology, 5(1), 45. https://doi.org/10.1038/s42003-021-02983-5
Fründt, T., Kuballa, L., Lütgehetman, M., Nörz, D., Arend, H., Brehm, T. T., Schulze Zur Wiesch, J., Horvatits, T., Horvatits, K., Huber, S., Wege, H., & Kluwe, J. (2021). Low incidence of COVID-19 in a prospective cohort of patients with liver cirrhosis and hepatocellular carcinoma treated at a tertiary medical center during the 2020 pandemic. PloS one, 16(12), e0258450. https://doi.org/10.1371/journal.pone.0258450
Koerber, N., Priller, A., Yazici, S., Bauer, T., Cheng, C. C., Mijočević, H., Wintersteller, H., Jeske, S., Vogel, E., Feuerherd, M., Tinnefeld, K., Winter, C., Ruland, J., Gerhard, M., Haller, B., Christa, C., Zelger, O., Roggendorf, H., Halle, M., Erber, J., … Knolle, P. A. (2022). Dynamics of spike-and nucleocapsid specific immunity during long-term follow-up and vaccination of SARS-CoV-2 convalescents. Nature communications, 13(1), 153. https://doi.org/10.1038/s41467-021-27649-y
Forster, J., Streng, A., Rudolph, P., Rücker, V., Wallstabe, J., Timme, S., Pietsch, F., Hartmann, K., Krauthausen, M., Schmidt, J., Ludwig, T., Gierszewski, D., Jans, T., Engels, G., Weißbrich, B., Romanos, M., Dölken, L., Heuschmann, P., Härtel, C., Gágyor, I., … Wü-KiTa-CoV Study Group (2022). Feasibility of SARS-CoV-2 Surveillance Testing Among Children and Childcare Workers at German Day Care Centers: A Nonrandomized Controlled Trial. JAMA network open, 5(1), e2142057. https://doi.org/10.1001/jamanetworkopen.2021.42057
Head, R. J., Lumbers, E. R., Jarrott, B., Tretter, F., Smith, G., Pringle, K. G., Islam, S., & Martin, J. H. (2022). Systems analysis shows that thermodynamic physiological and pharmacological fundamentals drive COVID-19 and response to treatment. Pharmacology research & perspectives, 10(1), e00922. https://doi.org/10.1002/prp2.922
Xu, G., Qi, F., Wang, H., Liu, Y., Wang, X., Zou, R., Yuan, J., Liao, X., Liu, Y., Zhang, S., & Zhang, Z. (2022). The Transient IFN Response and the Delay of Adaptive Immunity Feature the Severity of COVID-19. Frontiers in immunology, 12, 816745. https://doi.org/10.3389/fimmu.2021.816745
Henriques-Pons, A., Beghini, D. G., Silva, V., Iwao Horita, S., & da Silva, F. (2022). Pulmonary Mesenchymal Stem Cells in Mild Cases of COVID-19 Are Dedicated to Proliferation; In Severe Cases, They Control Inflammation, Make Cell Dispersion, and Tissue Regeneration. Frontiers in immunology, 12, 780900. https://doi.org/10.3389/fimmu.2021.780900
Zhao, M., Liu, Z., Shao, F., Zhou, W., Chen, Z., Xia, P., Wang, S., & Yang, P. (2022). Communication Pattern Changes Along With Declined IGF1 of Immune Cells in COVID-19 Patients During Disease Progression. Frontiers in immunology, 12, 729990. https://doi.org/10.3389/fimmu.2021.729990
Hofer U. (2022). SARS-CoV-2 ‘super-permissive’ cells. Nature reviews. Microbiology, 1. Advance online publication. https://doi.org/10.1038/s41579-022-00698-w
Ganier, C., Harun, N., Peplow, I., Du-Harpur, X., Arthurs, C., Watt, F. M., & Lynch, M. D. (2022). Angiotensin-Converting Enzyme 2 Expression Is Detectable in Keratinocytes, Cutaneous Appendages, and Blood Vessels by Multiplex RNA in Situ Hybridization. Advances in skin & wound care, 10.1097/01.ASW.0000819776.56007.18. Advance online publication. https://doi.org/10.1097/01.ASW.0000819776.56007.18
Databases, Tools and other Resources
Overview of resources for COVID-19 (single cell) research which are provided by members of the scientific community.
- COVID-19 Cell Atlas (Wellcome Sanger Institute, HCA, CZI)
- COVID-19 Data Portal (EMBL-EBI)
- DeCOI – Deutsche COVID-19 Omics Initiative
- Galaxy Europe server mirrors locally many COVID-19 datasets in the Galaxy data libraries
- Single Cell Portal – Special section devoted to COVID-19 studies (Broad Institute)
- de.NBI list of bioinformatic tools for coronavirus and COVID-19 research
- ELIXIR tools registry – contains COVID-19-specific software and analysis tools
- Galaxy Workflow to analyse genomics and cheminformatics data related to COVID-19
- Magellan: COVID-19 Omics Explorer (BIH/de.NBI) – web application for the display and analysis of next-generation sequencing data with a focus on COVID-19
- BIP! Finder for COVID-19 – aims to ease the exploration of COVID-19-related literature by enabling ranking articles
- Cell Press Coronavirus Resource Hub – latest COVID-19 content published by Cell Press journals, including protocols and articles
- CORD-19 – COVID-19 Open Research Dataset (Allen institute for AI) – free resource of more than 280,000 scholarly articles about the novel coronavirus for use by the global research community
- Covid Triage – search engine developed as part of SIBiLS (Swiss Institute of Bioinformatics Literature Services) to rank the COVID-19 literature (Medline, PMC, Cord-19) according to the 9 axes of the COVoc ontology (controlled vocabulary to support literature triage for COVID-19)
- Europe PMC COVID-19 preprints initiative – Indexing the full text of COVID-19 related preprints to make them searchable alongside peer-reviewed articles via Europe PMC
- iSearch COVID-19 Portfolio – comprehensive, expert-curated source for publications and preprints related to COVID-19 / SARS-CoV-2, with powerful search functionality and faceting, including articles from PubMed and preprints from arXiv, bioRxiv, ChemRxiv, medRxiv, Research Square, and SSRN
- LitCovid – curated literature hub for tracking up-to-date scientific information about the the Coronavirus, providing a central access to relevant articles in PubMed with further categorization by different research topics and geographic locations for improved access
- COVID-19 Disease Map – open access knowledgebase and computational repository
- COVID-19 Host Genetics Initiative – brings together the human genetics community to generate, share, and analyze data to learn the genetic determinants of COVID-19 susceptibility, severity, and outcomes
- ELIXIR support to COVID-19 research – range of services (data storage, access, tools etc.) for studying the SARS-CoV-2 coronavirus and the COVID-19 disease
- EMBL and COVID-19 – research and support services related to COVID-19 provided by EMBL, including in collaboration with institutes in the Member States
- HCA – LifeTime alliance on COVID-19 single cell and omics (meta)data – overview of resources for COVID-19 single-cell and omics data and meta-data that have been shared by members of their and related communities
- HCA – LifeTime COVID-10 joint registry – registry of researchers who are using single-cell approaches to study the disease
- NIH Open-Access Data and Computational Resources to Address COVID-19 – links to COVID-19 open-access data, computational, and supporting resources
- SIB resources supporting SARS-CoV-2 research – SIB (Swiss Institute of Bioinformatics) experts and resources are taking part in the global effort to develop dedicated data services, analysis tools and improve knowledge sharing to fight the COVID-19 pandemic
- UCSC COVID-19 Resources -Fast-tracking visualization of genome sequences and analyses in the UCSC Genome Browser for SARS-Cov-2, incorporation of relevant biomedical datasets such as single-cell lung gene expression and links to other SARS-CoV-2 related resources
- Workflow for single-cell transcriptomics on infectious diseases including COVID-19 (STAR-Protocol by SCOG-partner Joachim L. Schultze, DZNE/LIMES Bonn)