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

Türei, D., Valdeolivas, A., Gul, L., Palacio-Escat, N., Klein, M., Ivanova, O., Ölbei, M., Gábor, A., Theis, F., Módos, D., Korcsmáros, T., & Saez-Rodriguez, J. (2021). Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Molecular systems biology17(3), e9923. https://doi.org/10.15252/msb.20209923

Muus, C., Luecken, M. D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E. D., Subramanian, A., Smillie, C., Jagadeesh, K. A., Duong, E. T., Fiskin, E., Triglia, E. T., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., … Human Cell Atlas Lung Biological Network (2021). Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature medicine27(3), 546–559. https://doi.org/10.1038/s41591-020-01227-z

Wyler, E., Mösbauer, K., Franke, V., Diag, A., Gottula, L. T., Arsiè, R., Klironomos, F., Koppstein, D., Hönzke, K., Ayoub, S., Buccitelli, C., Hoffmann, K., Richter, A., Legnini, I., Ivanov, A., Mari, T., Del Giudice, S., Papies, J., Praktiknjo, S., Meyer, T. F., … Landthaler, M. (2021). Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy. iScience24(3), 102151. https://doi.org/10.1016/j.isci.2021.102151

Heming, M., Li, X., Räuber, S., Mausberg, A. K., Börsch, A. L., Hartlehnert, M., Singhal, A., Lu, I. N., Fleischer, M., Szepanowski, F., Witzke, O., Brenner, T., Dittmer, U., Yosef, N., Kleinschnitz, C., Wiendl, H., Stettner, M., & Meyer Zu Hörste, G. (2021). Neurological Manifestations of COVID-19 Feature T Cell Exhaustion and Dedifferentiated Monocytes in Cerebrospinal Fluid. Immunity54(1), 164–175.e6. https://doi.org/10.1016/j.immuni.2020.12.011

De Domenico, E., Bonaguro, L., Schulte-Schrepping, J., Becker, M., Händler, K., & Schultze, J. L. (2020). Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19. STAR protocols1(3), 100233. https://doi.org/10.1016/j.xpro.2020.100233

Bernardes, J. P., Mishra, N., Tran, F., Bahmer, T., Best, L., Blase, J. I., Bordoni, D., Franzenburg, J., Geisen, U., Josephs-Spaulding, J., Köhler, P., Künstner, A., Rosati, E., Aschenbrenner, A. C., Bacher, P., Baran, N., Boysen, T., Brandt, B., Bruse, N., Dörr, J., … Deutsche COVID-19 Omics Initiative (DeCOI) (2020). Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. Immunity53(6), 1296–1314.e9. https://doi.org/10.1016/j.immuni.2020.11.017

Schulte-Schrepping, J., Reusch, N., Paclik, D., Baßler, K., Schlickeiser, S., Zhang, B., Krämer, B., Krammer, T., Brumhard, S., Bonaguro, L., De Domenico, E., Wendisch, D., Grasshoff, M., Kapellos, T. S., Beckstette, M., Pecht, T., Saglam, A., Dietrich, O., Mei, H. E., Schulz, A. R., … Deutsche COVID-19 OMICS Initiative (DeCOI) (2020). Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell182(6), 1419–1440.e23. https://doi.org/10.1016/j.cell.2020.08.001

Ziegler, C., Allon, S. J., Nyquist, S. K., Mbano, I. M., Miao, V. N., Tzouanas, C. N., Cao, Y., Yousif, A. S., Bals, J., Hauser, B. M., Feldman, J., Muus, C., Wadsworth, M. H., 2nd, Kazer, S. W., Hughes, T. K., Doran, B., Gatter, G. J., Vukovic, M., Taliaferro, F., Mead, B. E., … HCA Lung Biological Network (2020). SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell181(5), 1016–1035.e19. https://doi.org/10.1016/j.cell.2020.04.035

Sungnak, W., Huang, N., Bécavin, C., Berg, M., Queen, R., Litvinukova, M., Talavera-López, C., Maatz, H., Reichart, D., Sampaziotis, F., Worlock, K. B., Yoshida, M., Barnes, J. L., & HCA Lung Biological Network (2020). SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature medicine26(5), 681–687. https://doi.org/10.1038/s41591-020-0868-6

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Varghese, J., Sandmann, S., Ochs, K., Schrempf, I. M., Frömmel, C., Dugas, M., Schmidt, H. H., Vollenberg, R., & Tepasse, P. R. (2021). Persistent symptoms and lab abnormalities in patients who recovered from COVID-19. Scientific reports11(1), 12775. https://doi.org/10.1038/s41598-021-91270-8

Rubio-Acero, R., Castelletti, N., Fingerle, V., Olbrich, L., Bakuli, A., Wölfel, R., Girl, P., Müller, K., Jochum, S., Strobl, M., Hoelscher, M., Wieser, A., & KoCo19 study team (2021). In Search of the SARS-CoV-2 Protection Correlate: Head-to-Head Comparison of Two Quantitative S1 Assays in Pre-characterized Oligo-/Asymptomatic Patients. Infectious diseases and therapy, 10.1007/s40121-021-00475-x. Advance online publication. https://doi.org/10.1007/s40121-021-00475-x

Theobald, S. J., Simonis, A., Georgomanolis, T., Kreer, C., Zehner, M., Eisfeld, H. S., Albert, M. C., Chhen, J., Motameny, S., Erger, F., Fischer, J., Malin, J. J., Gräb, J., Winter, S., Pouikli, A., David, F., Böll, B., Koehler, P., Vanshylla, K., Gruell, H., … Rybniker, J. (2021). Long-lived macrophage reprogramming drives spike protein-mediated inflammasome activation in COVID-19. EMBO molecular medicine, e14150. Advance online publication. https://doi.org/10.15252/emmm.202114150

Netea, M. G., & Li, Y. (2021). Immune memory in individuals with COVID-19. Nature cell biology23(6), 582–584. https://doi.org/10.1038/s41556-021-00689-8

Roncoroni, M., Droesbeke, B., Eguinoa, I., De Ruyck, K., D’Anna, F., Yusuf, D., Grüning, B., Backofen, R., & Coppens, F. (2021). A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinformatics (Oxford, England), btab421. Advance online publication. https://doi.org/10.1093/bioinformatics/btab421

Brand, I., Gilberg, L., Bruger, J., Garí, M., Wieser, A., Eser, T. M., Frese, J., Ahmed, M., Rubio-Acero, R., Guggenbuehl Noller, J. M., Castelletti, N., Diekmannshemke, J., Thiesbrummel, S., Huynh, D., Winter, S., Kroidl, I., Fuchs, C., Hoelscher, M., Roider, J., Kobold, S., … Geldmacher, C. (2021). Broad T Cell Targeting of Structural Proteins After SARS-CoV-2 Infection: High Throughput Assessment of T Cell Reactivity Using an Automated Interferon Gamma Release Assay. Frontiers in immunology12, 688436. https://doi.org/10.3389/fimmu.2021.688436

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Ma, D., Liu, S., Hu, L., He, Q., Shi, W., Yan, D., Cao, Y., Zhang, G., Wang, Z., Wu, J., & Jiang, C. (2021). Single-cell RNA sequencing identify SDCBP in ACE2-positive bronchial epithelial cells negatively correlates with COVID-19 severity. Journal of cellular and molecular medicine, 10.1111/jcmm.16714. Advance online publication. https://doi.org/10.1111/jcmm.16714

Wilk, A. J., Lee, M. J., Wei, B., Parks, B., Pi, R., Martínez-Colón, G. J., Ranganath, T., Zhao, N. Q., Taylor, S., Becker, W., Stanford COVID-19 Biobank, Jimenez-Morales, D., Blomkalns, A. L., O’Hara, R., Ashley, E. A., Nadeau, K. C., Yang, S., Holmes, S., Rabinovitch, M., Rogers, A. J., … Blish, C. A. (2021). Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. The Journal of experimental medicine218(8), e20210582. https://doi.org/10.1084/jem.20210582

Jin, K., Bardes, E. E., Mitelpunkt, A., Wang, J. Y., Bhatnagar, S., Sengupta, S., Krummel, D. P., Rothenberg, M. E., & Aronow, B. J. (2021). A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses. bioRxiv : the preprint server for biology, 2021.06.07.447287. https://doi.org/10.1101/2021.06.07.447287

Li, R., Liclican, A., Xu, Y., Pitts, J., Niu, C., Zhang, J., Kim, C., Zhao, X., Soohoo, D., Babusis, D., Yue, Q., Ma, B., Murray, B. P., Subramanian, R., Xie, X., Zou, J., Bilello, J. P., Li, L., Schultz, B. E., Sakowicz, R., … Feng, J. Y. (2021). Key Metabolic Enzymes Involved in Remdesivir Activation in Human Lung Cells. Antimicrobial agents and chemotherapy, AAC0060221. Advance online publication. https://doi.org/10.1128/AAC.00602-21

Davidson, S. M., Padró, T., Bollini, S., Vilahur, G., Duncker, D. J., Evans, P. C., Guzik, T., Hoefer, I. E., Waltenberger, J., Wojta, J., & Weber, C. (2021). Progress in cardiac research – from rebooting cardiac regeneration to a complete cell atlas of the heart. Cardiovascular research, cvab200. Advance online publication. https://doi.org/10.1093/cvr/cvab200

Huo, L., Jiao Li, J., Chen, L., Yu, Z., Hutvagner, G., & Li, J. (2021). Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects. Briefings in bioinformatics, bbab229. Advance online publication. https://doi.org/10.1093/bib/bbab229

Yang, B., Fan, J., Huang, J., Guo, E., Fu, Y., Liu, S., Xiao, R., Liu, C., Lu, F., Qin, T., He, C., Wang, Z., Qin, X., Hu, D., You, L., Li, X., Wang, T., Wu, P., Chen, G., Zhou, J., … Sun, C. (2021). Clinical and molecular characteristics of COVID-19 patients with persistent SARS-CoV-2 infection. Nature communications12(1), 3501. https://doi.org/10.1038/s41467-021-23621-y

Zhou, Y., Xu, J., Hou, Y., Leverenz, J. B., Kallianpur, A., Mehra, R., Liu, Y., Yu, H., Pieper, A. A., Jehi, L., & Cheng, F. (2021). Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. Alzheimer’s research & therapy13(1), 110. https://doi.org/10.1186/s13195-021-00850-3

Wang, Q., Li, L., Qu, T., Li, J., Wu, L., Li, K., Wang, Z., Zhu, M., Huang, B., Wu, W., Wu, M., Ding, R., Zhang, Z., Wang, Q., Xia, X., Li, P., Zhang, Z., & Guo, R. (2021). High Expression of ACE2 and TMPRSS2 at the Resection Margin Makes Lung Cancer Survivors Susceptible to SARS-CoV-2 With Unfavorable Prognosis. Frontiers in oncology11, 644575. https://doi.org/10.3389/fonc.2021.644575

Zheng M. (2021). Cellular Tropism of SARS-CoV-2 across Human Tissues and Age-related Expression of ACE2 and TMPRSS2 in Immune-inflammatory Stromal Cells. Aging and disease12(3), 718–725. https://doi.org/10.14336/AD.2021.0429

He, J., Lin, Y., Meng, M., Li, J., Yang, J. Y., & Wang, H. (2021). Construction of a Human Cell Landscape of COVID-19 Infection at Single-cell Level. Aging and disease12(3), 705–709. https://doi.org/10.14336/AD.2021.0301

Zhu, D., Yan, H., Zhou, Z., Tang, J., Liu, X., Hartmann, R., Parak, W. J., Shen, Y., & Feliu, N. (2021). Influence of the Modulation of the Protein Corona on Gene Expression Using Polyethylenimine (PEI) Polyplexes as Delivery Vehicle. Advanced healthcare materials, e2100125. Advance online publication. https://doi.org/10.1002/adhm.202100125

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Databases, Tools and other Resources

Overview of resources for COVID-19 (single cell) research which are provided by members of the scientific community.

  • 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