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Cited by 200

The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Open access
Butler, Daniel, Mozsary, Christopher, Meydan, Cem, Foox, Jonathan, Rosiene, Joel, Shaiber, Alon, Danko, David, Afshinnekoo, Ebrahim, MacKay, Matthew, Sedlazeck, Fritz J., Ivanov, Nikolay A., Sierra, Maria, Pohle, Diana, Zietz, Michael, Gisladottir, Undina, Ramlall, Vijendra, Sholle, Evan T., Schenck, Edward J., Westover, Craig D., Hassan, Ciaran, Ryon, Krista, Young, Benjamin, Bhattacharya, Chandrima, Ng, Dianna L., Granados, Andrea C., Santos, Yale A., Servellita, Venice, Federman, Scot, Ruggiero, Phyllis, Fungtammasan, Arkarachai, Chin, Chen-Shan, Pearson, Nathaniel M., Langhorst, Bradley W., Tanner, Nathan A., Kim, Youngmi, Reeves, Jason W., Hether, Tyler D., Warren, Sarah E., Bailey, Michael, Gawrys, Justyna, Meleshko, Dmitry, Xu, Dong, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya, Barrows, Joseph, Wells, Heather, O’Hara, Niamh B., Rosenfeld, Jeffrey A., Chen, Ying, Steel, Peter A. D., Shemesh, Amos J., Xiang, Jenny, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Iftner, Angelika, Bezdan, Daniela, Sanchez, Elizabeth, Campion, Thomas R., Sipley, John, Cong, Lin, Craney, Arryn, Velu, Priya, Melnick, Ari M., Shapira, Sagi, Hajirasouliha, Iman, Borczuk, Alain, Iftner, Thomas, Salvatore, Mirella, Loda, Massimo, Westblade, Lars F., Cushing, Melissa, Wu, Shixiu, Levy, Shawn, Chiu, Charles, Schwartz, Robert E., Tatonetti, Nicholas, Rennert, Hanna, Imielinski, Marcin, Mason, Christopher E.·2021·Nature Communications
DOI 10.1038/s41467-021-21361-7
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Abstract

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin–angiotensin–aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

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Authors
Butler, D., Mozsary, C., Meydan, C., Foox, J., Rosiene, J., Shaiber, A., Danko, D., Afshinnekoo, E., MacKay, M., Sedlazeck, F. J., Ivanov, N. A., Sierra, M., Pohle, D., Zietz, M., Gisladottir, U., Ramlall, V., Sholle, E. T., Schenck, E. J., Westover, C. D., Hassan, C., Ryon, K., Young, B., Bhattacharya, C., Ng, D. L., Granados, A. C., Santos, Y. A., Servellita, V., Federman, S., Ruggiero, P., Fungtammasan, A., Chin, C.-S., Pearson, N. M., Langhorst, B. W., Tanner, N. A., Kim, Y., Reeves, J. W., Hether, T. D., Warren, S. E., Bailey, M., Gawrys, J., Meleshko, D., Xu, D., Couto-Rodriguez, M., Nagy-Szakal, D., Barrows, J., Wells, H., O’Hara, N. B., Rosenfeld, J. A., Chen, Y., Steel, P. A. D., Shemesh, A. J., Xiang, J., Thierry-Mieg, J., Thierry-Mieg, D., Iftner, A., Bezdan, D., Sanchez, E., Campion, T. R., Sipley, J., Cong, L., Craney, A., Velu, P., Melnick, A. M., Shapira, S., Hajirasouliha, I., Borczuk, A., Iftner, T., Salvatore, M., Loda, M., Westblade, L. F., Cushing, M., Wu, S., Levy, S., Chiu, C., Schwartz, R. E., Tatonetti, N., Rennert, H., Imielinski, M., & Mason, C. E.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2021-03-12
Volume
12
Issue
1
Pages
1660-1660
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-021-21361-7
OpenAlex
W3133845106
Cited by
200
References
31
FWCI
11.85
Type
journal article
Language
en
Open access
gold

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CoChat. (2026). Citation check: Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. https://app.cochat.ai/papers/10.1038/s41467-021-21361-7
The paper
Butler, D., Mozsary, C., Meydan, C., Foox, J., Rosiene, J., Shaiber, A., Danko, D., Afshinnekoo, E., MacKay, M., Sedlazeck, F. J., Ivanov, N. A., Sierra, M., Pohle, D., Zietz, M., Gisladottir, U., Ramlall, V., Sholle, E. T., Schenck, E. J., Westover, C. D., . . . Mason, C. E. (2021). Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nature Communications. https://doi.org/10.1038/s41467-021-21361-7

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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.