{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T18:19:39Z","timestamp":1740161979385,"version":"3.37.3"},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T00:00:00Z","timestamp":1631059200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T00:00:00Z","timestamp":1631059200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"crossref","award":["LH2020C05"],"award-info":[{"award-number":["LH2020C05"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Cell Biosci"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Coronavirus disease 2019 (COVID-19) is an emerging infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and has posed a serious threat to global health. Here, we systematically characterized the transcription levels of the SARS-CoV-2 genes and identified the responsive human genes associated with virus infection. We inferred the possible biological functions of each viral gene and depicted the functional landscape based on guilt-by-association and functional enrichment analyses. Subsequently, the transcription factor regulatory network, protein\u2013protein interaction network, and non-coding RNA regulatory network were constructed to discover more potential antiviral targets. In addition, several potential drugs for COVID-19 treatment and prevention were recognized, including known cell proliferation-related, immune-related, and antiviral drugs, in which proteasome inhibitors (bortezomib, carfilzomib, and ixazomib citrate) may play an important role in the treatment of COVID-19. These results provided novel insights into the understanding of SARS-CoV-2 functional genomics and host-targeting antiviral strategies for SARS-CoV-2 infection.<\/jats:p>","DOI":"10.1186\/s13578-021-00684-4","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T07:02:39Z","timestamp":1631084559000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Inferring SARS-CoV-2 functional genomics from viral transcriptome with identification of potential antiviral drugs and therapeutic targets"],"prefix":"10.1186","volume":"11","author":[{"given":"Xu","family":"Pan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shangwei","family":"Ning","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9103-8642","authenticated-orcid":false,"given":"Hui","family":"Zhi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,9,8]]},"reference":[{"key":"684_CR1","first-page":"6219","volume":"69","author":"AD Davidson","year":"2020","unstructured":"Davidson AD, Williamson MK, Lewis S, Shoemark D, Carroll MW, Heesom K, Zambon M, Ellis J, Lewis PA, Hiscox JA, Matthews DA. Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site. bioRxiv. 2020;69:6219.","journal-title":"bioRxiv"},{"key":"684_CR2","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1038\/35001165","volume":"403","author":"S Oliver","year":"2000","unstructured":"Oliver S. Guilt-by-association goes global. Nature. 2000;403:601\u20133.","journal-title":"Nature"},{"key":"684_CR3","doi-asserted-by":"publisher","first-page":"102571","DOI":"10.1016\/j.autrev.2020.102571","volume":"19","author":"P Fagone","year":"2020","unstructured":"Fagone P, Ciurleo R, Lombardo SD, Iacobello C, Palermo CI, Shoenfeld Y, Bendtzen K, Bramanti P, Nicoletti F. Transcriptional landscape of SARS-CoV-2 infection dismantles pathogenic pathways activated by the virus, proposes unique sex-specific differences and predicts tailored therapeutic strategies. Autoimmun Rev. 2020;19:102571\u2013102571.","journal-title":"Autoimmun Rev"},{"key":"684_CR4","doi-asserted-by":"publisher","first-page":"108450","DOI":"10.1016\/j.clim.2020.108450","volume":"215","author":"S Mastaglio","year":"2020","unstructured":"Mastaglio S, Ruggeri A, Risitano AM, Angelillo P, Yancopoulou D, Mastellos DC, Huber-Lang M, Piemontese S, Assanelli A, Garlanda C, et al. The first case of COVID-19 treated with the complement C3 inhibitor AMY-101. Clinical Immunol. 2020;215:108450\u2013108450.","journal-title":"Clinical Immunol"},{"key":"684_CR5","doi-asserted-by":"publisher","first-page":"2637","DOI":"10.1007\/s42399-020-00610-8","volume":"2","author":"MH Ahmed","year":"2020","unstructured":"Ahmed MH, Hassan A. Dexamethasone for the treatment of coronavirus disease (COVID-19): a review. SN Compr Clin Med. 2020;2:2637\u201346.","journal-title":"SN Compr Clin Med"},{"key":"684_CR6","doi-asserted-by":"publisher","first-page":"e9357","DOI":"10.7717\/peerj.9357","volume":"8","author":"T Loganathan","year":"2020","unstructured":"Loganathan T, Ramachandran S, Shankaran P, Nagarajan D, Mohan SS. Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach. PeerJ. 2020;8:e9357.","journal-title":"PeerJ"},{"key":"684_CR7","doi-asserted-by":"publisher","first-page":"9606","DOI":"10.1038\/s41598-021-88313-5","volume":"11","author":"KK Oh","year":"2021","unstructured":"Oh KK, Adnan M, Cho DH. Network pharmacology approach to decipher signaling pathways associated with target proteins of NSAIDs against COVID-19. Sci Rep. 2021;11:9606.","journal-title":"Sci Rep"},{"key":"684_CR8","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/s41467-021-21085-8","volume":"12","author":"J Pang","year":"2021","unstructured":"Pang J, Xu F, Aondio G, Li Y, Fumagalli A, Lu M, Valmadre G, Wei J, Bian Y, Canesi M, et al. Efficacy and tolerability of bevacizumab in patients with severe Covid-19. Nat Commun. 2021;12:814.","journal-title":"Nat Commun"},{"key":"684_CR9","doi-asserted-by":"publisher","first-page":"3277","DOI":"10.1021\/acs.jcim.0c00179","volume":"60","author":"J Wang","year":"2020","unstructured":"Wang J. Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study. J Chem Inf Model. 2020;60:3277\u201386.","journal-title":"J Chem Inf Model"},{"key":"684_CR10","doi-asserted-by":"publisher","first-page":"e1001176","DOI":"10.1371\/journal.ppat.1001176","volume":"6","author":"AJ te Velthuis","year":"2010","unstructured":"te Velthuis AJ, van den Worm SH, Sims AC, Baric RS, Snijder EJ, van Hemert MJ. Zn(2+) inhibits coronavirus and arterivirus RNA polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture. PLoS Pathog. 2010;6:e1001176.","journal-title":"PLoS Pathog"},{"key":"684_CR11","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/j.ijid.2020.09.014","volume":"100","author":"D Jothimani","year":"2020","unstructured":"Jothimani D, Kailasam E, Danielraj S, Nallathambi B, Ramachandran H, Sekar P, Manoharan S, Ramani V, Narasimhan G, Kaliamoorthy I, Rela M. COVID-19: poor outcomes in patients with zinc deficiency. Int J Infect Dis. 2020;100:343\u20139.","journal-title":"Int J Infect Dis"},{"key":"684_CR12","doi-asserted-by":"publisher","first-page":"4326","DOI":"10.1002\/jmv.26932","volume":"93","author":"N Ali","year":"2021","unstructured":"Ali N, Fariha KA, Islam F, Mohanto NC, Ahmad I, Hosen MJ, Ahmed S. Assessment of the role of zinc in the prevention of COVID-19 infections and mortality: a retrospective study in the Asian and European population. J Med Virol. 2021;93:4326\u201333.","journal-title":"J Med Virol"}],"container-title":["Cell &amp; Bioscience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13578-021-00684-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13578-021-00684-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13578-021-00684-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T07:22:03Z","timestamp":1631085723000},"score":1,"resource":{"primary":{"URL":"https:\/\/cellandbioscience.biomedcentral.com\/articles\/10.1186\/s13578-021-00684-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,8]]},"references-count":12,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["684"],"URL":"https:\/\/doi.org\/10.1186\/s13578-021-00684-4","relation":{},"ISSN":["2045-3701"],"issn-type":[{"type":"electronic","value":"2045-3701"}],"subject":[],"published":{"date-parts":[[2021,9,8]]},"assertion":[{"value":"20 April 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 August 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 September 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declared no potential competing interests in terms of the research, authorship, and\/or publication of this article.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"171"}}