{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T18:05:58Z","timestamp":1786989958351,"version":"build-2736575974"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T00:00:00Z","timestamp":1715644800000},"content-version":"vor","delay-in-days":306,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,7,13]],"date-time":"2023-07-13T00:00:00Z","timestamp":1689206400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,7,7]],"date-time":"2023-07-07T00:00:00Z","timestamp":1688688000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFC0863300"],"award-info":[{"award-number":["2021YFC0863300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDB0490000"],"award-info":[{"award-number":["XDB0490000"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["2021-I2M-1-024"],"award-info":[{"award-number":["2021-I2M-1-024"]}]},{"name":"STI2030-Major Projects","award":["2021ZD0200900"],"award-info":[{"award-number":["2021ZD0200900"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82221004"],"award-info":[{"award-number":["82221004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32121001"],"award-info":[{"award-number":["32121001"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200460"],"award-info":[{"award-number":["32200460"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200460"],"award-info":[{"award-number":["32200460"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012692","name":"K. C. Wong Education Foundation","doi-asserted-by":"publisher","award":["GJTD-2019-08"],"award-info":[{"award-number":["GJTD-2019-08"]}],"id":[{"id":"10.13039\/501100012692","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project, China","award":["2017SHZDZX01"],"award-info":[{"award-number":["2017SHZDZX01"]}]},{"name":"China National Postdoctoral Program for Innovative Talents","award":["BX2021291"],"award-info":[{"award-number":["BX2021291"]}]},{"DOI":"10.13039\/501100012659","name":"Foundation for Innovative Research Groups of the National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82221004"],"award-info":[{"award-number":["82221004"]}],"id":[{"id":"10.13039\/501100012659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDB0490000"],"award-info":[{"award-number":["XDB0490000"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012692","name":"K. C. Wong Education Foundation","doi-asserted-by":"publisher","award":["GJTD-2019-08"],"award-info":[{"award-number":["GJTD-2019-08"]}],"id":[{"id":"10.13039\/501100012692","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003345","name":"Chinese Academy of Meteorological Sciences","doi-asserted-by":"publisher","award":["2021-I2M-1-024"],"award-info":[{"award-number":["2021-I2M-1-024"]}],"id":[{"id":"10.13039\/501100003345","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003345","name":"Chinese Academy of Meteorological Sciences","doi-asserted-by":"publisher","award":["2021ZD0200900"],"award-info":[{"award-number":["2021ZD0200900"]}],"id":[{"id":"10.13039\/501100003345","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["2017SHZDZX01"],"award-info":[{"award-number":["2017SHZDZX01"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012152","name":"National Postdoctoral Program for Innovative Talents","doi-asserted-by":"publisher","award":["BX2021291"],"award-info":[{"award-number":["BX2021291"]}],"id":[{"id":"10.13039\/501100012152","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFC0863300"],"award-info":[{"award-number":["2021YFC0863300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32121001"],"award-info":[{"award-number":["32121001"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200460"],"award-info":[{"award-number":["32200460"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2023,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the persistent coronavirus disease 2019 (COVID-19) pandemic, which has resulted in millions of deaths worldwide and brought an enormous public health and global economic burden. The recurring global wave of infections has been exacerbated by growing variants of SARS-CoV-2. In this study, the virological characteristics of the original SARS-CoV-2 strain and its variants of concern (VOCs; including Alpha, Beta, and Delta) in vitro, as well as differential transcriptomic landscapes in multiple organs (lung, right ventricle, blood, cerebral cortex, and cerebellum) from the infected rhesus macaques, were elucidated. The original strain of SARS-CoV-2 caused a stronger innate immune response in host cells, and its VOCs markedly increased the levels of subgenomic RNA \u00a0s, such as N, Orf9b, Orf6, and Orf7ab, which are known as the innate immune antagonists and the inhibitors of antiviral factors. Intriguingly, the original SARS-CoV-2 strain and Alpha variant induced larger alteration of RNA abundance in tissues of rhesus monkeys than Beta and Delta variants did. Moreover, a hyperinflammatory state and active immune response were shown in the right ventricles of rhesus monkeys by the up-regulation of inflammation- and immune-related RNAs. Furthermore, peripheral blood may mediate signaling transmission among tissues to coordinate the molecular changes in the infected individuals. Collectively, these data provide insights into the pathogenesis of COVID-19 at the early stage of infection by the original SARS-CoV-2 strain and its VOCs.<\/jats:p>","DOI":"10.1016\/j.gpb.2023.06.002","type":"journal-article","created":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T21:57:11Z","timestamp":1689199031000},"page":"1014-1029","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"title":["Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques"],"prefix":"10.1093","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9814-0081","authenticated-orcid":false,"given":"Tingfu","family":"Du","sequence":"first","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"},{"name":"State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College , Beijing, 100005 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5591-1034","authenticated-orcid":false,"given":"Chunchun","family":"Gao","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing, 100101 , China"},{"name":"Sino-Danish College, University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1675-9735","authenticated-orcid":false,"given":"Shuaiyao","family":"Lu","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4104-7692","authenticated-orcid":false,"given":"Qianlan","family":"Liu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing, 100101 , China"},{"name":"Sino-Danish College, University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9986-5930","authenticated-orcid":false,"given":"Yun","family":"Yang","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3205-2062","authenticated-orcid":false,"given":"Wenhai","family":"Yu","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3811-4970","authenticated-orcid":false,"given":"Wenjie","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6864-306X","authenticated-orcid":false,"given":"Yong","family":"Qiao Sun","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2718-2820","authenticated-orcid":false,"given":"Cong","family":"Tang","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9668-0666","authenticated-orcid":false,"given":"Junbin","family":"Wang","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7305-1269","authenticated-orcid":false,"given":"Jiahong","family":"Gao","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1983-4817","authenticated-orcid":false,"given":"Yong","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8367-0311","authenticated-orcid":false,"given":"Fangyu","family":"Luo","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8104-5985","authenticated-orcid":false,"given":"Ying","family":"Yang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing, 100101 , China"},{"name":"Sino-Danish College, University of Chinese Academy of Sciences , Beijing, 100049 , China"},{"name":"Institute of Stem Cell and Regeneration, Chinese Academy of Sciences , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2821-8541","authenticated-orcid":false,"given":"Yun-Gui","family":"Yang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing, 100101 , China"},{"name":"Sino-Danish College, University of Chinese Academy of Sciences , Beijing, 100049 , China"},{"name":"Institute of Stem Cell and Regeneration, Chinese Academy of Sciences , Beijing, 100101 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9592-9554","authenticated-orcid":false,"given":"Xiaozhong","family":"Peng","sequence":"additional","affiliation":[{"name":"National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Kunming, 650118 , China"},{"name":"State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College , Beijing, 100005 , China"},{"name":"Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, 100021 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,7,13]]},"reference":[{"key":"2024051404191113400_b0005","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.834098","article-title":"SARS-CoV-2\u2019s variants of concern: a brief characterization","volume":"13","author":"Scovino","year":"2022","journal-title":"Front Immunol"},{"key":"2024051404191113400_b0010","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/s41591-020-0796-5","article-title":"Emergence of a novel human coronavirus threatening human health","volume":"26","author":"Poon","year":"2020","journal-title":"Nat Med"},{"key":"2024051404191113400_b0015","article-title":"The biological functions and clinical significance of SARS-CoV-2 variants of corcern","volume":"9","author":"Akkiz","year":"2022","journal-title":"Front Med (Lausanne)"},{"key":"2024051404191113400_b0020","article-title":"SARS-CoV-2 variants of concern: a review","author":"Sarkar","year":"2023;93:2337","journal-title":"Monaldi Arch Chest Dis"},{"key":"2024051404191113400_b0025","doi-asserted-by":"crossref","DOI":"10.1016\/j.intimp.2022.108565","article-title":"A review on evolution of emerging SARS-CoV-2 variants based on spike glycoprotein","volume":"105","author":"Ghosh","year":"2022","journal-title":"Int Immunopharmacol"},{"key":"2024051404191113400_b0030","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/s11658-022-00352-6","article-title":"SARS-CoV-2: phenotype, genotype, and characterization of different variants","volume":"27","author":"Saberiyan","year":"2022","journal-title":"Cell Mol Biol Lett"},{"key":"2024051404191113400_b0035","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1038\/s41392-022-01039-2","article-title":"Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants","volume":"7","author":"Sun","year":"2022","journal-title":"Signal Transduct Target Ther"},{"key":"2024051404191113400_b0040","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1016\/S1473-3099(21)00170-5","article-title":"Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study","volume":"21","author":"Frampton","year":"2021","journal-title":"Lancet Infect Dis"},{"key":"2024051404191113400_b0045","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/s41586-021-03402-9","article-title":"Detection of a SARS-CoV-2 variant of concern in South Africa","volume":"592","author":"Tegally","year":"2021","journal-title":"Nature"},{"key":"2024051404191113400_b0050","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/s41586-021-03470-x","article-title":"Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England","volume":"593","author":"Volz","year":"2021","journal-title":"Nature"},{"key":"2024051404191113400_b0055","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/d41586-021-01274-7","article-title":"Coronavirus variants are spreading in India - what scientists know so far","volume":"593","author":"Vaidyanathan","year":"2021","journal-title":"Nature"},{"key":"2024051404191113400_b0060","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"Harvey","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"2024051404191113400_b0065","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1016\/j.cell.2020.07.012","article-title":"The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity","volume":"182","author":"Li","year":"2020","journal-title":"Cell"},{"key":"2024051404191113400_b0070","doi-asserted-by":"crossref","first-page":"6229","DOI":"10.1016\/j.cell.2021.11.026","article-title":"Population impact of SARS-CoV-2 variants with enhanced transmissibility and\/or partial immune escape","volume":"184","author":"Bushman","year":"2021","journal-title":"Cell"},{"key":"2024051404191113400_b0075","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel coronavirus from patients with pneumonia in China, 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"N Engl J Med"},{"key":"2024051404191113400_b0080","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/S2468-1253(20)30057-1","article-title":"Liver injury in COVID-19: management and challenges","volume":"5","author":"Zhang","year":"2020","journal-title":"Lancet Gastroenterol Hepatol"},{"key":"2024051404191113400_b0085","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1016\/S2213-2600(20)30229-0","article-title":"Management of acute kidney injury in patients with COVID-19","volume":"8","author":"Ronco","year":"2020","journal-title":"Lancet Respir Med"},{"key":"2024051404191113400_b0090","doi-asserted-by":"crossref","first-page":"9970","DOI":"10.12998\/wjcc.v10.i28.9970","article-title":"COVID-19 and the heart","volume":"10","author":"Xanthopoulos","year":"2022","journal-title":"World J Clin Cases"},{"key":"2024051404191113400_b0095","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/cid\/ciab437","article-title":"Increased peripheral blood neutrophil activation phenotypes and neutrophil extracellular trap formation in critically ill coronavirus disease 2019 (COVID-19) patients: a case series and review of the literature","volume":"74","author":"Masso-Silva","year":"2022","journal-title":"Clin Infect Dis"},{"key":"2024051404191113400_b0100","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1038\/s41586-022-05542-y","article-title":"SARS-CoV-2 infection and persistence in the human body and brain at autopsy","volume":"612","author":"Stein","year":"2022","journal-title":"Nature"},{"key":"2024051404191113400_b0105","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1007\/s13238-022-00915-5","article-title":"Differential transcriptomic landscapes of multiple organs from SARS-CoV-2 early infected rhesus macaques","volume":"13","author":"Gao","year":"2022","journal-title":"Protein Cell"},{"key":"2024051404191113400_b0110","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1126\/science.abb2507","article-title":"Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation","volume":"367","author":"Wrapp","year":"2020","journal-title":"Science"},{"key":"2024051404191113400_b0115","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/s41422-021-00595-6","article-title":"Receptome profiling identifies KREMEN1 and ASGR1 as alternative functional receptors of SARS-CoV-2","volume":"32","author":"Gu","year":"2022","journal-title":"Cell Res"},{"key":"2024051404191113400_b0120","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/s41590-021-01091-0","article-title":"Innate immunity: the first line of defense against SARS-CoV-2","volume":"23","author":"Diamond","year":"2022","journal-title":"Nat Immunol"},{"key":"2024051404191113400_b0125","first-page":"11:3810","article-title":"Activation and evasion of type I interferon responses by SARS-CoV-2","author":"Lei","year":"2020","journal-title":"Nat Commun"},{"key":"2024051404191113400_b0130","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-021-04352-y","article-title":"Evolution of enhanced innate immune evasion by SARS-CoV-2","author":"Thorne","year":"2022;602:487\u2013495","journal-title":"Nature"},{"key":"2024051404191113400_b0135","doi-asserted-by":"crossref","first-page":"e0018821","DOI":"10.1128\/cmr.00188-21","article-title":"SARS-CoV-2 infection and lung regeneration","volume":"35","author":"Zhao","year":"2022","journal-title":"Clin Microbiol Rev"},{"key":"2024051404191113400_b0140","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1111\/cei.13523","article-title":"Innate immunity during SARS-CoV-2: evasion strategies and activation trigger hypoxia and vascular damage","volume":"202","author":"Amor","year":"2020","journal-title":"Clin Exp Immunol"},{"key":"2024051404191113400_b0145","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gkaa970","article-title":"KEGG: integrating viruses and cellular organisms","volume":"49","author":"Kanehisa","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024051404191113400_b0150","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nmeth.3337","article-title":"Robust enumeration of cell subsets from tissue expression profiles","volume":"12","author":"Newman","year":"2015","journal-title":"Nat Methods"},{"key":"2024051404191113400_b0155","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejphar.2020.173090","article-title":"Macrophage M1\/M2 polarization","volume":"877","author":"Yunna","year":"2020","journal-title":"Eur J Pharmacol"},{"key":"2024051404191113400_b0160","first-page":"13:1490","article-title":"Detection of IFN\u03b3-secreting CD4+ and CD8+ memory T cells in COVID-19 convalescents after stimulation of peripheral blood mononuclear cells with live SARS-CoV-2","author":"Matyushenko","year":"2021","journal-title":"Viruses"},{"key":"2024051404191113400_b0165","article-title":"CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice","volume":"22:bbaa269","author":"Shao","year":"2021","journal-title":"Brief Bioinform"},{"key":"2024051404191113400_b0170","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1111\/bph.15998","article-title":"Pathogenic roles of neutrophil-derived alarmins (S100A8\/A9) in heart failure: from molecular mechanisms to therapeutic insights","volume":"180","author":"Bai","year":"2023","journal-title":"Br J Pharmacol"},{"key":"2024051404191113400_b0175","doi-asserted-by":"crossref","first-page":"e23764","DOI":"10.1002\/jcla.23764","article-title":"The clinical significance of spondin 2 eccentric expression in peripheral blood mononuclear cells in bronchial asthma","volume":"35","author":"Zhou","year":"2021","journal-title":"J Clin Lab Anal"},{"key":"2024051404191113400_b0180","doi-asserted-by":"crossref","first-page":"2305","DOI":"10.1158\/0008-5472.CAN-17-2867","article-title":"SPON2 promotes M1-like macrophage recruitment and inhibits hepatocellular carcinoma metastasis by distinct integrin-Rho GTPase-Hippo pathways","volume":"78","author":"Zhang","year":"2018","journal-title":"Cancer Res"},{"key":"2024051404191113400_b0185","doi-asserted-by":"crossref","first-page":"1462","DOI":"10.1080\/15548627.2018.1475816","article-title":"LC3-associated phagocytosis initiated by integrin ITGAM-ITGB2\/Mac-1 enhances immunity to Listeria monocytogenes","volume":"14","author":"Herb","year":"2018","journal-title":"Autophagy"},{"key":"2024051404191113400_b0190","doi-asserted-by":"crossref","DOI":"10.1016\/j.beha.2022.101401","article-title":"COVID-19 disease and immune dysregulation","volume":"35","author":"Davitt","year":"2022","journal-title":"Best Pract Res Clin Haematol"},{"key":"2024051404191113400_b0195","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1016\/j.chom.2020.05.008","article-title":"Type I and type III interferons \u2013 induction, signaling, evasion, and application to combat COVID-19","volume":"27","author":"Park","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2024051404191113400_b0200","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1186\/s12967-022-03767-z","article-title":"Innate immunity, cytokine storm, and inflammatory cell death in COVID-19","volume":"20","author":"Karki","year":"2022","journal-title":"J Transl Med"},{"key":"2024051404191113400_b0205","doi-asserted-by":"crossref","first-page":"eabo6294","DOI":"10.1126\/sciimmunol.abo6294","article-title":"ZBP1-dependent inflammatory cell death, PANoptosis, and cytokine storm disrupt IFN therapeutic efficacy during coronavirus infection","volume":"7","author":"Karki","year":"2022","journal-title":"Sci Immunol"},{"key":"2024051404191113400_b0210","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1016\/j.chom.2021.05.004","article-title":"Innate immune and inflammatory responses to SARS-CoV-2: implications for COVID-19","volume":"29","author":"Lowery","year":"2021","journal-title":"Cell Host Microbe"},{"key":"2024051404191113400_b0215","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.3390\/v13071192","article-title":"Immune evasion of SARS-CoV-2 emerging variants: what have we learnt so far?","volume":"13","author":"Lazarevic","year":"2021","journal-title":"Viruses"},{"key":"2024051404191113400_b0220","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/s41586-021-04245-0","article-title":"The N501Y spike substitution enhances SARS-CoV-2 infection and transmission","volume":"602","author":"Liu","year":"2022","journal-title":"Nature"},{"key":"2024051404191113400_b0225","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/s41392-021-00644-x","article-title":"Fast-spreading SARS-CoV-2 variants: challenges to and new design strategies of COVID-19 vaccines","volume":"6","author":"Zhou","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"2024051404191113400_b0230","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/s41577-021-00556-5","article-title":"Will SARS-CoV-2 variants of concern affect the promise of vaccines?","volume":"21","author":"Gupta","year":"2021","journal-title":"Nat Rev Immunol"},{"issue":"2","key":"2024051404191113400_b0235","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1002\/mco2.95","article-title":"The challenges of COVID-19 Delta variant: prevention and vaccine development","author":"He","year":"2021","journal-title":"MedComm (2020)"},{"key":"2024051404191113400_b0240","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1038\/s41467-022-28089-y","article-title":"Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant","volume":"13","author":"Li","year":"2022","journal-title":"Nat Commun"},{"key":"2024051404191113400_b0245","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1038\/s42003-022-03565-9","article-title":"Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7\/Alpha variant infections","volume":"5","author":"Parker","year":"2022","journal-title":"Commun Biol"},{"key":"2024051404191113400_b0250","article-title":"SARS-CoV-2 ORF6 disrupts bidirectional nucleocytoplasmic transport through interactions with Rae1 and Nup98","volume":"12:e00065-21","author":"Addetia","year":"2021","journal-title":"mBio"},{"key":"2024051404191113400_b0255","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.108916","article-title":"Sarbecovirus ORF6 proteins hamper induction of interferon signaling","volume":"34","author":"Kimura","year":"2021","journal-title":"Cell Rep"},{"key":"2024051404191113400_b0260","doi-asserted-by":"crossref","first-page":"4782","DOI":"10.1038\/s41467-022-32489-5","article-title":"Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport","volume":"13","author":"Gao","year":"2022","journal-title":"Nat Commun"},{"key":"2024051404191113400_b0265","doi-asserted-by":"crossref","first-page":"28344","DOI":"10.1073\/pnas.2016650117","article-title":"SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling","volume":"117","author":"Miorin","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024051404191113400_b0270","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1038\/s41423-020-0514-8","article-title":"SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70","volume":"17","author":"Jiang","year":"2020","journal-title":"Cell Mol Immunol"},{"key":"2024051404191113400_b0275","doi-asserted-by":"crossref","first-page":"2935","DOI":"10.1038\/s41467-022-30609-9","article-title":"SARS-CoV-2 ORF7a potently inhibits the antiviral effect of the host factor SERINC5","volume":"13","author":"Timilsina","year":"2022","journal-title":"Nat Commun"},{"key":"2024051404191113400_b0280","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1080\/15548627.2022.2084686","article-title":"The ORF7a protein of SARS-CoV-2 initiates autophagy and limits autophagosome-lysosome fusion via degradation of SNAP29 to promote virus replication","volume":"19","author":"Hou","year":"2023","journal-title":"Autophagy"},{"key":"2024051404191113400_b0285","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1001\/jamaneurol.2020.1127","article-title":"Neurologic manifestations of hospitalized patients with coronavirus disease 2019 in Wuhan, China","volume":"77","author":"Mao","year":"2020","journal-title":"JAMA Neurol"},{"key":"2024051404191113400_b0290","doi-asserted-by":"crossref","first-page":"2268","DOI":"10.1056\/NEJMc2008597","article-title":"Neurologic features in severe SARS-CoV-2 infection","volume":"382","author":"Helms","year":"2020","journal-title":"N Engl J Med"},{"key":"2024051404191113400_b0295","article-title":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and glial cells: insights and perspectives","volume":"7","author":"Vargas","year":"2020","journal-title":"Brain Behav Immun Health"},{"key":"2024051404191113400_b0300","first-page":"12:730088","article-title":"Cellular and molecular effects of SARS-CoV-2 linking lung infection to the brain","author":"Francistiov\u00e1","year":"2021","journal-title":"Front Immunol"},{"key":"2024051404191113400_b0305","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1016\/j.medcli.2022.07.002","article-title":"The heart and SARS-CoV-2","volume":"159","author":"Gonz\u00e1lez-Calle","year":"2022","journal-title":"Med Clin (Barc)"},{"key":"2024051404191113400_b0310","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/j.jacbts.2021.10.011","article-title":"The pathogenesis and long-term consequences of COVID-19 cardiac injury","volume":"7","author":"Siripanthong","year":"2022","journal-title":"JACC Basic Transl Sci"},{"key":"2024051404191113400_b0315","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","article-title":"SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor","volume":"181","author":"Hoffmann","year":"2020","journal-title":"Cell"},{"key":"2024051404191113400_b0320","doi-asserted-by":"crossref","first-page":"1578","DOI":"10.1002\/ajh.25982","article-title":"Thrombosis in COVID-19","volume":"95","author":"Hanff","year":"2020","journal-title":"Am J Hematol"},{"key":"2024051404191113400_b0325","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1016\/j.hrthm.2020.05.001","article-title":"Recognizing COVID-19-related myocarditis: the possible pathophysiology and proposed guideline for diagnosis and management","volume":"17","author":"Siripanthong","year":"2020","journal-title":"Heart Rhythm"},{"key":"2024051404191113400_b0330","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1001\/jamacardio.2020.3551","article-title":"Association of cardiac infection with SARS-CoV-2 in confirmed COVID-19 autopsy cases","volume":"5","author":"Lindner","year":"2020","journal-title":"JAMA Cardiol"},{"key":"2024051404191113400_b0335","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/s41569-020-00435-x","article-title":"Myocarditis and inflammatory cardiomyopathy: current evidence and future directions","volume":"18","author":"Tschope","year":"2021","journal-title":"Nat Rev Cardiol"},{"key":"2024051404191113400_b0340","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.964265","article-title":"Where do T cell subsets stand in SARS-CoV-2 infection: an update","volume":"12","author":"Tarique","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"2024051404191113400_b0345","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/s41392-021-00792-0","article-title":"Myeloid cells in COVID-19 microenvironment","volume":"6","author":"Qin","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"2024051404191113400_b0350","doi-asserted-by":"crossref","first-page":"e12989","DOI":"10.1111\/sji.12989","article-title":"T cell immunobiology and cytokine storm of COVID-19","volume":"93","author":"Luo","year":"2021","journal-title":"Scand J Immunol"},{"key":"2024051404191113400_b0355","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet"},{"key":"2024051404191113400_b0360","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2024051404191113400_b0365","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024051404191113400_b0370","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2024051404191113400_b0375","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1007\/s00122-020-03716-8","article-title":"Linear models for diallel crosses: a review with R functions","volume":"134","author":"Onofri","year":"2021","journal-title":"Theor Appl Genet"},{"key":"2024051404191113400_b0380","first-page":"D682","article-title":"Ensembl 2020","volume":"48","author":"Yates","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024051404191113400_b0385","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-019-1910-1","article-title":"Transcriptome assembly from long-read RNA-seq alignments with StringTie2","volume":"20","author":"Kovaka","year":"2019","journal-title":"Genome Biol"},{"key":"2024051404191113400_b0390","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"2024051404191113400_b0395","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2024051404191113400_b0400","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"2024051404191113400_b0405","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1002\/sam.11379","article-title":"The next-generation K-means algorithm","volume":"11","author":"Demidenko","year":"2018","journal-title":"Stat Anal Data Min"},{"key":"2024051404191113400_b0410","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2024051404191113400_b0415","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"2024051404191113400_b0420","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsdottir","year":"2013","journal-title":"Brief Bioinform"},{"key":"2024051404191113400_b0425","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2024051404191113400_b0430","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","article-title":"The Genome Sequence Archive Family: toward explosive data growth and diverse data types","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022923000955?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022923000955?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/21\/5\/1014\/57590378\/gpb_21_5_1014.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/21\/5\/1014\/57590378\/gpb_21_5_1014.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T21:28:07Z","timestamp":1729718887000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/21\/5\/1014\/7632877"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,13]]},"references-count":86,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,10,1]]}},"URL":"https:\/\/doi.org\/10.1016\/j.gpb.2023.06.002","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,10]]},"published":{"date-parts":[[2023,7,13]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques","name":"articletitle","label":"Article Title"},{"value":"Genomics, Proteomics & Bioinformatics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.gpb.2023.06.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences \/ China National Center for Bioinformation and Genetics Society of China.","name":"copyright","label":"Copyright"}]}}