{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T14:03:55Z","timestamp":1778940235419,"version":"3.51.4"},"reference-count":39,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T00:00:00Z","timestamp":1666396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-2012298"],"award-info":[{"award-number":["DMS-2012298"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Vaccines"],"abstract":"<jats:p>COVID-19 vaccines can be the tugboats for preventing SARS-CoV-2 infections when they are practical and, more importantly, without adverse effects. However, the reality is that they may result in short-term or long-term impacts on COVID-19-related diseases and even trigger the formation of new variants of SARS-CoV-2. Using published data, we use a set of optimized-performance COVID-19 genomic biomarkers (MND1, CDC6, ZNF282) to study the benefits and adverse effects of the BNT162b2 vaccine. We found that the vaccine lowered the expression values of genes MND1 and CDC6 while heightening the expression values of ZNF282 in individuals who are SARS-CoV-2 na\u00efve, which is expected and satisfies the biological equivalence between the COVID-19 disease and the genomic signature patterns established in the literature. However, we also found that COVID-19-convalescent octogenarians responded reversely. The vaccine heightened the expression values of MND1 and CDC6. In addition, it lowered the expression values of ZNF282. Such adverse effects raise outstanding concerns about whether or not COVID-19-convalescent individuals should take the current vaccine or when they can take it. These findings are new at the genomic level and can provide insights into developing next-generation vaccines, antiviral drugs, and pandemic management guidance.<\/jats:p>","DOI":"10.3390\/vaccines10111774","type":"journal-article","created":{"date-parts":[[2022,10,24]],"date-time":"2022-10-24T11:53:55Z","timestamp":1666612435000},"page":"1774","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Genomic Transcriptome Benefits and Potential Harms of COVID-19 Vaccines Indicated from Optimized Genomic Biomarkers"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2615-1539","authenticated-orcid":false,"given":"Zhengjun","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Statistics, School of Computer, Data & Information Sciences, University of Wisconsin, Madison, WI 53706, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/s41586-022-05053-w","article-title":"Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4, & BA.5","volume":"608","author":"Wang","year":"2022","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1002\/jmv.27526","article-title":"Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein","volume":"94","author":"Kumar","year":"2022","journal-title":"J. Med. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"eabq1841","DOI":"10.1126\/science.abq1841","article-title":"Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure","volume":"377","author":"Reynolds","year":"2022","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1038\/d41586-021-01827-w","article-title":"The quest to find genes that drive severe covid","volume":"595","author":"Callaway","year":"2021","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"COVID-19 Host Genetics Initiative (2021). Mapping the human genetic architecture of COVID-19. Nature, 600, 474\u2013477.","DOI":"10.1038\/s41586-021-03767-x"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/s41586-020-03065-y","article-title":"Genetic mechanisms of critical illness in COVID-19","volume":"591","author":"Clohisey","year":"2021","journal-title":"Nature"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"The RECOVERY Collaborative Group (2021). Dexamethasone in hospitalized patients with COVID-19. N. Engl. J. Med., 384, 693\u2013704.","DOI":"10.1056\/NEJMoa2021436"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e162","DOI":"10.1017\/S095026882100145X","article-title":"Development and validation of a clinical and genetic model for predicting risk of severe COVID-19","volume":"149","author":"Dite","year":"2021","journal-title":"Epidemiol. Infect."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"eabd4570","DOI":"10.1126\/science.abd4570","article-title":"Inborn errors of type i ifn immunity in patients with life-threatening COVID-19","volume":"370","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"eabd4585","DOI":"10.1126\/science.abd4585","article-title":"Autoantibodies against type i ifns in patients with life-threatening COVID-19","volume":"370","author":"Bastard","year":"2020","journal-title":"Science"},{"key":"ref_11","unstructured":"Povysil, G., Butler-Laporte, G., Shang, N., Weng, C., Khan, A., Alaamery, M., Nakanishi, T., Zhou, S., Forgetta, V., and Kiryluk, K. (2020, December 21). Failure to replicate the association of rare loss-of-function variants in type IIFN immunity genes with severe COVID-19. medRxiv, Available online: https:\/\/www.medrxiv.org\/content\/early\/2020\/12\/21\/2020.12.18.20248226."},{"key":"ref_12","unstructured":"Kosmicki, J.A., Horowitz, J.E., Banerjee, N., Lanche, R., Marcketta, A., Maxwell, E., Bai, X., Sun, D., Backman, J.D., and Ferreira, M. (2020). Genetic association analysis of SARS-CoV-2 infection in 455,838 UK biobank participants. medRxiv, Available online: https:\/\/www.medrxiv.org\/content\/early\/2020\/11\/03\/2020.10.28.2022180420248226."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e67569","DOI":"10.7554\/eLife.67569","article-title":"Association of toll-like receptor 7 variants with life-threatening COVID-19 disease in males: Findings from a nested case-control study","volume":"10","author":"Fallerini","year":"2021","journal-title":"eLife"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/s41593-020-00771-8","article-title":"The S1 protein of SARS-CoV-2 crosses the blood\u2013brain barrier in mice","volume":"24","author":"Rhea","year":"2021","journal-title":"Nat. Neurosci."},{"key":"ref_15","unstructured":"Rowland, C. (2020, November 21). Doctors and Nurses Want More Data before Championing Vaccines to End the Pandemic: Health Systems Are Launching Bids to Assure Their Medical Workers that Vaccines Will Be Safe and Effective. CNN. Available online: https:\/\/www.washingtonpost.com\/business\/2020\/11\/21\/vaccines-advocates-nurses-doctorscoronavirus\/."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"(2021). COVID-19 Vaccines Complicate Mammograms. Cancer Discov., 11, 1868. Available online: https:\/\/cancerdiscovery.aacrjournals.org\/content\/11\/8\/1868.1.","DOI":"10.1158\/2159-8290.CD-NB2021-0366"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e2130645","DOI":"10.1001\/jamanetworkopen.2021.30645","article-title":"Assessment of Cognitive Function in Patients After COVID-19 Infection","volume":"4","author":"Becker","year":"2021","journal-title":"JAMA Netw. Open"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Chertow, D., Stein, S., Ramelli, S., Grazioli, A., Chung, J.Y., Singh, M., Yinda, C.K., Winkler, C., Dickey, J., and Kleiner, D. (2021). SARS-CoV-2 infection and persistence throughout the human body and brain. Res. Sq.","DOI":"10.21203\/rs.3.rs-1139035\/v1"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1056\/NEJMoa2117128","article-title":"Effectiveness of COVID-19 Vaccines over a 9-Month Period in North Carolina","volume":"386","author":"Lin","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/s41586-021-04352-y","article-title":"Evolution of enhanced innate immune evasion by SARS-CoV-2","volume":"602","author":"Thorne","year":"2022","journal-title":"Nature"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/s41586-022-04856-1","article-title":"Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA.2","volume":"607","author":"Uraki","year":"2022","journal-title":"Nature"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"4686","DOI":"10.1038\/s41467-022-32396-9","article-title":"Omicron BA.4\/BA.5 escape neutralizing immunity elicited by BA.1 infection","volume":"13","author":"Khan","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"4203","DOI":"10.1016\/j.cell.2021.06.021","article-title":"In vitro and in vivo functions of SARS-CoV-2 infection- enhancing and neutralizing antibodies","volume":"184","author":"Li","year":"2021","journal-title":"Cell"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/j.jinf.2021.08.010","article-title":"Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan\/D614G strain and Delta variants. A potential risk for mass vaccination?","volume":"83","author":"Yahi","year":"2021","journal-title":"J. Infect."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"142","DOI":"10.6339\/21-JDS1005","article-title":"Five critical genes related to seven COVID-19 subtypes: A data science discovery","volume":"19","author":"Zhang","year":"2021","journal-title":"J. Data Sci."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Zhang, Z. (2022). The existence of at least three genomic signature patterns and at least seven subtypes of COVID-19 and the end of the disease. Vaccines, 10.","DOI":"10.1101\/2022.01.24.477579"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Zhang, Z. (2022). Genomic Biomarker Heterogeneities Between SARS-CoV-2 and COVID-19. Vaccines, 10.","DOI":"10.1101\/2022.01.13.476223"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1177\/11769351221076360","article-title":"Lift the veil of breast cancers using 4 or fewer critical genes","volume":"21","author":"Zhang","year":"2022","journal-title":"Cancer Inform."},{"key":"ref_29","first-page":"S14:100001","article-title":"Functional effects of four or fewer critical genes linked to lung cancers and new sub-types detected by a new machine learning classifier","volume":"11","author":"Zhang","year":"2021","journal-title":"J. Clin. Trials"},{"key":"ref_30","unstructured":"Zhang, Z., Xu, Y., Li, X., Chen, M., Wang, X., Zhang, N., and Liu, Y. (2022). PSMC2 and CXCL8-Modulated Four Critical Gene-Based High-Performance Biomarkers for Colorectal Cancers, submitted."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Liu, Y., Zhang, H., Xu, Y., Liu, Y.Z., Yeh, M.M., and Zhang, Z. (2022). The Interaction Effects of GMNN and CXCL12 Built in Five Critical Gene-based High-Performance Biomarkers for Hepatocellular Carcinoma, submitted.","DOI":"10.1177\/11769351231190477"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"110680","DOI":"10.1016\/j.celrep.2022.110680","article-title":"mRNA vaccination in octogenarians 15 and 20 months after recovery from COVID-19 elicits robust immune and antibody responses that include Omicron","volume":"39","author":"Lee","year":"2022","journal-title":"Cell Rep."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.cels.2020.10.003","article-title":"Large-scale multi-omic analysis of COVID-19 severity","volume":"12","author":"Overmyer","year":"2020","journal-title":"Cell Syst."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1126\/science.abc6261","article-title":"Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans","volume":"369","author":"Arunachalam","year":"2020","journal-title":"Science"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"5854","DOI":"10.1038\/s41467-020-19587-y","article-title":"Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses","volume":"11","author":"Mick","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Lieberman, N.A., Peddu, V., Xie, H., Shrestha, L., Huang, M.L., Mears, M.C., Cajimat, M.N., Bente, D.A., Shi, P.Y., and Bovier, F. (2020). In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PLoS Biol., 18.","DOI":"10.1101\/2020.06.22.165225"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"916686","DOI":"10.3389\/fimmu.2022.916686","article-title":"Prior Vaccination Exceeds Prior Infection in Eliciting Innate and Humoral Immune Responses in Omicron Infected Outpatients","volume":"13","author":"Lee","year":"2022","journal-title":"Front. Immunol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Klein, J., Wood, J., Jaycox, J., Lu, P., Dhodapkar, R.M., Gehlhausen, J.R., Tabachnikova, A., Tabacof, A., Malik, A.A., and Iwasaki, A. (2022). Distinguishing features of Long COVID identified through immune profiling. medRxiv.","DOI":"10.1101\/2022.08.09.22278592"},{"key":"ref_39","unstructured":"Couzin-Frankel, J. (2022, August 16). Blood Abnormalities Found in People with Long COVID Study: Implicates Lack of Key Hormone, Battle-weary Immune Cells, and Reawakened Viruses. Available online: https:\/\/www.science.org\/content\/article\/blood-abnormalities-found-people-long-covid."}],"container-title":["Vaccines"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-393X\/10\/11\/1774\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:00:47Z","timestamp":1760144447000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-393X\/10\/11\/1774"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,22]]},"references-count":39,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11]]}},"alternative-id":["vaccines10111774"],"URL":"https:\/\/doi.org\/10.3390\/vaccines10111774","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-1918598\/v1","asserted-by":"object"}]},"ISSN":["2076-393X"],"issn-type":[{"value":"2076-393X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,22]]}}}