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This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprograming of the new host upon infection.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/sinc-lab\/sarscov2-mirna-discovery.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1002","type":"journal-article","created":{"date-parts":[[2020,11,18]],"date-time":"2020-11-18T21:55:27Z","timestamp":1605736527000},"page":"5571-5581","source":"Crossref","is-referenced-by-count":28,"title":["Novel SARS-CoV-2 encoded small RNAs in the passage to humans"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0130-6226","authenticated-orcid":false,"given":"Gabriela A","family":"Merino","sequence":"first","affiliation":[{"name":"Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL , Santa Fe 3000, Argentina"},{"name":"Bioengineering and Bioinformatics Research and Development Institute (IBB), FI-UNER, CONICET , Entre R\u00edos 3100, Argentina"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Cambridgeshire CB101SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9585-1531","authenticated-orcid":false,"given":"Jonathan","family":"Raad","sequence":"additional","affiliation":[{"name":"Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL , Santa Fe 3000, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5702-946X","authenticated-orcid":false,"given":"Leandro A","family":"Bugnon","sequence":"additional","affiliation":[{"name":"Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL , Santa Fe 3000, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4157-2350","authenticated-orcid":false,"given":"Cristian","family":"Yones","sequence":"additional","affiliation":[{"name":"Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL , Santa Fe 3000, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Kamenetzky","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones en Microbiolog\u00eda y Parasitolog\u00eda M\u00e9dica (IMPaM), Facultad de Medicina, UBA-CONICET , Ciudad Aut\u00f3noma de Buenos Aires 1121, Argentina"},{"name":"Laboratorio de Gen\u00f3mica y Bioinform\u00e1tica de Pat\u00f3genos, iB3, Instituto de Biociencias, Biotecnolog\u00eda y Biolog\u00eda traslacional, Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires 1121, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"Claus","sequence":"additional","affiliation":[{"name":"Laboratorio de Virolog\u00eda, FBCB, Ciudad Universitaria UNL , Santa Fe 3000, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Federico","family":"Ariel","sequence":"additional","affiliation":[{"name":"Instituto de Agrobiotecnolog\u00eda del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral , Santa Fe 3000, 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