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Rego N, Salazar C, Paz M, Costábile A, Fajardo A, Ferrés I, Perbolianachis P, Fernández-Calero T, Noya V, Machado MR, Brandes M, Arce R, Arleo M, Possi T, Reyes N, Bentancor MN, Lizasoain A, Bortagaray V, Moller A, Chappos O, Nin N, Hurtado J, Duquía M, González MB, Griffero L, Méndez M, Techera MP, Zanetti J, Pereira E, Rivera B, Maidana M, Alonso M, Smircich P, Arantes I, Mir D, Alonso C, Medina J, Albornoz H, Colina R, Bello G, Moreno P, Moratorio G, Iraola G, Spangenberg L. Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Viruses 2021; 13:1801. [PMID: 34578382 PMCID: PMC8473254 DOI: 10.3390/v13091801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/20/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022] Open
Abstract
Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020-February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguay's capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest.
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Affiliation(s)
- Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (N.R.); (T.F.-C.); (M.B.)
| | - Cecilia Salazar
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (C.S.); (I.F.)
- Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (M.P.); (A.C.)
| | - Mercedes Paz
- Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (M.P.); (A.C.)
| | - Alicia Costábile
- Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (M.P.); (A.C.)
- Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (A.F.); (P.P.); (R.A.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Alvaro Fajardo
- Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (A.F.); (P.P.); (R.A.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Ignacio Ferrés
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (C.S.); (I.F.)
- Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (M.P.); (A.C.)
| | - Paula Perbolianachis
- Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (A.F.); (P.P.); (R.A.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Tamara Fernández-Calero
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (N.R.); (T.F.-C.); (M.B.)
- Department of Exact and Natural Sciences, Universidad Católica del Uruguay, Montevideo 11600, Uruguay
| | - Veronica Noya
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo 11600, Uruguay; (V.N.); (M.A.); (T.P.); (N.R.); (M.N.B.)
| | - Matias R. Machado
- Protein Engineering, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;
| | - Mariana Brandes
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (N.R.); (T.F.-C.); (M.B.)
| | - Rodrigo Arce
- Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (A.F.); (P.P.); (R.A.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo 11600, Uruguay; (V.N.); (M.A.); (T.P.); (N.R.); (M.N.B.)
| | - Mailen Arleo
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo 11600, Uruguay; (V.N.); (M.A.); (T.P.); (N.R.); (M.N.B.)
| | - Tania Possi
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo 11600, Uruguay; (V.N.); (M.A.); (T.P.); (N.R.); (M.N.B.)
| | - Natalia Reyes
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo 11600, Uruguay; (V.N.); (M.A.); (T.P.); (N.R.); (M.N.B.)
| | - María Noel Bentancor
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo 11600, Uruguay; (V.N.); (M.A.); (T.P.); (N.R.); (M.N.B.)
| | - Andrés Lizasoain
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto 50000, Uruguay; (A.L.); (V.B.); (A.M.); (R.C.)
| | - Viviana Bortagaray
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto 50000, Uruguay; (A.L.); (V.B.); (A.M.); (R.C.)
| | - Ana Moller
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto 50000, Uruguay; (A.L.); (V.B.); (A.M.); (R.C.)
| | - Odhille Chappos
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Nicolas Nin
- Unidad de Cuidados Intensivos, Hospital Español “Juan J. Crottogini”, Montevideo 11800, Uruguay; (N.N.); (J.H.)
| | - Javier Hurtado
- Unidad de Cuidados Intensivos, Hospital Español “Juan J. Crottogini”, Montevideo 11800, Uruguay; (N.N.); (J.H.)
| | - Melissa Duquía
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Maria Belén González
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Luciana Griffero
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Mauricio Méndez
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Maria Pía Techera
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Juan Zanetti
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Emiliano Pereira
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Bernardina Rivera
- Laboratorio de Diagnóstico Molecular, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (B.R.); (M.M.); (M.A.)
| | - Matías Maidana
- Laboratorio de Diagnóstico Molecular, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (B.R.); (M.M.); (M.A.)
| | - Martina Alonso
- Laboratorio de Diagnóstico Molecular, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (B.R.); (M.M.); (M.A.)
| | - Pablo Smircich
- Bioinformatics Laboratory, Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo 11600, Uruguay;
- Laboratory of Molecular Interactions, Facultad de Ciencias, UdelaR, Montevideo 11400, Uruguay
| | - Ighor Arantes
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil; (I.A.); (G.B.)
| | - Daiana Mir
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto 50000, Uruguay;
| | - Cecilia Alonso
- Centro Universitario Regional Este, Universidad de la República, Rocha 27000, Uruguay; (O.C.); (M.D.); (M.B.G.); (L.G.); (M.M.); (M.P.T.); (J.Z.); (E.P.); (C.A.)
| | - Julio Medina
- Cátedra de Enfermedades Infecciosas, Facultad de Medicina, Universidad de la República, Montevideo 11300, Uruguay; (J.M.); (H.A.)
- Dirección General de Salud, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | - Henry Albornoz
- Cátedra de Enfermedades Infecciosas, Facultad de Medicina, Universidad de la República, Montevideo 11300, Uruguay; (J.M.); (H.A.)
- Dirección General de Salud, Ministerio de Salud Pública, Montevideo 11200, Uruguay
| | - Rodney Colina
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto 50000, Uruguay; (A.L.); (V.B.); (A.M.); (R.C.)
| | - Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, Brazil; (I.A.); (G.B.)
| | - Pilar Moreno
- Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (M.P.); (A.C.)
- Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (A.F.); (P.P.); (R.A.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Gonzalo Moratorio
- Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (M.P.); (A.C.)
- Laboratorio de Virología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (A.F.); (P.P.); (R.A.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Gregorio Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (C.S.); (I.F.)
- Centro de Innovación en Vigilancia Epidemiológica, Institut Pasteur Montevideo, Montevideo 11400, Uruguay; (M.P.); (A.C.)
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile 8580745, Chile
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lucía Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (N.R.); (T.F.-C.); (M.B.)
- Department of Informatics and Computer Science, Universidad Católica del Uruguay, Montevideo 11600, Uruguay
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Mir D, Rego N, Resende PC, Tort F, Fernández-Calero T, Noya V, Brandes M, Possi T, Arleo M, Reyes N, Victoria M, Lizasoain A, Castells M, Maya L, Salvo M, Schäffer Gregianini T, Mar da Rosa MT, Garay Martins L, Alonso C, Vega Y, Salazar C, Ferrés I, Smircich P, Sotelo Silveira J, Fort RS, Mathó C, Arantes I, Appolinario L, Mendonça AC, Benítez-Galeano MJ, Simoes C, Graña M, Motta F, Siqueira MM, Bello G, Colina R, Spangenberg L. Recurrent Dissemination of SARS-CoV-2 Through the Uruguayan-Brazilian Border. Front Microbiol 2021; 12:653986. [PMID: 34122369 PMCID: PMC8195593 DOI: 10.3389/fmicb.2021.653986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/08/2021] [Indexed: 12/21/2022] Open
Abstract
Uruguay is one of the few countries in the Americas that successfully contained the coronavirus disease 19 (COVID-19) epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this ∼1,100 km uninterrupted dry frontier. Using complete SARS-CoV-2 genomes from the Uruguayan-Brazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (May-July) of the pandemic. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan urban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) with respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America. Although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems is crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world.
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Affiliation(s)
- Daiana Mir
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Natalia Rego
- Unidad de Bioinformaítica, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Fernando Tort
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Tamara Fernández-Calero
- Unidad de Bioinformaítica, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Ciencias Exactas y Naturales, Universidad Católica del Uruguay, Montevideo, Uruguay
| | - Verónica Noya
- Unidad de Bioinformaítica, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo, Uruguay
| | - Mariana Brandes
- Unidad de Bioinformaítica, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Tania Possi
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo, Uruguay
| | - Mailen Arleo
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo, Uruguay
| | - Natalia Reyes
- Laboratorio de Biología Molecular, Sanatorio Americano, Montevideo, Uruguay
| | - Matías Victoria
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Andres Lizasoain
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Matías Castells
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Leticia Maya
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Matías Salvo
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Brazil
| | - Marilda Tereza Mar da Rosa
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Brazil
| | - Letícia Garay Martins
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cecilia Alonso
- CENUR Este-Sede Rocha-Universidad de la República, Montevideo, Uruguay
| | - Yasser Vega
- Laboratorio DILAVE/MGAP-INIA-Universidad de la República, Tacuarembó, Uruguay
| | - Cecilia Salazar
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Ignacio Ferrés
- Laboratorio de Genómica Microbiana, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Jose Sotelo Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC. Sección Biología Celular, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rafael Sebastián Fort
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Mathó
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC. Sección Biología Celular, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ighor Arantes
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Luciana Appolinario
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Ana Carolina Mendonça
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - María José Benítez-Galeano
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Camila Simoes
- Unidad de Bioinformaítica, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Martín Graña
- Unidad de Bioinformaítica, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Fernando Motta
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Rodney Colina
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Lucía Spangenberg
- Unidad de Bioinformaítica, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Informática y Ciencias de la Computación, Universidad Católica del Uruguay, Montevideo, Uruguay
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4
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Tosar JP, Segovia M, Castellano M, Gámbaro F, Akiyama Y, Fagúndez P, Olivera Á, Costa B, Possi T, Hill M, Ivanov P, Cayota A. Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome. Nucleic Acids Res 2020; 48:12874-12888. [PMID: 32785615 PMCID: PMC7736827 DOI: 10.1093/nar/gkaa674] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/19/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
A major proportion of extracellular RNAs (exRNAs) do not copurify with extracellular vesicles (EVs) and remain in ultracentrifugation supernatants of cell-conditioned medium or mammalian blood serum. However, little is known about exRNAs beyond EVs. We have previously shown that the composition of the nonvesicular exRNA fraction is highly biased toward specific tRNA-derived fragments capable of forming RNase-protecting dimers. To solve the problem of stability in exRNA analysis, we developed a method based on sequencing the size exclusion chromatography (SEC) fractions of nonvesicular extracellular samples treated with RNase inhibitors (RI). This method revealed dramatic compositional changes in exRNA population when enzymatic RNA degradation was inhibited. We demonstrated the presence of ribosomes and full-length tRNAs in cell-conditioned medium of a variety of mammalian cell lines. Their fragmentation generates some small RNAs that are highly resistant to degradation. The extracellular biogenesis of some of the most abundant exRNAs demonstrates that extracellular abundance is not a reliable input to estimate RNA secretion rates. Finally, we showed that chromatographic fractions containing extracellular ribosomes are probably not silent from an immunological perspective and could possibly be decoded as damage-associated molecular patterns.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mercedes Segovia
- Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo, Uruguay. Immunobiology Department, Faculty of Medicine, Universidad de la República, Uruguay
| | - Mauricio Castellano
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Fabiana Gámbaro
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Molecular Virology Laboratory, Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
| | - Yasutoshi Akiyama
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pablo Fagúndez
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Álvaro Olivera
- Centro Universitario Regional Este, Universidad de la República, Uruguay
| | - Bruno Costa
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Tania Possi
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Marcelo Hill
- Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo, Uruguay. Immunobiology Department, Faculty of Medicine, Universidad de la República, Uruguay
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and M.I.T., Cambridge, MA, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Uruguay
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