1
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Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing. Wellcome Open Res 2023; 6:241. [PMID: 37224315 PMCID: PMC10189296 DOI: 10.12688/wellcomeopenres.17170.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 12/08/2023] Open
Abstract
Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5' end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach 'SMART-9N' and a version compatible rapid adapters available from Oxford Nanopore Technologies 'Rapid SMART-9N'. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.
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Affiliation(s)
- Ingra M. Claro
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Camila A. M. da Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Ian N. Valenca
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Darlan S. Candido
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Flavia C. S. Sales
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Jaqueline G. de Jesus
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Anderson de Paula
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Pamela dos Santos Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, 01246-904, Brazil
| | - Mariana C. Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - William M. Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Mariene R. Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, 13083-862, Brazil
| | - Esper G. Kallas
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - José Eduardo Levi
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- DASA, Sao Paulo, 06455-010, Brazil
| | - Nuno Rodrigues Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Nicholas J. Loman
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joshua Quick
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing. Wellcome Open Res 2023; 6:241. [PMID: 37224315 PMCID: PMC10189296 DOI: 10.12688/wellcomeopenres.17170.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 05/26/2023] Open
Abstract
Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5' end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach 'SMART-9N' and a version compatible rapid adapters available from Oxford Nanopore Technologies 'Rapid SMART-9N'. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.
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Affiliation(s)
- Ingra M. Claro
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Camila A. M. da Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Ian N. Valenca
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Darlan S. Candido
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Flavia C. S. Sales
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Jaqueline G. de Jesus
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Anderson de Paula
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Pamela dos Santos Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, 01246-904, Brazil
| | - Mariana C. Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - William M. Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Mariene R. Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, 13083-862, Brazil
| | - Esper G. Kallas
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - José Eduardo Levi
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- DASA, Sao Paulo, 06455-010, Brazil
| | - Nuno Rodrigues Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Nicholas J. Loman
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joshua Quick
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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Salgado BB, Maués FCDJ, Jordão M, Pereira RL, Toledo-Teixeira DA, Parise PL, Granja F, Souza HFS, Yamamoto MM, Chiang JO, Martins LC, Boscardin SB, Lalwani JDB, Vasconcelos PFC, Proença-Modena JL, Lalwani P. Antibody cross-reactivity and evidence of susceptibility to emerging Flaviviruses in the dengue-endemic Brazilian Amazon. Int J Infect Dis 2023; 129:142-151. [PMID: 36736575 DOI: 10.1016/j.ijid.2023.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES Several Flaviviruses can co-circulate. Pre-existing immunity to one virus can modulate the response to a heterologous virus; however, the serological cross-reaction between these emerging viruses in dengue virus (DENV)-endemic regions are poorly understood. METHODS A cross-sectional study was performed among the residents of Manaus city in the state of Amazonas, Brazil. The serological response was assessed by hemagglutination inhibition assay (HIA), enzyme-linked immunosorbent assay, and neutralization assay. RESULTS A total of 74.52% of the participants were immunoglobulin G-positive (310/416), as estimated by lateral flow tests. Overall, 93.7% of the participants were seropositive (419/447) for at least one DENV serotype, and the DENV seropositivity ranged between 84.8% and 91.0%, as determined by HIA. About 93% had antiyellow fever virus 17D-reactive antibodies, whereas 80.5% reacted to wild-type yellow fever virus. Zika virus (ZIKV) had the lowest seropositivity percentage (52.6%) compared with other Flaviviruses. Individuals who were DENV-positive with high antibody titers by HIA or envelope protein domain III enzyme-linked immunosorbent assay reacted strongly with ZIKV, whereas individuals with low anti-DENV antibody titers reacted poorly toward ZIKV. Live virus neutralization assay with ZIKV confirmed that dengue serogroup and ZIKV-spondweni serogroup are far apart; hence, individuals who are DENV-positive do not cross-neutralize ZIKV efficiently. CONCLUSION Taken together, we observed a high prevalence of DENV in the Manaus-Amazon region and a varying degree of cross-reactivity against emerging and endemic Flaviviruses. Epidemiological and exposure conditions in Manaus make its population susceptible to emerging and endemic arboviruses.
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Affiliation(s)
- Barbara Batista Salgado
- Leônidas e Maria Deane Institute (ILMD), Fiocruz Amazônia, Manaus, Amazonas, Brazil; Laboratory of infectious diseases and immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus, Brazil
| | - Fábio Carmona de Jesus Maués
- Leônidas e Maria Deane Institute (ILMD), Fiocruz Amazônia, Manaus, Amazonas, Brazil; Laboratory of infectious diseases and immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus, Brazil
| | - Maele Jordão
- Leônidas e Maria Deane Institute (ILMD), Fiocruz Amazônia, Manaus, Amazonas, Brazil; Laboratory of infectious diseases and immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus, Brazil
| | - Renato Lemos Pereira
- Leônidas e Maria Deane Institute (ILMD), Fiocruz Amazônia, Manaus, Amazonas, Brazil; Laboratory of infectious diseases and immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Pierina L Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Biodiversity Research Center, Federal University of Roraima, Roraima, Brazil
| | | | | | - Jannifer Oliveira Chiang
- Evandro Chagas Institute (IEC), Arbovirology and Hemorrhagic Fever Sector, Ananindeua, Pará, Brazil
| | - Livia Caricio Martins
- Evandro Chagas Institute (IEC), Arbovirology and Hemorrhagic Fever Sector, Ananindeua, Pará, Brazil
| | | | - Jaila Dias Borges Lalwani
- Pharmaceutical Science College (FCF), Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | | | - José Luiz Proença-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, São Paulo, Brazil
| | - Pritesh Lalwani
- Leônidas e Maria Deane Institute (ILMD), Fiocruz Amazônia, Manaus, Amazonas, Brazil; Laboratory of infectious diseases and immunology, ILMD/Fiocruz Amazônia and PPGIBA/ICB-UFAM, Manaus, Brazil.
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Negi V, Kuhn RJ, Fekete DM. Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear. Viruses 2023; 15:247. [PMID: 36680287 PMCID: PMC9867072 DOI: 10.3390/v15010247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The transmembrane protein Axl was proposed as an entry receptor for Zika virus (ZIKV) infection in vitro, but conflicting results from in vivo studies have made it difficult to establish Axl as a physiologically relevant ZIKV receptor. Both the functional redundancy of receptors and the experimental model used can lead to variable results. Therefore, it can be informative to explore alternative animal models to analyze ZIKV receptor candidates as an aid in discovering antivirals. This study used chicken embryos to examine the role of chicken Tyro3 (cTyro3), the equivalent of human Axl. Results show that endogenous cTyro3 mRNA expression overlaps with previously described hot spots of ZIKV infectivity in the brain and inner ear. We asked if ectopic expression or knockdown of cTyro3 influenced ZIKV infection in embryos. Tol2 vectors or replication-competent avian retroviruses were used in ovo to introduce full-length or truncated (presumed dominant-negative) cTyro3, respectively, into the neural tube on embryonic day two (E2). ZIKV was delivered to the brain 24 h later. cTyro3 manipulations did not alter ZIKV infection or cell death in the E5/E6 brain. Moreover, delivery of truncated cTyro3 variants to the E3 otocyst had no effect on inner ear formation on E6 or E10.
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Affiliation(s)
| | | | - Donna M. Fekete
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47906, USA
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Delafiori J, Faria AVDS, de Oliveira AN, Sales GM, Dias-Audibert FL, Catharino RR. Unraveling the Metabolic Alterations Induced by Zika Infection in Prostate Epithelial (PNT1a) and Adenocarcinoma (PC-3) Cell Lines. J Proteome Res 2023; 22:193-203. [PMID: 36469742 DOI: 10.1021/acs.jproteome.2c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outbreak of Zika virus infection in 2016 led to the identification of its presence in several types of biofluids, including semen. Later discoveries associated Zika infection with sexual transmission and persistent replication in cells of the male reproductive tract. Prostate epithelial and carcinoma cells are favorable to virus replication, with studies pointing to transcriptomics alterations of immune and inflammation genes upon persistence. However, metabolome alterations promoted by the Zika virus in prostate cells are unknown. Given its chronic effects and oncolytic potential, we aim to investigate the metabolic alterations induced by the Zika virus in prostate epithelial (PNT1a) and adenocarcinoma (PC-3) cells using an untargeted metabolomics approach and high-resolution mass spectrometry. PNT1a cells were viable up to 15 days post ZIKV infection, in contrast to its antiproliferative effect in the PC-3 cell lineage. Remarkable alterations in the PNT1a cell metabolism were observed upon infection, especially regarding glycerolipids, fatty acids, and acylcarnitines, which could be related to viral cellular resource exploitation, in addition to the over-time increase in oxidative stress metabolites associated with carcinogenesis. The upregulation of FA20:5 at 5 dpi in PC-3 cells corroborates the antiproliferative effect observed since this metabolite was previously reported to induce PC-3 cell death. Overall, Zika virus promotes extensive lipid alterations on both PNT1a and PC-3 cells, promoting different outcomes based on the cellular metabolic state.
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Affiliation(s)
- Jeany Delafiori
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, SP 13083-970, Brazil
| | - Alessandra V de S Faria
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Arthur N de Oliveira
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, SP 13083-970, Brazil
| | - Geovana M Sales
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, SP 13083-970, Brazil
| | - Flávia Luísa Dias-Audibert
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, SP 13083-970, Brazil
| | - Rodrigo R Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, SP 13083-970, Brazil
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m 6A Demethylase ALKBH5 Restrains PEDV Infection by Regulating GAS6 Expression in Porcine Alveolar Macrophages. Int J Mol Sci 2022; 23:ijms23116191. [PMID: 35682869 PMCID: PMC9181496 DOI: 10.3390/ijms23116191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/22/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a burdensome coronavirus for the global pig industry. Although its fecal-oral route has been well-recognized, increasing evidence suggests that PEDV can also spread through airborne routes, indicating that the infection may also occur in the respiratory tract. N6-methyladenosine (m6A) has been known to regulate viral replication and host immunity, yet its regulatory role and molecular mechanism regarding PEDV infection outside the gastrointestinal tract remain unexplored. In this study, we demonstrate that PEDV can infect porcine lung tissue and the 3D4/21 alveolar macrophage cell line, and the key m6A demethylase ALKBH5 is remarkably induced after PEDV infection. Interestingly, the disruption of ALKBH5 expression remarkably increases the infection’s capacity for PEDV. Transcriptome profiling identified dozens of putative targets of ALKBH5, including GAS6, which is known to regulate virus infectivity. Further, MeRIP-qPCR and mRNA stability analyses suggest that ALKBH5 regulates the expression of GAS6 via an m6A-YTHDF2-dependent mechanism. Overall, our study demonstrates that PEDV can infect porcine lung tissue and 3D4/21 cells and reveals the crucial role of ALKBH5 in restraining PEDV infections, at least partly, by influencing GAS6 through an m6A-YTHDF2-dependent mechanism.
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SOUZA MAYQUEPAULOMDE, FREITAS BÁRBARACAROLINEG, HOLANDA GUSTAVOM, DINIZ JUNIOR JOSÉANTÔNIOP, CRUZ ANACECÍLIAR. Correlation of cGAS, STING, INF-α and INF-β gene expression with Zika virus kinetics in primary culture of microglia and neurons from BALB/c mice. AN ACAD BRAS CIENC 2022; 94:e20211189. [DOI: 10.1590/0001-3765202220211189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
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8
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Polonio CM, Peron JPS. ZIKV Infection and miRNA Network in Pathogenesis and Immune Response. Viruses 2021; 13:v13101992. [PMID: 34696422 PMCID: PMC8541119 DOI: 10.3390/v13101992] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/14/2021] [Accepted: 09/28/2021] [Indexed: 01/01/2023] Open
Abstract
Over the years, viral infections have caused severe illness in humans. Zika Virus (ZIKV) is a flavivirus transmitted by mosquito vectors that leads to notable neurological impairment, whose most dramatic impact is the Congenital ZIKV Syndrome (CZS). ZIKV targets neuronal precursor cells leading to apoptosis and further impairment of neuronal development, causing microcephaly, lissencephaly, ventriculomegaly, and calcifications. Several regulators of biological processes are involved in CZS development, and in this context, microRNAs (miRNAs) seem to have a fundamental role. miRNAs are important regulators of protein translation, as they form the RISC silencing complex and interact with complementary mRNA target sequences to further post-transcriptional repression. In this context, little is known about their participation in the pathogenesis of viral infections. In this review, we discuss how miRNAs could relate to ZIKV and other flavivirus infections.
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Affiliation(s)
- Carolina Manganeli Polonio
- Neuroimmune Interactions Laboratory, Department of Immunology, University of São Paulo, São Paulo 05508-000, Brazil;
- Laboratory of Neuroimmunology of Arboviruses, Scientific Platform Pasteur-USP (SPPU), University of São Paulo, São Paulo 05508-020, Brazil
| | - Jean Pierre Schatzmann Peron
- Neuroimmune Interactions Laboratory, Department of Immunology, University of São Paulo, São Paulo 05508-000, Brazil;
- Laboratory of Neuroimmunology of Arboviruses, Scientific Platform Pasteur-USP (SPPU), University of São Paulo, São Paulo 05508-020, Brazil
- Immunopathology and Allergy Post Graduate Program, School of Medicine, University of São Paulo, São Paulo 01246-000, Brazil
- Correspondence:
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Hirschenberger M, Hunszinger V, Sparrer KMJ. Implications of Innate Immunity in Post-Acute Sequelae of Non-Persistent Viral Infections. Cells 2021; 10:2134. [PMID: 34440903 PMCID: PMC8391718 DOI: 10.3390/cells10082134] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Non-persistent viruses classically cause transient, acute infections triggering immune responses aimed at the elimination of the pathogen. Successful viruses evolved strategies to manipulate and evade these anti-viral defenses. Symptoms during the acute phase are often linked to dysregulated immune responses that disappear once the patient recovers. In some patients, however, symptoms persist or new symptoms emerge beyond the acute phase. Conditions resulting from previous transient infection are termed post-acute sequelae (PAS) and were reported for a wide range of non-persistent viruses such as rota-, influenza- or polioviruses. Here we provide an overview of non-persistent viral pathogens reported to be associated with diverse PAS, among them chronic fatigue, auto-immune disorders, or neurological complications and highlight known mechanistic details. Recently, the emergence of post-acute sequelae of COVID-19 (PASC) or long COVID highlighted the impact of PAS. Notably, PAS of non-persistent infections often resemble symptoms of persistent viral infections, defined by chronic inflammation. Inflammation maintained after the acute phase may be a key driver of PAS of non-persistent viruses. Therefore, we explore current insights into aberrant activation of innate immune signaling pathways in the post-acute phase of non-persistent viruses. Finally, conclusions are drawn and future perspectives for treatment and prevention of PAS are discussed.
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