1
|
Mirza JD, de Oliveira Guimarães L, Wilkinson S, Rocha EC, Bertanhe M, Helfstein VC, de-Deus JT, Claro IM, Cumley N, Quick J, Faria NR, Sabino EC, Kirchgatter K, Loman NJ. Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes. Microb Genom 2024; 10:001184. [PMID: 38240642 PMCID: PMC10868619 DOI: 10.1099/mgen.0.001184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.
Collapse
Affiliation(s)
- Jeremy D. Mirza
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Sam Wilkinson
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Esmenia C. Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mayara Bertanhe
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Ingra M. Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
| | - Nicola Cumley
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Joshua Quick
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Karin Kirchgatter
- Instituto Pasteur, São Paulo, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | |
Collapse
|
2
|
Villanova F, Marcatti R, Bertanhe M, Morais VDS, Milagres FADP, Brustulin R, Araújo ELL, Tahmasebi R, Witkin SS, Deng X, Delwart E, Sabino EC, Abreu-Junior CH, Leal É, da Costa AC. New Variants of Squash Mosaic Viruses Detected in Human Fecal Samples. Microorganisms 2021; 9:microorganisms9071349. [PMID: 34206387 PMCID: PMC8307838 DOI: 10.3390/microorganisms9071349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/01/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 11/16/2022] Open
Abstract
Squash mosaic virus (SqMV) is a phytovirus that infects great diversity of plants worldwide. In Brazil, the SqMV has been identified in the states of Ceará, Maranhão, Piauí, Rio Grande do Norte, and Tocantins. The presence of non-pathogenic viruses in animals, such as phytoviruses, may not be completely risk-free. Similarities in gene repertories between these viruses and viruses that affect animal species have been reported. The present study describes the fully sequenced genomes of SqMV found in human feces, collected in Tocantins, and analyzes the viral profile by metagenomics in the context of diarrhea symptomatology. The complete SqMV genome was obtained in 39 of 253 analyzed samples (15.5%); 97.4% of them belonged to children under 5 years old. There was no evidence that the observed symptoms were related to the presence of SqMV. Of the different virus species detected in these fecal samples, at least 4 (rotavirus, sapovirus, norovirus, parechovirus) are widely known to cause gastrointestinal symptoms. The presence of SqMV nucleic acid in fecal samples is likely due to recent dietary consumption and it is not evidence of viral replication in the human intestinal cells. Identifying the presence of SqMV in human feces and characterization of its genome is a relevant precursor to determining whether and how plant viruses interact with host cells or microorganisms in the human gastrointestinal tract.
Collapse
Affiliation(s)
- Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil;
| | - Roberta Marcatti
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Mayara Bertanhe
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
- School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo 05508-270, SP, Brazil
| | - Vanessa dos Santos Morais
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Flavio Augusto de Padua Milagres
- Instituto de Ciências Biológicas, Universidade Federal do Tocantins, Palmas 77001-090, TO, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, TO, Brazil
| | - Rafael Brustulin
- Instituto de Ciências Biológicas, Universidade Federal do Tocantins, Palmas 77001-090, TO, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, TO, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, DF, Brazil;
| | - Roozbeh Tahmasebi
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Steven S. Witkin
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ester Cerdeira Sabino
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | | | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil;
- Correspondence:
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| |
Collapse
|
3
|
do Socorro Fôro Ramos E, Rosa UA, de Oliveira Ribeiro G, Villanova F, de Pádua Milagres FA, Brustulin R, Dos Santos Morais V, Bertanhe M, Marcatti R, Araújo ELL, Witkin SS, Delwart E, Luchs A, da Costa AC, Leal É. High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis. Viruses 2021; 13:v13040595. [PMID: 33807396 PMCID: PMC8067319 DOI: 10.3390/v13040595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 01/07/2023] Open
Abstract
Echoviruses (E) are a diverse group of viruses responsible for various pathological conditions in humans including aseptic meningitis, myocarditis, and acute flaccid paralysis. The detection and identification of echovirus genotypes in clinical samples is challenging due to its high genetic diversity. Here, we report the complete genome sequences of nine echoviruses, obtained by next-generation sequencing of 238 fecal samples from individuals with gastroenteritis in regions of Brazil. Detected viruses were classified into six genotypes: Three E1 sequences (BRA/TO-028, BRA/TO-069 and BRA/TO-236), one E3 (BRA/TO-018), one E11 (BRA/TO-086), one E20 (BRA/TO-016), two E29 (BRA/TO-030 and BRA/TO-193), and one E30 sequence (BRA/TO-032). Phylogenetic analysis indicated that the echoviruses E1 and E29 circulating in Brazil are divergent from strains circulating worldwide. The genotype diversity identified in our study may under-represent the total echovirus diversity in Brazil because of the small sample size and the restricted geographical distribution covered by the survey.
Collapse
Affiliation(s)
- Endrya do Socorro Fôro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Ulisses Alves Rosa
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Flávio Augusto de Pádua Milagres
- Secretaria de Saúde do Tocantins, Palmas 77453-000, Tocantins, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas 77016-330, Tocantins, Brazil
| | - Rafael Brustulin
- Secretaria de Saúde do Tocantins, Palmas 77453-000, Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Mayara Bertanhe
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Roberta Marcatti
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation, Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Federal District, Brazil
| | - Steven S Witkin
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Laboratório de Doenças Entéricas, Centro de Virologia, Instituto Adolfo Lutz, São Paulo 01246-000, Brazil
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| |
Collapse
|