Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil

Imagem de Miniatura
Arquivos
art_ADELINO_Field_and_classroom_initiatives_for_portable_sequencebased_monitoring_2021.PDF (2.45 MB)
Citações na Scopus
22
Tipo de produção
article
Data de publicação
2021
DOI
Scopus
Web of Science
PubMed
Título da Revista
ISSN da Revista
Título do Volume
Editora
NATURE RESEARCH
Autores
ADELINO, Talita Emile Ribeiro
GIOVANETTI, Marta
FONSECA, Vagner
XAVIER, Joilson
ABREU, Alvaro Salgado de
NASCIMENTO, Valdinete Alves do
DEMARCHI, Luiz Henrique Ferraz
OLIVEIRA, Marluce Aparecida Assuncao
SILVA, Vinicius Lemes da
MELLO, Arabela Leal e Silva de
Citação
NATURE COMMUNICATIONS, v.12, n.1, article ID 2296, 12p, 2021
Projetos de Pesquisa
Unidades Organizacionais
Fascículo
Resumo
Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015-2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses. Here, the authors present results of the ZiBRA-2 project (https://www.zibra2project.org) which is an arbovirus surveillance project, across the Midwest of Brazil using a mobile genomics laboratory, combined with a genomic surveillance training program that targeted post-graduate students, laboratory technicians, and health practitioners in universities and laboratories.
Palavras-chave
URI
https://observatorio.fm.usp.br/handle/OPI/40876
Referências
  1. Allicock OM, 2012, MOL BIOL EVOL, V29, P1533, DOI 10.1093/molbev/msr320
  2. Baele G, 2013, MOL BIOL EVOL, V30, P239, DOI 10.1093/molbev/mss243
  3. Betts MJ, 2007, BIOINFORMATICS GENET, DOI [10.1002/0470867302.ch14, DOI 10.1002/0470867302.CH14, 10.1002/9780470059180.ch13]
  4. Borchering RK, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-13628-x
  5. Bouckaert R, 2014, PLOS COMPUT BIOL, V10, DOI 10.1371/journal.pcbi.1003537
  6. Brasil. Ministerio da Saude, 2020, MON CAS ARB URB TRAR
  7. Brasil. Ministerio da Saude, 2019, VIG SAUD NO BRAS 200
  8. Colizzi V, 2019, JMIR RES PROTOC, V8, DOI 10.2196/11745
  9. de Bruycker-Nogueira F, 2016, INFECT GENET EVOL, V45, P454, DOI 10.1016/j.meegid.2016.09.025
  10. de Jesus JG, 2020, MEM I OSWALDO CRUZ, V115, DOI 10.1590/0074-02760190423
  11. Dejnirattisai W, 2016, NAT IMMUNOL, V17, P1102, DOI 10.1038/ni.3515
  12. dos Santos FB, 2011, VIROL J, V8, DOI 10.1186/1743-422X-8-387
  13. Drumond BP, 2013, PLOS ONE, V8, DOI 10.1371/journal.pone.0059422
  14. Drumond BP, 2012, ARCH VIROL, V157, P2061, DOI 10.1007/s00705-012-1393-9
  15. Dutra KR, 2017, J MED VIROL, V89, P966, DOI 10.1002/jmv.24729
  16. Faria NR, 2018, SCIENCE, V361, P894, DOI 10.1126/science.aat7115
  17. Faria NR, 2017, NATURE, V546, P406, DOI 10.1038/nature22401
  18. Faria NR, 2016, GENOME MED, V8, DOI 10.1186/s13073-016-0356-2
  19. FernandesBrito A, 2020, LYING WAIT RESURGENC, DOI [10.1101/2020.08.10.20172247v1, DOI 10.1101/2020.08.10.20172247V1]
  20. Fonseca V, 2019, PLOS NEGLECT TROP D, V13, DOI 10.1371/journal.pntd.0007231
  21. Hill SC, 2019, EMERG INFECT DIS, V25, P784, DOI 10.3201/eid2504.180958
  22. Kalyaanamoorthy S, 2017, NAT METHODS, V14, P587, DOI [10.1038/nmeth.4285, 10.1038/NMETH.4285]
  23. Katoh K, 2013, MOL BIOL EVOL, V30, P772, DOI 10.1093/molbev/mst010
  24. Kraemer MUG, 2015, ELIFE, V4, DOI 10.7554/eLife.08347
  25. Nguyen LT, 2015, MOL BIOL EVOL, V32, P268, DOI 10.1093/molbev/msu300
  26. Larsson A, 2014, BIOINFORMATICS, V30, P3276, DOI 10.1093/bioinformatics/btu531
  27. Lemey P, 2009, PLOS COMPUT BIOL, V5, DOI 10.1371/journal.pcbi.1000520
  28. Lourenco J, 2018, EVOL APPL, V11, P516, DOI 10.1111/eva.12554
  29. San Martin JL, 2010, AM J TROP MED HYG, V82, P128, DOI 10.4269/ajtmh.2010.09-0346
  30. Martinez DR, 2020, CELL REP, V33, DOI 10.1016/j.celrep.2020.108226
  31. NOGUEIRA RMR, 1990, MEM I OSWALDO CRUZ, V85, P253, DOI 10.1590/S0074-02761990000200022
  32. Nogueira RMR, 2001, MEM I OSWALDO CRUZ, V96, P925, DOI 10.1590/S0074-02762001000700007
  33. Nunes MRT, 2014, PLOS NEGLECT TROP D, V8, DOI 10.1371/journal.pntd.0002769
  34. Oboist U, 2019, METHODS ECOL EVOL, V10, P1357, DOI 10.1111/2041-210X.13205
  35. Osanai C H, 1983, Rev Inst Med Trop Sao Paulo, V25, P53
  36. PAHO/WHO, REP CAS DENG FEV AM
  37. Petrone ME, 2021, NAT COMMUN, V12, DOI 10.1038/s41467-020-20391-x
  38. Pinheiro F., 1997, DENGUE BULL, V21
  39. Quick J, 2017, NAT PROTOC, V12, P1261, DOI 10.1038/nprot.2017.066
  40. Rambaut A, 2016, VIRUS EVOL, V2, DOI 10.1093/ve/vew007
  41. RICE CM, 1985, SCIENCE, V229, P726, DOI 10.1126/science.4023707
  42. RICOHESSE R, 1990, VIROLOGY, V174, P479, DOI 10.1016/0042-6822(90)90102-W
  43. Salles TS, 2018, PARASITE VECTOR, V11, DOI 10.1186/s13071-018-2830-8
  44. SCHATZMAYR H G, 1986, Memorias do Instituto Oswaldo Cruz, V81, P245, DOI 10.1590/S0074-02761986000200019
  45. Suchard MA, 2018, VIRUS EVOL, V4, DOI 10.1093/ve/vey016
  46. Nunes MRT, 2015, BMC MED, V13, DOI 10.1186/s12916-015-0348-x
  47. Nunes MRT, 2012, EMERG INFECT DIS, V18, P1858, DOI 10.3201/eid1811.120217
  48. Torres MC, 2019, PLOS ONE, V14, DOI 10.1371/journal.pone.0225879
  49. Vilsker M, 2019, BIOINFORMATICS, V35, P871, DOI 10.1093/bioinformatics/bty695
  50. WHO, 2009, DENGUE GUIDELINES DI

Coleções
Artigos e Materiais de Revistas Científicas - FM/Outros
Artigos e Materiais de Revistas Científicas - LIM/46
Artigos e Materiais de Revistas Científicas - ODS/03