Updating the Phylodynamics of Yellow Fever Virus 2016-2019 Brazilian Outbreak With New 2018 and 2019 Sao Paulo Genomes

Imagem de Miniatura
Arquivos
art_SALLES_Updating_the_Phylodynamics_of_Yellow_Fever_Virus_20162019_2022.PDF (7.39 MB)
Citações na Scopus
1
Tipo de produção
article
Data de publicação
2022
DOI
Scopus
Web of Science
PubMed
Título da Revista
ISSN da Revista
Título do Volume
Editora
FRONTIERS MEDIA SA
Autores
AMGARTEN, Deyvid Emanuel
AREVALO, Santiago Justo
Citação
FRONTIERS IN MICROBIOLOGY, v.13, article ID 811318, 9p, 2022
Projetos de Pesquisa
Unidades Organizacionais
Fascículo
Resumo
The recent outbreak of yellow fever (YF) in Sao Paulo during 2016-2019 has been one of the most severe in the last decades, spreading to areas with low vaccine coverage. The aim of this study was to assess the genetic diversity of the yellow fever virus (YFV) from Sao Paulo 2016-2019 outbreak, integrating the available genomic data with new genomes from patients from the Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP). Using phylodynamics, we proposed the existence of new IE subclades, described their sequence signatures, and determined their locations and time of origin. Plasma or urine samples from acute severe YF cases (n = 56) with polymerase chain reaction (PCR) positive to YFV were submitted to viral genome amplification using 12 sets of primers. Thirty-nine amplified genomes were subsequently sequenced using next-generation sequencing (NGS). These 39 sequences, together with all the complete genomes publicly available, were aligned and used to determine nucleotide/amino acids substitutions and perform phylogenetic and phylodynamic analysis. All YFV genomes generated in this study belonged to the genotype South American I subgroup E. Twenty-one non-synonymous substitutions were identified among the new generated genomes. We analyzed two major clades of the genotypes IE, IE1, and IE2 and proposed the existence of subclades based on their sequence signatures. Also, we described the location and time of origin of these subclades. Overall, our findings provide an overview of YFV genomic characterization and phylodynamics of the 2016-2019 outbreak contributing to future virological and epidemiological studies.
Palavras-chave
yellow fever virus, next generation sequencing, outbreak, Sao Paulo, vaccine coverage
URI
https://observatorio.fm.usp.br/handle/OPI/47129
Referências
  1. Auguste AJ, 2010, J VIROL, V84, P9967, DOI 10.1128/JVI.00588-10
  2. Baleotti FG, 2003, MEM I OSWALDO CRUZ, V98, P379, DOI 10.1590/S0074-02762003000300015
  3. Beasley DWC, 2015, ANTIVIR RES, V115, P48, DOI 10.1016/j.antiviral.2014.12.010
  4. Casadio LVB, 2019, MEM I OSWALDO CRUZ, V114, DOI 10.1590/0074-02760190033
  5. Bonato V, 2004, J MAMMAL, V85, P708, DOI 10.1644/BWG-121
  6. Bouckaert R, 2014, PLOS COMPUT BIOL, V10, DOI 10.1371/journal.pcbi.1003537
  7. Brand C, 2017, WIRES RNA, V8, DOI 10.1002/wrna.1437
  8. Bryant JE, 2007, PLOS PATHOG, V3, P668, DOI 10.1371/journal.ppat.0030075
  9. CHAMBERS TJ, 1990, ANNU REV MICROBIOL, V44, P649, DOI 10.1146/annurev.mi.44.100190.003245
  10. Chen S, 2017, VIRUSES-BASEL, V9, DOI 10.3390/v9100291
  11. Cunha MS, 2019, SCI REP-UK, V9, DOI 10.1038/s41598-019-41950-3
  12. Cunha MD, 2019, SCI REP-UK, V9, DOI 10.1038/s41598-019-56650-1
  13. de Rezende IM, 2018, PLOS NEGLECT TROP D, V12, DOI 10.1371/journal.pntd.0006538
  14. de Souza RP, 2010, J MED VIROL, V82, P175, DOI 10.1002/jmv.21606
  15. Delatorre E, 2019, FRONT MICROBIOL, V10, DOI 10.3389/fmicb.2019.01079
  16. Hoang DT, 2018, MOL BIOL EVOL, V35, P518, DOI 10.1093/molbev/msx281
  17. Drummond AJ, 2005, MOL BIOL EVOL, V22, P1185, DOI [10.1093/molbev/msi103, 10.1093/molbev/mss075]
  18. Drummond AJ, 2006, PLOS BIOL, V4, P699, DOI 10.1371/journal.pbio.0040088
  19. Drummond AJ, 2012, MOL BIOL EVOL, V29, P1969, DOI 10.1093/molbev/mss075
  20. Ferreira MAR, 2008, CAN J STAT, V36, P355, DOI 10.1002/cjs.5550360302
  21. Garrison E, 2012, HAPLOTYPE BASED VARI, DOI 10.1101/2021.05.21.445151
  22. Gomez MM, 2018, J GEN VIROL, V99, P536, DOI 10.1099/jgv.0.001033
  23. Google, 2020, GOOGL MAPS
  24. Governo do Estado de Sao Paulo, 2019, B EP FEBR AM
  25. Guindon S, 2010, SYST BIOL, V59, P307, DOI 10.1093/sysbio/syq010
  26. Hill SC, 2020, PLOS PATHOG, V16, DOI 10.1371/journal.ppat.1008699
  27. Hunt M, 2015, BIOINFORMATICS, V31, P2374, DOI 10.1093/bioinformatics/btv120
  28. Kalyaanamoorthy S, 2017, NAT METHODS, V14, P587, DOI [10.1038/NMETH.4285, 10.1038/nmeth.4285]
  29. Katoh K, 2013, MOL BIOL EVOL, V30, P772, DOI 10.1093/molbev/mst010
  30. Kumar S, 2016, MOL BIOL EVOL, V33, P1870, DOI [10.1093/molbev/msw054, 10.1093/molbev/msv279]
  31. Larkin MA, 2007, BIOINFORMATICS, V23, P2947, DOI 10.1093/bioinformatics/btm404
  32. Lemey P, 2009, PLOS COMPUT BIOL, V5, DOI 10.1371/journal.pcbi.1000520
  33. Li H, 2011, BIOINFORMATICS, V27, P2987, DOI 10.1093/bioinformatics/btr509
  34. Li H, 2009, BIOINFORMATICS, V25, P2078, DOI 10.1093/bioinformatics/btp352
  35. Li H, 2009, BIOINFORMATICS, V25, P1094, DOI [10.1093/bioinformatics/btp100, 10.1093/bioinformatics/btp324]
  36. McKenna A, 2010, GENOME RES, V20, P1297, DOI 10.1101/gr.107524.110
  37. Minh BQ, 2020, MOL BIOL EVOL, V37, P1530, DOI 10.1093/molbev/msaa015
  38. Mir D, 2017, SCI REP-UK, V7, DOI 10.1038/s41598-017-07873-7
  39. Monath TP, 2015, J CLIN VIROL, V64, P160, DOI 10.1016/j.jcv.2014.08.030
  40. Mutebi JP, 2001, J VIROL, V75, P6999, DOI 10.1128/JVI.75.15.6999-7008.2001
  41. Nunes MRT, 2012, J VIROL, V86, P13263, DOI 10.1128/JVI.00565-12
  42. Nurk S, 2013, J COMPUT BIOL, V20, P714, DOI 10.1089/cmb.2013.0084
  43. Silva NIO, 2020, VIROL J, V17, DOI 10.1186/s12985-019-1277-7
  44. Patkar CG, 2007, J VIROL, V81, P6471, DOI 10.1128/JVI.02120-06
  45. Rambaut A, 2018, SYST BIOL, V67, P901, DOI 10.1093/sysbio/syy032
  46. Russel PM, 2019, SYST BIOL, V68, P219, DOI 10.1093/sysbio/syy050
  47. de Abreu FVS, 2019, EMERG MICROBES INFEC, V8, P218, DOI 10.1080/22221751.2019.1568180
  48. Suchard MA, 2009, BIOINFORMATICS, V25, P1370, DOI 10.1093/bioinformatics/btp244
  49. Tabachnick WJ, 2016, ANNU REV VIROL, V3, P125, DOI 10.1146/annurev-virology-110615-035630
  50. Thorvaldsdottir H, 2013, BRIEF BIOINFORM, V14, P178, DOI 10.1093/bib/bbs017
  51. Vasconcelos Pedro Fernando da Costa, 2003, Rev. Soc. Bras. Med. Trop., V36, P275, DOI 10.1590/S0037-86822003000200012
  52. von Lindern JJ, 2006, J GEN VIROL, V87, P895, DOI 10.1099/vir.0.81236-0
  53. Yu Guangchuang, 2020, Curr Protoc Bioinformatics, V69, pe96, DOI 10.1002/cpbi.96

Coleções
Artigos e Materiais de Revistas Científicas - FM/MGT
Artigos e Materiais de Revistas Científicas - HC/ICHC
Artigos e Materiais de Revistas Científicas - LIM/03
Artigos e Materiais de Revistas Científicas - LIM/07
Artigos e Materiais de Revistas Científicas - ODS/03