Genomic and Phylogenetic Characterization of Brazilian Yellow Fever Virus Strains

Overview

Journal J Virol

Publisher American Society for Microbiology

Date 2012 Sep 28

PMID 23015713

Citations 22

Authors

Marcio R T Nunes

Gustavo Palacios

Jedson F Cardoso

Livia C Martins

Edivaldo C Sousa Jr

Clayton P S de Lima

Daniele B A Medeiros

Nazir Savji

Aaloki Desai

Sueli G Rodrigues

Valeria L Carvalho

W Ian Lipkin

Pedro F C Vasconcelos

Affiliations

Soon will be listed here.

Abstract

Globally, yellow fever virus infects nearly 200,000 people, leading to 30,000 deaths annually. Although the virus is endemic to Latin America, only a single genome from this region has been sequenced. Here, we report 12 Brazilian yellow fever virus complete genomes, their genetic traits, phylogenetic characterization, and phylogeographic dynamics. Variable 3' noncoding region (3'NCR) patterns and specific mutations throughout the open reading frame altered predicted secondary structures. Our findings suggest that whereas the introduction of yellow fever virus in Brazil led to genotype I-predominant dispersal throughout South and Central Americas, genotype II remained confined to Bolivia, Peru, and the western Brazilian Amazon.

Citing Articles

Phylodynamic Investigation of Yellow Fever Virus Sheds New Insight on Geographic Dispersal Across Africa.

Motayo B, Opayele A, Akinduti P, Faneye A, Omoregie I Evol Bioinform Online. 2024; 20:11769343241309247.

PMID: 39691473 PMC: 11650462. DOI: 10.1177/11769343241309247.

Wild Brazilian yellow fever virus infection in Syrian hamsters (Mesocricetus auratus): Clinical and histopathological analyses.

de Oliveira Bottino F, Euzebio Pereira Dias de Oliveira B, Rodrigues Dos Santos J, Barata Viana Tiradentes M, Rodrigues Maia de Souza Y, Silva Galdino de Paula T Virus Res. 2024; 350:199505.

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Phylogeographic patterns of the yellow fever virus around the metropolitan region of São Paulo, Brazil, 2016-2019.

Cunha M, Duarte-Neto A, Zaki Pour S, Pereira B, Ho Y, Perondi B PLoS Negl Trop Dis. 2022; 16(9):e0010705.

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Continuous Circulation of Yellow Fever among Rural Populations in the Central African Republic.

Simo Tchetgna H, Descorps-Declere S, Selekon B, Garba-Ouangole S, Konamna X, Soungouza M Viruses. 2022; 14(9).

PMID: 36146820 PMC: 9503741. DOI: 10.3390/v14092014.

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

Salles A, Nastri A, Ho Y, Vilas Boas Casadio L, Amgarten D, Justo Arevalo S Front Microbiol. 2022; 13:811318.

PMID: 35633726 PMC: 9132216. DOI: 10.3389/fmicb.2022.811318.

References

Lepiniec L, Dalgarno L, Huong V, Monath T, Digoutte J, Deubel V . Geographic distribution and evolution of yellow fever viruses based on direct sequencing of genomic cDNA fragments. J Gen Virol. 1994; 75 ( Pt 2):417-23. DOI: 10.1099/0022-1317-75-2-417. View

Yu L, Markoff L . The topology of bulges in the long stem of the flavivirus 3' stem-loop is a major determinant of RNA replication competence. J Virol. 2005; 79(4):2309-24. PMC: 546603. DOI: 10.1128/JVI.79.4.2309-2324.2005. View

Wang E, Ryman K, Jennings A, Wood D, Taffs F, Minor P . Comparison of the genomes of the wild-type French viscerotropic strain of yellow fever virus with its vaccine derivative French neurotropic vaccine. J Gen Virol. 1995; 76 ( Pt 11):2749-55. DOI: 10.1099/0022-1317-76-11-2749. View

Schwede T, Kopp J, Guex N, Peitsch M . SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 2003; 31(13):3381-5. PMC: 168927. DOI: 10.1093/nar/gkg520. View

Bae H, Drosten C, Emmerich P, Colebunders R, Hantson P, Pest S . Analysis of two imported cases of yellow fever infection from Ivory Coast and The Gambia to Germany and Belgium. J Clin Virol. 2005; 33(4):274-80. DOI: 10.1016/j.jcv.2004.12.001. View

Bryant J, Vasconcelos P, Rijnbrand R, Mutebi J, Higgs S, Barrett A . Size heterogeneity in the 3' noncoding region of South American isolates of yellow fever virus. J Virol. 2005; 79(6):3807-21. PMC: 1075708. DOI: 10.1128/JVI.79.6.3807-3821.2005. View

Arnold K, Bordoli L, Kopp J, Schwede T . The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics. 2005; 22(2):195-201. DOI: 10.1093/bioinformatics/bti770. View

Ronquist F, Huelsenbeck J . MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003; 19(12):1572-4. DOI: 10.1093/bioinformatics/btg180. View

Bruen T, Philippe H, Bryant D . A simple and robust statistical test for detecting the presence of recombination. Genetics. 2006; 172(4):2665-81. PMC: 1456386. DOI: 10.1534/genetics.105.048975. View

10.

Wang H, Jennings A, Ryman K, Late C, Wang E, Ni H . Genetic variation among strains of wild-type yellow fever virus from Senegal. J Gen Virol. 1997; 78 ( Pt 6):1349-52. DOI: 10.1099/0022-1317-78-6-1349. View

11.

Drummond A, Rambaut A, Shapiro B, Pybus O . Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005; 22(5):1185-92. DOI: 10.1093/molbev/msi103. View

12.

Franco O . [History of the Yellow fever in Brazil]. Rev Bras Malariol Doencas Trop. 1969; 21(2):315-512. View

13.

Pisano M, Mercier V, Deubel V, Tolou H . Complete nucleotide sequence and phylogeny of an American strain of yellow fever virus, TRINID79A. Arch Virol. 1999; 144(9):1837-43. DOI: 10.1007/s007050050708. View

14.

Silva P, Molenkamp R, Dalebout T, Charlier N, Neyts J, Spaan W . Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3' stem-loop structure is not required for replication. J Gen Virol. 2007; 88(Pt 6):1738-1747. DOI: 10.1099/vir.0.82811-0. View

15.

Lemey P, Rambaut A, Drummond A, Suchard M . Bayesian phylogeography finds its roots. PLoS Comput Biol. 2009; 5(9):e1000520. PMC: 2740835. DOI: 10.1371/journal.pcbi.1000520. View

16.

McArthur M, Suderman M, Mutebi J, Xiao S, Barrett A . Molecular characterization of a hamster viscerotropic strain of yellow fever virus. J Virol. 2002; 77(2):1462-8. PMC: 140822. DOI: 10.1128/jvi.77.2.1462-1468.2003. View

17.

da C Cardoso J, Almeida M, Dos Santos E, da Fonseca D, Sallum M, Noll C . Yellow fever virus in Haemagogus leucocelaenus and Aedes serratus mosquitoes, southern Brazil, 2008. Emerg Infect Dis. 2010; 16(12):1918-24. PMC: 3294583. DOI: 10.3201/eid1612.100608. View

18.

Beasley D, Whiteman M, Zhang S, Huang C, Schneider B, Smith D . Envelope protein glycosylation status influences mouse neuroinvasion phenotype of genetic lineage 1 West Nile virus strains. J Virol. 2005; 79(13):8339-47. PMC: 1143769. DOI: 10.1128/JVI.79.13.8339-8347.2005. View

19.

Mutebi J, Wang H, Li L, Bryant J, Barrett A . Phylogenetic and evolutionary relationships among yellow fever virus isolates in Africa. J Virol. 2001; 75(15):6999-7008. PMC: 114428. DOI: 10.1128/JVI.75.15.6999-7008.2001. View

20.

Vasconcelos P, Bryant J, da Rosa T, Tesh R, Rodrigues S, Barrett A . Genetic divergence and dispersal of yellow fever virus, Brazil. Emerg Infect Dis. 2004; 10(9):1578-84. PMC: 3320275. DOI: 10.3201/eid1009.040197. View