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18 authors, including:
Renato Pereira de Souza
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Gizelda Katz
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INTRODUCTION
Yellow fever virus (YFV) is the prototype member of
the family Flaviviridae, genus Flavivirus, which
includes approximately 70 human and veterinary
pathogens. Flaviviruses have a single-stranded, positive sense RNA genome of about 11 kb in length,
arranged into a short 50 non-coding region (50 NCR), a
single open-reading frame encoding the structural
proteins capsid (C), premembrane (prM), membrane
(M), envelope (E), the non-structural (NS) proteins NS1,
2009 WILEY-LISS, INC.
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de Souza et al.
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Sequence ID
Location/yeara
Source
prM/E junction
30 NCR
Brazil00B
Brazil00C
Brazil04
Brazil08A
Brazil08B
Brazil08C
Brazil08D
Brazil08E
Brazil08F
Brazil08G
Brazil08H
SP/2000
SP/2000
AM/2004
MT/2008
MS/2008
GO/2008
GO/2008
SP/2008
SP/2008
SP/2008
SP/2008
Human
Human
Human
Human
Human
Human
Human
Monkey
Monkey
Monkey
Monkey
FJ875515
FJ875516
FJ875517
nd
nd
nd
nd
FJ875518
FJ875519
nd
FJ875520
FJ875521
FJ875522
FJ875523
FJ875524
FJ875525
FJ875526
FJ875527
FJ875528
FJ875529
FJ875530
FJ875531
Data Analysis
Nucleotide sequence of prM/E junction fragment was
translated into the amino acid sequence by using the
program Edit Seq (Lasergene, DNASTAR, Inc., Madison, WI). This program was also used to determine the
end of the NS5 gene and the beginning of the 30 NCR in
the nucleotide sequence obtained with primers set VD8/
EMF1. The portion of the NS5 gene was eliminated and
further analysis was undertaken using the region of the
30 NCR of about 300-bp starting with the stop codon to
the end of the CS2 motif.
Phylogenetic Analysis
The sources, geographic origins, and GenBank accession numbers for which prM/E junction and 30 NCR
178
de Souza et al.
0
TABLE II. prM/E Junction and 3 NCR Sequences Used in This Study
GenBank accession no.
Isolate
Sequence ID
JSS
BeH111
BeAn23536
BeAr44824
BeH203416
BeAr233436
BeH233393
BeH350698
BeH379501
BeH413820
BeH 425381
BeAr424492
BeH422312
BeAr 424083
BeH511843
BeAr512943
BeH512772
BeAr527198
BeH 535010
BeAr 544276
Tennessee
BeAn604552
BeH603325
BeH605427
BeAr614320
BeAR628124
BeAr630768
BeAr631464
BeAr645693
V528A
Trinidad79
CAREC 788379
1345
OBD 5041
614819
1368
1899/81
1914
Peru95(153)
ARV 0548
03-5350-98
IQT 5591
OBS7687
OBS8026
35720
Asibi
M 90-5
69056
IB AR 45244
H117505
Uga
ggA 709-4-A2
STA-LSF-4-4143
Serie 227
Senegal65
SH 1446
Ar B 8883
Brazil35
Brazil54
Brazil60
Brazil62
Brazil71
Brazil73A
Brazil73B
Brazil78
Brazil80
Brazil83
Brazil84A
Brazil84B
Brazil84C
Brazil84D
Brazil91
Brazil92A
Brazil92B
Brazil94
Brazil95
Brazil96A
Brazil96B
Brazil98A
Brazil98B
Brazil98C
Brazil99
Brazil00A
Brazil01A
Brazil01B
Brazil01C
Colombia79
Trinidad79A
Trinidad79B
Ecuador81
Ecuador97
Panama74
Peru77
Peru81A
Peru81B
Peru95A
Peru95B
Peru98A
Peru98B
Bolivia99A
Bolivia99B
Venezuela98
Ghana27
Sudan40
Nigeria46
Nigeria69
Nigeria87
Uganda48A
Uganda48B
Zaire58
Ethiopia61
Senegal65A
Senegal65B
CAR77A
Ar B 9005
CAR77B
85-82H
IvoryC1999
IvoryCoast82
IvoryCoast99
Origin/year of
isolation
Brazil/1935
Brazil/1954
Brazil/1960
Brazil/1962
Brazil/1971
Brazil/1973
Brazil/1973
Brazil/1978
Brazil/1980
Brazil/1983
Brazil/1984
Brazil/1984
Brazil/1984
Brazil/1984
Brazil/1991
Brazil/1992
Brazil/1992
Brazil/1994
Brazil/1995
Brazil/1996
Brazil/1996
Brazil/1998
Brazil/1998
Brazil/1998
Brazil/1999
Brazil/2000
Brazil/2001
Brazil/2001
Brazil/2001
Colombia/1979
Trinidad/1979
Trinidad/1979
Ecuador/1981
Ecuador/1997
Panama/1974
Peru/1977
Peru/1981
Peru/1981
Peru/1995
Peru/1995
Peru/1998
Peru/1998
Bolivia/1999
Bolivia/1999
Venezuela/1998
Ghana/1927
Sudan/1940
Nigeria/1946
Nigeria/1969
Nigeria/1987
Uganda48
Uganda/1948
Zaire/1958
Ethiopia/1961
Senegal/1965
Senegal/1965
Central African
Republic/1977
Central African
Republic/1977
Ivory Coast/1982
Ivory Coast/1999
Source
prM/E junction
30 NCR
Human
Human
Cebus spp.
Haemagogus spp.
Human
Haemagogus spp.
Human
Human
Human
Human
Human
Hg. janthinomys
Human
Hg. albomaculatus
Human
Hg. janthinomys
Human
Haemagogus spp.
Human
Hg. janthinomys
Human
Alouatta belzebul
Human
Human
Haemagogus spp.
Hg. janthinomys
Hg. janthinomys
Sa. chloropterus
Haemagogus sp.
Human
Hg. spegazzini
Haemagogus
Human
Human
Human
Human
Human
Sentinel mice
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Mosquito
Human
Human
Aedes africanus
Human
Human
Human
Human
Ae. africanus
AY540437
AY540441
AY540443
AY540449
AY540452
AY540453
AY540456
AY540457
AY540458
AY540459
AY540461
AY540463
AY540465
AY540469
AY540471
AY540472
AY540473
AY540436
AY540475
DQ872412
AY540477
AY540478
AY540479
AY161928
AY161933
AY161946
AY161948
AY161950
AY540431
AY540434
AY540489
AY640589
AF369692
U52403
AF369677
AF369684
AF369694
AF369697
AF369674
AF369687
U52392
U52390
AY541335
AY541338
AY541340
AY541344
AY541347
AY541348
AY541352
AY541358
AY566273
AY541366
AY541369
AY541377
AY541379
AY541381
AY541387
AY541394
AY541397
AY541398
AY541399
AY541328
AY541332
AY541333
AY541334
AY541403
U52420
AY541405
AY541406
AY541412
AY541414
U52411
U52407
AY541430
AY541432
AY541434
AY541326
AY541327
AY541443
AY326411
AY326414
U52403
AY541410
U52423
AY541445
AY541407
U52414
U52393
U52395
U52396
U54798
AY603338
U54798
Ae. africanus
Human
Human
179
180
de Souza et al.
Fig. 1. Bayesian analysis of the prM/E junction sequences. This analysis used the GTR G I model, as
suggested by Modeltest. Duplicate sequences were collapsed before analysis (as shown by compound leaf
names). Details of the MCMC are given in the Materials and Methods Section. The consensus of post-burnin trees is shown, with nodes with less than 70% support collapsed. Numbers above the nodes represent
posterior probabilities of those branches. Black squares indicate the new sequences generated for this
study.
181
Fig. 2. Bayesian analysis of the 30 NCR sequences. Conditions were as described in Figure 1, using the
GTR G model. Numbers above the nodes represent posterior probabilities of those branches. Black
squares indicate the new sequences generated for this study.
182
de Souza et al.
183
Fig. 3. Maximum clade credibility (MCC) tree from a Bayesian analysis using a molecular clock model for
the prM/E junction. Numbers above the branches show the posterior probability of those branches.
Numbers to the right of nodes are the estimated dates of divergence. The gray bars represent the 95%
confidence region for those estimates. (The confidence interval for the root is not shown because it is very
big; instead the confidence interval is shown in parentheses.) For the genotype nomenclature, we adopted
the classification of Vasconcelos et al. [2004]. Numbers inside the circles represent the nodes for which
molecular divergence times were estimated as indicated in Table III.
184
de Souza et al.
TABLE III. Estimated Molecular Divergence Times for YFV of the Clades Old Para and Subclades of Clade I of the
South American Genotype I
Nodea
1
2
3
4
5
6
7
8
9
Dateb
Clade/subclades
Old Para, clade 1
Old Para
Clade 1
1A (1C, 1D, 1E)
1C (1D, 1E)
Brazil84 (1D, 1E)
1D, 1E
Venezuela98 (Brazil04 Brazil08E, Brazil08F, Brazil08H)
Brazil04 (Brazil08E, Brazil08F, Brazil08H)
1904 (18511953)
1935 (19151950)
1950 (19271965)
1954 (19351967)
1957 (19411969)
1969 (19511981)
1975 (1963-1985)
1985 (19801989)
1997 (19882003)
As indicated in Figure 3.
Estimates of the median time of the most recent common ancestor under relaxed molecular clock using the GTR I G model. 95% HPD
confidence intervals are shown between parentheses.
185
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