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. 2009 Oct 13;4(10):e7299.
doi: 10.1371/journal.pone.0007299.

New genotype of dengue type 3 virus circulating in Brazil and Colombia showed a close relationship to old Asian viruses

Victor Hugo Aquino  1 , Alberto Anastacio Amarilla, Helda Liz Alfonso, Weber Cheli Batista, Luiz Tadeu Moraes Figueiredo
Affiliations

New genotype of dengue type 3 virus circulating in Brazil and Colombia showed a close relationship to old Asian viruses

Victor Hugo Aquino et al. PLoS One. .

Abstract

Dengue type 3 genotype V viruses have been recently detected in Brazil and Colombia. In this study, we described another Brazilian isolate belonging to this genotype. Phylogenetic analysis including dengue type 3 viruses isolated worldwide showed that Brazilian and Colombian viruses were closely related to viruses isolated in Asia more than two decades ago. The characteristic evolutionary pattern of dengue type 3 virus cannot explain the close similarity of new circulating viruses with old viruses. Further studies are needed to confirm the origin of the new dengue type III genotype circulating in Brazil and Colombia.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Bayesian phylogenetic trees derived from 154 global samples of DENV-3 E gene partial sequences (1023 nucleotides) inferred with MrBayes program.
The posterior probabilities are expressed in percent and indicated at important nodes. DENV-1 (ThD1_0127_80_D4, AY732411), DENV-2 (JAM1983_D2, AY484605) and DENV-4 (1503_YUCATAN_MX_84_D4, DQ341212) were used as outgroup. Horizontal branch lengths are drawn to scale. Aligned sequences were analyzed in the MrModeltest 2.3 program to identify the best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction . The nucleotide substitution model used was under a General Time Reversible model of nucleotide substitution with gamma-distributed rate variation (G = 1.2411) and a proportion of invariable sites (I = 0.3656) (GTR+G+I), using Akaike's Information Criterion (AIC) . Five runs of 4 chains each (one cold and tree heated, temperature = 0.20) were run for 1.5×106 generations, with a burn-in of 6000 generations. Characteristic amino acid substitutions at important nodes are indicated. GenBank accession numbers: BH 16 2003 (EF625832), BH 19 2003 (EF625833), BH 24 2003 (EF625834), BR 00 68784 (AY038605), D3BR RP1 03 (DQ118877), BR74886 02 (AY679147), China 80 2 (AF317645), Cuba21 02 (AY702031), D3BR PV7 03 (EU570161), BR DEN3 RO1 02 (EF629373), BR DEN3 RO2-02 (EF629373), ET ET209 00 (EF440434), ET_D3_Hu_TL129NIID_2005 (AB214882), ET_D3_Hu_TL018NIID_2005 (AB214879), ET_D3_OPD007NIID 2005 (AB219131), ET SV0153 05 (DQ453981), ET SV0160 05 (DQ453980), ET SV0174 05 (DQ453973), ET SV0177 05 (DQ453972), ET SV0193 05 (DQ453970), ET SV0194 05 (DQ453969), ET_D3_TL029NIID_2005 (AB214880), Fiji 92 (L11422), PF89 27643 89 (AY744677), PF89 320219 89 (AY744678), PF90 3050 90 (AY744679), PF90 3056 90 (AY744680), PF90 6056 90 (AY744681), PF92 2956 92 (AY744682), PF92 2986 92 (AY744683), PF94 136116 94 (AY744685), India 84 (L11424), Indo0312a TW 03 (DQ518677), Indo0508a_TW (DQ518678), IN 9108a_Tw 91 (DQ518674), IN 9909a_Tw 99 (DQ518675), IN BA51 04 (AY858037), IN DEN3 98 (AY858039), IN FW01 04 (AY858040), IN FW06 04 (AY858041), IN KJ30i 04 (AY858042), Indo_KJ71 04 (AY858044), ET_D3_Indonésia_NIID01 2005 (AB219137), ET_D3_Indonésia_NIID02 2005 (AB219138), ET_D3_Indonésia_NIID04 2005 (AB219139), IN PH86 04 (AY858045), IN PI64 04 (AY858046), IN Sleman 78 (AY648961), IN TB16 04 (AY858047), IN TB55i 04 (AY858048), Indo_73 (L11425), Indo_78 (L11426), Indo_85 (L11428), JP 73NIID 1973 (AB111085), Malasya 74 (L11429), Malasya 81 (L11427), D3_H_IMTSSA_MART_2000_1567 (AY099338), D3_H_IMTSSA_MART_2000_1706 (AY099339), D3_H_IMTSSA_MART_1999_1243 (AY099337), MG 20 2004 (EF625835), MEX6097_95 (AY146763), 6584_YUCATAN_MX 96 (DQ341203), Nicaragua 94 (AY702033), Panama 94 (DQ341209), Philip 56 H87 (L11423), Philp_05_0508aTw (DQ518673), Philp_96_9609aTw (DQ518668), Philp_98_9808aTw (DQ518671), Philp_98_9809aTw (DQ518669), PtoRico 63 (L11433), D3PY AS10 03 (DQ118883), SAMOA_86 (L11435), SOMALIA 93 S142 (DQ341208), SriLan 99 9912a (DQ518679), D3_H_IMTTSSA_Sri_2000_1266 (AY099336), SriLanka 81 (L11431), SriLanka 85 (L11436), SriLanka 89 (L11437), SriLanka 91 (L11438), Venez_C02 003_Maracay_2001 (DQ367720), Venez C23 009 Maracay_2001 (DQ367721), Venz_LARD5990_00 (AY146764), In_98901437 DSS DV_3_98 (AB189126), In_98901517 DHF DV_3_98 (AB189127), In_98901403 DSS DV_3_98 (AB189125), NAMRU_2 98901620 (AY265857), Tw_05_812KH0508a_Tw (DQ518672), ET_SV0171_05 (DQ453974), In_den3_88 (AY858038), Thail_D88_303_88 (AY145714), In_98902890 DF DV_3_98 (AB189128), 95TW466_95(DQ675519), Tw_94_813KH9408a_Tw (DQ518667), In_InJ_I6_82 (DQ401694), PF92_4190_92 (AY744684), Taiwan_739079A (AY776329), BR_D3BR_ST14_04 (DQ118882), PY_D3PY_AS12_02 (DQ118884), Cuba580_01 (AY702030), 6883_YUCATAN_MX_97 (DQ341204), 4841_YUCATAN_MX_95 (DQ341202), Ja_00_28_1HuNIID_00 (AB111081), PtoRico_77_1339 (AY146761), Tahiti_65 (L11439), ThD3_1687_98 (AY676348), ThD3_0115_99 (AY676387), ThD3_1959_01 (AY676402), ThD3_0328_02 (AY676383), ThD3_0989_00 (AY676414), ThD3_0077_98 (AY676389), ThD3_0654_01 (AY676394), ThD3_0111_02 (AY676420), ThD3_0188_91 (AY676367), ThD3_0182_96 (AY676369), Thail_03_0308a_Tw (DQ518660), TW_05_807KH0509a_Tw (DQ518659), VietN_BID V1018_2006 (EU482462), Thal_D93_044_93 (AY145720), Ja_00_40_1HuNIID_00 (AB111082), Ja_96_17_1HuNIID_96(AB111084), BDH_Apu_01 (AY656672), Thail_D92_423_92 (AY145718), Thail_D94_283_94 (AY145723), Thail_D95_0014 _95(AY145724), Thail_D97_0144_97 (AY145729), Thail_D93_674 _93 (AY145721), Thail_D94_122 _94(AY145722), Thail_D97_0291 _97(AY145730), Thail_D95_0400 _95 (AY145725), Ja_00_27_1HuNIID_00 (AB111080), BDH02_1_02 (AY496871), Myan_05_0508a_Tw, DQ518666), Mal_LN7933_94 (AY338494), Ma_LN2632_93 (AF147459), Sing_8120_95 (AY766104), ThD3_0029_90 (AY676421), ThD3_0183_85 (AY676368), Thail_87_1384_87 (AF533079), Thail_D91_538_91 (AY145717), Thail_D92_431_92 (AY145719), ThD3_0065_86 (AY676354), ThD3_0040_80 (AY676359), 98TW182_98 (DQ675520), Thail_PaH881_88 (AF349753), ThD3_0046_83 (AY676358), Thail_D89_273_89 (AY145715), ThD3_0137_84 (AY676371), ThD3_0059_81 (AY676356), ThD3_285M_77 (AY676384), ThD3_0059_82 (AY676355), ThD3_0033_74 (AY676360), 1503_YUCATAN_MX_84_D4 (DQ341212), JAM1983_D2 (AY484605), ThD1_0127_80 _D1 (AY732411).
Figure 2
Figure 2. Maximum Likelihood phylogenetic tree derived from 80 global samples of DENV-3 using 306 nucleotides of E/NS1 junction with a bootstrap analysis of 500 replicates.
A DENV-1 strain (M87512) was used as outgroup. Horizontal branch lengths are drawn to scale. Aligned sequences were analyzed in the Modeltest 2.3 program and found that the best fit-model of nucleotide substitution for phylogenetic reconstruction was Tamura & Nei (TrN+I) with a proportion of invariable sites (I) of 0.5203 and gamma distribution with equal rates for all sites, using Akaike's Information Criterion (AIC). GenBank accession numbers: In_98901403_DSS_DV_3_98 (AB189125), In_98901437_DSS_DV_3_98 (AB189126), In_98901517_DHF_DV_3_98 (AB189127), In_FW01_04 (AY858040), In_FW06_04 (AY858041), In_KJ30i_04 (AY858042), In_KJ71_04 (AY858044), In_PH86_04 (AY858045), In_PI64_04 (AY858046), In_TB16_04 (AY858047), In_TB55i_04 (AY858048), In_BA51_04 (AY858037), In_den3_98 (AY858039), ET_D3_Hu_TL109NIID_2005 (AB214881), China_80_2_ (AF317645), BR_DEN3_RO1_02 (EF629370), BR_DEN3_RO2_02_ (EF629373), BDH02_1_02 (AY496871), BDH02_7_02 (AY496877), ThD3_0104_93_ (AY676350), ThD3_0055_93_ (AY676351), Thail_C0331_94_94 (AY876494), ThD3_0010_87_ (AY676352), VietN_BID_V1008_2006 (EU482452), VietN_BID_V1009_2006 (EU482453), VietN_BID_V1011_2006 (EU482455), VietN_BID_V1014_2006 (EU482458), VietN_BID_V1015_2006 (EU482459), VietN_BID_V1016_2006 (EU482460), VietN_BID_V1017_2006 (EU482461), VietN_BID_V1018_2006 (EU482462), VietN_BID_V1010_2006 (EU482454), VietN_BID_V1012_2006 (EU482456), VietN_BID_V1013_2006 (EU482457), Sing_8120_95 (AY766104), D3_H_IMTSSA_SRI_2000_1266 (AY099336), NC_001475 (NC_001475), Singapore (AY662691), D3_SG_SS710_2004 (EU081181), D3_SG_05K791DK1_2005 (EU081182), BR74886_02 (AY679147), BR_DEN3_95_04 (EF629366), BR_DEN3_97_04 (EF629367), BR_DEN3_98_04_ (EF629368), BR_DEN3_290_02 (EF629369), PtoR_BID_V1043_2006 (EU482555), PtoR_BID_V1078_2003 (EU482564), PtoR_BID_V1075_1998 (EU482563), PtoR_BID_V1088_1998 (EU482566), PtoR_BID_V859_1998 (EU482596), VEN_BID_V904_2001 (EU482612), PtoR_BID_V858_2003 (EU482595), D3/Hu/TL029NIID/2005 (AB214880), Indo_98_98901640 (AY912455), In KJ46 (AY858045), Philp56 H87 (L11423), 375 And03 (EU003494), 389 Guaj03 (EU003495), 395 NSan04 (EU003496), 400 Guaj04 (EU003497), 417 Guav04 (EU003498), 429 Huil04 (EU003499), 591 DV20 Ant05 (EU003513), DV06 Ant05 (EU003514), C0360 94 (AY923865), ThD3 1283 98 (AY676349), 98TW182 (DQ675520), Thail 98 KPS 4 0657 207 (AY912458), 99TW628 99 (DQ675533), D3 H IMTSSA MART 1999 1243 (AY099337), D3 H IMTSSA MART 2000 1567 (AY099338), D3 H IMTSSA MART 2000 1706 (AY099339), D3 H IMTSSA MART 2001 2012 (AY099340), D3 H IMTSSA MART 2001 2336 (AY099342), D3 H IMTSSA MART 2001 2023 (AY099341), BDH02_8_02 (AY496878), BDH02_6_02 (AY496876), ThD3_1687_98 (AY676348), DENV1 (M87512).
Figure 3
Figure 3. Bayesian phylogenetic trees derived from 79 global samples of DENV-3 NS1 gene sequences inferred with MrBayes program.
The posterior probabilities expressed in percent are indicated at important nodes. DENV-1 (M87512) and DENV-4 (AY618992) strains were used as outgroup. Horizontal branch lengths are drawn to scale. Aligned sequences were analyzed in the MrModeltest 2.3 program to identify the best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction. The nucleotide substitution model used was under a General Time Reversible model of nucleotide substitution with gamma-distributed rate variation (G = 1.9241) and a proportion of invariable sites (I = 0.4401) (GTR+G+I), using Akaike's Information Criterion (AIC). Five runs of 4 chains each (one cold and tree heated, temperature = 0.20) were run for 1.5×106 generations, with a burn-in of 6000 generations. GenBank accession numbers: D3BR PV7 03 (FJ481174), In_98901403_DSS_DV_3_98 (AB189125), In_98901437_DSS_DV_3_98 (AB189126), In_98901517_DHF_DV_3_98 (AB189127), In_98902890_DF_DV_3_98 (AB189128), ET_D3_Hu_TL018NIID_2005 (AB214879), ET_D3_Hu_TL109NIID_2005 (AB214881), ET_D3_Hu_TL029NIID_2005 (AB214880), ET_D3_Hu_TL129NIID_2005 (AB214882), China_80_2_ (AF317645), D3_H_IMTSSA_SRI_2000_1266 (AY099336), D3_H_IMTSSA_MART_1999_1243 (AY099337), BDH02_1_02 (AY496871), BDH02_3_02 (AY496873), BDH02_4_2 (AY496874), BDH02_7_02 (AY496877), In_Sleman_78 (AY648961), Singapore (AY662691), ThD3_0104_93_ (AY676350), ThD3_0055_93_ (AY676351), BR74886_02 (AY679147), PF89_320219_89 (AY744678), PF90_3056_90 (AY744680), PF92_4190_92 (AY744684), PF94_136116_94 (AY744685), In_BA51_04 (AY858037), In_den3_98 (AY858039), In_FW01_04 (AY858040), In_FW06_04 (AY858041), In_KJ30i_04 (AY858042), In_KJ71_04 (AY858044), In_PH86_04 (AY858045), In_PI64_04 (AY858046), In_TB16_04 (AY858047), In_TB55i_04 (AY858048), Thail_C0331_94_94 (AY876494), In_InJ_16_82 (DQ401690), PhMH_J1_97 (DQ401695), BR_DEN3_95_04 (EF629366), BR_DEN3_97_04 (EF629367), BR_DEN3_98_04_ (EF629368), BR_DEN3_290_02 (EF629369), BR_DEN3_RO1_02 (EF629370), BR_DEN3_RO2_02_ (EF629373), D3_SG_SS710_2004 (EU081181), D3_SG_05K791DK1_2005 (EU081182), D3_SG_05K843DK1_2005 (EU081187), D3_SG_05K4648DK1_2005 (EU081225), VietN_BID_V1008_2006 (EU482452), VietN_BID_V1009_2006 (EU482453), VietN_BID_V1010_2006 (EU482454), VietN_BID_V1011_2006 (EU482455), VietN_BID_V1012_2006 (EU482456), VietN_BID_V1013_2006 (EU482457), VietN_BID_V1014_2006 (EU482458), VietN_BID_V1015_2006 (EU482459), VietN_BID_V1016_2006 (EU482460), VietN_BID_V1017_2006 (EU482461), VietN_BID_V1018_2006 (EU482462), PtoR_BID_V1043_2006 (EU482555), PtoR_BID_V1049_1998 (EU482558), PtoR_BID_V1050_1998 (EU482559), PtoR_BID_V1075_1998 (EU482563), PtoR_BID_V1078_2003 (EU482564), PtoR_BID_V1088_1998 (EU482566), PtoR_BID_V858_2003 (EU482595), PtoR_BID_V859_1998 (EU482596), VEN_BID_V904_2001 (EU482612), VEN_BID_V906_2001 (EU482613), VEN_BID_V913_2001 (EU482614), Philip56_H87 (M93130), NC_001475 (NC_001475), ThD3_1687_98 (AY676348), 98TWmosq_98 (DQ675532), ThD3_1283_98 (AY676349), In_KJ46_04 (AY858043), Thail C0360 94 (AY923865), DENV1 (M87512), DENV4 (AY618992).
Figure 4
Figure 4. Bayesian phylogenetic trees derived from 31 global samples of DENV-3 based on the 3′UTR sequences inferred with MrBayes program.
The posterior probabilities expressed in percent are indicated key nodes. The DENV-1 (M87512) and DENV4 (AY618992) strains were used as outgroup. Horizontal branch lengths are drawn to scale. Aligned sequences were analyzed in the MrModeltest 2.3 program to identify the best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction. The nucleotide substitution model used was under a General Time Reversible model of nucleotide substitution with a proportion of invariable sites (I = 0.6264) (GTR+I), using Akaike's Information Criterion (AIC). Five runs of 4 chains each (one cold and tree heated, temperature = 0.20) were run for 1.5×106 generations, with a burn-in of 6000 generations. GenBank accession numbers: D3BR PV7 03 (FJ481175), In_98901437_DSS_DV_3_98 (AB189126), In_98901403_DSS_DV_3_98 (AB189125), ET_D3_Hu_TL018NIID_2005 (AB214879), ET_D3_Hu_TL029NIID_2005 (AB214880), China_80_2_(AF317645), D3_H_IMTSSA_MART_1999_1243 (AY099337), D3_H_IMTSSA_SRI_2000_1266 (AY099336), BR74886_02 (AY679147), Philip56_H87 (M93130), BR_DEN3_95_04 (EF629366), BR_DEN3_290_02 (EF629369), BR_DEN3_RO1_02 (EF629370), BR_DEN3_RO2_02_(EF629373), D3_SG_SS710_2004 (EU081181), Singapore (AY662691), PtoR_BID_V859_1998 (EU482596), PtoR_BID_V1088_1998 (EU482566), PtoR_BID_V1078_2003 (EU482564), PtoR_BID_V1075_1998 (EU482563), PtoR_BID_V1043_2006 (EU482555), PtoR_BID_V1049_1998 (EU482558), PtoR_BID_V1050_1998 (EU482559), VEN_BID_V904_2001 (EU482612), PhMH_J1_97 (DQ401695), BDH02_1_02 (AY496871), BDH02_3_02 (AY496873), BDH02_4_2 (AY496874), BDH02_7_02 (AY496877), DENV1 (M87512), DENV4 (AY618992).
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