| 1 | AB074760.1 | Mochizuki | 2001 | Japan | Asia | JA01 |
| 2 | JN054255.1 | DV1_SL_2010b | 2010 | Sri Lanka | Asia | SL10 |
| 3 | KC759167.1 | DF1203 | 2012 | China | Asia | CH12 |
| 4 | KF887994.1 | DENV-1/8/Thailand/01/2013 | 2013 | Thailand | Asia | TH13 |
| 5 | KF955446.1 | DENV-1/VN/BID-V3909/2008 | 2008 | Vietnam | Asia | VN08 |
| 6 | KJ649286.1 | DENV-1-Jeddah | 2011 | Saudi Arabia | Asia | SA11 |
| 7 | AB074761.1 | A88 | 2001 | Japan | South Pacific | JA01A |
| 8 | AB189121.1 | 98901530 DFDV-1 | 1998 | Indonesia | South Pacific | ID98 |
| 9 | JQ915074.1 | PF08/180908-01 | 2008 | French-Moorea | South Pacific | FM08 |
| 10 | JQ915076.1 | PF09/090609-76 | 2009 | French-Tahiti | South Pacific | FT09 |
| 11 | FJ810415.1 | DENV-1/VE/BID-V2253/2005 | 2005 | Venezuela | America/Africa | VE05 |
| 12 | JN903579.1 | RGCB419 | 2008 | India | America/Africa | IN08 |
| 13 | KF184975.1 | Angola_2013 | 2013 | Angola | America/Africa | AN13 |
| 14 | KJ189367.1 | DENV-1/PR/BID-V8188/2010 | 2010 | Puerto Rico | America/Africa | PR10 |
| 15 | KJ189368.1 | DENV-1/MX/BID-V8195/2012 | 2012 | Mexico | America/Africa | ME12 |
| 16 | KJ189367.1 | DENV-1/PR/BID-V8188/2010 | 2010 | Puerto Rico | America/Africa | PR10 |
| 17 | KF041233.1 | D2/Pakistan/2011-3/2011 | 2011 | Pakistan | Cosmopolitan-I | PA11 |
| 18 | KJ010186.1 | DENV-2/PK/2013 | 2013 | Pakistan | Cosmopolitan-I | PA13 |
| 19 | JQ955624.1 | Od2112 | 2011 | India | Cosmopolitan-I | IN11 |
| 20 | KF479233.1 | QHD13CAIQ | 2013 | China | Cosmopolitan-I | CH13 |
| 21 | EU056810.1 | 1349 | 1983 | Burkina.Faso | Cosmopolitan-II | BF83 |
| 22 | GQ398258.1 | DENV-2/ID/1016DN/1975 | 1975 | Indonesia | Cosmopolitan-II | IN75 |
| 23 | GQ398259.1 | DENV-2/ID/1017DN/1976 | 1976 | Indonesia | Cosmopolitan-II | IN76 |
| 24 | GQ398260.1 | DENV-2/ID/1070DN/1976 | 1976 | Indonesia | Cosmopolitan-II | IN76A |
| 25 | AY858035.2 | BA05i | 2004 | Indonesia | Cosmopolitan-III | IN04 |
| 26 | EU179857.1 | DS31-291005 | 2005 | Brunei | Cosmopolitan-III | BR05 |
| 27 | EU482672.1 | DENV-2/VN/BID-V735/2006 | 2006 | Vietnam | Cosmopolitan-III | VN06 |
| 28 | FJ196853.1 | GD01/03 | 2003 | China | Cosmopolitan-III | CH03 |
| 29 | JF327392.1 | DENV-2/SG/D2Y98P-PP1/2009 | 2009 | Singapore | Cosmopolitan-III | SI09 |
| 30 | AF100467.1 | IQT1797 | 1998 | Peru | American | PE98 |
| 31 | GQ868592.1 | DENV-2/CO/BID-V3358/1986 | 1986 | Columbia | American | CO86 |
| 32 | HM582099.1 | D2/FJ/UH21/1971 | 1971 | Fiji | American | FI71 |
| 33 | AF119661.1 | China 04 | 1985 | China | Asian-American | CH85 |
| 34 | HQ999999.1 | DENV-2/GU/FDA-GUA09/2009 | 2009 | Guatemala | Asian-American | GU09 |
| 35 | KC294221.1 | DENV-2/PE/IQA 2080/2010 | 2010 | Peru | Asian-American | PE10 |
| 36 | KC294223.1 | DENV-2/PE/NFI1159/2010 | 2010 | Peru | Asian-American | PE10A |
| 37 | GQ868591.1 | DENV-2/TH/BID-V3357/1964 | 1964 | Thailand | Asian-I | TH64 |
| 38 | AF204177.1 | 44 | 1989 | China | Asian-II | CH89 |
| 39 | AF204178.1 | 43 | 1987 | China | Asian-II | CH87 |
| 40 | HQ891024.1 | DENV-2/TW/BID-V5056/2008 | 2008 | Taiwan | Asian-II | TA08 |
| 41 | JF730050.1 | DENV-2/US/BID-V5412/2007 | 2007 | US | Asian-II | US07 |
| 42 | JN796245.1 | DENV-3/US/BID-V5055/2008 | 2008 | US | II | US08 |
| 43 | EU482458.1 | DENV-3/VN/BID-V1014/2006 | 2006 | Vietnam | II | VN06 |
| 44 | HM181935.1 | DENV-3/KH/BID-V3829/2007 | 2007 | Cambodia | II | CA07 |
| 45 | GU131905.1 | DENV-3/IPC/BID-V3808/2008 | 2008 | Cambodia | II | CA08 |
| 46 | AY923865.1 | C0360/94 | 1994 | Thailand | II | TH94 |
| 47 | FJ744740.1 | DENV-3/TH/BID-V2329/2001 | 2001 | Thailand | II | TH01 |
| 48 | AY766104.1 | Singapore 8120/95 | 1995 | Singapore | II | SI95 |
| 49 | AY496879.2 | PhMH-J1-97 | 1997 | Philippines | I | PH97 |
| 50 | DQ401690.1 | InJ-16-82 | 2006 | Indonesia | I | IN06 |
| 51 | AY858042.2 | KJ30i | 2004 | Indonesia | I | IN04 |
| 52 | AB214882.1 | D3/Hu/TL129NIID/2005 | 2005 | East Timor | I | TL05 |
| 53 | EF629370.1 | BR DEN3 RO1-02 | 2007 | Brazil | V | BR07 |
| 54 | M93130.1 | H87 | 1990 | Philippines | V | PH90 |
| 55 | AF317645.1 | 80-2 | 2001 | China | V | CH01 |
| 56 | EU081198.1 | D3/SG/05K2933DK1/2005 | 2005 | Singapore | III | SI05 |
| 57 | GU363549.1 | GZ1D3 | 2009 | China | III | CH09 |
| 58 | EU529702.1 | DENV-3/US/BID-V1089/2003 | 2003 | US | III | US03 |
| 59 | EU529699.1 | DENV-3/US/BID-V1080/2006 | 2006 | US | III | US06 |
| 60 | FJ182011.1 | DENV-3/US/BID-V1621/2005 | 2005 | US | III | US05 |
| 61 | GQ868587.1 | DENV-3/VE/BID-V2483/2007 | 2007 | Venezuela | III | VE07 |
| 62 | GQ868578.1 | DENV-3/CO/BID-V3405/2007 | 2007 | Colombia | III | CO07 |
| 63 | FJ373304.1 | DENV-3/VE/BID-V1590/2004 | 2004 | Venezuela | III | VE04 |
| 64 | GU131954.1 | DENV-3/CO/BID-V3404/2006 | 2006 | Colombia | III | CO06 |
| 65 | AY618992.1 | ThD4_0485_01 | 2001 | Thailand | I | TH01 |
| 66 | JQ513345.1 | H781363 | 2011 | Brazil | I | BR11 |
| 67 | AY618991.1 | ThD4_0087_77 | 1977 | Thailand | I | TH77 |
| 68 | AY776330.1 | Taiwan-2K0713 | 2004 | Taiwan | II | TA04 |
| 69 | GQ398256.1 | DENV-4/SG/06K2270DK1/2005 | 2005 | Singapore | II | SI05 |
| 70 | FJ882599.1 | DENV-4/US/BID-V2446/1999 | 1999 | Puerto Rico | II | PR99 |
| 71 | JQ513341.1 | H780120 | 2010 | Brazil | II | BR10 |
| 72 | JQ513340.1 | H780090 | 2010 | Brazil | II | BR10A |
| 73 | JQ513339.1 | H779652 | 2011 | Brazil | II | BR11 |
| 74 | AY618989.1 | ThD4_0017_97 | 1997 | Thailand | II | TH97 |
| 75 | AY618988.1 | ThD4_0476_97 | 1997 | Thailand | III | TH97A |
| 76 | AY618989.1 | ThD4_0017_97 | 1997 | Thailand | III | TH97B |
| 77 | AB189124.1 | 98900666 DSS DV-2 | 1998 | Indonesia | Outgroup | IN98 |
| 78 | KF955458.1 | DENV-3/VN/BID-V1876/2007 | 2007 | Vietnam | Outgroup | VN07 |
| 79 | Our sample | VT-HT-00518/14 D1(1F1) | 2014 | Vietnam | | 0518/14 |
| 80 | Our sample | BD-DNT-5527/14 D1(1F1) | 2014 | Vietnam | | 5527/14 |
| 81 | Our sample | ST-HT-1191/15 D1(1F1) | 2015 | Vietnam | | 1191/15 |
| 82 | Our sample | TN-HT-9062/15 D1(1F1) | 2015 | Vietnam | | 9062/15 |
| 83 | Our sample | VT-HT-4577/14 D2 | 2014 | Vietnam | | 4577/14 |
| 84 | Our sample | BD-HT-4598/14 D2 | 2014 | Vietnam | | 4598/14 |
| 85 | Our sample | ÐN-HT-4581/15 D2 | 2015 | Vietnam | | 4581/15 |
| 86 | Our sample | BD-HT-258/14 D3 | 2014 | Vietnam | | 0258/14 |
| 87 | Our sample | VT-HT-6426/14 D3 | 2014 | Vietnam | | 6426/14 |
| 88 | Our sample | ÐN-HT-1070/15 D3 | 2015 | Vietnam | | 1070/15 |
| 89 | Our sample | BD-HT-5786/15 D3 | 2015 | Vietnam | | 5786/15 |
| 90 | Our sample | ÐT-HT-6970/15 D3 | 2015 | Vietnam | | 6970/15 |
| 91 | Our sample | BD-HT-3268/14 D4 | 2014 | Vietnam | | 3268/14 |
| 92 | Our sample | VT-HT-3837/14 D4 | 2014 | Vietnam | | 3837/14 |
| 93 | Our sample | LA-HT-1128/15 D4 | 2015 | Vietnam | | 1128/15 |
| 94 | Our sample | BD-HT-5297/15D4 | 2015 | Vietnam | | 5297/15 |
| 95 | Our sample | BD-HT-7053/15 D4 | 2015 | Vietnam | | 7053/15 |