Population Genomics of Dengue Virus Serotype 4: Insights Into Genetic Structure and Evolution

Population genomics of Dengue virus serotype 4: insights into genetic structure and evolution

Journal: Archives of Virology

Vaishali P Waman1, Sunitha Manjari K1,2, Mohan M Kale3, Urmila Kulkarni-Kale1§

1Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune-411007, India

2Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune-411007, India

3Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune-411007, India

§Corresponding author

Email: ,

Online resource 1:TableS1. The dataset of 134 strains of Dengue virus 4 (DENV-4) used in this study. The table enlists the assigned serial number, GenBank accession number, name, country, collection date, genotype and subpopulation (assigned using STRUCTURE program). The serial numbers are used to represent the corresponding strain in the bar plot given in Fig. 2.

Serial
number / GenBank Accession number / DENV-4 strain/isolate name / Country / Collection date / Genotype / Subpopulation assigned using STRUCTURE program
1 / JF262780 / Dengue virus 4 isolate P73-1120 / Malaysia / 1973 / S / GS
2 / JF262779 / Dengue virus 4 isolate P75-514 / Malaysia / 1975 / S / GS
3 / EF457906 / Dengue virus type 4 isolate P75-215 / Malaysia / 1975 / S / GS
4 / JQ922560 / Dengue virus 4 isolate DENV-4/IND/0952326/2009 / India / 2009 / I / GI-A
5 / JQ922559 / Dengue virus 4 isolate DENV-4/IND/793679/1979 / India / 1979 / I / GI-A
6 / JQ513345 / Dengue virus 4 strain H781363 / Brazil / 18-03-2011 / I / GI-A
7 / JF262783 / Dengue virus 4 isolate INDIA G11337 / India / 1961 / I / GI-B
8 / GQ868594 / Dengue virus 4 isolate DENV-4/PH/BID-V3361/1956 / Philippines / 1956 / I / GI-A
9 / FJ196850 / Dengue virus 4 isolate GD09/90 / China / 1990 / I / GI-A
10 / AY947539 / Dengue virus type 4 strain H241 / Philippines / NA / I / GI-A
11 / AY618992 / Dengue virus type 4 strain ThD4_0485_01 / Thailand / 2001 / I / GI-A
12 / AY618991 / Dengue virus type 4 strain ThD4_0087_77 / Thailand / 1977 / I / GI-A
13 / AY618990 / Dengue virus type 4 strain ThD4_0348_91 / Thailand / 1991 / I / GI-A
14 / AF289029 / dengue virus type 4 China Guangzhou B5 strain / China / NA / I / GI-A
15 / M14931 / NA / NA / NA / II / GII-A2
16 / KC333651 / Dengue virus 4 strain GZ/9809/2012 / China / 2012 / II / GII-A1
17 / JX024758 / Dengue virus 4 isolate EHI310A129SY10 / Singapore / 2010/12 / II / GII-A1
18 / JX024757 / Dengue virus 4 isolate EHI310A129CY10 / Singapore / 2010/12 / II / GII-A1
19 / JQ922558 / Dengue virus 4 isolate DENV-4/IND/624000/1962 / India / 1962 / I / GI-B
20 / JQ915090 / Dengue virus 4 isolate WF09/010409-0001 / Wallis and Futuna / 01-04-2009 / II / GII-A1
21 / JQ915089 / Dengue virus 4 isolate NC09/230909-14518 / New Caledonia / 23-09-2009 / II / GII-A1
22 / JQ915088 / Dengue virus 4 isolate NC09/020409-9266 / New Caledonia / 02-04-2009 / II / GII-A1
23 / JQ915087 / Dengue virus 4 isolate NC09/170309-6652 / New Caledonia / 17-03-2009 / II / GII-A1
24 / JQ915086 / Dengue virus 4 isolate NC09/050209-1413 / New Caledonia / 05-02-2009 / II / GII-A1
25 / JQ915085 / Dengue virus 4 isolate NC08/200208-409 / New Caledonia / 20-02-2008 / II / GII-A1
26 / JQ915084 / Dengue virus 4 isolate PF10/150610-28 / French Polynesia / 15-06-2010 / II / GII-A1
27 / JQ915083 / Dengue virus 4 isolate PF09/080409-93 / French Polynesia / 08-04-2009 / II / GII-A1
28 / JQ915082 / Dengue virus 4 isolate PF09/230309-126 / French Polynesia / 23-03-2009 / II / GII-A1
29 / JQ915081 / Dengue virus 4 isolate PF09/290109-69 / French Polynesia / 29-01-2009 / II / GII-A1
30 / JQ822247 / Dengue virus 4 isolate GZ30 / China / 2010 / II / GII-A1
31 / JQ513344 / Dengue virus 4 strain H780571 / Brazil / 13-01-2011 / II / GII-A3
32 / JQ513343 / Dengue virus 4 strain H780563 / Brazil / 29-01-2011 / II / GII-A3
33 / JQ513342 / Dengue virus 4 strain H780556 / Brazil / 29-01-2011 / II / GII-A3
34 / JQ513341 / Dengue virus 4 strain H780120 / Brazil / 21-11-2010 / II / GII-A3
35 / JQ513340 / Dengue virus 4 strain H780090 / Brazil / 29-11-2010 / II / GII-A3
36 / JQ513339 / Dengue virus 4 strain H779652 / Brazil / 24-01-2011 / II / GII-A3
37 / JQ513338 / Dengue virus 4 strain H779228 / Brazil / 14-01-2011 / II / GII-A3
38 / JQ513337 / Dengue virus 4 strain H778887 / Brazil / 20-01-2011 / II / GII-A2
39 / JQ513336 / Dengue virus 4 strain H778504 / Brazil / 11-01-2011 / II / GII-A2
40 / JQ513335 / Dengue virus 4 strain H778494 / Brazil / 12-01-2011 / II / GII-A2
41 / JQ513334 / Dengue virus 4 strain H775222 / Brazil / 10-11-2010 / II / GII-A2
42 / JQ513333 / Dengue virus 4 strain H774846 / Brazil / 24-08-2010 / II / GII-A3
43 / JQ513332 / Dengue virus 4 strain H773583 / Brazil / 20-08-2010 / II / GII-A3
44 / JQ513331 / Dengue virus 4 strain H772852 / Brazil / 18-07-2010 / II / GII-A3
45 / JQ513330 / Dengue virus 4 strain H772846 / Brazil / 17-07-2010 / II / GII-A3
46 / JN983813 / Dengue virus 4 isolate Br246RR/10 / Brazil / 08-09-2010 / II / GII-A3
47 / JN819409 / Dengue virus 4 isolate DENV-4/VE/BID-V2167/1998 / Venezuela / 1998 / II / GII-A2
48 / JN819406 / Dengue virus 4 isolate DENV-4/VE/BID-V2607/2006 / Venezuela / 2006 / II / GII-A3
49 / JN559741 / Dengue virus 4 strain H772854 / Brazil / 21-07-2010 / II / GII-A3
50 / JN559740 / Dengue virus 4 strain H402276 / Brazil / 26-03-1982 / II / GII-A2
51 / JF741967 / Dengue virus 4 isolate GZ1D4 / China / 26-09-2010 / II / GII-A1
52 / JF262782 / Dengue virus 4 isolate Haiti73 / Haiti / 1994 / II / GII-A2
53 / JF262781 / Dengue virus 4 isolate INH6412 / Venezuela / 1995 / II / GII-A2
54 / HQ332176 / Dengue virus 4 strain VE_61054_2007 / Venezuela / 2007 / II / GII-A3
55 / HQ332175 / Dengue virus 4 strain VE_61013_2007 / Venezuela / 2007 / II / GII-A3
56 / HQ332174 / Dengue virus 4 strain VE_61073_2007 / Venezuela / 2007 / II / GII-A3
57 / HQ332173 / Dengue virus 4 strain VE_61110_2007 / Venezuela / 2007 / II / GII-A3
58 / HQ332172 / Dengue virus 4 strain VE_61027_2007 / Venezuela / 2007 / II / GII-A3
59 / GU289913 / Dengue virus 4 strain 341750 / Colombia / 1982 / II / GII-A2
60 / GQ868645 / Dengue virus 4 isolate DENV-4/VE/BID-V1156/2007 / Venezuela / 2007 / II / GII-A3
61 / GQ868644 / Dengue virus 4 isolate DENV-4/VE/BID-V1155/2007 / Venezuela / 2007 / II / GII-A3
62 / GQ868643 / Dengue virus 4 isolate DENV-4/VE/BID-V1154/2007 / Venezuela / 2007 / II / GII-A3
63 / GQ868642 / Dengue virus 4 isolate DENV-4/VE/BID-V1153/2007 / Venezuela / 2007 / II / GII-A3
64 / GQ868585 / Dengue virus 4 isolate DENV-4/CO/BID-V3412/2005 / Colombia / 2005 / II / GII-A3
65 / GQ868584 / Dengue virus 4 isolate DENV-4/CO/BID-V3411/2004 / Colombia / 2004 / II / GII-A3
66 / GQ868583 / Dengue virus 4 isolate DENV-4/CO/BID-V3410/2004 / Colombia / 2004 / II / GII-A3
67 / GQ868582 / Dengue virus 4 isolate DENV-4/CO/BID-V3409/2001 / Colombia / 2001 / II / GII-A2
68 / GQ868581 / Dengue virus 4 isolate DENV-4/CO/BID-V3408/2001 / Colombia / 2001 / II / GII-A2
69 / GQ868580 / Dengue virus 4 isolate DENV-4/CO/BID-V3407/2001 / Colombia / 2001 / II / GII-A2
70 / GQ868579 / Dengue virus 4 isolate DENV-4/CO/BID-V3406/2001 / Colombia / 2001 / II / GII-A2
71 / GQ398256 / Dengue virus 4 strain DENV-4/SG/06K2270DK1/2005 / Singapore / 2005 / II / GII-A1
72 / GQ252675 / Dengue virus 4 isolate DENV-4/US/BID-V2432/1995 / USA / 1995 / II / GII-A2
73 / GQ199885 / Dengue virus 4 isolate DENV-4/US/BID-V2439/1996 / USA / 1996 / II / GII-A2
74 / GQ199884 / Dengue virus 4 isolate DENV-4/US/BID-V2438/1996 / USA / 1996 / II / GII-A2
75 / GQ199883 / Dengue virus 4 isolate DENV-4/US/BID-V2437/1996 / USA / 1996 / II / GII-A2
76 / GQ199882 / Dengue virus 4 isolate DENV-4/US/BID-V2436/1996 / USA / 1996 / II / GII-A2
77 / GQ199881 / Dengue virus 4 isolate DENV-4/US/BID-V2435/1996 / USA / 1996 / II / GII-A2
78 / GQ199880 / Dengue virus 4 isolate DENV-4/US/BID-V2431/1995 / USA / 1995 / II / GII-A2
79 / GQ199879 / Dengue virus 4 isolate DENV-4/US/BID-V2430/1994 / USA / 1994 / II / GII-A2
80 / GQ199878 / Dengue virus 4 isolate DENV-4/US/BID-V2429/1994 / USA / 1994 / II / GII-A2
81 / GQ199876 / Dengue virus 4 isolate DENV-4/VE/BID-V2610/2007 / Venezuela / 2007 / II / GII-A3
82 / FJ882601 / Dengue virus 4 isolate DENV-4/US/BID-V2448/1999 / USA / 1999 / II / GII-A2
83 / FJ882600 / Dengue virus 4 isolate DENV-4/US/BID-V2447/1999 / USA / 1999 / II / GII-A2
84 / FJ882599 / Dengue virus 4 isolate DENV-4/US/BID-V2446/1999 / USA / 1999 / II / GII-A2
85 / FJ882598 / Dengue virus 4 isolate DENV-4/US/BID-V2445/1998 / USA / 1998 / II / GII-A2
86 / FJ882597 / Dengue virus 4 isolate DENV-4/US/BID-V2444/1998 / USA / 1998 / II / GII-A2
87 / FJ882596 / Dengue virus 4 isolate DENV-4/US/BID-V2442/1998 / USA / 1998 / II / GII-A2
88 / FJ882595 / Dengue virus 4 isolate DENV-4/US/BID-V2441/1998 / USA / 1998 / II / GII-A2
89 / FJ882592 / Dengue virus 4 isolate DENV-4/VE/BID-V2501/2008 / Venezuela / 2008 / II / GII-A3
90 / FJ882591 / Dengue virus 4 isolate DENV-4/VE/BID-V2500/2007 / Venezuela / 2007 / II / GII-A3
91 / FJ882590 / Dengue virus 4 isolate DENV-4/VE/BID-V2499/2007 / Venezuela / 2007 / II / GII-A3
92 / FJ882589 / Dengue virus 4 isolate DENV-4/VE/BID-V2498/2007 / Venezuela / 2007 / II / GII-A3
93 / FJ882588 / Dengue virus 4 isolate DENV-4/VE/BID-V2497/2007 / Venezuela / 2007 / II / GII-A3
94 / FJ882587 / Dengue virus 4 isolate DENV-4/VE/BID-V2496/2007 / Venezuela / 2007 / II / GII-A3
95 / FJ882586 / Dengue virus 4 isolate DENV-4/VE/BID-V2495/2007 / Venezuela / 2007 / II / GII-A3
96 / FJ882585 / Dengue virus 4 isolate DENV-4/VE/BID-V2494/2007 / Venezuela / 2007 / II / GII-A3
97 / FJ882584 / Dengue virus 4 isolate DENV-4/VE/BID-V2493/2007 / Venezuela / 2007 / II / GII-A3
98 / FJ882583 / Dengue virus 4 isolate DENV-4/VE/BID-V2492/2007 / Venezuela / 2007 / II / GII-A3
99 / FJ882582 / Dengue virus 4 isolate DENV-4/VE/BID-V2491/2007 / Venezuela / 2007 / II / GII-A3
100 / FJ882581 / Dengue virus 4 isolate DENV-4/VE/BID-V2490/2007 / Venezuela / 2007 / II / GII-A3
101 / FJ882580 / Dengue virus 4 isolate DENV-4/VE/BID-V2489/2007 / Venezuela / 2007 / II / GII-A3
102 / FJ850095 / Dengue virus 4 isolate DENV-4/VE/BID-V2176/2000 / Venezuela / 2000 / II / GII-A3
103 / FJ850059 / Dengue virus 4 isolate DENV-4/US/BID-V2443/1998 / USA / 1998 / II / GII-A2
104 / FJ850058 / Dengue virus 4 isolate DENV-4/US/BID-V2440/1996 / USA / 1996 / II / GII-A2
105 / FJ850057 / Dengue virus 4 isolate DENV-4/US/BID-V2434/1995 / USA / 1995 / II / GII-A2
106 / FJ810417 / Dengue virus 4 isolate DENV-4/US/BID-V2433/1995 / USA / 1995 / II / GII-A2
107 / FJ639773 / Dengue virus 4 isolate DENV-4/VE/BID-V2206/2001 / Venezuela / 2001 / II / GII-A3
108 / FJ639764 / Dengue virus 4 isolate DENV-4/VE/BID-V2194/2001 / Venezuela / 2001 / II / GII-A2
109 / FJ639748 / Dengue virus 4 isolate DENV-4/VE/BID-V2177/2000 / Venezuela / 2000 / II / GII-A2
110 / FJ639745 / Dengue virus 4 isolate DENV-4/VE/BID-V2173/1999 / Venezuela / 1999 / II / GII-A2
111 / FJ639744 / Dengue virus 4 isolate DENV-4/VE/BID-V2172/1999 / Venezuela / 1999 / II / GII-A2
112 / FJ639742 / Dengue virus 4 isolate DENV-4/VE/BID-V2170/1999 / Venezuela / 1999 / II / GII-A2
113 / FJ639739 / Dengue virus 4 isolate DENV-4/VE/BID-V2166/1998 / Venezuela / 1998 / II / GII-A2
114 / FJ639738 / Dengue virus 4 isolate DENV-4/VE/BID-V2165/1998 / Venezuela / 1998 / II / GII-A2
115 / FJ639737 / Dengue virus 4 isolate DENV-4/VE/BID-V2164/1998 / Venezuela / 1998 / II / GII-A2
116 / FJ639736 / Dengue virus 4 isolate DENV-4/VE/BID-V2163/1998 / Venezuela / 1998 / II / GII-A2
117 / FJ226067 / Dengue virus 4 isolate DENV-4/US/BID-V860/1994 / USA / 1994 / II / GII-A2
118 / FJ196849 / Dengue virus 4 isolate GD07/78 / China / 1978 / II / GII-A4
119 / FJ182017 / Dengue virus 4 isolate DENV-4/VE/BID-V1160/2007 / Venezuela / 2007 / II / GII-A3
120 / FJ182016 / Dengue virus 4 isolate DENV-4/VE/BID-V1158/2007 / Venezuela / 2007 / II / GII-A3
121 / FJ024476 / Dengue virus 4 isolate DENV-4/CO/BID-V1600/1997 / Colombia / 1997 / II / GII-A2
122 / FJ024424 / Dengue virus 4 isolate DENV-4/US/BID-V1082/1998 / USA / 1998 / II / GII-A2
123 / EU854301 / Dengue virus 4 isolate DENV-4/VE/BID-V1161/2007 / Venezuela / 2007 / II / GII-A3
124 / EU854300 / Dengue virus 4 isolate DENV-4/VE/BID-V1159/2007 / Venezuela / 2007 / II / GII-A3
125 / EU854299 / Dengue virus 4 isolate DENV-4/VE/BID-V1157/2007 / Venezuela / 2007 / II / GII-A3
126 / EU854297 / Dengue virus 4 isolate DENV-4/US/BID-V1094/1998 / USA / 1998 / II / GII-A2
127 / EU854296 / Dengue virus 4 isolate DENV-4/US/BID-V1093/1998 / USA / 1998 / II / GII-A2
128 / EU854295 / Dengue virus 4 isolate DENV-4/US/BID-V1083/1986 / USA / 1986 / II / GII-A2
129 / AY776330 / Dengue virus type 4 strain Taiwan-2K0713 / Taiwan / NA / II / GII-A1
130 / AY762085 / Dengue virus type 4 strain Singapore 8976/95 / Singapore / 1995 / II / GII-A2
131 / AY618993 / Dengue virus type 4 strain ThD4_0734_00 / Thailand / 2000 / II / GII-A1
132 / AF326573 / Dengue virus type 4 strain 814669 / NA / 1981 / II / GII-A2
133 / AY618989 / Dengue virus type 4 strain ThD4_0017_97 / Thailand / 1997 / III / GIII
134 / AY618988 / Dengue virus type 4 strain ThD4_0476_97 / Thailand / 1997 / III / GIII