diff --git a/auspice/CHIKV.json b/auspice/CHIKV.json index 41646c6..7ca8fff 100644 --- a/auspice/CHIKV.json +++ b/auspice/CHIKV.json @@ -19,6 +19,10 @@ { "key": "country", "scale": [ + [ + "Paraguay", + "#e31a1c" + ], [ "Bolivia", "#e31a1c" @@ -283,6 +287,10 @@ "Madagascar", "#99d8c9" ], + [ + "Djibouti", + "#99d8c9" + ], [ "Mauritius", "#99d8c9" @@ -547,12 +555,12 @@ "longitude": -61.796428 }, "Aruba": { - "latitude": 12.512306, - "longitude": -69.975188 + "latitude": 12.52111, + "longitude": -69.968338 }, "Australia": { - "latitude": -25.047944, - "longitude": 134.003347 + "latitude": -25.274398, + "longitude": 133.775136 }, "Bahamas": { "latitude": 25.0, @@ -563,12 +571,12 @@ "longitude": 90.283221 }, "Barbados": { - "latitude": 13.169025, - "longitude": -59.555144 + "latitude": 13.193887, + "longitude": -59.543198 }, "Bolivia": { - "latitude": -17.0, - "longitude": -65.0 + "latitude": -16.290154, + "longitude": -63.588653 }, "Borneo": { "latitude": 48.977748, @@ -587,24 +595,24 @@ "longitude": 104.910399 }, "Cameroon": { - "latitude": 4.717083, - "longitude": 11.74702 + "latitude": 7.369722, + "longitude": 12.354722 }, "Cayman_Islands": { - "latitude": 19.269665, - "longitude": -81.276855 + "latitude": 19.513469, + "longitude": -80.566956 }, "Central_African_Republic": { "latitude": 7.028514, "longitude": 20.580697 }, "China": { - "latitude": 34.740765, - "longitude": 101.319735 + "latitude": 35.86166, + "longitude": 104.195397 }, "Colombia": { - "latitude": 3.501314, - "longitude": -72.872505 + "latitude": 4.570868, + "longitude": -74.297333 }, "Comoros": { "latitude": -12.226076, @@ -615,32 +623,36 @@ "longitude": -5.566505 }, "Cuba": { - "latitude": 22.0, - "longitude": -79.5 + "latitude": 21.521757, + "longitude": -77.781167 }, "Democratic_Republic_of_the_Congo": { "latitude": -1.471684, "longitude": 23.213382 }, + "Djibouti": { + "latitude": 11.825138, + "longitude": 42.590275 + }, "Dominica": { - "latitude": 15.426354, - "longitude": -61.357071 + "latitude": 15.414999, + "longitude": -61.370976 }, "Dominican_Republic": { "latitude": 18.892313, "longitude": -70.206847 }, "Ecuador": { - "latitude": -1.3397667, - "longitude": -79.3666964 + "latitude": -1.831239, + "longitude": -78.183406 }, "El_Salvador": { "latitude": 13.63171, "longitude": -88.910934 }, "Finland": { - "latitude": 63.2467777, - "longitude": 25.9209164 + "latitude": 61.92411, + "longitude": 25.748151 }, "France": { "latitude": 46.648713, @@ -655,36 +667,36 @@ "longitude": -149.406843 }, "Gabon": { - "latitude": -1.343877, - "longitude": 11.721494 + "latitude": -0.803689, + "longitude": 11.609444 }, "Grenada": { - "latitude": 12.155863, - "longitude": -61.654958 + "latitude": 12.262776, + "longitude": -61.604171 }, "Guadeloupe": { - "latitude": 16.154225, - "longitude": -61.677913 + "latitude": 16.995971, + "longitude": -62.067641 }, "Guatemala": { - "latitude": 15.609342, - "longitude": -90.560029 + "latitude": 15.783471, + "longitude": -90.230759 }, "Guyana": { - "latitude": 4.633369, - "longitude": -58.801275 + "latitude": 4.860416, + "longitude": -58.93018 }, "Haiti": { - "latitude": 18.964026, - "longitude": -71.997442 + "latitude": 18.971187, + "longitude": -72.285215 }, "Honduras": { - "latitude": 14.504704, - "longitude": -87.225643 + "latitude": 15.199999, + "longitude": -86.241905 }, "Hong_Kong": { - "latitude": 22.3964, - "longitude": 114.1095 + "latitude": 22.396428, + "longitude": 114.109497 }, "India": { "latitude": 23.041173, @@ -703,12 +715,12 @@ "longitude": -77.160905 }, "Japan": { - "latitude": 35.68536, - "longitude": 139.75309 + "latitude": 36.204824, + "longitude": 138.252924 }, "Kenya": { - "latitude": 1.0, - "longitude": 38.0 + "latitude": -0.023559, + "longitude": 37.906193 }, "Kiribati": { "latitude": 1.993671, @@ -719,44 +731,44 @@ "longitude": 102.63215 }, "Madagascar": { - "latitude": -19.863362, - "longitude": 46.526251 + "latitude": -18.766947, + "longitude": 46.869107 }, "Malaysia": { - "latitude": 3.98864, - "longitude": 102.064055 + "latitude": 4.210484, + "longitude": 101.975766 }, "Martinique": { - "latitude": 14.6415, - "longitude": -61.0242 + "latitude": 14.641528, + "longitude": -61.024174 }, "Mauritius": { - "latitude": -20.253752, - "longitude": 57.589972 + "latitude": -20.348404, + "longitude": 57.552152 }, "Mayotte": { "latitude": -12.812986, "longitude": 45.1406 }, "Mexico": { - "latitude": 22.40657, - "longitude": -101.844884 + "latitude": 23.634501, + "longitude": -102.552784 }, "Micronesia": { - "latitude": 6.888581, - "longitude": 158.243484 + "latitude": 7.425554, + "longitude": 150.550812 }, "Montserrat": { - "latitude": 16.737408, - "longitude": -62.192334 + "latitude": 16.742498, + "longitude": -62.187366 }, "Myanmar": { "latitude": 21.124585, "longitude": 96.253678 }, "New_Caledonia": { - "latitude": -20.9043, - "longitude": 165.618 + "latitude": -20.904305, + "longitude": 165.618042 }, "Nicaragua": { "latitude": 12.139432, @@ -771,36 +783,40 @@ "longitude": 69.913918 }, "Panama": { - "latitude": 8.641033, - "longitude": -80.40586 + "latitude": 8.537981, + "longitude": -80.782127 }, "Papua_New_Guinea": { "latitude": -6.269095, "longitude": 143.940287 }, + "Paraguay": { + "latitude": -23.442503, + "longitude": -58.443832 + }, "Philippines": { "latitude": 12.415512, "longitude": 123.431038 }, "Puerto_Rico": { - "latitude": 18.2459121, - "longitude": -66.4164147 + "latitude": 18.220833, + "longitude": -66.590149 }, "Republic_of_the_Congo": { "latitude": -0.22949, "longitude": 15.935776 }, "Russia": { - "latitude": 64.6863136, - "longitude": 97.7453061 + "latitude": 61.52401, + "longitude": 105.318756 }, "Saint_Kitts_and_Nevis": { "latitude": 17.315342, "longitude": -62.744355 }, "Saint_Lucia": { - "latitude": 13.895288, - "longitude": -60.964518 + "latitude": 13.909444, + "longitude": -60.978893 }, "Saint_Martin": { "latitude": 18.083183, @@ -811,20 +827,20 @@ "longitude": -61.189064 }, "Samoa": { - "latitude": -13.621469, - "longitude": -172.438935 + "latitude": -13.759029, + "longitude": -172.104629 }, "Senegal": { - "latitude": 14.502785, - "longitude": -14.654668 + "latitude": 14.497401, + "longitude": -14.452362 }, "Singapore": { "latitude": 1.356203, "longitude": 103.828142 }, "South_Africa": { - "latitude": -29.140993, - "longitude": 24.367459 + "latitude": -30.559482, + "longitude": 22.937506 }, "Sri_Lanka": { "latitude": 7.517242, @@ -835,36 +851,36 @@ "longitude": -62.820854 }, "Sudan": { - "latitude": 16.0, - "longitude": 30.0 + "latitude": 12.862807, + "longitude": 30.217636 }, "Suriname": { - "latitude": 4.1413, - "longitude": -56.047436 + "latitude": 3.919305, + "longitude": -56.027783 }, "Tanzania": { "latitude": -6.453096, "longitude": 34.894539 }, "Thailand": { - "latitude": 15.660392, - "longitude": 101.520053 + "latitude": 15.870032, + "longitude": 100.992541 }, "Timor-Leste": { - "latitude": -8.819164, - "longitude": 125.865833 + "latitude": -8.874217, + "longitude": 125.727539 }, "Tonga": { - "latitude": -19.9160818, - "longitude": -175.2026423 + "latitude": -21.178986, + "longitude": -175.198242 }, "Trinidad_and_Tobago": { - "latitude": 10.485968, - "longitude": -61.255908 + "latitude": 10.691803, + "longitude": -61.222503 }, "Turks_and_Caicos_Islands": { - "latitude": 21.800308, - "longitude": -71.71875 + "latitude": 21.694025, + "longitude": -71.797928 }, "USA": { "latitude": 39.999733, @@ -879,8 +895,8 @@ "longitude": -64.759199 }, "Yemen": { - "latitude": 15.744086, - "longitude": 47.66645 + "latitude": 15.552727, + "longitude": 48.516388 } }, "key": "country" @@ -981,7 +997,7 @@ "entropy" ], "title": "Molecular epidemiology of Chikungunya virus", - "updated": "2020-12-30" + "updated": "2021-02-16" }, "tree": { "branch_attrs": { @@ -991,7 +1007,7 @@ { "branch_attrs": { "labels": { - "aa": "CHIKVgp1: T128A, V176I, L233M, M292I, V410I, Q444P, Q488K, E518D, V604I, M643L, K705R, I714T, T753S, G761N, S998N, K1045R, Y1078H, I1116T, T1133N, A1180V, V1194I, V1218I, I1273V, M1465L, S1486A, I1504V, V1508I, A1529S, I1549V, R1658K, S1660P, S1663T, T1669S, I1686V, V1689A, D1694E, A1699I, L1700P, A1703T, L1704P, G1707R, H1710L, G1713E, L1715F, A1716S, S1724N, V1726A, R1737K, T1740N, I1750V, T1751L, E1762D, C1764H, P1765S, V1766I, T1773I, M1778A, P1784L, T1786V, L1790P, S1791N, H1792Q, P1793L, S1801N, L1830S, K1874R, S1879T, H1890Q, I1936V, R1941G, V1972I, S1996A, A2036S, S2041T, E2098K, S2258P, H2371Y, T2375A, E2403D, I2414V, Y2430H, V2462I, I2463V; CHIKVgp2: T20A, K71R, Q74K, N80D, T81P, N82K, K89Q, T124M, I265L, M268L, K294S, Q313K, V357I, N397S, M399T, F409L, S449T, D457E, K465R, S507T, V547I, I609T, E627Q, Q632H, M643T, L667M, V694I, V695I, M709T, M715V, I740L, I743V, A746T, Q752Y, V756A, R785K, L843Q, T954A, I971V, M1085I, L1105V, A1130T, E1152D, I1153V, E1188A, A1213T, V1229I" + "aa": "CHIKVgp1: T128A, V176I, L233M, M292I, V410I, Q444P, Q488K, E518D, V604I, M643L, K705R, I714T, T753S, G761N, S998N, K1045R, Y1078H, I1116T, T1133N, T1134I, A1180V, V1194I, V1218I, I1273V, M1465L, S1486A, I1504V, V1508I, A1529S, I1549V, R1658K, S1660P, S1663T, T1669S, I1686E, V1689A, D1694E, A1699I, L1700P, A1703T, L1704P, G1707R, H1710L, G1713E, L1715F, A1716S, S1724N, V1726A, R1737K, T1740N, I1750V, T1751L, E1762D, C1764H, P1765S, V1766I, T1773I, M1778A, P1784L, T1786V, S1791N, H1792Q, P1793L, S1801N, L1830S, K1874R, S1879T, H1890Q, I1936V, R1941G, V1972I, S1996A, A2036S, S2041T, E2098K, S2258P, H2371Y, T2375A, E2403D, I2414V, I2422T, Y2430H, V2462I, I2463V; CHIKVgp2: T20A, K71R, Q74K, N80D, T81P, N82K, K89Q, T124M, I265L, M268L, K294S, Q313K, V357I, N397S, M399T, F409L, S449T, D457E, K465R, S507T, V547I, I609T, E627Q, Q632H, M643T, L667M, V695I, M709T, M715V, I740L, I743V, A746T, Q752Y, V756A, L843Q, T954A, I971V, M1078I, M1085I, L1105V, A1130T, E1152D, I1153V, E1188A, A1213T, V1229I" }, "mutations": { "CHIKVgp1": [ @@ -1014,6 +1030,7 @@ "Y1078H", "I1116T", "T1133N", + "T1134I", "A1180V", "V1194I", "V1218I", @@ -1028,7 +1045,7 @@ "S1660P", "S1663T", "T1669S", - "I1686V", + "I1686E", "V1689A", "D1694E", "A1699I", @@ -1054,7 +1071,6 @@ "M1778A", "P1784L", "T1786V", - "L1790P", "S1791N", "H1792Q", "P1793L", @@ -1075,6 +1091,7 @@ "T2375A", "E2403D", "I2414V", + "I2422T", "Y2430H", "V2462I", "I2463V" @@ -1106,7 +1123,6 @@ "Q632H", "M643T", "L667M", - "V694I", "V695I", "M709T", "M715V", @@ -1115,10 +1131,10 @@ "A746T", "Q752Y", "V756A", - "R785K", "L843Q", "T954A", "I971V", + "M1078I", "M1085I", "L1105V", "A1130T", @@ -1156,7 +1172,6 @@ "G420A", "C423T", "T424C", - "C441T", "G444A", "A451G", "G453A", @@ -1227,7 +1242,7 @@ "C1053T", "G1059A", "G1071A", - "G1074T", + "G1074C", "G1077A", "C1098A", "C1101T", @@ -1259,7 +1274,6 @@ "T1326C", "A1329T", "A1335G", - "T1338C", "A1350G", "T1377C", "C1380T", @@ -1293,6 +1307,7 @@ "G1563A", "A1578G", "A1581G", + "G1584A", "T1590C", "C1596A", "C1605A", @@ -1318,7 +1333,6 @@ "G1848A", "T1854C", "G1866A", - "C1869T", "C1876A", "G1879A", "A1884T", @@ -1370,14 +1384,17 @@ "T2256A", "T2259C", "C2262T", + "A2271G", "G2289A", "T2295C", "C2298T", "A2326T", + "C2334T", "A2341C", "A2349G", "G2350A", "G2351A", + "T2352C", "A2355G", "T2370C", "T2376C", @@ -1415,9 +1432,7 @@ "G2748A", "C2751T", "A2769G", - "T2787C", "C2814T", - "C2820T", "A2823G", "T2827C", "A2841G", @@ -1451,7 +1466,6 @@ "C3060T", "G3062A", "T3063C", - "T3078C", "T3081C", "A3084G", "A3090G", @@ -1463,7 +1477,6 @@ "T3129C", "C3135A", "G3144A", - "C3154T", "T3159C", "T3162C", "T3183C", @@ -1478,6 +1491,7 @@ "G3258A", "T3261C", "A3264G", + "G3273A", "A3276G", "T3279C", "G3288A", @@ -1505,6 +1519,7 @@ "C3456T", "T3465G", "C3467A", + "C3470T", "G3483T", "A3501G", "C3504T", @@ -1528,13 +1543,13 @@ "A3645G", "T3648C", "G3649A", + "C3651T", "C3654G", "G3660T", "T3666C", "G3684A", "T3687C", "T3702C", - "G3708A", "G3721A", "C3723T", "T3741C", @@ -1577,7 +1592,7 @@ "A4035T", "C4038T", "A4044T", - "A4047C", + "A4047T", "A4065G", "A4086T", "G4104A", @@ -1602,6 +1617,8 @@ "G4299T", "T4305C", "G4311A", + "A4320G", + "G4326A", "C4332T", "T4335C", "A4347T", @@ -1611,7 +1628,6 @@ "T4389G", "C4395T", "A4401C", - "T4404C", "A4407G", "A4413T", "C4434T", @@ -1621,6 +1637,7 @@ "C4461A", "A4462T", "G4464A", + "C4467T", "G4470A", "G4473T", "C4482T", @@ -1631,7 +1648,6 @@ "G4539A", "C4543A", "G4557A", - "G4560A", "G4563A", "T4566C", "G4569A", @@ -1666,12 +1682,13 @@ "C4762T", "A4764G", "T4767C", - "C4770G", + "C4770A", "C4771T", "T4785A", "G4800A", "A4803G", "G4809A", + "T4818C", "A4830G", "T4833G", "G4839A", @@ -1686,10 +1703,8 @@ "T4929C", "T4932A", "T4938C", - "C4953T", "A4971G", "A4980G", - "C4983T", "C4986T", "G4989A", "A4992G", @@ -1710,22 +1725,21 @@ "T5094C", "T5106C", "A5109T", - "C5112T", "C5121T", "A5125G", + "T5126A", "T5135C", "C5136T", "A5142T", + "C5146T", "T5151A", "C5157T", "C5160T", - "A5163G", "G5164A", "C5165T", "C5166T", "T5168C", "A5169G", - "A5172G", "G5176A", "C5178A", "T5180C", @@ -1733,7 +1747,7 @@ "G5190A", "A5198T", "C5199T", - "A5202T", + "A5202G", "G5207A", "C5211T", "C5212T", @@ -1750,7 +1764,6 @@ "G5271A", "A5274T", "G5279A", - "C5284T", "C5288A", "G5292C", "A5295C", @@ -1779,7 +1792,6 @@ "T5391C", "C5394T", "A5397G", - "T5400C", "A5401G", "T5402C", "T5409C", @@ -1790,19 +1802,15 @@ "C5426T", "C5430T", "G5433A", - "T5438C", "G5439A", "G5441A", "T5445A", "C5447T", "C5457A", - "C5460T", "G5471A", "G5478T", "C5487A", "A5490G", - "T5493C", - "C5499T", "C5502T", "C5505T", "A5511G", @@ -1813,17 +1821,15 @@ "A5541G", "T5544C", "C5547T", + "A5550G", "C5557T", "T5558C", "A5559G", - "C5562A", + "C5562G", "T5565C", - "T5577C", "T5578C", "T5586C", - "C5592T", "C5604T", - "C5610T", "G5622A", "C5634T", "T5649C", @@ -1843,7 +1849,7 @@ "C5721T", "C5725T", "C5736T", - "C5739A", + "C5739G", "G5748A", "C5764T", "A5775G", @@ -1853,7 +1859,6 @@ "A5787G", "C5788T", "G5808A", - "C5823T", "T5838C", "G5841A", "A5844C", @@ -1865,13 +1870,11 @@ "A5886G", "A5890G", "A5892T", - "C5895T", "T5898C", - "A5904C", + "A5904T", "C5907T", "A5916G", "C5931T", - "T5937C", "G5943A", "C5946T", "G5958A", @@ -1895,8 +1898,8 @@ "T6081C", "T6090C", "A6093G", + "C6096T", "G6114A", - "T6117C", "G6123T", "A6129G", "A6135G", @@ -1916,7 +1919,6 @@ "T6204C", "A6216G", "A6228G", - "C6229T", "A6231G", "T6237C", "A6246T", @@ -1942,6 +1944,7 @@ "A6393G", "T6402C", "A6405G", + "C6411T", "T6420A", "G6429A", "G6432A", @@ -1952,11 +1955,12 @@ "T6468C", "G6474A", "A6486G", + "A6489G", + "A6492G", "T6498C", "C6504T", "A6507T", "T6513C", - "T6525C", "T6540G", "T6543G", "A6546G", @@ -1970,7 +1974,6 @@ "A6615G", "T6624C", "C6634T", - "T6639C", "G6642A", "C6651T", "C6654A", @@ -1981,8 +1984,9 @@ "A6681G", "C6705T", "T6708C", - "A6717C", + "A6717T", "A6723G", + "A6735G", "A6738G", "T6744C", "T6747A", @@ -2011,9 +2015,7 @@ "C6909T", "C6912T", "A6933G", - "C6945T", "T6951C", - "C6963T", "T6967C", "T6975C", "C6984A", @@ -2031,6 +2033,7 @@ "T7074C", "T7078C", "C7089A", + "C7095T", "T7101A", "A7134G", "T7137C", @@ -2059,10 +2062,11 @@ "C7266T", "T7275C", "A7278C", - "T7281C", "A7290T", "G7293A", "A7309G", + "C7311T", + "T7334C", "G7344A", "G7347A", "T7357C", @@ -2076,6 +2080,7 @@ "C7434T", "G7453A", "A7456G", + "T7461C", "T7462C", "C7470T", "T7506C", @@ -2091,6 +2096,7 @@ "T7539C", "A7562G", "C7565G", + "C7577T", "G7583A", "G7592A", "T7595C", @@ -2108,7 +2114,6 @@ "T7670C", "A7685T", "T7691C", - "T7694C", "C7698T", "A7703C", "A7730T", @@ -2119,7 +2124,6 @@ "A7763G", "C7767A", "A7778G", - "C7784T", "A7785G", "A7788C", "C7793G", @@ -2130,7 +2134,7 @@ "A7835G", "G7841A", "G7844A", - "A7871G", + "A7853G", "C7874T", "T7910C", "G7913A", @@ -2149,16 +2153,14 @@ "G7988C", "C7991T", "C7997T", - "A8018G", "G8024A", "C8030T", "C8039T", "G8042A", - "C8051G", + "C8051A", "C8066T", "C8069T", "T8072C", - "C8081T", "T8087C", "G8096C", "C8108T", @@ -2195,6 +2197,7 @@ "T8348C", "A8349T", "T8366C", + "C8369T", "G8372A", "C8384T", "C8390G", @@ -2210,16 +2213,15 @@ "T8493C", "A8495G", "A8498T", + "T8501C", "G8516A", "C8517A", "C8537T", "C8540T", - "C8567T", "C8576T", "C8582T", "T8588C", "C8600T", - "T8609C", "T8612C", "C8615T", "G8616A", @@ -2240,18 +2242,17 @@ "C8735T", "A8737G", "T8738C", - "C8741T", "T8743C", "A8750G", "A8756G", "A8760C", "G8762A", "G8768A", - "C8769T", "A8771G", "T8772C", "A8780G", "A8783T", + "T8801C", "T8804C", "A8807G", "A8810C", @@ -2268,6 +2269,7 @@ "G8879A", "T8888C", "T8892A", + "T8897C", "G8900A", "A8906G", "T8909C", @@ -2287,7 +2289,6 @@ "C8963T", "C8973T", "A9008C", - "G9017A", "A9029G", "C9044T", "C9047T", @@ -2295,7 +2296,6 @@ "A9059G", "T9060C", "T9066A", - "A9068G", "A9071G", "C9077T", "A9086G", @@ -2318,7 +2318,6 @@ "G9230A", "T9233C", "C9243T", - "G9245A", "T9254C", "T9257C", "A9275T", @@ -2330,7 +2329,6 @@ "T9311C", "A9317T", "G9323A", - "G9326A", "T9329A", "G9338A", "C9347A", @@ -2340,6 +2338,7 @@ "A9398G", "C9405T", "C9410T", + "C9413T", "G9416T", "T9419C", "G9426C", @@ -2350,7 +2349,6 @@ "A9446G", "G9458A", "T9461C", - "C9473T", "T9475C", "G9476C", "A9479G", @@ -2373,7 +2371,6 @@ "T9590C", "T9596C", "T9614C", - "G9627A", "A9629C", "G9630A", "A9638G", @@ -2382,7 +2379,6 @@ "T9671C", "T9673C", "G9674A", - "G9683A", "C9689T", "A9690G", "T9695C", @@ -2399,7 +2395,6 @@ "T9758C", "A9764G", "A9765C", - "C9770T", "A9774G", "A9782G", "G9783A", @@ -2409,11 +2404,8 @@ "C9801T", "A9803C", "T9814C", - "A9815G", - "C9818T", "G9821A", "G9830A", - "G9833A", "T9839C", "T9840C", "T9845C", @@ -2425,7 +2417,7 @@ "C9876T", "T9881C", "A9887G", - "G9901A", + "A9902G", "A9908G", "T9917C", "A9923G", @@ -2439,6 +2431,8 @@ "T10085C", "G10091A", "G10097A", + "C10098T", + "A10100G", "G10103A", "T10109C", "C10133T", @@ -2446,7 +2440,6 @@ "T10145C", "A10157G", "C10163T", - "C10191T", "T10196A", "T10208C", "C10217T", @@ -2457,6 +2450,7 @@ "A10289G", "G10298A", "G10304A", + "C10307T", "A10313T", "A10325G", "A10334G", @@ -2473,13 +2467,12 @@ "A10407G", "T10415C", "A10418T", - "C10427T", "T10442A", "A10454G", "C10457T", "A10458G", "T10460C", - "G10466A", + "G10466C", "T10475C", "A10478C", "C10493T", @@ -2536,6 +2529,7 @@ "T10898C", "A10904C", "T10928C", + "T10934C", "G10935A", "C10940T", "C10952T", @@ -2593,6 +2587,7 @@ "T11297C", "C11300T", "A11301G", + "C11303T", "T11304A", "T11308C", "T11310C", @@ -2603,16 +2598,15 @@ "A11355C", "T11357C", "C11358T", - "T11369A", - "A11370T", + "A11360T", "C11386T", "T11407C", - "A11446G", - "G11447A", + "C11441A", "A11452T", "T11453C", "A11454T", "T11461C", + "C11469A", "A11502G", "G11534A", "A11535T", @@ -2639,9 +2633,15 @@ "C11880T", "T11917C", "A11946T", - "A12001T", - "T12028A", - "G12031A", + "G12005A", + "T12006A", + "T12014A", + "C12016A", + "C12021A", + "T12022A", + "T12025A", + "C12028A", + "G12029A", "T12032A", "C12034A", "C12035A", @@ -2655,21 +2655,9 @@ "G12049A", "G12050A", "G12053A", - "G12055A", - "T12057A", - "G12058A", - "T12059A", - "G12061A", - "G12062A", - "T12063A", - "C12065A", - "T12066A", "G12069A", "C12070A", "T12071A", - "G12080A", - "C12081A", - "G12083A", "G12105A", "G12106A", "C12107A", @@ -2679,7 +2667,8 @@ "T12114A", "C12116A", "C12117A", - "G12118A" + "G12118A", + "C12121A" ] } }, @@ -2687,195 +2676,525 @@ { "branch_attrs": { "labels": { - "aa": "CHIKVgp1: F391L, I967V, V1667I, D1835E; CHIKVgp2: A552V, K1221R" + "aa": "CHIKVgp1: L313I, A1100V, V1767E, M1931T; CHIKVgp2: P77S, T417M, A1151V" }, "mutations": { "CHIKVgp1": [ - "F391L", - "I967V", - "V1667I", - "D1835E" + "L313I", + "A1100V", + "V1767E", + "M1931T" ], "CHIKVgp2": [ - "A552V", - "K1221R" + "P77S", + "T417M", + "A1151V" ], "nuc": [ - "C267T", - "C378T", - "G651A", - "A759G", - "C1068T", - "C1153T", - "G1185A", - "T1240C", - "C2011T", - "T2140C", - "C2458T", - "T2601C", - "A2968G", - "C3216T", - "A3285G", - "T3414C", - "T3477C", - "C3810T", - "A4338C", - "G4701A", - "G5068A", - "C5298T", - "T5505C", - "T5574A", - "G6135A", - "C6237T", - "C6624T", - "A6972G", - "T7338C", - "G7377A", - "C7580T", - "G8216A", - "C9202T", - "T9243C", - "A9674G", - "T10163C", + "C528T", + "T708C", + "C1006A", + "T1230A", + "T1701C", + "G1782A", + "C1953T", + "C1956T", + "C2136T", + "A2289C", + "C2313T", + "C2331T", + "A2583G", + "A2913G", + "C3368T", + "G3444A", + "A3669G", + "C3672T", + "T3909C", + "C3948T", + "A4005C", + "T4035C", + "T4086C", + "G4419A", + "T4452A", + "A4479T", + "C4500T", + "T4618C", + "C4845A", + "G5046A", + "T5355C", + "T5369A", + "C5619T", + "G5805A", + "T5861C", + "C6000T", + "T6045C", + "C6138T", + "A6447T", + "G6450A", + "G6645A", + "C6657T", + "A6993G", + "C7222T", + "G7437A", + "A7446G", + "T7529C", + "T7533C", + "T7661A", + "C7776T", + "G8390A", + "C8633T", + "C8717T", + "C8797T", + "G9017A", + "C9179T", + "C9575T", + "G9692A", + "C10082T", "C10205T", - "C10346T", - "T10418C", - "A10862G", - "C11072T", - "T11141C", - "A11209G", - "A11228G", - "G11288A", - "C11561T", - "C11567T" + "C10253T", + "T10295C", + "C10713A", + "C10999T", + "A11860G", + "C11961T" ] } }, - "name": "HM045815.1", + "name": "HM045817.1", "node_attrs": { "author": { "author": "Volk,S.M., Chen,R., Tsetsarkin,K.A., Adams,A.P., Garcia,T.I., Sall,A.A., Nasar,F., Schuh,A.J., Holmes,E.C., Higgs,S., Maharaj,P.D., 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"C1869T", + "C2820T", + "G3708A", + "G4560A", + "C4953T", + "C4983T", + "A5163G", + "C5284T", + "T5400C", + "T5438C", + "T5493C", + "C5499T", + "T5577C", + "C5823T", + "C5895T", + "T5937C", + "T6525C", + "T6639C", + "T7281C", + "T7694C", + "C8567T", + "T8609C", + "C8741T", + "C8769T", + "A9068G", + "G9245A", + "G9683A", + "C9818T", + "G9901A", + "A10779G" + ] + } }, "children": [ { "branch_attrs": { - "labels": { - "aa": "CHIKVgp1: V1391I; CHIKVgp2: M610L" - }, "mutations": { - "CHIKVgp1": [ - "V1391I" - ], - "CHIKVgp2": [ - "M610L" - ], "nuc": [ - "T852C", - "C1968T", - "C2640T", - "C2865T", - "T2955C", - "C3066T", - "A3141G", - "G4240A", - "G4740A", - "A4926G", - "G5082A", - "T6381A", - "T7616C", - "C8150T", - "A9375C" + "T1701C", + "C2403T", + "C2743T", + "G3897A", + "T4618C", + "T4782C", + "T7528C", + "T7529C", + "T7661A", + "C8402A", + "C11117T" ] } }, - "name": "HM045785.1", - "node_attrs": { - "author": { - "author": "Volk,S.M., Chen,R., Tsetsarkin,K.A., Adams,A.P., Garcia,T.I., Sall,A.A., Nasar,F., Schuh,A.J., Holmes,E.C., Higgs,S., Maharaj,P.D., Brault,A.C. and Weaver,S.C.", - "value": "Volk,S.M., Chen,R., Tsetsarkin,K.A., Adams,A.P., Garcia,T.I., Sall,A.A., Nasar,F., Schuh,A.J., Holmes,E.C., Higgs,S., Maharaj,P.D., Brault,A.C. and Weaver,S.C." - }, - "country": { - "confidence": { - "Senegal": 1.0 + "children": [ + { + "branch_attrs": { + "labels": { + "aa": "CHIKVgp1: K299E, T301S, S454G, T1110I, E1656V, P1704Q, V1709A; CHIKVgp2: N67S, K525R, A795V, G991D, N1158S" + }, + "mutations": { + "CHIKVgp1": [ + "K299E", + "T301S", + "S454G", + "T1110I", + "E1656V", + "P1704Q", + "V1709A" + ], + "CHIKVgp2": [ + "N67S", + "K525R", + "A795V", + "G991D", + "N1158S" + ], + "nuc": [ + "C519T", + "T742C", + "G765A", + "T864C", + "A964G", + "A970T", + "T1104C", + "G1164A", + "A1429G", + "T2466C", + "C3398T", + "T4068C", + "T4347C", + "C4611T", + "A5036T", + "A5085G", + "C5180A", + "T5195C", + "C5367T", + "C5460T", + "T5700C", + "T5721C", + "T5811C", + "C6687T", + 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"value": "Volk,S.M., Chen,R., Tsetsarkin,K.A., Adams,A.P., Garcia,T.I., Sall,A.A., Nasar,F., Schuh,A.J., Holmes,E.C., Higgs,S., Maharaj,P.D., Brault,A.C. and Weaver,S.C." + }, + "country": { + "value": "Cote_d'Ivoire" + }, + "div": 0.09319805165442965, + "lineage": { + "value": "WA" + }, + "num_date": { + "confidence": [ + 1981.6671232876713, + 1981.7386301369863 + ], + "value": 1981.6671232876713 + }, + "region": { + "value": "WAf" + }, + "year": { + "value": "1981" + } + } + }, + { + "branch_attrs": { + "labels": { + "aa": "CHIKVgp1: S171G, V451A, K1340R, A1664V, D1762N, P2136S, A2375V; CHIKVgp2: P458S" + }, + "mutations": { + "CHIKVgp1": [ + "S171G", + "V451A", + "K1340R", + "A1664V", + "D1762N", + "P2136S", + "A2375V" + ], + "CHIKVgp2": [ + "P458S" + ], + "nuc": [ + "T391C", + "A498G", + "A549G", + "A580G", + "A609G", + "A759G", + "G807A", + "C978T", + "A1386G", + "T1421C", + "T1515C", + "C2085T", + "T2448C", + "A3012T", + "T3192C", + "T3456C", + "A4005G", + "A4088G", + "T4590C", + 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