3-I 3 3-II Farm S1-25f swine (AY858911) Mexico

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3-I 3 3-II 4 1 2 Farm 11 100 76 0.1 S1-25f swine (AY858911) Mexico DQ832264 DQ832265 DQ832262 DQ860011 DQ832269 AF466664 DQ860012 AB094207 AB094211 AB094203 AB094268 AB094271 AB094267 AB094274 AB094215 AB094249 AB094240 DQ860005 AF516178 AF516179 |AY641398. AF466659 AB194489 AB194488 AF466683 AB194283.1 AB105903 AB105892.1 AB105891.1 AB074918 AB194293.1 AB074920 AB194296.1 AB476445 AB107368.1 AB115541.1 AB089824 AF466661 1559-07-31 AF466660 AB094212 AB094214 AF466678 AF060669 AF466681 AY870833 AF466679 DQ859994 AB194529 AB107366.1 AB115543.1 AB194497 AF466663 AF060668 AB196843.1 DQ860004 AB481228 AB194491 AB194493 AB194492 FJ426403 AF466674 AF466668 AF466675 AF466672 AY871094 AF466666 AY870835 AF466665 AF466667 AF466685 AF466684 AY575859 AY575858 AF082843 AY575857 AF466676 AB094218 AB094217 AB094238 DQ859990 AY858934 AF336299 AF336291 AF466662 DQ859998 DQ860010 DQ859997 DQ859992 DQ860009 DQ859996 DQ860002 AY714271.1 AY714270.1 AY714268.1 AY714272.1 AY858926 AY858911 AY858924 AY858923 AY858922 AY858929 AY858932 AY858931 FJ426404 AY858894 AY858897 AY858896 AY858893 AY858899 AY858901 AY858898 AY858892 AB220070 AB220063 AB220066 AB220068.2 EU497922 DQ860001 DQ860000 AY115488 DQ859991 DQ859995 311-07.315 310-07.315 315-07.315 AB270968 AB270965 AB270975 AB270966 AB270967 AB270977 AB270978 AB270973 AB194528 AB096756 AB194525 AB091394 AB194524 AB154830.1 AB094316 AB094310.1 AB177373 AB177372 AB177368 AB194496 AB222182 AB094337 AB094328 AB094333 AB094321 AB094325 AB094275 AB094278 AB094277 AB094276 AB194508 AB194505 AB194515 AB194514 AB194511 AB194510 AB194509 AB481229 AB094304 AB194486 AB194485 AB194526 AB246676 AB115544.1 AB194495 AB425830 AB301710 AB437316 AB073910 AB219129.1 AB236320 AB194530 AB222183 AB291963 AB196839.1 AB105900 AB189072 AB189074 AB189073 AB189070 AB189075 AB189071 AB219128.1 AB476446 AB079763.1 AP003430 AB088418.1 AB154829.1 AB369691 AB196841.1 AB112743.1 AB270988 AB270970 AB270979 AB270981 AB270983 AB270976 AB270971 AB270984 AB270989 AB270986 AB270987 AB270980 AB194502 FJ527832 AB094266 AB194490 AB105898 EF187823 AB222184 EU034717 AB194494 AB105901 DQ860006 AB194484 AB194483 AB194482 AB194476 AB177357 AB115542.1 AB194500 AB177363 AB073912 AB073909 AB194522 AB291957 AB443624 AB443623 AB291954 AB291960 AB094279 AB443626 AB291952 AB291956 AB443627 AB443625 AB291951 AB291955 AB291953 AB094305 AB194518 AB194517 AB194478 AB291962 AB194527 AB194523 DQ079632 AB369689 AF296166 AF296165 AF296167 AB290080 AB290083 AB290075 AB290312 AB290073 AB290090 AB290094 AB290067 AB290086 AB290102 AB290081 AB290106 FJ998011 FJ998010 FJ998012 FJ998008 FJ998018 EF494703 1179-08-31 AF336297 AF336298 AF336293 AY032756 EF491206 1092-08-31 1153-08-31 56-2007-31 1152-08 26-02-k 292-07.315 293-07-315 294-07.315 298-07.315 285-07-315 287-07-315 284-07.315 288-07.315 EU360977 svensk-hev 291-08.315 668-08.315 560-05.315 EU723512 291-09-315 326-07.315 326-072-31 296-09-315 667-05.HE1 69-2007.31 317-07.315 325-07.315 292-08.315 392-08.315 288-08.315 289-08.315 290-08.315 300-09S2-3 328-072-31 292-09S2-3 331-072-31 299-09S2-3 1969-072-3 297-09S2-3 293-09-315 294-09S2-3 1969-07.31 331-07.315 328-07.315 330-07-315 38-08.3158 293-08.315 296-08.315 295-08.315 EU723515 EU723514 EU723513 EU723516 EU495148 AF336296 EF050797 AY323506 EF523417 EF523418 1459-06-k 995-09-315 AY032758 AY032757 FJ956757 EU708713 EU708712 AB369687 AF332620 EF494704 AF336294 AF336292 AF336295 EU375463 AY032759 FJ998017 751-08-315 525-07-315 AB291961 889-08-315 EF523412 AB094235.1 AB094237 AB094233.1 AB248521 AB094230.1 AB094234.1 AB094226 AB094231.1 AB481226 AB094228.1 AB094216 AB248522 AB094253.1 AB094250 AB094252.1 AB194284.1 670-05.110 300-07rev. 299-07.315 1970-07.31 AF503512 FJ998019 FJ998014 FJ998015 FJ998016 FJ998013 AB093535 AB476447 AB073911 AB291958 AB248520 AF503511 EF494700 AB290313 AB290107 AB290119 AB290115 AF455784 DQ061078.1 AB220975 AB105895.1 AB194290.1 AB194295.1 AB220978 AB194291.1 AB161717 AB105889.1 AB074917 AB107367.1 AB105890.1 AB105896.1 AB220972 AB161718 AB161719 AB194285.1 AB105893.1 AB220973 AB291967 AB194298.1 AB220977 AB291968 AB291965 AB291966 AB220976 AB194289.1 AB291959 AB105902 AB105894.1 AB194297.1 AB220979 AB194299.1 AB194292.1 AB194521 AB079762.1 AB074915 EU034709 EU034707 DQ450079 DQ450081 AJ428855 AB097811 AB220971 AB094254 AB097812 AB094255 AB194282.1 AB206467.1 AB193176 AB099347 AB193178 AB091395 AB200239 AB193177 AB094225 AB094219 AB080575 AB481227 AB194897.1 AB108537 AB220974 AF117278 AY052774 AF117276 AF296162 AF302068 AF296163 AB197673 EF488819 EU366959 EU380903 EU375565 EU380902 EU326142 DQ445492 DQ445495 AF117279 DQ445491 EF077630 EU332152 EU332144 EU332143 AB197674 AF117280 AF117281 AF296161 EU676172 AJ428856 DQ279091 AB253420 AB291964 AB298181 AB298180 AB298183 j|AB124818 AB124818 EU034712 EU034713 EF570133.s EU034711 EU034708 DQ450075 DQ450072 DQ450077 AB369690 EU034715 AY596311 AY596313 AY596320 AY596309 AY596319 AY596315 AY596312 AY594199 AY596314 AY596308 AY621100 AY621102 AY621097 AY621096 DQ450080 AJ272108 FJ610232 AB194831.1 AB298182 AB369688 EU003605 AF324504 EU003603 AY723745 AF407562 AF407564 AF505860 AF505861 AF407569 AF407566 AF324502 AY753554 AB116175.1 |AB116184. AB116173.1 306-05.110 342-05.110 AB085977.1 701-95-315 195-95-k 670-96-315 AB116178.1 AB116177.1 AB116176.1 AB116181.1 AB116189.1 1230-03-k AB116221.1 AB116201.1 AB116217.1 j|AB116218 AB116219.1 AB116185.1 AB116183.1 AB116192.1 AB116160.1 113-05.110 233-04.110 1735-08-31 333-08.315 929-08-315 AB116207.1 AB116225.1 AB116199.1 1297-07-31 3-07-k.seq 1668-08-31 410-02-k 20-03-041 AB116190.1 132-04.110 AB116186.1 319-05.110 346-08.315 368-08.315 1962-07-31 610-08.315 1099-03-k3 118-05.110 83-04.110- 5-05.110-3 1927-07-31 FJ457024 AB085955.1 AB085967.1 AB085952.1 795-99-k AB085951.1 AB085958.1 AB085966.1 AB085960.1 254-98-315 AB116168.1 AB116188.1 DQ459342 AF076239 AF459438 228-95-k AB085999.1 AF051830 398-95-k HPESVP M73218 D10330 AB085950.1 290-98-k 589-08.315 492-05.110 175-06.315 1248-08-31 708-05.110 X99441 AF185822 6894-93-k 1062-94-k 689-96-k 470-96-HE1 AB085974.1 AB085973.1 386-99-k 344-05.110 583-05.110 787-05.HE1 607-08.315 492-94-k 4308-97-k 499-98-k 821-99-k 4745-97-k AB085985.1 AB085965.1 AF302069 AB085981.1 AB085993.1 AB085996.1 AB085975.1 AB085962.1 AB085949.1 AB085953.1 AB085976.1 377-94-kne X98292 557-94-k 559-94-k HPCEGENOM HPEGENSA L08816 M94177 NC 001434 D11092 HPECG L25595 L25547 D11093 HPEUIGH M80581 AF444002 AF444003 AY697427 AY230202 AY204877 M74506 HPENSSP 3 3-I 3-II 4 2 1 S1-25f swine (AY858911) Mexico S4-25f swine (AY858926) Mexico S4-23f swine (AY858924) Mexico S4-22f swine (AY858923) Mexico S4-21f swine (AY858922) Mexico S4-29f swine (AY858929) Mexico G2-10f swine (AY858932) Mexico G2-8f swine (AY858931) Mexico OKIswN3 swine (AB220070) Japan OKIsw14 swine (AB220063) Japan OKIsw29 swine (AB220066) Japan OKIsw33 swine (AB220068) Japan swTW1-8 swine (EU497922) Taiwan swSTHY21 swine (DQ860001) Canada swSTHY20 swine (DQ860000) Canada Arkell swine (AY115488) Canada swSTHY9 swine (DQ859991) Canada swSTHY13 swine (DQ859995) Canada swJTY1-1 swine (AB194523) Japan swJSM1-1 swine (AB194527) Japan E088 human (AB369689) Japan G3-4531 swine (DQ079632) Japan 311-07 swine 11:3 Sweden 310-07 swine 11:2 Sweden 315-07 Swine 11:10 Sweden 366-09 male Sweden 241-2007 wild boar Östergötland Sweden TW13SW swine (AF296166) Taiwan TW12SW swine (AF296165) Taiwan TW3SW swine (AF296167) Taiwan 100 Farm 11 76 Supplementary Fig. 1. UPGMA dendrogram based on 276 nucleotides of ORF 2 in 640 HEV strains. The genotypes and subdivision of genotype 3 into two groups are shown on the branches. The details of the branch formed by 3-I strains are shown in the figure. The subtypes are indicated on the branches. Origin of strains from Swedish pigs is indicated on the branch, by the designation of the pig farm. Strains sequenced and described in this study are marked in bold. Strains from animals are indicated in italic. Boot strap values of 1000 replica are indicated below the branches.