TABLE 1.
Nucleotide sequences for phylogenetic analysis
| Full name | Short name | Country | Length (nt) | Accession number | |
|---|---|---|---|---|---|
| 1 | Porcine deltacoronavirus strain USA/NorthCarolina452/2014, complete genome | PDCoV/USA/NorthCarolina452/2014 | USA | 25394 | KR265858.1 |
| 2 | Porcine deltacoronavirus strain USA/Minnesota/2013, complete genome | PDCoV/USA/Minnesota/2013 | USA | 25394 | KR265853.1 |
| 3 | Porcine deltacoronavirus strain USA/Illinois449/2014, complete genome | PDCoV/USA/Illinois449/2014 | USA | 25394 | KR265852.1 |
| 4 | Porcine deltacoronavirus strain USA/Minnesota159/2014, complete genome | PDCoV/USA/Minnesota159/2014 | USA | 25401 | KR265859.1 |
| 5 | Deltacoronavirus PDCoV/USA/Illinois134/2014 from USA, complete genome | PDCoV/USA/Illinois134/2014 | USA | 25404 | KJ601778.1 |
| 6 | Porcine deltacoronavirus strain USA/Nebraska210/2014, complete genome | PDCoV/USA/Nebraska210/2019 | USA | 25404 | KR265861.1 |
| 7 | Porcine deltacoronavirus genomic RNA, complete genome, strain: YMG/JPN/2014 | PDCoV/JPN/YMG/2014 | Japan | 25362 | LC260044.1 |
| 8 | Porcine deltacoronavirus strain USA/Michigan448/2014, complete genome | PDCoV/USA/Michigan448/2014 | USA | 25394 | KR265850.1 |
| 9 | Porcine deltacoronavirus strain USA/Michigan447/2014, complete genome | PDCoV/USA/Michigan447/2014 | USA | 25393 | KR265849.1 |
| 10 | Deltacoronavirus PDCoV/USA/Ohio137/2014 from USA, complete genome | PDCoV/USA/Ohio137/2014 | USA | 25404 | KJ601780.1 |
| 11 | Porcine deltacoronavirus strain USA/Indiana453/2014, complete genome | PDCoV/USA/Indiana453/2014 | USA | 25394 | KR265851.1 |
| 12 | Porcine deltacoronavirus strain USA/Minnesota455/2014, complete genome | PDCoV/USA/Minnesota455/2014 | USA | 25394 | KR265855.1 |
| 13 | Porcine deltacoronavirus strain USA/Minnesota454/2014, complete genome | PDCoV/USA/Minnesota454/2014 | USA | 25394 | KR265854.1 |
| 14 | Porcine deltacoronavirus strain USA/Arkansas61/2015, complete genome | PDCoV/USA/Arkansas61/2015 | USA | 25398 | KR150443.1 |
| 15 | Deltacoronavirus PDCoV/USA/Illinois121/2014 from USA complete genome | PDCoV/USA/Illinois121/2014 | USA | 25406 | KJ481931.1 |
| 16 | Porcine deltacoronavirus 8734/USA‐IA/2014 complete genome | PDCoV/USA‐IA/8734 | USA | 25422 | KJ567050.1 |
| 17 | Porcine deltacoronavirus strain OH‐FD22 P7 complete genome | PDCoV/USA/OH‐FD22 | USA | 25438 | MZ291567.1 |
| 18 | Porcine deltacoronavirus strain SHJS/SL/2016, complete genome | PDCoV/SHJS/SL/2016 | China | 25414 | MF041982.1 |
| 19 | Porcine deltacoronavirus strain CH/SXD1/2015, complete genome | PDCoV/CH/SXD1/2015 | China | 25419 | KT021234.1 |
| 20 | Porcine deltacoronavirus strain CHN‐LYG‐2014, complete genome | PDCoV/CHN‐LYG/2014 | China | 25370 | KU665558.1 |
| 21 | Porcine deltacoronavirus isolate PDCoV/CHJXNI2/2015, complete genome | PDCoV/CHJXNI2/2015 | China | 25438 | KR131621.1 |
| 22 | Porcine deltacoronavirus isolate CHN‐AH‐2004, complete genome | PDCoV/CHN‐AH/2004 | China | 25420 | KP757890.1 |
| 23 | Porcine deltacoronavirus strain CH/Hunan/2014 complete genome | PDCoV/CH/Hunan/2014 | China | 25413 | KY513724.1 |
| 24 | Porcine deltacoronavirus PDCoV/CH/SXD1/2015 | PDCoV/CH/SXD1/2015 | China | 25419 | KT021234.1 |
| 25 | Porcine deltacoronavirus isolate 104–553 complete genome | PDCoV/104‐553 | China | 25418 | MW854634.1 |
| 26 | Porcine deltacoronavirus strain CHN/GS/2017/1 complete genome | PDCoV/CHN/GS/2017 | China | 25420 | MF642324.1 |
| 27 | Porcine deltacoronavirus strain CHN/QH/2017/1 complete genome | PDCoV/CHN/QH/2017 | China | 25420 | MF642325.1 |
| 28 | Porcine deltacoronavirus isolate CHN‐HN‐1601 complete genome | PDCoV/CHN/HN1601/2017 | China | 25419 | MG832584.1 |
| 29 | Porcine deltacoronavirus isolate CHN/Sichuan/2019 complete genome | PDCoV/ CHN/Sichuan/2019 | China | 25380 | MK993519.1 |
| 30 | Porcine deltacoronavirus isolate CH/JXJGS01/2016 complete genome | PDCoV/CH/JXJGS01/2016 | China | 25446 | MK625641.1 |
| 31 | Porcine deltacoronavirus isolate P1 16 BTL 0115/PDCoV/2016/Lao complete genome | PDCoV/Lao/2016 | Lao | 25405 | KX118627.1 |
| 32 | Porcine deltacoronavirus strain PDCoV/Swine/Vietnam/HaNoi6/2015, complete genome | PDCoV/Vietnam/HaNoi6/2015 | Vietnam | 25406 | KX834351.1 |
| 33 | Porcine deltacoronavirus strain PDCoV/Swine/Vietnam/Binh21/2015, complete genome | PDCoV/Vietnam/Binh21/2015 | Vietnam | 25406 | KX834352.1 |
| 34 | Porcine deltacoronavirus strain PDCoV/Swine/Thailand/S5015L/2015, complete genome | PDCoV/Thailand/S5015L/2015 | Thailand | 25405 | KU051649.1 |
| 35 | Porcine deltacoronavirus strain PDCoV/Swine/Thailand/S5011/2015, complete genome | PDCoV/Thailand/S5011/2015 | Thailand | 25405 | KU051641.1 |
| 36 | Porcine deltacoronavirus isolate KNU16‐07 complete genome | PDCoV/SouthKorea/KNU16‐07 | South Korea | 25422 | KY364365.1 |
| 37 | Porcine deltacoronavirus isolate KNU16‐11 complete genome | PDCoV/SouthKorea/KNU16‐11 | South Korea | 25419 | KY926512.1 |
| 38 | Porcine deltacoronavirus genomic RNA complete genome strain: IWT/JPN/2014 | PDCoV/JPN/IWT/2014 | Japan | 25362 | LC260041.1 |
| 39 | Porcine deltacoronavirus genomic RNA complete genome strain: MYZ/JPN/2014 | PDCoV/JPN/MYZ/2014 | Japan | 25362 | LC260042.1 |
| 40 | Porcine deltacoronavirus genomic RNA complete genome strain: AKT/JPN/2014 | PDCoV/JPN/AKT/2014 | Japan | 25362 | LC260038.1 |
| 41 | Porcine deltacoronavirus genomic RNA complete genome strain: OKN/JPN/2014 | PDCoV/JPN/OKN/2014 | Japan | 25362 | LC260043.1 |
| 42 | Porcine deltacoronavirus isolate PDCoV/Haiti/Human/0256‐1/2015 complete genome | PDCoV/Haiti/Human/0256‐1/2015 | Haiti | 25447 | MW685623.1 |
| 43 | Porcine deltacoronavirus isolate PDCoV/Haiti/Human/0329‐4/2015 complete genome | PDCoV/Haiti/Human/0329‐4/2015 | Haiti | 25444 | MW685624.1 |
| 44 | Porcine deltacoronavirus isolate PDCoV/Haiti/Human/0081‐4/2014 complete genome | PDCoV/Haiti/Human/0081‐4/2014 | Haiti | 25444 | MW685622.1 |
| 45† | Porcine deltacoronavirus isolate CD‐HNZK‐02 S protein gene complete cds | PDCoV/CD‐HZNK‐02 | China | 3480 | MZ326690.1 |
| 46† | Porcine deltacoronavirus strain CC‐HNZK‐02 S protein gene complete cds | PDCoV/CC‐HNZK‐02 | China | 3480 | MK248485.1 |
| 47† | Porcine deltacoronavirus isolate SD‐01‐2018 spike glycoprotein gene complete cds | PDCoV/SD/01/2018 | China | 3480 | MN173803.1 |
| 48† | Porcine deltacoronavirus strain CH‐XS‐2018 spike protein gene complete cds | PDCoV/CH/XS/2018 | China | 3480 | MK040452.1 |
| 49† | Porcine deltacoronavirus strain CH‐HX‐2018 spike protein gene complete cds | PDCoV/CH/HX/2018 | China | 3480 | MK040448.1 |
| 50† | Porcine deltacoronavirus strain CH‐WH‐2017 spike protein gene complete cds | PDCoV/CH/WH/2017 | China | 3480 | MK040451.1 |
| 51† | Pocine deltacoronavirus PDCoV/CH HN 2016 S protein (S) gene complete cds | PDCoV/CH HN 2016 | China | 3480 | KY496312.1 |
| 52† | Porcine deltacoronavirus isolate CHN‐GD16‐13 spike protein gene complete cds | PDCoV/CHN‐GC16‐13 | China | 3480 | KY078916.1 |
| 53† | Porcine deltacoronavirus isolate CHN‐GC16‐12 spike protein gene complete cds | PDCoV/CHN‐GC16‐12 | China | 3480 | KY078915.1 |
| 54† | Porcine deltacoronavirus isolate CH/XJYN/2016 spike protein (S) gene complete cds | PDCoV/CH/XJYN/2016 | China | 3483 | MN064712.1 |
| 55† | Porcine deltacoronavirus isolate GX05‐2017 spike glycoprotein gene complete cds | PDCoV/GX05‐2017 | China | 3480 | MT505449.1 |
| 56† | Porcine deltacoronavirus strain CH‐DH2‐2017 spike protein gene complete cds | PDCoV/CH‐DH2‐2017 | China | 3480 | MK040450.1 |
| 57† | Porcine deltacoronavirus isolate SD‐12‐2018 spike glycoprotein gene complete cds | PDCoV/SD‐12‐2018 | China | 3480 | MN173812.1 |
| 58† | Porcine deltacoronavirus isolate SD‐10‐2018 spike glycoprotein gene complete cds | PDCoV/SD‐10‐2018 | China | 3480 | MN173810.1 |
| 59† | Porcine deltacoronavirus isolate GX03‐2017 spike glycoprotein gene complete cds | PDCoV/GX03‐2017 | China | 3474 | MT505447.1 |
| 60† | Porcine deltacoronavirus isolate GX05‐2019 spike glycoprotein gene complete cds | PDCoV/GX05‐2019 | China | 3483 | MT505460.1 |
| 61† | Porcine deltacoronavirus isolate GX03‐2018 spike glycoprotein gene complete cds | PDCoV/GX03‐2018 | China | 3483 | MT505452.1 |
| 62† | Porcine deltacoronavirus isolate GX03‐2019 spike glycoprotein gene complete cds | PDCoV/GX03‐2019 | China | 3483 | MT505458.1 |
| 63† | Porcine deltacoronavirus isolate GX05‐2018 spike glycoprotein gene complete cds | PDCoV/GX05‐2018 | China | 3483 | MT505454.1 |
| 64† | Porcine deltacoronavirus isolate GX04‐2019 spike glycoprotein gene complete cds | PDCoV/GX04‐2019 | China | 3483 | MT505459.1 |
| 65† | Porcine deltacoronavirus CH‐HA2‐2017 spike protein gene complete cds | PDCoV/CH‐HA2‐2017 | China | 3480 | MK040454.1 |
| 66† | Porcine deltacoronavirus strain CH‐HA3‐2017 spike protein gene complete cds | PDCoV/CH‐HA3‐2017 | China | 3483 | MK040455.1 |
| 67† | Porcine deltacoronavirus isolate YUC/UICMPR/2015 spike glycoprotein (S) gene, complete cds | PDCoV/Mexico/YUC/UICMPR/2015 | Mexico | 3483 | MK478381.1 |
| 68† | Porcine deltacoronavirus isolate MEXICO/OAX/UI1253CMPR/2017 spike glycoprotein (S) gene, complete cds | PDCoV/Mexico/OAX/UI1253CMPR/2017 | Mexico | 3483 | MK478383.1 |
| 69† | Porcine deltacoronavirus isolate EDOMEX/UI202CMPR/2017 spike glycoprotein (S) gene, complete cds | PDCoV/Mexico/UI202CMPR/2017 | Mexico | 3482 | MK478382.1 |
| 70† | Porcine deltacoronavirus isolate QRO/UI689CMPR/2017 spike glycoprotein (S) gene, complete cds | PDCoV/Mexico/QRO/UI689CMPR/2017 | Mexico | 3482 | MK478380.1 |
| 71† | Porcine deltacoronavirus isolate KNU16‐08 spike protein (S) gene complete cds | PDCoV/SouthKorea/KNU16‐08 | South Korea | 3480 | KY926511.1 |
| 72† | Porcine deltacoronavirus isolate SL5 spike protein gene complete cds | PDCoV/SouthKorea/SL5 | South Korea | 3483 | KR060083.1 |
| 73† | Porcine deltacoronavirus isolate SL2 spike protein gene complete cds | PDCoV/SouthKorea/SL2 | South Korea | 3483 | KR060082.1 |
†
Nucleotide sequences included for phylogenetic analysis of S gene.