F22083 R22181 | TTAAAATATATTCTAAGCACACGC [22083–22106] CATTTCGCTGATTTTGGGGTCC [22157–22181] | Ins214 S | FAM/ TATTATAGT/ZEN/ GCGTGAGCCAGAAGATCTCC/3IABkFQ [28215–28244] | (Yaniv et al. 2022) |
nCoV_N2-F nCoV_N2-R | TTACAAACATTGGCCGCAAA [29164–29183] GCGCGACATTCCGAAGAA [29230 − 29213] | nCoV_N2-P | FAM/ACAATTTGCCCCCAGCGCTTCAG/3IABkFQ [29188–29210] |
Improved N3-F N3-R | GGGAGCCTTGAATACACCAAAAG [28681–28703] TGTAGCACGATTGCAGCATTG [28752 − 28732] | Improved N3 | FAM/TCACATTGGCACCCGCAATCCTGC/3IABkFQ [28705–28728] |
NTD fwd NTD rev | TCA ACT CAG GAC TTG TTC T(OMe-U)A C TGG TAG GAC AGG GTT AT(OMe-C) AAA C | A67V-del69-70 probe | Atto425- TGG TCC CAG A(+ G)A T(+ A)(+ A) C(+ A)T -BHQ1 | (Nörz et al. 2022) |
RBD-452 fwd RBD-484 fwd RBD-484-rev RBD-univ-rev | GAT T(+ C)T AAG GTT GGT GG(2OMe-U) AAT CTA TCA GGC CGG TAR (2OMe-C)A GTC GGA AAC TAT ATG ATC GTA AA(OMe-G) G AGT TGC TGG TGC ATG TA(OMe-G) AA | E484A probe | YakYellow- AT(+ G) GTG TT(+ G) (+ C)(+ A)G (+ G)TT -BHQ1 |
P681R probe | FAM- A(+ T)T CT(+ C) (+ G)(+ T)C GGC G -BHQ1 |
N679K-P681H probe | Atto620- A(+ G)T CT(+ C) (+ A)(+ T)C GG(+ C) G -BHQ2 |
FCS fwd FCS rev | TGC AGG TAT ATG CGC TAG T(OMe-U)A GTG ACA TAG TGT AGG CAA TGA (OMe-U)G |
OmN-F OmN-R | GGACCCTCAGATTCAACTGG GCAGTATTATTGGGTAAACCTTGG | OmNm-Pr | TexasRed-ATCGCGCCCCACCATTCT | (Tsui et al. 2022) |
hCoV-Spike-D | | | | |
22,632S 22,659S 22,659S-Omi SP35AS SP36AS 22,687S 22,712S SP37AS SP38AS | GAATCAGCAACTGTGTTGCTG [22,632–22,652] CTGTCCTATATAATTCCGCATC [22,659–22,680] CTGTCCTATATAATCTCGCACC [22,659–22,680] TGACTAGCTACACTACGTGC [23,612–23,631] TTAGTCTGAGTCTGATAACTAG [23,577–23,598] CACTTTTAAGTGTTATGGAGTG [22,687–22,708] CCTACTAAATTAAATGATCTCTG [22,712–22,734] GCATATACCTGCACCAATGG [23,556–23,575] TATGTCACACTCATATGAGTTG [23,533–23,554] | NA | NA | (Ko et al. 2022) |
hCoV-full-a | |
45S a-1-2 85S a-2-2 | CAACTTTCGATCTCTTGTAGATCTGTTC [37–64] TGTAAAACACGCACAGAATTTTGAGCAG [1926–1953] TTAAAATCTGTGTGGCTGTCACTCGG [77–102] CGGGAGAAAATTGATCGTACAACAC [1890–1914] |
hCoV-full-b | |
b-1-1 b-1-2 b-2-1 b-2-2 | GCTTTTGTGGAAACTGTGAAAGG [1721–1743] GCTTAACTTCCTCTTTAGGAATCTC [3878–3902] AAACAAATTGTTGAATCCTGTGG [1763–1785] CAACTTGCTTTTCACTCTTCATTTCC [3838–3863] |
hCoV-full-c | |
c-1-1 c-1-2 c-2-1 c-2-2 | AAGACATTCAACTTCTTAAGAGTGC [3642–3666] AATAGGACCTTTGTATTCTGAGGAC [5830–5854] CAGCACGAAGTTCTACTTGCACCA [3683–3706] TTATAGTGACCACACTGGTAATTACC [5750–5775] |
hCoV-full-d | |
d-1-1 d-1-2 d-2-1 d-2-2 | GTACATGGGCACACTTTCTTATGAAC [5572–5597] CAGCTTTATCAAAGTAAAGATGGATGG [7764–7790] GTGTTCAGATACCTTGTACGTGTGG [5610–5634] CTGTAACACTATCAACGATGTAAGAAG [7725–7751] |
hCoV-full-e | |
e-1-1 e-1-2 e-2-1 e-2-2 | GTACAACTATTGTTAATGGTGTTAGAAG [7533–7560] CTCTTTAGGTAATTACTAAAGAACC [9729–9753] TGTCTATGCTAATGGAGGTAAAGGC [7570–7594] GCTTTGTGGAAATACAAATGATATAAGC [9692–9719] |
hCoV-full-f | |
f-1-1 f-1-2 f-2-1 f-2-2 | TTCCTTATGTCATTCACTGTACTCTG [9518–9543] ACACCAAGAGTCAGTCTAAAGTAGCG [11,669–11,694] ACTCATTCTTACCTGGTGTTTATTCTG [9558–9584] ACAAAAGAGGCCAAAGTAACAAGTAC [11,634–11,659] |
hCoV-full-g | |
g-1-1 g-1-2 g-2-1 g-2-2 | TCCATGTGGGCTCTTATAATCTCTG [11,459–11,483] CTTCGTCCTTTTCTTGGAAGCGACAAC [13,598–13,624] CTACTCAGGTGTAGTTACAACTGTC [11,494–11,518] TAGCAAAACCAGCTACTTTATCATTG [13,554–13,579] |
hCoV-full-h | |
h-1-1 h-1-2 h-2-1 h-2-2 | CGGTATGTGGAAAGGTTATGGCTG [13,384–13,407] ACTTATCGGCAATTTTGTTACCATCAG [15,569–15,595] CAACTCCGCGAACCCATGCTTCAG [13,418–13,441] AAAAGTGCATTAACATTGGCCGTGAC [15,538–15,563] |
hCoV-full-i | |
i-1-1 i-1-2 i-2-1 i-2-2 | ATTATGGCCTCACTTGTTCTTGCTCG [15,334–15,359] CTATAGTTTTCATAAGTCTACACACTCC [17,506–17,533] GCTTGTCACACCGTTTCTATAGATTAG [15,380–15,406] CTTAGTTAGCAATGTGCGTGGTGCAG [17,453–17,478] |
hCoV-full-j | |
j-1-1 j-1-2 j-2-1 j-2-2 | GTGAATTCAACATTAGAACAGTATGTC [17,278–17,304] GCATGATGTCTACAGACAGCACCACC [19,477–19,502] AATGCATTGCCTGAGACGACAGCAG [17,317–17,341] ATTGCAACGTGTTATACACGTAGCAG [19,448–19,473] |
hCoV-full-k | |
k-1-1 k-1-2 k-2-1 k-2-2 | ATTTGACACTAGAGTGCTATCTAACC [19,239–19,264] TCTTTTAAAGACATAACAGCAGTACCC [21,423–21,449] TGGTTGTGATGGTGGCAGTTTGTATG [19,275–19,300] GGGGAAATTTACTCATGTCAAATAAAG [ 21,386–21,412] |
hCoV-full-l | |
l-1-1 l-1-2 l-2-1 l-2-2 | ATTACATTACACATAAACGAACTTATGG [25,369–25,396] GCTCACAAGTAGCGAGTGTTATCAGTG [27,416–27,442] TTTGTTTATGAGAATCTTCACAATTGG [25,398–25,424] ATCAATCTCCATTGGTTGCTCTTCATC [27,358–27,384] |
hCoV-full-m | |
m-1-1 m-1-2 m-2-1 m-2-2 | CTTTGCTTGTACAGTAAGTGACAACAG [27,175–27,201] CTTCTGCGTAGAAGCCTTTTGGCAATG [28,771–28,797] CTCGTTGACTTTCAGGTTACTATAGC [27,211–27,236] TTGAGGAAGTTGTAGCACGATTGCAGC [28,737–28,763] |
hCoV-full-n | |
n-1-1 n-1-2 n-2-1 n-2-2 | AGAGCTACCAGACGAATTCGTGGTG [28,539–28,563] TTTTTTTTTTTGTCATTCTCCTAAGAAGC [29,854–29,882] ATGGTATTTCTACTACCTAGGAACTGG [28,595–28,621] ATTAAAATCACATGGGGATAGCACTAC [29,826–29,852] |
hCoV-full-S1 | |
20,963S 21,018S 23,504AS 21,050S 21,018S 23,461AS | TCTTAATGACTTTGTCTCTGATGCAG [20,955–20,980] GTACATACAGCTAATAAATGGGATC [21,010–21,034] CCCTATTAAACAGCCTGCACGTG [23,496–23,518] TAGTGATATGTACGAC CCTAAGAC [21,042–21,065] GTACATACAGCTAATAAATGGGATC [21,010–21,034] TGTAGAATAAACACGCCAAGTAGG [23,453–23,476] |
hCoV-full-S2 | |
23,254S 25,666AS 23,283S 25,619AS | TTYCAACAATTTGGCAGAGACATTG [23,246–23,270] CGAGCAAAAGGTGTGAGTAAACTG [25,658–25,681] CACTACTGATGCTGTCCGTGATC [23,275–23,297] AAACAAAGTGAACACCCTTGGAG [25,611–25,633] |
E_Sarbeco-F E_Sarbeco-R | ATAGGTACGTTAATAGTTAATAGCGT TGTGTGCGTACTGCTGCAATAT | E_Sarbeco-P | ACACTAGCCATCCTTACTGCGCTTCG | (Tao et al. 2022) |
nCoV_IP2-F nCoV_IP2-R | ATGAGCTTAGTCCTGTTG ACAACACAACAAAGGGAG/ACAACACAACAAAGGGAT | nCoV_IP2-P | AGATGTCTTGTGCTGCCGGTA |
nCoV_IP4-F nCoV_IP4-R | GGTAACTGGTATGATTTCG CCTATATTAACCTTGACCAG/ CCTATATTAACCTTGACTAG | nCoV_IP4-P | TCATACAAACCACGCCAGG/TCGTACAAACCACGCCAGG |
RdRp-CoV-19-F RdRp-CoV-19-R | GTGAAATGGTCATGTGTGGCGG/ GTGAAATGGTCATGTGTGGCRG TATGCTAATAGTGTTTTTAACATTTG/ TATGCTAATAGTGTTTATAACATTTG | RdRp-CoV-19-P | CAGGTGGAACCTCATCAGGAGATGC/ |
ORF1ab-F ORF1ab-R | CCCTGTGGGTTTTACACTTAA/ CCCTGTGGGTTTTATACTTAA TCAGCTGATGCACAATCGT | ORF1ab-P | CCGTCTGCGGTATGTGGAAAGGTTATGG/ CTGTCTGCGGTATGTGGAAAGGTTATGG |
ORF1b-nsp14-F ORF1b-nsp14-R | TGGGGTTTTACAGGTAACCT/ TGGGGTTTTATAGGTAACCT GAGTGCTTTGTTAAGCGTGTT | ORF1b-nsp14-P | TAGTTGTGATGCAATCATGACTAG |
HKU-N-F HKU-N-R | TAATCAGACAAGGAACTGATT CATGGAAGTCACACCTTCG/ CATGGAAGTCACACCTTCT/ CATGGAAGTCACACCTTTG | HKU-N-P | CCGCAAATTGCACAATTTGC |
NIID_2019-nCoV_2-F NIID_2019-nCoV_2-R | AAATTTTGGGGACCAGGAAC/ AAATTTTGGGGACCACGAAC GTTGACCTACACAGGTGCCA | NIID_2019-nCoV_2-P | ATGTCGCGCATTGGCATGGA/ATGTCTCGCATTGGCATGGA |
N-F N-R | GGGGAACTTCTCCTGCTAGAAT CAGCTTGAGAGCAAAATGTCTG | N-P | TTGCTGCTGCTTGACAGATT/TTGCTGCTACTTGACAGATT/ TTGCTGTTACTTGACAGATT |
2019-nCoV_N1-F 2019-nCoV_N1-R | GACCCCAAAATCAGCGAAAT/ WRSCCCAAAATCAGCGAAAT CAGATTCAACTGGCAGTAACCAGA/ CAGATTCAATTGGCAGTAACCAGA/ CAGATTCTACTGGCAGTAACCAGA | 2019-nCoV_N1-P | ACTCCGCATTACGTTTGGTGGACC/ ACCCCGCATTACGTTTGGTGGACC/ ACYCCGCATTACGTTTGGTGGACC/ ACTCCGCATTACGTTTGGTGGACT/ |
2019-nCoV_N2-F 2019-nCoV_N2-R | TTACAAACATTGGCCGCAAA/ TTACAAATATTGGCCGCAAA TTATAAACATTGGCCGCAAA TTCTTCGGAATGTCGCGC/ TTCTTCGGAATGTCTCGC | 2019-nCoV_N2-P | ACAATTTGCCCCCAGCGCTTCAG/ ACAATTTGCCCCTAGCGCTTCAG |
2019-nCoV_N3-F 2019-nCoV_N3-R | GGGAGCCTTGAATACACCAAAA/ GGGAGCCTTGAATATACCAAAA/ TGGAGCCTTGAATACACCAAAA/ GGGGGCCTTGAATACACCAAAA/ CAATGCTGCAATCGTGCTACA | 2019-nCoV_N3-P | ATCACATTGGCACCCGCAATCCTG/ ATCATATTGGCACCCGCAATCCTG/ TTCATATTGGCACCCGCAATCCTG |
WH-NIC N-F WH-NIC N-R | CGTTTGGTGGACCCTCAGAT/ CGTTTGGTGGACTCTCAGAT/ CKTTTGGTGGACCCTCAGAT AATGGAGAACGCAGTGGGG/ AATGGTGAACGAAGTGGGG | WH-NIC N-P | CAACTGGCAGTAACCA/CAATTGGCAGTAACCA/ CTACTGGCAGTAACCA |
N501Y-F N501Y-R | TGTTACTTTCCTTTACAATCATATGGTTT GAAAGTACTACTACTCTGTATGGTTGGTA | N501Y-P | FAM/CCAACCCAC/ZEN/TTATGGTGTTGG/3lABkFQ | (Chung et al. 2022) |
69-70-F 69-70-R | TCAACTCAGGACTTGTTCTTAC TGGTAGGACAGGGTTATCAAAC | 69-70-P | FAM/GTCCCAGAG/ZEN/ACATGTATAGCAT/3lABkFQ |
K417N-F K417N-R | TGCAGATTCATTTGTAATTAGAGG ATAACGCAGCCTGTAAAATCATC | K417N-P | FAM/GCAAACTGG/ZEN/AAATATTGCT/3lABkFQ |
P681H-F P681H-R | CCCATTGGTGCAGGTATATG TAGTGTAGGCAATGATGGATTGA | P681H-P | FAM/ACTCAGACT/ZEN/AATTCTCATCG/3lABkFQ |