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. 2020 Sep 20;112(6):5204–5213. doi: 10.1016/j.ygeno.2020.09.028

Table 2.

Summary of mutations on COVID-19 diagnostic primers and probes and their occurrence frequencies in clusters. Here, SC is the sample counts and MC is the mutation counts.

Primer MC SC Cluster I Cluster II Cluster III Cluster IV Cluster V Cluster VI
RX7038-N1 primer (Fw)a 15 79 5 14 12 28 14 6
RX7038-N1 primer (Rv)a 17 113 1 66 14 9 2 21
RX7038-N2 primer (Fw)a 7 60 3 10 24 21 1 1
RX7038-N2 primer (Rv)a 6 50 2 17 6 15 3 7
RX7038-N3 primer (Fw) [9] 13 287 4 224 13 26 14 6
RX7038-N3 primer (Rv) [9] 12 70 4 10 7 39 6 4
N1-U.S.-P [5] 15 856 4 782 20 31 15 4
N2-U.S.-P [5] 11 70 10 40 4 12 4 0
N3-U.S.-P [5] 16 84 5 27 15 21 10 6
N-Sarbeco-Fb [4] 12 63 4 20 10 15 10 4
N-Sarbeco-Pb [4] 12 116 1 19 30 42 15 9
N-Sarbeco-Rb [4] 17 156 37 26 4 80 5 4
N-China-F [5] 23 26,280 38 226 10,873 139 17 14,987
N-China-R [5] 17 217 5 15 17 157 8 15
N-China-P [5] 7 20 1 4 6 8 1 0
N-HK-F [5] 5 149 1 2 74 7 1 64
N-HK-R [5] 14 84 14 12 14 35 4 5
N-JP-F [5] 10 66 5 10 9 16 26 0
N-JP-P [5] 9 32 0 5 1 16 3 7
N-TL-F [5] 17 149 1 84 14 31 13 6
N-TL-R [5] 17 115 29 7 7 66 3 3
N-TL-P [5] 11 45 1 5 13 5 1 20
E-Sarbeco-F1c 5 23 0 0 10 9 2 2
E-Sarbeco-R2c 4 18 0 6 5 1 6 0
E-Sarbeco-P1c 9 48 1 29 6 9 3 0
nCoV-IP2-12669Fwc 3 50 0 17 12 11 0 10
nCoV-IP2-12759Rvc 11 739 123 244 77 168 127 0
nCoV-IP2-12696bProbe(+)c 8 17 2 4 1 6 4 0
nCoV-IP4-14059Fwc 3 9 0 0 7 2 0 0
nCoV-IP4-14146Rvc 11 38 7 7 9 9 1 5
nCoV-IP4-14084Probe(+)c 11 49 3 12 6 19 5 4
RdRP-SARSr-F2d 5 89 2 1 5 37 44 0
RdRP-SARSr-R1d [4] 3 4 2 0 0 2 0 0
RdRP-SARSr-P2d [4] 4 10 0 6 2 2 0 0
ORF1ab-China-F [5] 4 19 0 4 2 6 5 2
ORF1ab-China-R [5] 0 0 0 0 0 0 0 0
ORF1ab-China-P [5] 14 61 1 6 30 11 3 10
ORF1b-nsp14-HK-F [5] 6 12 2 1 6 3 0 0
ORF1b-nsp14-HK-R [5] 9 89 3 9 52 14 6 5
ORF1b-nsp14-HK-P [5] 6 37 2 1 9 13 0 12
SC2-Fe 11 88 0 5 34 29 13 7
SC2-Re 0 0 0 0 0 0 0 0
NIID_WH-1_F501 [10] 13 255 0 205 25 18 3 4
NIID_WH-1_R913 [10] 14 128 1 94 9 18 4 2
NIID_WH-1_F509 [10] 10 30 7 5 7 6 3 2
NIID_WH-1_R854 [10] 9 261 63 25 33 117 5 18
NIID_WH-1_Seq F519 [10] 19 130 8 89 17 11 3 2
NIID_WH-1_Seq R840 [10] 12 66 6 9 21 8 3 19
WuhanCoV-spk1-f [10] 14 433 265 22 11 123 8 4
WuhanCoV-spk1-r [10] 4 10 0 2 3 1 2 2
NIID_WH-1_F24381 [10] 20 494 275 30 16 153 13 7
NIID_WH-1_R24873 [10] 5 15 1 4 3 7 0 0
NIID_WH-1_Seq_F24383 [10] 21 503 275 30 22 153 13 10
NIID_WH-1_Seq_R24865 [10] 6 17 2 4 5 6 0 0