Figure 2 shows a nucleotide sequence alignment of the RdRp, E, and N gene regions that span the designed real-time RT-PCR primers, for a number of SARS-CoV-2 and bat CoV sequences. Looking at the RdRp sequence primer regions, which CoV sequence is most different to the SARS-CoV-2 and why? (up to 50 words).
FIGURE 2
Partial alignments of oligonucleotide binding regions, SARS-related coronaviruses (n = 9)
RdRp_SARSr-
A. RdRp gene
RdRp_SARSr-F
P1:
RdRp_SARSr-R
...R................. P2:..... WH-Human_1|China|2019-Dec GTGAAATGGTCATGTGTGGCGG CCAGGTGGAACCTCATCAGGAGATGC BetaCoV/Wuhan/IPBCAMS-WH-01/2019|EPI_ISL_402123 BetaCoV/Wuhan/IVDC-HB-01/2019|EPI_ISL_402119 BetaCoV/Wuhan/IVDC-HB-04/2020|EPI_ISL_402120 BetaCoV/Wuhan/IVDC-HB-05/2019|EPI_ISL_402121 BetaCoV/Wuhan/WIV04/2019|EPI_ISL_402124 MG772933 Bat SARS-related CoV (bat-SL-CoVZC45) NC_004718 Human SARS-related CoV (e.g. Frankfurt-1 NC_014470 Bat SARS-related CoV (BM48-31/BGR/2008)
TATGCTAATAGTGTTTTTAACATTTG
E_Sarbeco_F B. E gene WH-Human_1|China|2019-Dec ACAGGTACGT TAATAGT TAATAGCGT BetaCoV/Wuhan/IPBCAMS-WH-01/2019|EPI_ISL_402123 BetaCoV/Wuhan/IVDC-HB-01/2019|EPI_ISL_402119 BetaCoV/Wuhan/IVDC-HB-04/2020jEPI_ISL_402120 BetaCoV/Wuhan/IVDC-HB-05/2019|EPI_ISL_402121 BetaCoV/Wuhan/WIV04/2019|EPI_ISL_402124 MG772933 Bat SARS-related CoV (bat-SL-CoVZC45) NC_004718 Human SARS-related CoV (e.g. Frankfurt-1) NC_014470 Bat SARS-related CoV (BM48-31/BGR/2008
E_Sarbeco_P1
E_Sarbeco_R
ACA
TGCGTACTGCTGCAATAT
N_Sarbeco_F
N_Sarbeco_P
N_Sarbeco_R
C.N gene WH-Human_1|China|2019-Dec BetaCoV/Wuhan/IPBCAMS-WH-01/2019|EPI_ISL_402123 BetaCoVMuhan/IVDC-HB-01/2019|EPI_ISL_402119 BetaCoVMuhan/IVDC-HB-04/2020|EPI_ISL_402120 BetaCoV/Wuhan/IVDC-HB-05/2019|EPI_ISL_402121 BetaCoV/Wuhan/WIV04/2019|EPI_iSL_402124 MG772933 Bat SARSrelated CoV(bat-SL-CoVZC45 NC_004718 Human SARS-related CoV (e.g. Frankfurt-1) NC_014470 Bat SARS-related CoV (BM48-31/BGR/2008)
.......
....
CACATTGGCACCCGCAATC
ACTTCCTCAAGGAACAACATTGCCA
CAAGCCTCTTCTCGTTCCTC
TAA
which can be used as a positive control for all three RT-PCR assays. The alignment also contains a closely related bat virus (Bat SARS-related clade, detected in Bulgaria (GenBank accession number NC_o1447o). Dots represent identical nucleotides compared with the WH_Human_1 sequence. Nucleotide substitutions are specified. Blue arrows: oligonucleotides as specified in Table 1. More comprehensive alignments can be found in the Supplement.