Primers & Probes for SARS-CoV-2 (COVID-19) Genome
Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome.
RT-PCR primers and probes for SARS-CoV-2 (COVID-19), assembled by Martin Reijns at the MRC Human Genetics Unit at the University of Edinburgh. UPDATED JAN 2021.
Sequence Author: Martin Reijns
Explore Over 2.7k Plasmids: Coronavirus Resources | More Plasmid Sets
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| 2019-nCoV_N2-R 18-mer / 56% GC 1 binding site 29,213 .. 29,230 = 18 annealed bases Tm = 57°C Reverse primer, N gene amplicon 2 (67 bp; USA-CDC) https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| 2019-nCoV_N2-P 23-mer / 57% GC 1 binding site 29,188 .. 29,210 = 23 annealed bases Tm = 65°C Probe, N gene amplicon 2 (USA-CDC) https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| 2019-nCoV_N2-F 20-mer / 40% GC 1 binding site 29,164 .. 29,183 = 20 annealed bases Tm = 56°C Forward primer, N gene amplicon 2 (67 bp; USA-CDC) https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| N-R 22-mer / 45% GC 1 binding site 28,958 .. 28,979 = 22 annealed bases Tm = 56°C Zhu et al (2020) N Engl J Med 2020;382:727-33. DOI: 10.1056/NEJMoa2001017 |
| N-probe 20-mer / 45% GC 1 binding site 28,934 .. 28,953 = 20 annealed bases Tm = 58°C Zhu et al (2020) N Engl J Med 2020;382:727-33. DOI: 10.1056/NEJMoa2001017 |
| N-F 22-mer / 50% GC 1 binding site 28,881 .. 28,902 = 22 annealed bases Tm = 57°C Zhu et al (2020) N Engl J Med 2020;382:727-33. DOI: 10.1056/NEJMoa2001017 |
| 2019-nCoV_N1-R 24-mer / 46% GC 1 binding site 28,335 .. 28,358 = 24 annealed bases Tm = 59°C Reverse primer, N gene amplicon 1 (72 bp; USA-CDC) https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| 2019-nCoV_N1-P 24-mer / 58% GC 1 binding site 28,309 .. 28,332 = 24 annealed bases Tm = 65°C Probe, N gene amplicon 1 (USA-CDC) https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| 2019-nCoV_N1-F 20-mer / 45% GC 1 binding site 28,287 .. 28,306 = 20 annealed bases Tm = 56°C Forward primer, N gene amplicon 1 (72 bp; USA-CDC) https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| M-574-R 20-mer / 60% GC 1 binding site 27,077 .. 27,096 = 20 annealed bases Tm = 59°C https://doi.org/10.3390/ijms21124396 |
| M-507-P 20-mer / 50% GC 1 binding site 27,029 .. 27,048 = 20 annealed bases Tm = 58°C https://doi.org/10.3390/ijms21124396 |
| M-475-F 20-mer / 55% GC 1 binding site 26,997 .. 27,016 = 20 annealed bases Tm = 59°C https://doi.org/10.3390/ijms21124396 |
| E_Sarbeco_R2 22-mer / 45% GC 1 binding site 26,360 .. 26,381 = 22 annealed bases Tm = 59°C Reverse primer, E gene amplicon (113 bp) Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019 nCoV) by real time RT PCR. Euro Surveill. 2020 https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045 also, https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf |
| E_Sarbeco_P1 26-mer / 54% GC 1 binding site 26,332 .. 26,357 = 26 annealed bases Tm = 64°C E gene probe Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019 nCoV) by real time RT PCR. Euro Surveill. 2020 https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045 also, https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf |
| E_Sarbeco_F1 26-mer / 35% GC 1 binding site 26,269 .. 26,294 = 26 annealed bases Tm = 56°C Forward primer, E gene amplicon (113 bp) Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019 nCoV) by real time RT PCR. Euro Surveill. 2020 https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045 also, https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf |
| S-gene-R 22-mer / 45% GC 1 binding site 21,796 .. 21,817 = 22 annealed bases Tm = 56°C https://doi.org/10.1016/j.jmoldx.2020.09.004 |
| S-gene-P 24-mer / 46% GC 1 binding site 21,759 .. 21,782 = 24 annealed bases Tm = 59°C https://doi.org/10.1016/j.jmoldx.2020.09.004 |
| S‐Gene‐F 22-mer / 41% GC 1 binding site 21,710 .. 21,731 = 22 annealed bases Tm = 54°C https://doi.org/10.1016/j.jmoldx.2020.09.004 |
| RdRp_SARSr-R1 26-mer / 29% GC 1 binding site 15,505 .. 15,530 = 25 annealed bases (26% GC) Tm = 45°C Reverse primer, RdRp amplicon (100 bp) Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019 nCoV) by real time RT PCR. Euro Surveill. 2020 https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045 also, https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf |
| RdRp_SARSr-P2 25-mer / 56% GC 1 binding site 15,470 .. 15,494 = 25 annealed bases Tm = 62°C RdRp probe Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019 nCoV) by real time RT PCR. Euro Surveill. 2020 https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045 also, https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf |
| RdRp_SARSr-F2 22-mer / 57% GC 1 binding site 15,431 .. 15,452 = 22 annealed bases Tm = 61°C Forward primer, RdRp amplicon (100 bp) Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019 nCoV) by real time RT PCR. Euro Surveill. 2020 https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045 also, https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf |
| nCoV_IP4-14146Rv 20-mer / 40% GC 1 binding site 14,167 .. 14,186 = 20 annealed bases Tm = 49°C Institut Pasteur, Paris, France https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| nCoV_IP4-14084Probe(+) 19-mer / 53% GC 1 binding site 14,105 .. 14,123 = 19 annealed bases Tm = 58°C Institut Pasteur, Paris, France https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| nCoV_IP4-14059Fw 19-mer / 42% GC 1 binding site 14,080 .. 14,098 = 19 annealed bases Tm = 51°C Institut Pasteur, Paris, France https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| ORF1ab-R 19-mer / 47% GC 1 binding site 13,442 .. 13,460 = 19 annealed bases Tm = 54°C Zhu et al (2020) N Engl J Med 2020;382:727-33. DOI: 10.1056/NEJMoa2001017 |
| ORF1ab-probe 28-mer / 54% GC 1 binding site 13,377 .. 13,404 = 28 annealed bases Tm = 64°C Zhu et al (2020) N Engl J Med 2020;382:727-33. DOI: 10.1056/NEJMoa2001017 |
| ORF1ab-F 21-mer / 43% GC 1 binding site 13,342 .. 13,362 = 21 annealed bases Tm = 53°C Zhu et al (2020) N Engl J Med 2020;382:727-33. DOI: 10.1056/NEJMoa2001017 |
| nCoV_IP2-12759Rv 18-mer / 44% GC 1 binding site 12,780 .. 12,797 = 18 annealed bases Tm = 52°C Institut Pasteur, Paris, France https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| nCoV_IP2-12696bProbe(+) 21-mer / 52% GC 1 binding site 12,717 .. 12,737 = 21 annealed bases Tm = 58°C Institut Pasteur, Paris, France https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| nCoV_IP2-12669Fw 18-mer / 44% GC 1 binding site 12,690 .. 12,707 = 18 annealed bases Tm = 51°C Institut Pasteur, Paris, France https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2 |
| 5' UTR 1 .. 265 = 265 bp |
| 5' UTR 1 .. 265 = 265 bp |
| ORF1ab 266 .. 21,555 = 21,290 bp 7096 amino acids = 794.1 kDa 2 segments Segment 1: 266 .. 13,468 = 13,203 bp 4401 amino acids = 489.6 kDa Product: ORF1ab polyprotein pp1ab; translated by -1 ribosomal frameshift |
| ORF1ab 266 .. 21,555 = 21,290 bp 7096 amino acids = 794.1 kDa 2 segments Segment 2: 13,468 .. 21,555 = 8088 bp 2695 amino acids = 304.5 kDa Product: ORF1ab polyprotein pp1ab; translated by -1 ribosomal frameshift |
| ORF1ab 266 .. 21,555 = 21,290 bp 7096 amino acids = 794.1 kDa 2 segments Product: ORF1ab polyprotein pp1ab; translated by -1 ribosomal frameshift |
| S 21,563 .. 25,384 = 3822 bp 1273 amino acids = 141.2 kDa Product: surface glycoprotein structural protein; spike protein |
| S 21,563 .. 25,384 = 3822 bp 1273 amino acids = 141.2 kDa Product: surface glycoprotein structural protein; spike protein |
| ORF3a 25,393 .. 26,220 = 828 bp 275 amino acids = 31.1 kDa Product: ORF3a protein |
| ORF3a 25,393 .. 26,220 = 828 bp 275 amino acids = 31.1 kDa Product: ORF3a protein |
| E 26,245 .. 26,472 = 228 bp 75 amino acids = 8.4 kDa Product: envelope protein ORF4; structural protein; E protein |
| E 26,245 .. 26,472 = 228 bp 75 amino acids = 8.4 kDa Product: envelope protein ORF4; structural protein; E protein |
| M 26,523 .. 27,191 = 669 bp 222 amino acids = 25.1 kDa Product: membrane glycoprotein ORF5; structural protein |
| M 26,523 .. 27,191 = 669 bp 222 amino acids = 25.1 kDa Product: membrane glycoprotein ORF5; structural protein |
| ORF6 27,202 .. 27,387 = 186 bp 61 amino acids = 7.3 kDa Product: ORF6 protein |
| ORF6 27,202 .. 27,387 = 186 bp 61 amino acids = 7.3 kDa Product: ORF6 protein |
| ORF7a 27,394 .. 27,759 = 366 bp 121 amino acids = 13.7 kDa Product: ORF7a protein |
| ORF7a 27,394 .. 27,759 = 366 bp 121 amino acids = 13.7 kDa Product: ORF7a protein |
| ORF8 27,894 .. 28,259 = 366 bp 121 amino acids = 13.8 kDa Product: ORF8 protein |
| ORF8 27,894 .. 28,259 = 366 bp 121 amino acids = 13.8 kDa Product: ORF8 protein |
| N 28,274 .. 29,533 = 1260 bp 419 amino acids = 45.6 kDa Product: nucleocapsid phosphoprotein ORF9; structural protein |
| N 28,274 .. 29,533 = 1260 bp 419 amino acids = 45.6 kDa Product: nucleocapsid phosphoprotein ORF9; structural protein |
| ORF10 29,558 .. 29,674 = 117 bp 38 amino acids = 4.4 kDa Product: ORF10 protein |
| ORF10 29,558 .. 29,674 = 117 bp 38 amino acids = 4.4 kDa Product: ORF10 protein |
| 3' UTR 29,675 .. 29,903 = 229 bp |
| 3' UTR 29,675 .. 29,903 = 229 bp |
| ORF1ab 266 .. 13,483 = 13,218 bp 4405 amino acids = 490.0 kDa Product: ORF1a polyprotein pp1a |
| ORF1ab 266 .. 13,483 = 13,218 bp 4405 amino acids = 490.0 kDa Product: ORF1a polyprotein pp1a |
| stem loop 13,488 .. 13,542 = 55 bp Function: Coronavirus frameshifting stimulation element stem-loop 2 |
| stem loop 13,488 .. 13,542 = 55 bp Function: Coronavirus frameshifting stimulation element stem-loop 2 |
| B.1.1.7 lineage synonymous mutation C14676T 14,676 .. 14,676 = 1 bp VUI-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation C14676T 14,676 .. 14,676 = 1 bp VUI-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation C15279T 15,279 .. 15,279 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation C15279T 15,279 .. 15,279 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation C16176T 16,176 .. 16,176 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation C16176T 16,176 .. 16,176 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| mature peptide 16,237 .. 18,039 = 1803 bp Product: helicase nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding domain (ZD), NTPase/helicase domain (HEL), RNA 5'-triphosphatase; produced by pp1ab only /protein_id=YP_009725308.1 |
| mature peptide 16,237 .. 18,039 = 1803 bp Product: helicase nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding domain (ZD), NTPase/helicase domain (HEL), RNA 5'-triphosphatase; produced by pp1ab only /protein_id=YP_009725308.1 |
| mature peptide 18,040 .. 19,620 = 1581 bp Product: 3'-to-5' exonuclease nsp14A2_ExoN and nsp14B_NMT; produced by pp1ab only /protein_id=YP_009725309.1 |
| mature peptide 18,040 .. 19,620 = 1581 bp Product: 3'-to-5' exonuclease nsp14A2_ExoN and nsp14B_NMT; produced by pp1ab only /protein_id=YP_009725309.1 |
| mature peptide 19,621 .. 20,658 = 1038 bp Product: endoRNAse nsp15-A1 and nsp15B-NendoU; produced by pp1ab only /protein_id=YP_009725310.1 |
| mature peptide 19,621 .. 20,658 = 1038 bp Product: endoRNAse nsp15-A1 and nsp15B-NendoU; produced by pp1ab only /protein_id=YP_009725310.1 |
| mature peptide 20,659 .. 21,552 = 894 bp Product: 2'-O-ribose methyltransferase nsp16_OMT; 2'-o-MT; produced by pp1ab only /protein_id=YP_009725311.1 |
| mature peptide 20,659 .. 21,552 = 894 bp Product: 2'-O-ribose methyltransferase nsp16_OMT; 2'-o-MT; produced by pp1ab only /protein_id=YP_009725311.1 |
| 501_V2 lineage mutation C21614T (L18F) 21,614 .. 21,614 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C21614T (L18F) 21,614 .. 21,614 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 lineage 21765-21770 del (HV69-70del) 21,765 .. 21,770 = 6 bp VOC-202012/01 Also present in Danish mink variant, Danish mink cluster 5 and various variants with spike amino acid change N439K Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| B.1.1.7 lineage 21765-21770 del (HV69-70del) 21,765 .. 21,770 = 6 bp VOC-202012/01 Also present in Danish mink variant, Danish mink cluster 5 and various variants with spike amino acid change N439K Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| 501_V2 lineage mutation A21801C (D80A) 21,801 .. 21,801 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation A21801C (D80A) 21,801 .. 21,801 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 lineage 21991-21993 del (Y144del) 21,991 .. 21,993 = 3 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage 21991-21993 del (Y144del) 21,991 .. 21,993 = 3 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| 501_V2 lineage mutation A22206G (D215G) 22,206 .. 22,206 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation A22206G (D215G) 22,206 .. 22,206 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 20A.EU1 lineage mutation C22227T (A222V) 22,227 .. 22,227 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| 20A.EU1 lineage mutation C22227T (A222V) 22,227 .. 22,227 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| 501_V2 lineage mutation 22286-94 del (LAL del) 22,286 .. 22,294 = 9 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation 22286-94 del (LAL del) 22,286 .. 22,294 = 9 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation G22299T (R246I) 22,299 .. 22,299 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation G22299T (R246I) 22,299 .. 22,299 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation G22813T (K417N) 22,813 .. 22,813 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation G22813T (K417N) 22,813 .. 22,813 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| Danish mink variant mutation A22920T (Y453F) 22,920 .. 22,920 = 1 bp https://www.biorxiv.org/content/10.1101/2020.11.16.384743v1 https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| Danish mink variant mutation A22920T (Y453F) 22,920 .. 22,920 = 1 bp https://www.biorxiv.org/content/10.1101/2020.11.16.384743v1 https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| 20A_EU2 lineage mutation G22992A (S477N) 22,992 .. 22,992 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| 20A_EU2 lineage mutation G22992A (S477N) 22,992 .. 22,992 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| 501_V2 lineage mutation G23012A (E484K) 23,012 .. 23,012 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation G23012A (E484K) 23,012 .. 23,012 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 + 501_V2 lineage mutation A23063T (N501Y) 23,063 .. 23,063 = 1 bp VOC-202012/01 Also present in 501.V2 (Report of increased transmissibility from South Africa) Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| B.1.1.7 + 501_V2 lineage mutation A23063T (N501Y) 23,063 .. 23,063 = 1 bp VOC-202012/01 Also present in 501.V2 (Report of increased transmissibility from South Africa) Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| B.1.1.7 lineage mutation C23271A (A570D) 23,271 .. 23,271 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation C23271A (A570D) 23,271 .. 23,271 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| A23403G (D614G) 23,403 .. 23,403 = 1 bp Present in B.1.1.7 lineage (VOC-202012/01) and many other strains Rapid increase during the early stages of the pandemic in the EU/EEA and then worldwide, probably due to a mix of founder effects and increased transmissibility. https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| A23403G (D614G) 23,403 .. 23,403 = 1 bp Present in B.1.1.7 lineage (VOC-202012/01) and many other strains Rapid increase during the early stages of the pandemic in the EU/EEA and then worldwide, probably due to a mix of founder effects and increased transmissibility. https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf |
| B.1.1.7 lineage muation C23604A (P681H) 23,604 .. 23,604 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage muation C23604A (P681H) 23,604 .. 23,604 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| 501_V2 lineage mutation C23664T (A701V) 23,664 .. 23,664 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C23664T (A701V) 23,664 .. 23,664 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 lineage mutation C23709T (T716I) 23,709 .. 23,709 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation C23709T (T716I) 23,709 .. 23,709 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation T24506G (S982A) 24,506 .. 24,506 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation T24506G (S982A) 24,506 .. 24,506 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation G24914C (D1118H) 24,914 .. 24,914 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation G24914C (D1118H) 24,914 .. 24,914 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| 501_V2 lineage mutation G25563T (Q57H) 25,563 .. 25,563 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation G25563T (Q57H) 25,563 .. 25,563 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C25904T (S171L) 25,904 .. 25,904 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C25904T (S171L) 25,904 .. 25,904 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C26456T (P71L) 26,456 .. 26,456 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C26456T (P71L) 26,456 .. 26,456 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 lineage synonymous mutation T26801C 26,801 .. 26,801 = 1 bp VUI-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation T26801C 26,801 .. 26,801 = 1 bp VUI-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| ORF7b 27,756 .. 27,887 = 132 bp 43 amino acids = 5.2 kDa Product: ORF7b |
| ORF7b 27,756 .. 27,887 = 132 bp 43 amino acids = 5.2 kDa Product: ORF7b |
| B.1.1.7 lineage mutation C27972T (Q27stop) 27,972 .. 27,972 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation C27972T (Q27stop) 27,972 .. 27,972 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation G28048T (R52I) 28,048 .. 28,048 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation G28048T (R52I) 28,048 .. 28,048 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation A28111G (Y73C) 28,111 .. 28,111 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation A28111G (Y73C) 28,111 .. 28,111 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation 28280 GAT->CTA (D3L) 28,280 .. 28,282 = 3 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation 28280 GAT->CTA (D3L) 28,280 .. 28,282 = 3 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| 501_V2 lineage mutation C28887T (T205I) 28,887 .. 28,887 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C28887T (T205I) 28,887 .. 28,887 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 20A.EU1 lineage mutation C28932T (A220V) 28,932 .. 28,932 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| 20A.EU1 lineage mutation C28932T (A220V) 28,932 .. 28,932 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| B.1.1.7 lineage mutation C28977T (S235F) 28,977 .. 28,977 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation C28977T (S235F) 28,977 .. 28,977 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| stem loop 29,609 .. 29,644 = 36 bp Function: Coronavirus 3' UTR pseudoknot stem-loop 1 |
| stem loop 29,609 .. 29,644 = 36 bp Function: Coronavirus 3' UTR pseudoknot stem-loop 1 |
| 20A_EU1 lineage mutation G29645T (L68F) 29,645 .. 29,645 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| 20A_EU1 lineage mutation G29645T (L68F) 29,645 .. 29,645 = 1 bp https://www.medrxiv.org/content/10.1101/2020.10.25.20219063v1.full.pdf |
| stem loop 29,728 .. 29,768 = 41 bp Function: Coronavirus 3' stem-loop II-like motif (s2m) basepair exception: alignment to the Rfam model implies coordinates 29740:29758 form a noncanonical C:T basepair, but the homologous positions form a highly conserved C:G basepair in other viruses, including SARS (NC_004718.3) |
| stem loop 29,728 .. 29,768 = 41 bp Function: Coronavirus 3' stem-loop II-like motif (s2m) basepair exception: alignment to the Rfam model implies coordinates 29740:29758 form a noncanonical C:T basepair, but the homologous positions form a highly conserved C:G basepair in other viruses, including SARS (NC_004718.3) |
| mature peptide 266 .. 805 = 540 bp Product: leader protein nsp1; produced by both pp1a and pp1ab /protein_id=YP_009742608.1 |
| mature peptide 266 .. 805 = 540 bp Product: leader protein nsp1; produced by both pp1a and pp1ab /protein_id=YP_009742608.1 |
| mature peptide 806 .. 2719 = 1914 bp Product: nsp2 produced by both pp1a and pp1ab /protein_id=YP_009725298.1 |
| mature peptide 806 .. 2719 = 1914 bp Product: nsp2 produced by both pp1a and pp1ab /protein_id=YP_009725298.1 |
| mature peptide 2720 .. 8554 = 5835 bp Product: nsp3 former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab /protein_id=YP_009742610.1 |
| mature peptide 2720 .. 8554 = 5835 bp Product: nsp3 former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab /protein_id=YP_009742610.1 |
| mature peptide 8555 .. 10,054 = 1500 bp Product: nsp4 nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab /protein_id=YP_009742611.1 |
| mature peptide 8555 .. 10,054 = 1500 bp Product: nsp4 nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab /protein_id=YP_009742611.1 |
| mature peptide 10,055 .. 10,972 = 918 bp Product: 3C-like proteinase nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab /protein_id=YP_009725301.1 |
| mature peptide 10,055 .. 10,972 = 918 bp Product: 3C-like proteinase nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab /protein_id=YP_009725301.1 |
| mature peptide 10,973 .. 11,842 = 870 bp Product: nsp6 nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab /protein_id=YP_009742613.1 |
| mature peptide 10,973 .. 11,842 = 870 bp Product: nsp6 nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab /protein_id=YP_009742613.1 |
| mature peptide 11,843 .. 12,091 = 249 bp Product: nsp7 produced by both pp1a and pp1ab /protein_id=YP_009742614.1 |
| mature peptide 11,843 .. 12,091 = 249 bp Product: nsp7 produced by both pp1a and pp1ab /protein_id=YP_009742614.1 |
| mature peptide 12,092 .. 12,685 = 594 bp Product: nsp8 produced by both pp1a and pp1ab /protein_id=YP_009725304.1 |
| mature peptide 12,092 .. 12,685 = 594 bp Product: nsp8 produced by both pp1a and pp1ab /protein_id=YP_009725304.1 |
| mature peptide 12,686 .. 13,024 = 339 bp Product: nsp9 ssRNA-binding protein; produced by both pp1a and pp1ab /protein_id=YP_009725305.1 |
| mature peptide 12,686 .. 13,024 = 339 bp Product: nsp9 ssRNA-binding protein; produced by both pp1a and pp1ab /protein_id=YP_009725305.1 |
| mature peptide 13,025 .. 13,441 = 417 bp Product: nsp10 nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab /protein_id=YP_009742617.1 |
| mature peptide 13,025 .. 13,441 = 417 bp Product: nsp10 nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab /protein_id=YP_009742617.1 |
| mature peptide 13,442 .. 16,236 = 2795 bp 2 segments Segment 1: 13,442 .. 13,468 = 27 bp Product: RNA-dependent RNA polymerase nsp12; NiRAN and RdRp; produced by pp1ab only /protein_id=YP_009725307.1 |
| mature peptide 13,442 .. 16,236 = 2795 bp 2 segments Segment 2: 13,468 .. 16,236 = 2769 bp Product: RNA-dependent RNA polymerase nsp12; NiRAN and RdRp; produced by pp1ab only /protein_id=YP_009725307.1 |
| mature peptide 13,442 .. 16,236 = 2795 bp 2 segments Product: RNA-dependent RNA polymerase nsp12; NiRAN and RdRp; produced by pp1ab only /protein_id=YP_009725307.1 |
| stem loop 29,629 .. 29,657 = 29 bp Function: Coronavirus 3' UTR pseudoknot stem-loop 2 |
| stem loop 29,629 .. 29,657 = 29 bp Function: Coronavirus 3' UTR pseudoknot stem-loop 2 |
| mature peptide 266 .. 805 = 540 bp Product: leader protein nsp1; produced by both pp1a and pp1ab /protein_id=YP_009725297.1 |
| mature peptide 266 .. 805 = 540 bp Product: leader protein nsp1; produced by both pp1a and pp1ab /protein_id=YP_009725297.1 |
| mature peptide 806 .. 2719 = 1914 bp Product: nsp2 produced by both pp1a and pp1ab /protein_id=YP_009742609.1 |
| mature peptide 806 .. 2719 = 1914 bp Product: nsp2 produced by both pp1a and pp1ab /protein_id=YP_009742609.1 |
| mature peptide 2720 .. 8554 = 5835 bp Product: nsp3 former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab /protein_id=YP_009725299.1 |
| mature peptide 2720 .. 8554 = 5835 bp Product: nsp3 former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab /protein_id=YP_009725299.1 |
| mature peptide 8555 .. 10,054 = 1500 bp Product: nsp4 nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab /protein_id=YP_009725300.1 |
| mature peptide 8555 .. 10,054 = 1500 bp Product: nsp4 nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab /protein_id=YP_009725300.1 |
| mature peptide 10,055 .. 10,972 = 918 bp Product: 3C-like proteinase nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab /protein_id=YP_009742612.1 |
| mature peptide 10,055 .. 10,972 = 918 bp Product: 3C-like proteinase nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab /protein_id=YP_009742612.1 |
| mature peptide 10,973 .. 11,842 = 870 bp Product: nsp6 nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab /protein_id=YP_009725302.1 |
| mature peptide 10,973 .. 11,842 = 870 bp Product: nsp6 nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab /protein_id=YP_009725302.1 |
| mature peptide 11,843 .. 12,091 = 249 bp Product: nsp7 produced by both pp1a and pp1ab /protein_id=YP_009725303.1 |
| mature peptide 11,843 .. 12,091 = 249 bp Product: nsp7 produced by both pp1a and pp1ab /protein_id=YP_009725303.1 |
| mature peptide 12,092 .. 12,685 = 594 bp Product: nsp8 produced by both pp1a and pp1ab /protein_id=YP_009742615.1 |
| mature peptide 12,092 .. 12,685 = 594 bp Product: nsp8 produced by both pp1a and pp1ab /protein_id=YP_009742615.1 |
| mature peptide 12,686 .. 13,024 = 339 bp Product: nsp9 ssRNA-binding protein; produced by both pp1a and pp1ab /protein_id=YP_009742616.1 |
| mature peptide 12,686 .. 13,024 = 339 bp Product: nsp9 ssRNA-binding protein; produced by both pp1a and pp1ab /protein_id=YP_009742616.1 |
| mature peptide 13,025 .. 13,441 = 417 bp Product: nsp10 nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab /protein_id=YP_009725306.1 |
| mature peptide 13,025 .. 13,441 = 417 bp Product: nsp10 nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab /protein_id=YP_009725306.1 |
| mature peptide 13,442 .. 13,480 = 39 bp Product: nsp11 produced by pp1a only /protein_id=YP_009725312.1 |
| mature peptide 13,442 .. 13,480 = 39 bp Product: nsp11 produced by pp1a only /protein_id=YP_009725312.1 |
| B.1.1.7 lineage synomymous mutation C913T 913 .. 913 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synomymous mutation C913T 913 .. 913 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| 501_V2 lineage mutation C1059T (T265I) 1059 .. 1059 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation C1059T (T265I) 1059 .. 1059 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 lineage mutation C3267T (T1001I) 3276 .. 3276 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation C3267T (T1001I) 3276 .. 3276 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| 501_V2 lineage mutation G5230T (K1655N) 5230 .. 5230 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation G5230T (K1655N) 5230 .. 5230 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 lineage mutation C5388A (A1708D) 5388 .. 5388 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation C5388A (A1708D) 5388 .. 5388 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation C5986T 5986 .. 5986 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage synonymous mutation C5986T 5986 .. 5986 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation T6954C (I2230T) 6954 .. 6954 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage mutation T6954C (I2230T) 6954 .. 6954 = 1 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| 501_V2 lineage mutation A10323G (K3353R) 10,323 .. 10,323 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| 501_V2 lineage mutation A10323G (K3353R) 10,323 .. 10,323 = 1 bp https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 |
| B.1.1.7 lineage 11288-11296 del (SGF 3675-3677del) 11,288 .. 11,296 = 9 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| B.1.1.7 lineage 11288-11296 del (SGF 3675-3677del) 11,288 .. 11,296 = 9 bp VOC-202012/01 Rambaut et al (2020) https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 |
| stem loop 13,476 .. 13,503 = 28 bp Function: Coronavirus frameshifting stimulation element stem-loop 1 |
| stem loop 13,476 .. 13,503 = 28 bp Function: Coronavirus frameshifting stimulation element stem-loop 1 |
| ORF: 13,768 .. 21,555 = 7788 bp ORF: 2595 amino acids = 293.0 kDa |
| ORF: 25,393 .. 26,220 = 828 bp ORF: 275 amino acids = 31.1 kDa |
| ORF: 26,245 .. 26,472 = 228 bp ORF: 75 amino acids = 8.4 kDa |
| ORF: 27,394 .. 27,759 = 366 bp ORF: 121 amino acids = 13.7 kDa |
| ORF: 266 .. 13,483 = 13,218 bp ORF: 4405 amino acids = 490.0 kDa |
| ORF: 21,536 .. 25,384 = 3849 bp ORF: 1282 amino acids = 142.3 kDa |
| ORF: 28,274 .. 29,533 = 1260 bp ORF: 419 amino acids = 45.6 kDa |
| ORF: 2958 .. 3206 = 249 bp ORF: 82 amino acids = 9.6 kDa |
| ORF: 21,936 .. 22,199 = 264 bp ORF: 87 amino acids = 10.2 kDa |
| ORF: 26,523 .. 27,191 = 669 bp ORF: 222 amino acids = 25.1 kDa |
| ORF: 27,894 .. 28,259 = 366 bp ORF: 121 amino acids = 13.8 kDa |
| ORF: 28,284 .. 28,577 = 294 bp ORF: 97 amino acids = 10.8 kDa |
| ORF: 422 .. 667 = 246 bp ORF: 81 amino acids = 9.6 kDa |
| ORF: 23,198 .. 23,437 = 240 bp ORF: 79 amino acids = 9.1 kDa |
| ORF: 6187 .. 6489 = 303 bp ORF: 100 amino acids = 10.8 kDa |
| ORF: 23,074 .. 23,322 = 249 bp ORF: 82 amino acids = 8.9 kDa |
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Individual Sequences & Maps
Plasmid Sets
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