Table 2.
Major coronavirus variants of concern, mutation sites in surface spike protein and unique peptide masses that distinguish such strains
| Lineage | Origin | Mutations | Tryptic + GluC segmenta | Sequence (mutations shown underlined, except deletions)b | Mass [M + H]+ mono. | Strain distinguishing peptide massesc |
|---|---|---|---|---|---|---|
| B.1.17 (Alpha) | UK | HV69–70 del. | 54–77 minus 69–70 | LFLPFFSNVTWFHAISGTNGTK | 2484.2711 | 2484.2711 |
| Y144 del. | 139–147 minus 144 | PFLGVYHK | 960.5302 | 960.5302 | ||
| N501Y | 499–504 | STYLVK | 710.4084 | |||
| A570D | 569–570 | ID | 247.1289 | (247.1289) | ||
| D614G | 587–619 | ITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTE | 3356.6138 | |||
| P681H | 664–682 | IPIGAGICASYQTQTNSHR | 2016.9920 | 2016.9920 | ||
| T716I | 703–725 | NSVAYSNNSIAIPINFTISVTTE | 2455.2352 | 2455.2352 | ||
| S982A | 979–982 | ILAR | 472.3242 | (472.3242) | ||
| D1118H | 1112–1127 | PQIITTHNTFVSGNCD | 1746.8116 | 1746.8116 | ||
| B.1.351 (Beta) | South Africa | L18F | 1–21 | MFVFLVLLPLVSSQCVNFTTR | 2414.2975 | |
| D80A | 79–88 | FANPVLPFND | 1133.5626 | 1133.5626 | ||
| D215G | 215–224 | GLPQGFSALE | 1018.5204 | 1018.5204 | ||
| LAL 242–244 del. | 238–246 minus 242–244 | FQTLHR | 801.4366 | 801.4366 | ||
| R246I | 238–253 | FQTLLALHISYLTPGD | 1788.9531 | 1788.9531 | ||
| K417N | 409–419 | QIAPGQTGNIAD | 1184.5906 | 1184.5906 | ||
| E484K | 472–484 | IYQAGSTPCNGVK | 1337.6519 | 1337.6519 | ||
| N501Y | 499–504 | STYLVK | 710.4084 | |||
| D614G | 587–619 | ITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTE | 3356.6138 | |||
| A701V | 686–702 | SVASQSIIAYTMSLGVE | 1755.8834 | 1755.8834 | ||
| B.1.617 (Delta) | India | T95I | 89–96 | GVYFASIE | 885.4353 | 885.4353 |
| G142D | 139–142 | PFLD | 491.2501 | |||
| E154K | 151–154 | SWMK | 551.2647 | 551.2647 | ||
| L452R | 429–452 | FTGCVIAWNSNNR | 1481.6955 | |||
| E484Q | 472–509 | IYQAGSTPCNGVQGFNCYFPLQSYGFQPTNGVGYQPYR | 4221.9222 | 4221.9222 | ||
| D614G | 587–619 | ITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTE | 3356.6138 | |||
| P681R | 664–681 | IPIGAGICASYQTQTNSR | 1879.9331 | |||
| B.1.617.2 (Delta plus) | India | T19R | 1–19 | MFVFLVLLPLVSSQCVNLR | 2178.2178 | 2178.2178 |
| G142D | 139–142 | PFLD | 491.2501 | |||
| EF156–157 del. | 155–158 minus 156–157 | SR | 262.1510 | (262.1510) | ||
| R158G | 154–169 | SEFGVYSSANNCTFE | 1654.6690 | 1654.6690 | ||
| L452R | 429–452 | FTGCVIAWNSNNR | 1481.6955 | |||
| T478K | 472–478 | IYQAGSK | 766.4094 | 766.4094 | ||
| D614G | 587–619 | ITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTE | 3356.6138 | |||
| P681R | 664–681 | IPIGAGICASYQTQTNSR | 1879.9331 | |||
| D950N | 948–964 | LQNVVNQNAQALNTLVK | 1867.0396 | 1867.0396 | ||
| P.1 (Gamma) | Brazil | L18F | 1–21 | MFVFLVLLPLVSSQCVNFTTR | 2414.2975 | |
| T20N | 1–21 | MFVFLVLLPLVSSQCVNLTNR | 2393.3084 | 2393.3084 | ||
| P26S | 22–34 | TQLPSAYTNSFTR | 1485.7333 | 1485.7333 | ||
| D138Y | 133–147 | FQFCNYPFLGVYYHK | 1925.9043 | 1925.9043 | ||
| R190S | 188–191 | NLSE | 462.2195 | (462.2195) | ||
| K417T | 409–420 | QIAPGQTGTIAD | 1171.5954 | 1171.5954 | ||
| E484K | 472–484 | IYQAGSTPCNGVK | 1337.6519 | 1337.6519 | ||
| N501Y | 499–504 | STYLVK | 710.4084 | 710.4084 | ||
| D614G | 587–619 | ITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTE | 3356.6138 | |||
| H655Y | 655–661 | YVNNSYE | 888.3734 | 888.3734 | ||
| T1027I | 1019–1028 | ASANLAAIK | 858.5044 | 858.5044 | ||
| V1176F | 1169–1181 | ISGINASFVNIQK | 1390.7689 | 1390.7689 |
aResidue numbering is based on the originating strain and may differ in some variants due to the presence of deletion sites
bAll strain distinguishing peptides do not contain proline (F817P, A892P, A899P, A942P, K986P, V987P) or alanine substitutions (R683A and R685A) added to the recombinant forms for the variants introduced to stabilize the S-protein trimer
cThose with masses lower than 500 are bracketed since they typically appear among matrix background ions in MALDI mass spectra. All other peptides differ in mass by at least 83 ppm, as is the case for mass 1133.5626 and that of 1133.6565 for missed cleaved peptide 821–830 (of sequence LLFNKVTLAD) for the spike protein of the original reference strain