Table 2.
Breakpoint information from the SARS-CoV-2 Pre-VOC to Recombinant.
| Lineage SARS-CoV-2 variant | Breakpoint position | Total length | No. of mutation | Variants with MAF > 0.05 | Gene region | Amino acid |
|---|---|---|---|---|---|---|
| Pre-VOC | 1,175–2,275 | 1,100 | 1 | C1191T | ORF1ab(nsp2) | P309L |
| 3,350–4,875 | 1,525 | 1 | G4184A | ORF1ab(nsp3) | G1307S | |
| 4,950–5,375 | 425 | 1 | C5184T | ORF1ab(nsp3) | P1640L | |
| 6,500–8,400 | 1900 | 2 | C7124T, G8393A | ORF1ab(nsp3) | P2287S,A2710T | |
| 8,650–8,885 | 235 | – | – | ORF1ab(nsp4) | ||
| 11,950–13,225 | 1,275 | 1 | C12880T | ORF1ab(nsp7) | 4205I | |
| 13,400–13,650 | 250 | – | – | ORF1ab(nsp12) | ||
| 14,250–15,200 | 950 | – | – | ORF1ab(nsp12) | ||
| 16,350–16,550 | 200 | 1 | C16466T | ORF1ab(nsp13) | P5401L | |
| 16,850–19,550 | 2,700 | 2 | C17410T | ORF1ab(nsp13) | R5716C | |
| A18163G | ORF1ab(nsp14) | I5967V | ||||
| 20,575–21,475 | 900 | – | – | ORF1ab-S | ||
| Alpha | 500–1950 | 1,450 | 1 | C913T | ORF1ab(nsp2) | 216S |
| 2,775–7,625 | 4,850 | 7 | C3037T, A5041G, C5388A,T5952G, C5986T, T6954C, G7560A | ORF1ab(nsp3) | 924F,1592Q,A1708D,L1896W,1907F,I2230T,R2432K | |
| 8,075–10,775 | 2,700 | 3 | G8131T, T9853C, C10450T | ORF1ab(nsp3-5) | K2622N,3196D,3395P | |
| Beta | 11,175–11,950 | 775 | 2 | G11417T, G11540T | ORF1ab(nsp6) | V3718F,V3759F |
| 18,725–18,750 | 25 | – | – | ORF1ab(nsp14) | ||
| 21,525–22,275 | 750 | 1 | C21714T | S | T51I | |
| Delta | 1,275–1,300 | 25 | – | – | ORF1ab(nsp2) | |
| 7,050–7,250 | 200 | 1 | C7124T | ORF1ab(nsp3) | P2287S | |
| 9,200–9,275 | 75 | – | – | ORF1ab(nsp4) | ||
| 20,200–20,250 | 50 | 1 | A20262G | ORF1ab(nsp15) | 6,666 L | |
| 20,400–20,475 | 75 | – | – | ORF1ab(nsp15) | ||
| 21,125–23,100 | 1975 | 7 | C21618G, C21846T, G21987A, C22227T, T22917G, C22995A, G23012A | S | T19R,T95I,G142D,A222V,L452R,T478K,E484K | |
| 25,675–26,575 | 900 | 1 | C26054A | ORF3a | T221K | |
| 26,800–28,700 | 1900 | 6 | T27638C, C27739T, C27752T,C27874T, A28271T, A28461G | ORF7a,Intergenic &N | V82A,L116F,T120I,Intergenic,Intergenic,N:D63G | |
| BA.1 | 6,025–6,325 | 300 | – | – | ORF1ab(nsp3) | |
| 10,825–11,725 | 900 | 1 | G11291A | ORF1ab(nsp5) | G3676S | |
| 11,975–12,200 | 225 | – | – | ORF1ab(nsp6) | ||
| 18,425–18,475 | 50 | – | – | ORF1ab(nsp14) | ||
| 21,300–22,600 | 1,300 | 7 | C21595T, C21762T, C21846T, G21987A, T22200G, G22578A, G22599A | S | 11 V,A67V,T95I,G142D,V213G,G339D,R346K | |
| 23,775–24,275 | 500 | 2 | C23854A, C24130A | S | N764K,N856K | |
| C24130A | S | N856K | ||||
| 25,600–25,625 | 25 | – | – | ORF3a | ||
| 26,500–26,600 | 100 | 2 | A26530G | M | D3G | |
| C26577G | M | Q19E | ||||
| 28,175–28,275 | 100 | 1 | A28271T | Intergenic | ||
| BA.2 | 8,600–8,700 | 100 | – | ORF1ab(nsp4) | ||
| Recombinant | 500–2,275 | 1775 | 1 | T670G | ORF1ab(nsp1) | S135R |
| 3,125–26,875 | 23,750 | 42 | G4184A, G4184A, C4321T, T5386G, G8393A, C9344T, A9424G, C9534T, C9866T, G10447A, C10449A, G11291A, C12880T, C15714T, T16342C, C17410T, A18163G, C19955T, A20055G, C21618G, G21987A, T22200G, C22674T,T22679C C22686T, A22688G, G22775A, A22786C, G22813T, T22917G, G22992A, C22995A, A23013C, A23040G,A23055G A23063T, T23075C, C25000T, C25416T, C26060T, C26270T, C26577G, C26858T | ORF1ab(nsp3)-M | ORF1ab:G1307S, 1352A, 1707A, A2710T, L3027F, 3,050 V, T3090I, L3201F, 3394R, P3395H, G3676S, 4205I, 5,150 L S5360P, R5716C, I5967V, T6564I, 6597E, S:T19R, G142D, V213G, S371F, S373P, S375F, T376A, D405N, R408S, K417N, L452R, S477N, T478K, E484A, Q493R, Q498R, N501Y, H505Y, 1146D, ORF3a:8F, T223I, E:T9I, M:Q19E, 112F |
|
| 27,900–29,225 | 1,325 | 4 | C28311T, G28881T, G28882A, G28883C | N | P13L, R203M, 203R, G204R |