Table 2.
Detected SARS CoV-2 variants and mutational patterns from December 28, 2020 to September 28, 2021.
| Variant | Month and province of first detection during the study period | December 28-FebruaryN = 291 (100%) | March-JuneN = 781 (100%) | July-SeptemberN = 334 (100%) | TotalN = 1406 (100%) |
|---|---|---|---|---|---|
| D614Ga | December, Havana | 182 (63.2) | 84 (10.7) | 0 (0.0) | 266 (19.06) |
| Alpha B.1.1.7 | December, Havana | 3 (1.03) | 24 (3.07) | 0 (0.0) | 27 (1.92) |
| Beta B.1.351 |
December, Havana | 23 (7.90) | 424 (54.28) | 42 (12.57) | 489 (34.77) |
| A.2.5 | December, Ciego de Avila | 11 (3.78) | 71 (9.09) | 1 (0.29) | 83 (5.90) |
| Wuhana | January, Havana | 1 (0.34) | 0 (0.0) | 0 (0.0) | 1 (0.07) |
| Zeta/P2 | January, Cienfuegos | 3 (1.03) | 8 (1.02) | 0 (0.0) | 11 (0.78) |
| B.1.575.1 | January, Havana | 8 (2.74) | 4 (0.51) | 0 (0.0) | 12 (0.85) |
| Pattern 1b | January, Pinar del Rio | 22 (7.56) | 16 (2.04) | 0 (0.0) | 38 (2.70) |
| Pattern 2c | January, Pinar del Rio | 2 (0.68) | 3 (0.38) | 0 (0.0) | 5 (0.35) |
| Pattern 3d | January, Havana | 29 (9.96) | 14 (1.79) | 0 (0.0) | 43 (3.05) |
| Pattern 4e | February, Camagüey | 5 (1.71) | 11 (1.40) | 0 (0.0) | 16 (1.13) |
| B.1.1.519 | March, Havana | 0 (0.0) | 1 (0.12) | 0 (0.0) | 1 (0.07) |
| B.1.623 | February, Mayabeque | 2 (0.68) | 39 (4.99) | 0 (0.0) | 41 (2.91) |
| Delta B.1.617.2 |
April, Matanzas | 0 (0.0) | 59 (7.55) | 291 (87.12) | 350 (24.89) |
| Gamma/P1 | May, Havana | 0 (0.0) | 2 (0.25) | 0 (0.0) | 2 (0.14) |
| Lambda C37 |
May, Havana | 0 (0.0) | 2 (0.25) | 0 (0.0) | 2 (0.14) |
| B.1.523 | May, Camagüey | 0 (0.0) | 19 (2.43) | 0 (0.0) | 19 (1.35) |
a
Wuhan and D614G SARS CoV-2 variants had already been detected in 2020 in Cuba. In the table we refer only to samples collected for the present study.
b
Pattern 1 (D614G+T470K).
c
Pattern 2 (S477N+D614G).
d
Pattern 3 (D614G+T732A).
e
Pattern 4 (D614G+Q677H). GISAID describes two sub lineages of B.1.1 (lineages B.1.1.222 and B.1.1.322) which have the D614G+T732A mutations in the S gene fragment. In the present study, it was not possible to reach this classification because it would be necessary to sequence another gene. For this reason, the assignment of pattern 3 was maintained for all the samples with this combination of mutations.