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. 2021 Nov 30;7(11):000684. doi: 10.1099/mgen.0.000684

Table 1.

Mutations of concern with multiple occurrences in Mexico during the pre-vaccination stage of the Covid-19 pandemic.

Protein and amino acid (region)*

Mutation

VOC/VOI with this mutation†

Clades/lineages in Mexico‡

No. of sequences (State)§

S: 13 (NTD)

S → I

20C/452R, B.1.427/9

20C/B.1.427/9

44 (BCN, NLE, JAL, CMX,

QUE, BCS, ROO)

S → G

20B/B.1.1.222

1 (CMX)

S: 18 (NTD)

L → F

20h/501Y.V2, B.1.351

20G/B.1.2

2 (GUA, NLE)

20J/501Y.V3, P.1

20B/B.1.1.29

1 (CMX)

20B/B.1.1

1 (AGU)

20B/B.1.1.222

2 (CMX, MEX)

20B/B.1.1.237

1 (NLE)

20B/B.1

1 (OAX)

S: 20 (NTD)

T → I

20J/501Y.V3, P.1

20C/B.1.2

1 (NLE)

20A/B.1.189

1 (BCN)

T → N

20B/B.1.1.222

3 (NLE, COA, CMX)

20B/B.1

1 (OAX)

S: 26 (NTD)

P → S

20J/501Y.V3, P.1

20C/B.1.429

6 (CMX, NLE, QUE)

20B/B.1

1 (OAX)

S: 138 (NTD)

D → Y

20J/501Y.V3, P.1

20A/B.1.189

1 (CMX)

20A/B.1

1 (BCN)

20A/B.1.404

16 (BCN, AGU)

20B/B.1.1.244

1 (NLE)

D → H

20B/B.1.1.222

1 (COL)

S: 144 (NTD)

144 → X

20I/501Y.V1, B.1.1.7

20A/B.1.189

1 (NLE)

20A/484K, B.1.525

20B/B.1.1.222

1 (CMX)

S: 152 (NTD)

W → C

20C/452R, B.1.427/9

20C/B.1.427/9

44 (BCN, NLE, JAL, CMX,QUE, BCS, ROO)

W → R

20A/B.1.94

1 (HID)

20A/B.1.243

1 (BCN)

W → L

20A/B.1

2 (CMX)

20B/B.1.1.222

2 (CMX)

S: 190 (NTD)

R → M

20J/501Y.V3, P.1

20B/P.4

3 (JAL)

R→ S

20A/B.1.243

1 (BCN)

S: 215 (NTD)

D → G

20 h/501Y.V2, B.1.351

20C/B.1.429

1 (JAL)

D → Y

20A/B.1

1 (OAX)

20B/B.1.1.222

1 (CMX)

S: 417 (RBD)

K → N

20h/501Y.V2, B.1.351

20B/B.1.1.222

1 (CMX)

K → T

20J/501Y.V3 or P.1

S: 452 (RBD, RBM)

L → R

20C/452R, B.1.427/9

20C/B.1.427/9

44 (BCN, NLE, JAL, CMX,

21A/154K, B.1.617.1

QUE, BCS, ROO)

21A/478K, B.1.617.2

20A/B.1.189

1 (NLE)

20A/B.1.232

9 (BCN)

S: 477 (RBD, RBM)

S → N

20C/452R, B.1.427/9

20A/B.1

3 (BCN, SLP, VER)

S → I

20A/B.1.404

3 (AGU)

20B/B.1.1.222

1 (CMX)

S: 478 (RBD, RBM)

T → K

20B/478 K.V1, B.1.1.222

20B/B.1.1.29

1 (OAX)

21A/478K, B.1.617.2

20B/B.1.1.85

1 (CMX)

20B/B.1.1.222

494 (majority of states)

S: 484 (RBD, RBM)

E → K

20h/501Y.V2, B.1.351

20A/B.1

1 (SLP)

20J/501Y.V3, P.1

20A/B.1.396

1 (SLP)

20B/484K, P.2

20B/P.4

9 (JAL)

20A/484K, B.1.525

20C/484K, B.1.526

E → Q

21A/154K, B.1.617.1

20A/B.1.243

1 (OAX)

S: 501 (RBD, RBM)

N → Y

20J/501Y.V1, P.1

20J/B.1.1.28.1

1 (JAL)

20I/501YV3, B.1.1.7

20I/B.1.1.7

6 (TAM, NLE)

S: 614 (S1)

D → G

20I/501Y.V1, B.1.1.7

20A and 20B

1547 (majority of states)

20h/501Y.V2, B.1.351

20J/501Y.V3, P.1

20B/484K, P.2

20A/484K, B.1.525

20C/484K, B.1.526

21B/154K, B.1.617.1

21A/478K, B.1.617.2

S: 655 (S1)

H → Y

20J/501Y.V3, P.1

20B/B.1

1 (OAX)

H → R

S: 677 (S1)

Q → H

20A/484K, B.1.525

20G/B.1.2

1 (NLE)

20A/B.1.189

2 (CMX)

20A/B.1.241

1 (CMX)

20A/B.1

3 (COA, SLP)

20A/B.1.232

3 (COA, BCS).

20B/B.1.1.220

2 (AGS, SLP)

20B/B.1.1

1 (CMX)

20B/B.1.1.28

1 (CMX)

Q → P

20B/B.1.1.222

3 (GRO, CMX)

20B/B.1.1.85

5 (NLE, COL, BCN, COA)

20G/B.1.2

2 (COA, QUE)

S: 681 (S1)

P → H

20I/501Y.V1, B.1.1.7

20G/B.1.2

2 (YUC, QUE)

20A/B.1.189

2 (QUE, NLE)

20A/B.1.243

11 (TAM, NLE, QUE, COA)

20B/B.1.1.29

1 (CMX)

20B/B.1.1.

6 (CMX, COA)

20B/B.1.1.344

1 (SLP)

20B/B.1.1.29

1 (OAX)

20B/B.1.1.85

1 (CMX)

20B/B.1.1.222

491 (majority of states)

P → R

21A/154K, B.1.617.1

20A/B.1

10 (CMX, MOR, BCN)

21A/478K, B.1.617.2

S: 701 (S2)

A → S

20 h/501Y.V2, B.1.351

20A/B.1

1 (MIC)

A → V

20A/B.1

3 (CMX, TAM, COA)

S: 732 (S2)

T → A

20B/478 K.V1, B.1.1.222

20B/B.1.1.29

1 (OAX)

20B/B.1.1.222

670 (majority of states)

T → S

20B/B.1.1.85

9 (QRO, CMX, QUE, COA, BCN, NLE, COL)

S: 1176 (S2)

V → F

20J/501Y.V3, P.1

20B/B.1.1.28

2 (CMX, NLE)

20B/484K, P.2

20B/P.4

9 (JAL)

N: 194 (IDR)

S → L

20@/B.1.1.289 (Mink)

20A/B.1||

342 (majority of states)

20A/B.1.36

*Mutations of concern in the spike (S) and nucleocapsid (N) proteins are based on previous reports (Plante et al., 2021) and in the co-variant data integrated by the Institute of Social and Preventive Medicine, University of Bern, Switzerland (Emma B. Hodcroft. 2021. ‘CoVariants: SARS-CoV-2 Mutations and Variants of Interest.’ https://covariants.org/). NTD, N-terminal domain (14–306). RBD, receptor binding domain (318–541). RBM, receptor binding motif (441–510). S1 (307–682) and S2 (683–1146) subunits. IDR, intrinsically disordered region. Only mutations occurring in more than one genome sequence during the period of study are reported.

†Known VOI or VOC that have been recorded in Mexico during the pre-vaccination stage are shown underlined, as these are part of the currently designated Covid-19 constellations (https://cov-lineages.org/constellations). VOI P.4 or B.1.1.28.4 is a sub-lineage closely related to the B.1.1.28.1 (P.1), B.1.1.28.2 (P.2) and B.1.1.28.3 (P.3) lineages.

‡Co-occurrence of mutations with T478K within 20B/B.1.1.222 or any other emerging lineage is shown in bold type. Refer to text for details on co-mutations, available in Table S3.

§Abbreviation of Mexican States (location) as recorded in GISAID, as follows (alphabetical order): AGS or AGU, Aguascalientes. BCN, Baja California. BCS, Baja California Sur. CMX, Mexico City. COA, Coahuila. COL, Colima. GUA, Guanajuato. GRO, Guerrero. HID, Hidalgo. JAL, Jalisco. MEX, Estado de Mexico. MIC, Michoacan. MOR, Morelos. NLE, Nuevo Leon. OAX, Oaxaca. QUE, Queretaro. QRO, Quintana Roo. SLP, San Luis Potosi. TAM, Tamaulipas. YUC, Yucatan. VER, Veracruz. The majority of S tates is used for 17 (out of 32) or more States.

||See Fig. 4 for a phylogenomic analysis of sub-clades 20A and lineages bearing the mutation N:S194L associated with the development of symptoms. Fig. S4 provides a phylogenomic analysis of all mutations included in Table 1.