Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants

Purpose: The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented.

Methods: The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread.

Results: BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed.

Conclusions: Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.

Citing Articles

The CABANA model 2017-2022: research and training synergy to facilitate bioinformatics applications in Latin America.

Campos-Sanchez R, Willis I, Gopalasingam P, Lopez-Juarez D, Cristancho M, Brooksbank C Front Educ (Lausanne). 2024; 9.

PMID: 39686965 PMC: 7617245. DOI: 10.3389/feduc.2024.1358620.

Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover.

Garcia-Lopez R, Taboada B, Zarate S, Munoz-Medina J, Salas-Lais A, Herrera-Estrella A Microb Genom. 2024; 10(3).

PMID: 38512312 PMC: 11004493. DOI: 10.1099/mgen.0.001220.

Differences in the Evolution of Clinical, Biochemical, and Hematological Indicators in Hospitalized Patients with COVID-19 According to Their Vaccination Scheme: A Cohort Study in One of the World's Highest Hospital Mortality Populations.

Mendoza-Hernandez M, Guzman-Esquivel J, Ramos-Rojas M, Santillan-Luna V, Sanchez-Ramirez C, Hernandez-Fuentes G Vaccines (Basel). 2024; 12(1).

PMID: 38250885 PMC: 10821037. DOI: 10.3390/vaccines12010072.

Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology.

Aguayo-Acosta A, Oyervides-Munoz M, Rodriguez-Aguillon K, Ovalle-Carcano A, Romero-Castillo K, Robles-Zamora A IJID Reg. 2023; 10:44-51.

PMID: 38149263 PMC: 10750064. DOI: 10.1016/j.ijregi.2023.11.005.

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico.

Taboada B, Zarate S, Garcia-Lopez R, Munoz-Medina J, Gomez-Gil B, Herrera-Estrella A Microb Genom. 2023; 9(12).

PMID: 38112714 PMC: 10763511. DOI: 10.1099/mgen.0.001120.

References

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

Cedro-Tanda A, Gomez-Romero L, Anda-Jauregui G, Garnica-Lopez D, Alfaro-Mora Y, Sanchez-Xochipa S . Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Viruses. 2022; 14(3). PMC: 8950183. DOI: 10.3390/v14030545. View

To T, Jung M, Lycett S, Gascuel O . Fast Dating Using Least-Squares Criteria and Algorithms. Syst Biol. 2015; 65(1):82-97. PMC: 4678253. DOI: 10.1093/sysbio/syv068. View

Meng B, Abdullahi A, Ferreira I, Goonawardane N, Saito A, Kimura I . Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature. 2022; 603(7902):706-714. PMC: 8942856. DOI: 10.1038/s41586-022-04474-x. View

Ulloa A, Buchan S, Daneman N, Brown K . Estimates of SARS-CoV-2 Omicron Variant Severity in Ontario, Canada. JAMA. 2022; 327(13):1286-1288. PMC: 8855311. DOI: 10.1001/jama.2022.2274. View

Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M . Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet. 2022; 399(10323):437-446. PMC: 8769664. DOI: 10.1016/S0140-6736(22)00017-4. View

Taboada B, Zarate S, Isa P, Boukadida C, Vazquez-Perez J, Munoz-Medina J . Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic. Viruses. 2021; 13(11). PMC: 8622467. DOI: 10.3390/v13112161. View

Brussow H . COVID-19: Omicron - the latest, the least virulent, but probably not the last variant of concern of SARS-CoV-2. Microb Biotechnol. 2022; 15(7):1927-1939. PMC: 9111164. DOI: 10.1111/1751-7915.14064. View

Minh B, Schmidt H, Chernomor O, Schrempf D, Woodhams M, von Haeseler A . IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020; 37(5):1530-1534. PMC: 7182206. DOI: 10.1093/molbev/msaa015. View

10.

Balint G, Voros-Horvath B, Szechenyi A . Omicron: increased transmissibility and decreased pathogenicity. Signal Transduct Target Ther. 2022; 7(1):151. PMC: 9077027. DOI: 10.1038/s41392-022-01009-8. View

11.

Ito K, Piantham C, Nishiura H . Estimating relative generation times and reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta variant in Denmark. Math Biosci Eng. 2022; 19(9):9005-9017. DOI: 10.3934/mbe.2022418. View

12.

Zarate S, Taboada B, Munoz-Medina J, Isa P, Sanchez-Flores A, Boukadida C . The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico. Microbiol Spectr. 2022; 10(2):e0224021. PMC: 9045257. DOI: 10.1128/spectrum.02240-21. View

13.

Richter J, Koptides D, Tryfonos C, Alexandrou D, Christodoulou C . Introduction, Spread and Impact of the SARS-CoV-2 Omicron Variants BA.1 and BA.2 in Cyprus. Microorganisms. 2022; 10(9). PMC: 9503937. DOI: 10.3390/microorganisms10091688. View

14.

Stefanelli P, Trentini F, Petrone D, Mammone A, Ambrosio L, Manica M . Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022. Euro Surveill. 2022; 27(45). PMC: 9650705. DOI: 10.2807/1560-7917.ES.2022.27.45.2200125. View

15.

Takashita E, Kinoshita N, Yamayoshi S, Sakai-Tagawa Y, Fujisaki S, Ito M . Efficacy of Antibodies and Antiviral Drugs against Covid-19 Omicron Variant. N Engl J Med. 2022; 386(10):995-998. PMC: 8809508. DOI: 10.1056/NEJMc2119407. View

16.

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J . Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021; 592(7854):438-443. DOI: 10.1038/s41586-021-03402-9. View

17.

Noureddine F, Chakkour M, El Roz A, Reda J, Al Sahily R, Assi A . The Emergence of SARS-CoV-2 Variant(s) and Its Impact on the Prevalence of COVID-19 Cases in the Nabatieh Region, Lebanon. Med Sci (Basel). 2021; 9(2). PMC: 8293406. DOI: 10.3390/medsci9020040. View

18.

Ranjan P, Neha , Devi C, Devar K, Das P . The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta variants: A computational approach. Microb Pathog. 2022; 169:105619. PMC: 9174103. DOI: 10.1016/j.micpath.2022.105619. View

19.

Su W, Choy K, Gu H, Sia S, Cheng K, Nizami S . Reduced Pathogenicity and Transmission Potential of Omicron BA.1 and BA.2 Sublineages Compared with the Early Severe Acute Respiratory Syndrome Coronavirus 2 D614G Variant in Syrian Hamsters. J Infect Dis. 2022; 227(10):1143-1152. PMC: 9278237. DOI: 10.1093/infdis/jiac276. View

20.

Willett B, Grove J, MacLean O, Wilkie C, De Lorenzo G, Furnon W . SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat Microbiol. 2022; 7(8):1161-1179. PMC: 9352574. DOI: 10.1038/s41564-022-01143-7. View