ABSTRACT
Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Hugo G Castelán-Sánchez hugo.castelan{at}conacyt.mx, Luis Delaye luis.delaye{at}cinvestav.mx, Rhys Inward rhys.inward{at}biology.ox.ac.uk, Simon Dellicour simon.dellicour{at}ulb.be, Bernardo Gutierrez bernardo.gutierrez{at}biology.ox.ac.uk, Natalia Martinez de la Vina nataliamv{at}gmail.com, Oliver G Pybus oliver.pybus{at}biology.ox.ac.uk, Guillermo de Anda Jáuregui gdeanda{at}inmegen.edu.mx, Plinio Guzmán pgzmnk{at}gmail.com, Marisol Flores-Garrido mflores{at}enesmorelia.unam.mx, Óscar Fontanelli ofontanelli{at}ciencias.unam.mx, Maribel Hernández Rosales maribel.hr{at}cinvestav.mx, Amilcar Meneses ameneses{at}cs.cinvestav.mx, Gabriela Olmedo-Alvarez golmedo{at}cinvestav.mx, Alfredo Herrera-Estrella alfredo.herrera{at}cinvestav.mx, Celia Boukadida celia.boukadida{at}cieni.org.mx, Alejandro Sánchez-Flores alejandro.sanchez{at}ibt.unam.mx, José Esteban Muñoz-Medina eban10{at}hotmail.com, Andreu Comas-García andreu.comas{at}uaslp.mx, Bruno Gómez-Gil bruno{at}ciad.mx, Selene Zárate selene.zarate{at}uacm.edu.mx, Blanca Taboada btaboada{at}ibt.unam.mx, Susana López susana.lopez{at}ibt.unam.mx, Carlos F Arias arias{at}ibt.unam.mx, Moritz Kraemer moritz.kraemer{at}biology.ox.ac.uk, Antonio Lazcano alar{at}ciencias.unam.mx, Marina Escalera-Zamudio marina.escalerazamudio{at}biology.ox.ac.uk
The main text has now been modified to frame the study within the hypothesis and goals stated. We have further aimed to connect key conclusions to public health implications, applied to the country and the extended geographic region of the Americas. We now include a new figure (Supplementary Figure 1 c) comparing the overall cumulative proportion of genomes generated per state between 2020-2021. Furthermore, we have also added additional maps representing the geographic distribution of the clades identified within Figures 2-4. The main text has been modified to provide further details on the sampling scheme, and we thoroughly discuss how this may impact our findings. We now provide a comparative analysis to validate our migration-informed genome subsampling approach. For this, we re-ran the time-scaled analysis applied to the B.1.617.2 dataset (representing the best sampled lineage in the country) using a different migration-informed sub-sampling scheme (including all countries). We then re-estimated the number of introduction events and compared the obtained value with our initial result. This is now presented in a new section in SI (Supplementary Text 2 and Figure 2). For the new dataset, a significantly lower number of introduction events into Mexico were inferred whilst C5d displayed a reduced diversity, further supporting for our migration-informed subsampling approach.