The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico

Abstract

The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

“…Phylogenetic analysis revealed a pattern similar to the one observed for the B. the state of Chihuahua, CHH) 32,46 and fall within the C2a identified here, with an MRCA dating to late January 2021 (Supplementary Data 2). Of note, the collection date of the earliest B.1.1.7 genome from Mexico coincides with at least four independent introduction events that occurred synchronously during December 2020 (Figure 3a).…”

Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

“…The haplotype network and mutation analysis showed limited regional clustering of AY.20 populations, but different spread chains could be observed. Interestingly, the AY.26 sublineage was detected early in the north of Mexico, particularly in the NW region, although the bordering USA states did not exhibit high frequencies of this sublineage (California and Arizona reported a frequency of AY.26 of 5% vs. 50% in NW Mexico, according to GISAID data), indicating that the exchange of AY.26 through the Mexico-US border was limited in contrast to what has been reported for the Alpha variant [14]. This data suggests that this sublineage originated in the NW of Mexico.…”

“…Most samples were collected in public clinics and hospitals of the Ministry of Health of Mexico [Instituto Mexicano del Seguro Social (IMSS) and Instituto Nacional de Enfermedades Respiratorias (INER)]. The RNA from 14,529 samples positive for SARS-CoV-2, as confirmed by real-time reverse transcription-polymerase chain reaction (RT-qPCR) and anonymized before the start of the study, were analyzed by the CoViGen-Mex consortium under the Mexican Official Norm NOM-017-SSA2-2012 [13] between February 2020 and November 2021, as previously described [14]. Sequencing was carried out using the Illumina COVIDSeq kit or Nextera XT (Illumina, Inc., San Diego, CA, USA) following the manufacturer's instructions, using different Illumina platforms and 2 × 150 cycles of paired-end runs.…”

“…To analyze the variation in the most prevalent Delta sublineages in Mexico, sequences from AY.3 (n = 1001), AY.20 (n = 9759), AY.26 (n = 4676), AY.62 (n = 224), AY.100 (n = 1650), AY.103 (n = 215), and AY.113 (n = 572) were specifically studied. Moreover, to inspect their geographical distribution and spread, the country was divided into seven regions (Figure S1) as previously reported [14], each including the following states: Northwest (NW): Baja California, Baja California Sur, Chihuahua, Durango, Sonora, and Sinaloa; Northeast (NE): Coahuila, Nuevo Leon, and Tamaulipas; Central North (CN): Aguascalientes, Guanajuato, Querétaro, San Luis Potosi, and Zacatecas; Central South (CS): Mexico City, State of Mexico, Morelos, Hidalgo, Puebla, and Tlaxcala; West (W): Colima, Jalisco, Michoacan, and Nayarit; South (S): Guerrero, Oaxaca, Chiapas, Veracruz, and Tabasco; Southeast (SE): Campeche, Yucatan, and Quintana Roo. A stack density plot was built for each region using ggplot2 v.3.3.5 [19] in R v.4.1.0.…”

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

“…3a, Supplementary Data 2). The earliest genome sequences were collected from the north-east region of the country (mostly represented by the state of Chihuahua, CHH) 32,46 and fall within the C2a identi ed here, with an MRCA dating to late January 2021 (Supplementary Data 2). Of note, the collection date of the earliest B.1.1.7 genome from Mexico coincides with at least four independent introduction events that occurred synchronously during December 2020 (Fig.…”