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• W4385885298 abstract "Full text Figures and data Side by side Abstract Editor's evaluation Introduction Results Discussion Methods Appendix 1 Data availability References Decision letter Author response Article and author information Metrics 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. Editor's evaluation Castelán-Sánchez et al. analyzed, in an important way, the SARS-CoV-2 genomes from Mexico collected between February 2020 and November 2021. This period spans three major spikes in daily COVID-19 cases in Mexico and the rise of three distinct variants of concern (VOCs; B.1.1.7, P.1., and B.1.617.2). The authors perform convincing appropriate methodology in line with the current state of the art by careful phylogenetic analyses of these three VOCs, as well as two other lineages that rose to substantial frequency in Mexico, focusing on identifying periods of cryptic transmission (before the lineage was first detected) and introductions to and from the neighboring United States. https://doi.org/10.7554/eLife.82069.sa0 Decision letter Reviews on Sciety eLife's review process Introduction Genome sequencing efforts for the surveillance of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has granted public access to a massive number of virus genomes generated worldwide (https://www.gisaid.org/). Exploring SARS-CoV-2 genome data using genomic epidemiology has allowed researchers to characterize increasing virus diversity (Hill et al., 2021), track emerging viral subpopulations, and explore virus evolution in real-time, both at local and global scales (for examples see Kraemer et al., 2021; du Plessis et al., 2021; Worobey et al., 2020; Candido et al., 2020; COVID-19 Genomics UK (COG-UK) consortiumcontact@cogconsortium.uk, 2020). Throughout the development of the COVID-19 pandemic, viral variants have emerged and circulated across different regions of the world (Kraemer et al., 2021; Chen et al., 2021), displaying specific mutations that define their phylogenetic patterns (Li et al., 2021; Tao et al., 2021). The emergence and spread of SARS-CoV-2 lineages has been routinely monitored since early 2021, informing public health authorities on their responses to the ongoing pandemic (Oude Munnink and Koopmans, 2023). Emerging virus lineages are classified using a dynamic nomenclature system (‘Pango system’, Phylogenetic Assignment of Named Global Outbreak Lineages), developed to consistently assign newly generated genomes to existing lineages, and to designate novel virus lineages according to their phylogenetic identity and epidemiological relevance (Rambaut et al., 2020; Ruis and Colquhoun, 2021). Virus lineages that may pose an increased risk to global health have been classified as Variants of Interest (VOI), Variants under Monitoring (VUM), and Variants of Concern (VOC), potentially displaying one or more of the following biological properties (Tao et al., 2021; Centers for Disease Control and Prevention, 2022): increased transmissibility (Horby et al., 2021), decreasing the effectiveness of available diagnostics or therapeutic agents (such as monoclonal antibodies) (Weisblum et al., 2020), and evasion of immune responses (including vaccine-derived immunity) (Oude Munnink and Koopmans, 2023; Greaney et al., 2021a; Greaney et al., 2021b). Up to date, five SARS-CoV-2 lineages (including all descending sub-lineages) have been designated as VOC: B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron) (Oude Munnink and Koopmans, 2023; World Health Organization, 2021; O’Toole et al., 2021a). Virus lineages that dominate across various geographic regions are likely to have an evolutionary advantage, driven in part by a genetic increase in virus fitness (i.e. mutations enhancing transmissibility and/or immune escape; Martin et al., 2021; Escalera-Zamudio et al., 2023; Kumar et al., 2021; Vöhringer et al., 2021; Caniels et al., 2021). Moreover, the spread of different VOC across the world has been linked to human movement, often resulting in the replacement of previously dominating virus lineages (Oude Munnink and Koopmans, 2023). However, exploring lineage replacement/fitness dynamics remains a challenge, as these are impacted by numerous factors, including differential and stochastic growth rates that vary across geographic regions, a shifting immune structure of the host population (linked to viral pre-exposure levels and vaccination rates), (Vöhringer et al., 2021; Caniels et al., 2021) and changing social behaviours (such as fluctuating human mobility patterns and the implementation of local non-pharmaceutical interventions across time) (Vöhringer et al., 2021; Zhang et al., 2020; Boutin et al., 2021). Thus, the epidemiological and evolutionary processes enabling some lineages to spread and become dominant across distinct geographic regions, whilst others fail to do so, remain largely understudied. Mexico has been severely impacted by the COVID-19 pandemic, evidenced by a high number of cumulative deaths relative to other countries in Latin America (Sánchez-Talanquer et al., 2021). Since the first introductions of the virus in early 2020 and up to November 2021 (Taboada et al., 2020), the local epidemiological curve fluctuated between three waves of infection (observed in July 2020, January 2021, and August 2021; Sánchez-Talanquer et al., 2021; Taboada et al., 2020; Ritchie, 2020). Prior to the first peak of infection, non-pharmaceutical interventions (including social distancing and suspension of non-essential activities) were implemented at a national scale from March 23, 2020 to May 30, 2020. Nonetheless, a reopening plan for the country was already announced in May 13, 2020, whilst the national vaccination campaign did not begin before December 2020 (Sánchez-Talanquer et al., 2021). The ‘Mexican Consortium for Genomic Surveillance’ (abbreviated CoViGen-Mex) Consorcio de Vigilancia Genómica MexCoV2, 2021a was launched in February 2021, establishing systematic sequencing effort for a genomic epidemiology-based surveillance of SARS-CoV-2 in Mexico. In close collaboration with the national ministry of health, and driven by the sequencing capacity in the country, the program aimed to sequence per month approximately 1200 representative samples derived from positive cases recorded throughout national territory, based on the proportion of cases reported across states. In May 2021, the sequencing scheme was upgraded to follow the official case report line, in order to better coordinate case reporting and genome sampling across the country. Derived from publicly accessible genome data from Mexico deposited in GISAID (https://www.gisaid.org/) from 2020 to 2021 (corresponding to the first year of the epidemic), over 48,000 viral genomes were available, resulting in an approximate average of 2000 viral genomes sequenced per month. However, starting February 2021, the CoViGen-Mex sampling scheme gradually increased its sequencing output from a mean of less than 500 genomes per month to over 1000 genomes from May 2021 onwards. As of the time of writing this manuscript, around 80,000 SARS-CoV-2 genomes from Mexico were available in GISAID, with one-third of these generated by CoViGen-Mex Consorcio de Vigilancia Genómica MexCoV2, 2021a (and other national institutions sequencing the rest). From these, approximately 95% of all SARS-CoV-2 genomes from Mexico were generated in the country and 5% in the USA. Investigating the dominance and replacement patterns of SARS-CoV-2 can provide valuable information for understanding viral spread and shed light on virus evolution and adaptation processes. During the first year of the epidemic in Mexico, over 200 different virus lineages were detected, including all VOCs O’Toole et al., 2021a; Consorcio de Vigilancia Genómica MexCoV2, 2021b. Various virus lineages co-circulated across the national territory, a noteworthy observation in light of recombinant SARS-CoV-2 lineages that emerged in North America during 2021 (Gutierrez et al., 2022). Additionally, some virus lineages displayed specific dominance and replacement patterns that differed from those observed in neighboring countries, specifically the USA (Consorcio de Vigilancia Genómica MexCoV2, 2021a; Consejo Nacional de Humanidades, Ciencias y Tecnologías, 2021; Taboada et al., 2021). With this in mind, our study aimed to examine the dominance and replacement patterns of SARS-CoV-2 in Mexico from 2020 to 2021. We explored whether the spread of dominant lineages was driven by specific mutations that impacted local growth rates (further shaped the immune landscape of the local host population, depending mostly on virus pre-exposure levels at this time). We also investigated whether viral diffusion processes within the country were associated with local human mobility patterns, anticipating that the SARS-CoV-2 epidemic in Mexico may have been impacted by the epidemiological behavior of the virus in neighboring countries. To achieve this, we investigated the introduction, spread, and replacement dynamics of five virus lineages that dominated during the first year of the epidemic: B.1.1.222, B.1.1.519, B.1.1.7 (VOC Alpha), P.1 (VOC Gamma), and B.1.617.2 (VOC Delta) (Consorcio de Vigilancia Genómica MexCoV2, 2021a; Consejo Nacional de Humanidades, Ciencias y Tecnologías, 2021; Taboada et al., 2021). We used a phylodynamic approach to analyze publicly available cumulative SARS-CoV-2 genome data from the country in the context of virus genome data collected worldwide. We also devised a human migration and phylogenetic-informed subsampling approach to increase the robustness of our tailored phylogeographic analyses. To investigate lineage-specific spatial epidemiology, we contrasted our phylodynamic results with epidemiological and human mobility data, focusing on quantifying lineage importations into Mexico and characterizing local extended transmission chains across geographic regions (i.e. states). Our analysis revealed similar dynamics for the B.1.1.222 and B.1.1.519 lineages, with both likely originating in Mexico and denoting single extended transmission chains sustained for over a year. For P.1, B.1.1.7, and B.1.617.2 lineages, multiple introduction events were identified, with the detection of a few large transmission chains across the country. For B.1.617.2, which represented the largest and most genetically diverse clades identified, we observed a within-the-country virus diffusion pattern seeding from the south with subsequent movement into the central and north. We further identify Mexico’s southern border may have played an important role in the introduction and spread of SARS-CoV-2 (and other epidemics) across the country. Results The sampling date of this study comprises January 2020 to November 2021, corresponding to the first year of the epidemic in Mexico, just before the introduction of ‘Omicron’ (B.1.1.529) into the country (Consorcio de Vigilancia Genómica MexCoV2, 2021a; Consejo Nacional de Humanidades, Ciencias y Tecnologías, 2021; Taboada et al., 2021). During this time, Mexico reported a daily mean test rate ranging between 0.13–0.18 test per 1,000 inhabitants (Ritchie, 2020). Despite a lower testing rate compared to other countries, the cumulative number of viral genomes generated throughout 2020 and 2021 (both by CoViGen-Mex and other national institutions) correlates with the number of cases recorded at a national scale, corresponding to approximately 100 viral genomes per 10,000 cases, or ~1% of the official COVID-19 cases (Figure 1—figure supplement 1). Although SARS-CoV-2 sequencing remained centralized to Mexico City, the proportion of viral genomes per state roughly coincided with the spatial distribution of confirmed cases (with Mexico City reporting most cases), as stated officially Informe Técnico Diario COVID-19 MÉXICO, 2021 (Figure 1—figure supplement 1). Therefore, SARS-CoV-2 sequencing in Mexico has been sufficient to explore the spatial and temporal frequency of viral lineages across national territory (Consorcio de Vigilancia Genómica MexCoV2, 2021a; Consejo Nacional de Humanidades, Ciencias y Tecnologías, 2021; Taboada et al., 2021), now to further investigate the number of lineage-specific introduction events, and to characterize the extension and geographic distribution of associated transmission chains under a genomic epidemiology approach, as presented in this study. Our comparative analysis on the temporal distribution of virus lineages in Mexico confirmed previous published observations (O’Toole et al., 2021a; Consejo Nacional de Humanidades, Ciencias y Tecnologías, 2021; Taboada et al., 2021) showing that relative to other virus lineages circulating at the time, only the B.1.1.222, B.1.1.519, B.1.1.7 (Alpha), P.1 (Gamma), and B.1.617.2 (Delta) lineages displayed a dominant prevalence pattern within the country. Moreover, for most of these dominant lineages, peaks in genome sampling frequency (defined here as the proportion of viral genomes assigned to a specific lineage, relative to the proportion of viral genomes assigned to any other virus lineage in a given time point) often coincided with the epidemiological waves of infection recorded (except for B.1.1.7 and P.1) (Figure 1a and b). Figure 1 with 2 supplements see all Download asset Open asset Overview of the SARS-CoV-2 epidemic in Mexico. (a) Time-scaled phylogeny of representative SARS-CoV-2 genomes from Mexico within a global context, highlighting the phylogenetic positioning of B.1.1.222, B.1.1.519, B.1.1.7, P.1, and B.1.617.2 sequences. Lineage B.1.1.222 is shown in light green, B.1.1.519 in yellow, P.1 in red (Gamma), B.1.1.7 (Alpha) in dark green, and B.1.617.2 (Delta) in teal (b) The epidemic curve for COVID-19 in Mexico from January 2020 up to November 2021, showing the average number of daily cases (red line) and associated excess mortality (represented by a punctuated grey curve, denoting weekly average values). The peak of the first (July 2020), the second (January 2021), and the third wave (August 2021) of infection are highlighted in yellow shadowing. The dashed red line corresponds to the start date national vaccination campaign (December 2020), whilst the dashed black line represents the implementation date of a systematic genome sampling and sequencing scheme for the surveillance of SARS-CoV-2 in Mexico (February 2021). The period for the implementation of non-pharmaceutical interventions at national scale is highlighted in grey shadowing. The lower panel represents the genome sampling frequency (defined here as the proportion of viral genomes assigned to a specific lineage, relative to the proportion of viral genomes assigned to any other virus lineage in a given time point) of dominant virus lineages detected in the country during the first year of the epidemic. Lineages displaying a lower sampling frequency are jointly shown in purple. (c) Heatmap displaying the volume of trips into a given state from any other state recorded from January 2020 up to November 2021 derived from anonymized mobile device geolocated and time-stamped data. B.1.1.222 The B.1.1.222 lineage circulated in North America between April 2020 and September 2021, mostly within the USA (~80% of all B.1.1.222-assigned genomes) and Mexico (~20% of all B.1.1.222-assigned genomes). With limited reports from other regions of the world, B.1.1.222 was thus considered as endemic to the region (https://cov-lineages.org/) O’Toole et al., 2021b. The first B.1.1.222-assigned genome was sampled from Mexico on April 2020 (Mexico/CMX-INER-0026/2020-04-04) O’Toole et al., 2021b, whilst the last B.1.1.222-assigned genome was sampled from the USA on September 2021 (USA/CA-CDPH-1002006730/2021-09-14). The latest sampling date for B.1.1.222 in Mexico corresponds to July 2021 (Mexico/CHH_INER_IMSS_1674/2021-07-26), two months before the latest sampling date of the lineage at an international scale. We observe that in Mexico, the B.1.1.222 lineage was continuously detected between April 2020 and May 2021, followed by a steady decline after July 2021 (Figure 1b). During its circulation period, most B.1.1.222 genomes were collected from the central region of the country, represented by Mexico City (CMX; Figure 2a). For B.1.1.222, a rising genome sampling frequency was observed from May 2020 onwards, coinciding with the first epidemiological wave recorded during July 2020. Subsequently, genome sampling frequency progressively increased to reach a highest of 35% recorded in October 2020, denoting established dominance before the emergence and spread of B.1.1.519 (Figure 1b). Figure 2 Download asset Open asset Time-scaled phylogenetic analyses for the B.1.1.222 and B.1.1.519 lineage. Maximum clade credibility (MCC) trees for the (a) B.1.1.222 and (b) B.1.1.519 lineages, in which clades corresponding to distinct introduction events into Mexico are highlighted. Nodes shown as outline circles correspond to the most recent common ancestor (MRCA) for clades representing independent re-introduction events into Mexico (in teal) or from the USA (in ochre). Based on the earliest and latest MRCAs, the estimated circulation period for each lineage is highlighted in yellow shadowing. The dashed purple line represents the date of the earliest viral genome sampled from Mexico, while its position in the tree indicated. The dashed yellow line represents the implementation date of a systematic virus genome sampling and sequencing scheme for the surveillance of SARS-CoV-2 in Mexico. The corresponding root-to-tip regression plots for each tree are shown, in which genomes sampled from Mexico are shown in blue, whilst genomes sampled elsewhere are shown in grey. Map graphs on the left show the cumulative proportion of genomes sampled across states per lineage of interest, corresponding to the period of circulation of the given lineage (relative to the total number of genomes taken from GISAID, corresponding to raw data before subsampling). Maps on the right represent the geographic distribution of the clades identified. Data from the first year of the epidemic (available until February 2021, as analyzed by Taboada et al., 2021; O’Toole et al., 2021a; Consejo Nacional de Humanidades, Ciencias y Tecnologías, 2021) initially revealed that the B.1.1.222 lineage had reached a maximum genome sampling frequency of approximately 10%. However, our results show an important frequency underestimation (10% vs 35%), since the vast majority of B.1.1.222-assigned genomes from Mexico (>80%) were generated, assigned, and submitted to GISAID after February 2021. These observations are based on publicly available genome data, and both these values may actually underestimate lineage prevalence. However, calculating 'real' frequency values goes beyond the scope of this study. Notably, in the USA, the B.1.1.222 lineage reached a maximum genome sampling frequency of 3.5%, compared to a 35% observed in Mexico. This four-fold difference in the number of B.1.1.222-assigned genomes between the USA and Mexico reflects a significant disparity in sequencing efforts between the two countries, and contrasts with region-specific epidemiological scenarios Hill et al., 2021. This is of great importance since sequencing disparities and sampling gaps between countries can hinder the development of global outbreak control strategies and exacerbate existing health inequalities. Phylodynamic analysis for the B.1.1.222 lineage revealed one main clade deriving from a single earliest MRCA (most recent common ancestor) with a ‘most likely’ location (supported by a relative Posterior Probability [PP] of 0.99) inferred to be ‘Mexico’, denoting lineage emergence in the country (Figure 2a). The inferred date for this MRCA corresponds to March 2020, further denoting a cryptic circulation period of a month (before the earliest sampling date for the lineage within the country, see Methods section Time-scaled analysis). Subsequent ‘introductions’ should be interpreted as ‘re-introduction’ events into the country (with dates ranging from October 2020 to July 2021). After emergence, B.1.1.222 was seeded into the USA from Mexico multiple times. In this context, we estimate a minimum of 237 introduction events from Mexico into the USA (95% HPD interval = [225-250]), and a minimum of 106 introduction events from the USA into Mexico (95% HPD interval = [93-120]; Figure 2a). Based on inferred node dates (for MRCAs) in the MCC tree, the B.1.1.222 lineage displayed a total persistence of up to 16 months. B.1.1.519 Directly descending from B.1.1.222 (Figure 1a), the B.1.1.519 lineage circulated in North America between August 2020 and November 2021, mostly within the USA (~60% of all B.1.1.519-assigned genomes) and Mexico (~30% of all B.1.1.519-assigned genomes). As for B.1.1.222, B.1.1.519 genome reporting from other countries was limited, and the B.1.1.519 lineage was also considered as endemic to the region (https://cov-lineages.org/) (Taboada et al., 2021; O’Toole et al., 2021l; Cedro-Tanda et al., 2021; Rodríguez-Maldonado et al., 2021). At an international scale, the earliest B.1.1.519-assigned genome was sampled from the USA on July 2020 (USA/TX-HMH-MCoV-45579/2020-07-31) O’Toole et al., 2021c, whilst the latest B.1.1.519-assigned genome was sampled from Mexico on December 2021 (Mexico/CHP_IBT_IMSS_5310/2021-12-27) Aceves et al., 2021. During initial phylogenetic assessment, we noted that most of B.1.1.519-assigned genomes collected after November 2021 came from outside North America (namely, from Turkey and Africa). These were further identified as outliers within the tree, likely to be sequencing errors resulting, and thus were excluded from further analyses. In Mexico, the B.1.1.519 lineage was first detected on August 2020 (Mexico/YUC-NYGC-39037-20/2020-08-28) (Taboada et al., 2021). Our analysis derived from cumulative genome data from Mexico shows that B.1.1.519 displayed an increasing genome sampling frequency observed between September 2020 and July 2021 (Figure 1b). During these months, the spread of B.1.1.519 raised awareness in public health authorities, leading to its designation as a VUM in June 2021 (Oude Munnink and Koopmans, 2023; Taboada et al., 2021; Cedro-Tanda et al., 2021; Rodríguez-Maldonado et al., 2021). During its circulation period, most B.1.1.519 genomes were sampled from the central region of the country, represented by the state of Puebla (PUE; Figure 2b). We further observed that by late January 2021, up to 75% of the virus genomes sequenced in Mexico were assigned as B.1.1.519, with the lineage dominating over the second wave of infection recorded (Figure 1b). Similar to B.1.1.222, in the USA, B.1.1.519 only reached a maximum genome sampling frequency of 5% (up to April 2021). Compared to the 75% observed in Mexico, this once again contrast to the epidemiological scenario observed in each country, further exposing sequencing disparities (O’Toole et al., 2021b; O’Toole et al., 2021c). Phylodynamic analysis for the B.1.1.519 lineage revealed a similar pattern to the one observed for B.1.1.222, with one main clade deriving from a single MRCA (Figure 2b). The inferred date for this MRCA corresponds to July 2020, again with a ‘most likely’ source location inferred to be ‘Mexico’ (PP: 0.99). Thus, our results suggest that B.1.1.519 circulated cryptically in Mexico for one month prior to its initial detection (Figure 2b). After its emergence, the B.1.1.519 lineage was seeded back and forth between the USA and Mexico, with subsequent ‘re-introduction events’ into the country occurring between July 2020 and November 2021. In this light, we estimate a minimum number of 121 introduction events from the USA into Mexico (95% HPD interval = [108-131]), compared to a minimum number of 391 introduction events from Mexico into the USA (95% HPD interval = [380-402]) (Figure 2b). Based on inferred node dates in the MCC tree, the B.1.1.519 lineage displayed a total persistence of over 16 months. B.1.1.7 The B.1.1.7 lineage was first detected in the UK in September 2020, spreading to more than 175 countries in over a year O’Toole et al., 2021d. The earliest B.1.1.7-assigned genome from Mexico was sampled on late December 2020 (Mexico/TAM-InDRE-94/2020-12-31), while the latest B.1.1.7-assigned genome was sampled on October 2021 (Mexico/QUE_InDRE_FB47996_S8900/2021-10-13). Our analysis derived from cumulative genome data from the country revealed a continuous detection between February and September 2021. A peak in genome sampling frequency was observed around May 2021, coinciding with a lower number of cases recorded at the time (Figure 1b). Our results further confirm that the B.1.1.7 lineage reached an overall lower sampling frequency of up to 25% (relative to other virus lineages circulating in the country), as noted prior to this study (e.g. see Zárate et al., 2022; Sánchez-Talanquer et al., 2021; Ritchie, 2020; Subsecretaria de Prevención y Promoción de la Salud, 2021b). Of interest, similar observations were independently made for other Latin American countries, such as Brazil, Chile, and Peru (https://www.gisaid.org/), likely denoting region-specific dynamics for this lineage. Phylodynamic analysis for B.1.1.7 revealed an earliest MRCA dating to late October 2020, denoting a cryptic circulation period of approximately two months prior to detection in the country. The earliest genome sampling date also coincides with at least four independent and synchronous introduction events that date back to December 2020 (Figure 3a). In total, we estimated a minimum of 224 introduction events into Mexico (95% HPD interval = [219-231]). Potentially linked to the establishment of a systematic genome sequencing in Mexico, most of these were identified after February 2021. Within the MCC, we further identified seven clades (C1a to C7a) representing extended local transmission chains, with C3 and C7 being the largest (Figure 3a, Supplementary file 2). Figure 3 with 2 supplements see all Download asset Open asset Time-scaled phylogenetic analyses for the B.1.1.7 and P.1 lineages. Maximum clade credibility (MCC) trees for the (a) B.1.1.7 and the (b) P.1 lineages, in which major clades identified as distinct introduction events into Mexico are highlighted. Nodes shown as red outline circles correspond to the most recent common ancestor (MRCA) for clades representing independent introduction events into Mexico. Based on the earliest and latest MRCAs, the estimated circulation period for each lineage is highlighted in yellow shadowing. The dashed purple line represents the date of the earliest viral genome sampled from Mexico, while its position in the tree indicated. The dashed yellow line represents the implementation date of a systematic virus genome sampling and sequencing scheme for the surveillance of SARS-CoV-2 in Mexico. The corresponding root-to-tip regression plots for each tree are shown, in which genomes sampled from Mexico are shown in blue, whilst genomes sampled elsewhere are shown in grey. Map graphs on the left show the cumulative proportion of genomes sampled across states per lineage of interest, corresponding to the period of circulation of the given lineage (relative to the total number of genomes taken from GISAID, corresponding to raw data before subsampling). Maps on the right represent the geographic distribution of the clades identified. During its circulation period, most B.1.1.7 genomes from Mexico were generated from the state of Chihuahua, with these also representing the earliest B.1.1.7-assigned genomes from the country (Taboada et al., 2021; Zárate et al., 2022). However, only a small proportion of these genomes grouped within a larger clade denoting an extended transmission chain (C2a), with the rest falling within minor clusters, or representing singleton events (Figure 3a). Relative to other states, Chihuahua generated an overall lower proportion of viral genomes throughout 2020–2021 (Figure 1—figure supplement 1). Between February 2021 and September 2021 (corresponding to the circulation period of the B.1.1.7 lineage/Alpha VOC in Mexico), Mexico City reported the highest number of COVID-19 cases (https://coronavirus.gob.mx/datos/#DOView). During this time, Mexico City also reported the highest number of cases related to the B.1.1.7 lineage/Alpha VOC, with 2452 confirmed cases, followed by the states of Mexico, Jalisco, and Nuevo Leon (https://coronavirus.gob.mx/variantes/). Therefore, neither phylogenetic nor epidemiological data from the country support the notion that Chihuahua may have been an initial sink-source for the B.1.1.7 lineage/Alpha VOC (or for any other virus lineage, when comparing DTA results). Various factors can impact virus lineage distribution in a given region at a sp" @default.
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• W4385885298 title "Editor's evaluation: Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico" @default.
• W4385885298 doi "https://doi.org/10.7554/elife.82069.sa0" @default.
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