Challenges and Opportunities of Genomic Surveillance SARS-CoV-2 in Mexico Meeting ^†

Abstract

In late 2019, a new virus, SARS-CoV-2, emerged in Wuhan, China, causing COVID-19 and the subsequent global pandemic. As of 30 April 2023, more than 774 million cases of COVID-19 had been reported worldwide, including over 7.5 million in Mexico. Despite advances in vaccination, epidemic surges of COVID-19 continued to occur globally, highlighting the importance of sharing and disseminating the experiences gained during these first years to better understand the virus’s evolution and respond accordingly. For this reason, the National Council for Science and Technology (CONACYT) organized the meeting “Challenges and Opportunities for Genomic Surveillance of SARS-CoV-2 in Mexico” from 15 to 17 August 2022, to present the efforts and results accumulated over more than two years of the pandemic. In this meeting report, we summarize the key findings of each participant and provide their contact information.

1. Introduction

COVID-19, the disease caused by the SARS-CoV-2 virus, emerged in late 2019 in Wuhan, China, and rapidly spread across the globe. As of 30 April 2023, the number of confirmed COVID-19 cases worldwide exceeded 774 million, involving 231 sovereign states and territories. During the pandemic, several variants of the original SARS-CoV-2 emerged and spread worldwide, yet, nowadays, Omicron remains the dominant variant across the globe. To identify new variants that might pose a risk for public health systems, the WHO continuously encourages countries to continue surveillance, testing, and sequencing. Nevertheless, it remains deficient worldwide, making monitoring this virus a challenge. Therefore, an appropriate articulation between governments, private entities, and academia may be an excellent strategy to join efforts in monitoring the emergence and evolution of SARS-CoV-2 variants.

On 15–17 August 2022, the National Council for Science and Technology (CONACYT; for its acronym in Spanish) held a meeting to expose and discuss the challenges and opportunities for genomic surveillance of SARS-CoV-2 in Mexico. Researchers from the Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Instituto de Biotecnología of the Universidad Nacional Autónoma de Mexico (IBT-UNAM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, Universidad Autónoma de la Ciudad de Mexico (UACM), Instituto Nacional de Enfermedades Respiratorias (INER), Universidad Autónoma del Estado de Morelos (UAEM), Hospital del Niño Morelense, the Center for Centro de Ciencias Matemáticas (CCM-UNAM), the private laboratory LABOPAT, as well as researchers from Colombia, of the Grupo de Genómica de Microorganismos Emergentes from Instituto Nacional de Salud, were invited as speakers to this meeting.

Government scientists, academic researchers, and industry members from multiple disciplines, such as bioinformatics, virology, immunology, and medical genomics, gathered to discuss the state of art in each of their respective subjects of expertise, as well as advances, challenges, applications, and new opportunities for the continuous monitoring of new SARS-CoV-2 variants and development of new strategies to combat the COVID-19 pandemic. This meeting addressed three main topics that are relevant for Mexico: (i) to call attention to CONACYT’s open science informatics resources, which are focused on COVID-19 epidemiology and SARS-CoV-2 genomics; (ii) to facilitate communication and collaboration between the different SARS-CoV-2 genotyping initiatives in Mexico and Colombia, by sharing research results on sequencing, epidemiology, and phylogenomics of the virus; (iii) to promote the development of platforms and strategies to help communicate and assist in problem solving and information flow.

In general, researchers presented new findings on methods of virus identification by next-generation sequencing (NGS), antibody testing, and epidemiological dynamics, such as the introduction of variants of concern (VOC) to Mexico. In addition, topics like addressing human mobility, affecting virus introduction and spread, and how epidemiological models can be used for vaccine deployment in Mexico were discussed. This article describes the highlights of the conference, a snapshot of some of the SARS-CoV-2 genomic epidemiology research carried out in Mexico and Colombia from the perspective of leading institutions involved in genomic surveillance of the virus. This series aimed to bring together a multidisciplinary group of scientists from Mexico and Colombia to foster collaboration among the various research groups.

2. Summary of the Scientific Program

Opening and Meeting Overview

Aideé Orozco-Hernández, Director of Technological Development, Linkage and Innovation, Consejo Nacional de Ciencia y Tecnología (CONACYT), and Irma López-Martínez, Director of Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), made the inaugural comments and welcomed speakers and participants to the meeting “Challenges and Opportunities for Genomic Surveillance of the Virus SARS-CoV-2 in Mexico”. Dr. Aidee Orozco highlighted that since March 2020, CONACYT has been committed to promoting the development and consolidation of genomic and bioinformatic resources through the National Computational Ecosystem COVID-19, which has led to the generation of public knowledge concerning SARS-CoV-2.

Over the next three days, participants would be expected to provide an overview of the approaches and perspectives of genomic surveillance projects on SARS-CoV-2 at various institutes and laboratories in Mexico and Colombia. This is part of a continuous effort, and it was essential to recognize the efforts of CONACYT and the commitment of the Mexican health sector, which enabled the forging of closer ties through inter-institutional work and cooperative agreements that may open new avenues of collaboration and cooperation for the benefit of the health of the Mexican population.

On her behalf, Irma López-Martínez (InDRE) mentioned the progress in the diagnosis and investigation of the SARS-CoV-2 virus that has been achieved in Mexico after more than two years of the pandemic. After the World Health Organization (WHO) raised the alarm in December 2019 due to the increase in cases of unknown pneumonia, it became clear that the world was dealing with a new virus. Work began to identify the virus, a fundamental challenge for epidemiology. Genomic surveillance was introduced nationally in many developed and developing countries, including Latin America. Mexico gathered a group of experts to sequence the virus and perform bioinformatics analysis, establishing a coordinated genomic surveillance network.

This network was a great help in continuing studies across the country and sharing advances, innovation, and research in health facilities and universities. In this way, it was possible to monitor the virus throughout the pandemic; moreover, the clinical and epidemiological data contributed to a better understanding of this disease, forming the basis for the surveillance of other diseases.

In the following days, advances in genomic surveillance, evolutionary analysis of the virus, development of bioinformatics tools to study the genomics of the virus, and epidemiological models of the virus were presented.

3. Results

3.1. Viral Emergence and Surveillance in Mexico

Claudia Wong-Arámbula (InDRE) pointed out that one of the critical differences in the COVID-19 pandemic was that this pandemic occurred in the genomic era, driven by continuous advances in next-generation sequencing [1]. InDRE is the Mexican government institute responsible for monitoring different pathogens through diverse strategies and protocols and contributing to accurately identifying emerging pathogenic strains or species and their genetic variation in real time. In addition, the rapid evolution of SARS-CoV-2’s genomic information globally during this pandemic highlighted the need for developing new tools to rapidly identify SARC-CoV-2 variants with greater accuracy, for example, the design of specific primers for various real-time PCR protocols for surveillance. Wong-Arámbula noted that the deletion at position 6970 nt of the spike (S) gene of the virus, used by some laboratories for diagnosis, was compromised when the Omicron variant emerged, since both the Alpha and Omicron variants have the same deletion, resulting in false negatives for the diagnosis of Omicron [2]. The protocol followed by InDRE (for target samples) was to amplify a 370 bp fragment of the spike protein and sequence the amplicon using the Sanger method. Subsequently, positive samples were subjected to whole genome sequencing (WGS) using high-throughput platforms for genomic characterization of the virus.

Active surveillance across the country and analyses of the epidemiological situation at the time of the meeting was focused on surveillance of the Omicron sublineages. In Mexico, the majority of samples obtained in the first months of 2021 corresponded to variant B.1.1.519 of SARS-CoV-2 [3], followed by Alpha and Gamma VOCs in mid-2021; then, the Delta VOC was prevalent during the second half of the year, while the Omicron variant was detected in November. Of the 4000 Omicron samples reported so far by InDRE, the sublineage with the highest prevalence was BA.1.1 (Omicron), and the spread was faster between December 2021 and February 2022.

Rodrigo García-López (IBt-UNAM), a member of the Mexican Consortium for Genomic Surveillance (CoViGen-Mex), talked about CoViGen’s pivotal contribution towards the national surveillance effort and provided a general overview and statistics of the turnover of SARS-CoV-2 variants during the COVID-19 pandemic in Mexico. CoViGen was described as a consortium comprised by multiple leading academic and health institutions in Mexico that focused on sequencing and analyzing genomes of pathogenic species bearing epidemiological interest. Garcia López highlighted that during the pandemic, the Instituto de Biotecnología IBt-UNAM, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Instituto Nacional de Enfermedades Respiratorias INER, and Centro de Investigación en Alimentación y Desarrollo Mazatlán (CIAD-Mazatlán) had sequenced over 35.38% (25,317) of the total SARS-CoV-2 genomes out of all samples collected in Mexico as of the time of the meeting (71,551), on par with INMEGEN (33.39%) and InDRE (19.89%). In other words, the consortium had sequenced on average around 1000 genomes per month from all regions in Mexico, with the highest coverage rate and quality thanks to its collaboration with the governmental Instituto Mexicano del Seguro Social (IMSS). The general overview of the epidemiology of the SARS-CoV-2 virus showed that Mexico had reported about 6.8 million cases and more than 328,000 deaths up until early August. García-López mentioned that Mexico’s average mortality had peaked during its second wave at an average 1400 deaths per day.

As was shown, throughout 2020, Mexico’s genomic surveillance was limited and had reported the concurrent circulation of multiple variants. However, as the country traversed two first epidemiological surges, variant B.1.1.222 was the first showing high prevalence exclusively in Mexico, which gave rise to B.1.1.519, which was in turn the first to reach a prevalence of ~80% of almost all sequences amongst the Mexican population on the first quarter of 2021. Subsequently, VOCs Alpha and Gamma reached Mexico and became the most widespread around mid-2021 [4]. By August 2021, the Delta variant had displaced all other extant variants and triggered the third wave. This variant remained unrivaled until the end of 2021, as it was swiftly displaced shortly after the onset of the first Omicron variants in Mexico. Omicron subvariants were solely responsible for the fourth (January 2022) and fifth (June 2022) COVID-19 waves in the country and have been the only variants circulating in Mexico ever since [5]. Since early 2021, CoViGen has been uploading the full genomic sequences derived from COVID-19-positive samples 16 to 21 days after collection to establish real-time genomic surveillance of the circulation of variants in Mexico.

Ugo Avila-Ponce de León (INMEGEN/UNAM) and Eric Avila-Vales (UADY) collaborated to develop a mathematical model at the onset of the pandemic in Mexico in March. This model aimed to analyze the potential virus transmission within Mexico [6,7]. In that first model, the initial goal was to figure out when the maximum hospital load would be surpassed in 2020. Over the years, the number of variables in the mathematical models had been increased, including factors such as the vaccination rate and the co-occurrence of different variants that may be affecting the spread of the virus [8,9]. His research group developed a modified mathematical SIR model (Susceptible-Infected-Recovered) comprising multiple differential equations, each considering compartments corresponding to the subpopulation that would be interacting at that time; in Mexico, these were typically asymptomatic patients, as on average 20% to 80% of infected individuals developed symptoms. The mathematical model included two separate sets of equations for the Omicron variants (BA.1 and BA.5) that affected the same susceptible and vaccinated (boosted or unboosted) subpopulations. Competition between Omicron subvariants would eventually lead to dominance by BA.5, while BA.2 would linger with a low number of infections as it would never reach a level of zero infections from this subvariant. In their model, they had evaluated the importance of pharmaceutical (multiple vaccines against COVID-19) and non-pharmaceutical (use of face masks) strategies for the containment of the second Omicron surge (fifth wave) in Mexico. Vaccination in Mexico had helped reduce hospitalizations. Their model showed that unvaccinated individuals had had a higher rate of hospitalization compared with vaccinated individuals. The same behavior was observed in vaccinated individuals with or without booster vaccination, with vaccinated individuals having a lower probability of hospitalization compared with unvaccinated individuals. They examined the differential efficacy of facemask usage and recommended the specific use of surgical facemasks because they had demonstrated to be effective in preventing viral infection while being inexpensive. Finally, their model predicted another Omicron wave due late 2022, but it would be 75% smaller than the previous (fifth) wave. Moreover, the size of these waves would be strongly influenced by immunity parameters such as waning immune and cross-reactive immunity. Apparently, the Mexican population had not developed sterilizing immunity when infected by earlier variants, stressing the importance of employing non-pharmaceutical strategies during the seasonal period of viral spread. This lack of sterilizing immunity, particularly during the first and second waves, was evidenced by recurring, even mild, infections and sustained transmission chains. Serological surveillance revealed that previously infected individuals were still susceptible, underscoring the importance of implementing non-pharmaceutical interventions such as masking and distancing, especially during peak seasonal transmission periods.

Luis A. Mendoza Torres (LABOPAT) discussed that a critical aspect of genomic surveillance (in the case of SARS-CoV-2) was the rapid response from sample collection to genome analysis. LABOPAT is a private laboratory that started sequencing samples of clinical interest. For this purpose, LABOPAT uses the Genexus Syste from Thermo Fisher Scientific [10]. This platform is based on the same principle as the Ion Torrent technology. It is a sequencing method based mainly on semiconductors and has a significant advantage over other platforms in the automatization of library preparations, allowing to process up to 16 RNA samples in 27 h. Mendoza-Torres mentioned that the bioinformatics analysis had been performed with the IRMA software [11], based on a reference sequence, and variant assignment had been performed with Pangolin, whereas phylogenetic trees had been generated with MEGA [12]. Mendoza-Torres listed the advantages of establishing schemes with optimized workflows to reduce the error rate. LABOPAT had reported 99 sequences from Puebla, Tlaxcala, and Mexico City thus far.

3.2. Molecular Evolution and Diagnostic of SARS-CoV-2 in Mexico

Margarita Valdés Alemán (Hospital del Niño Morelense, HNM) and Ramón A. González (Universidad Autónoma del Estado de Morelos, UAEM) presented work on serological studies to assess the seroprevalence of SARS-CoV-2 in children and adults from the state of Morelos, before the start of vaccination campaigns. For the adult population, seroconversion was followed along with each vaccination dose to assess their response to the vaccines. For this purpose, an ELISA test was developed using the RBD domain of the SARS-CoV-2 spike protein to coat the plates to which the serum samples from participants were added [13]. Measurements for the presence of IgG, IgM, and IgA antibodies recognizing the RBD in sera were performed in all cases. The adult population cohort consisted of healthcare personnel that participated in the hospital transfers of COVID-19-positive patients during the pandemic; therefore, it was considered a high-risk population. Samples of 114 participants were obtained during January and February of 2021, just before the start of vaccination campaigns. The population consisted of 40% females and 60% males between the ages of 19 to 59 years, most of them being below 40 years old. The two most frequently reported risk factors were obesity/overweight (57%) and smoking (56%). The seroprevalence analysis showed that 26% of the population resulted positive for IgG specific to SARS-CoV-2 (IgG 26.3%, IgM 19.3%, and IgA 13.2%). Subsequently, 73 of these participants were followed during the vaccination process, from the first to the third dose, obtaining samples 20–48 days after vaccination. The vaccine applied in the first and second dose to healthcare personnel in Mexico was the Pfizer-BioNTech (BNT162b2) vaccine. A comparison of IgG, IgM, and IgA levels after vaccination showed that the second dose had a significant effect on reaching higher antibody levels and reducing the variability of IgG and IgM antibodies. For the third dose, participants in the study group received either Pfizer-BioNTech, Oxford/Astra-Zeneca ChAdOx1-S (AZD1222), CanSino (Ad5-nCoV-S), or Moderna (ARNm-1273) vaccines. However, the results showed that regardless of the type of vaccine applied for the third dose, the study group had comparable or higher levels of IgG and IgM than after the second dose. In contrast to IgG and IgM levels, the IgA levels in serum samples showed a broad spectrum of measurements. High IgA levels pre-vaccination were only found in participants with recent and moderated cases of COVID-19. During vaccination only around 1/3 of the subjects reached high levels of IgA, although the median of IgA levels did increase after the third dose. The study on children consisted of sampling hospitalized children or children that attended the hospital for medical consultation from March 2021 to May 2022. None of the children had the vaccine applied. A total of 115 samples were obtained. The age range varied from 3 months to 16 years, but most were below 11 years old. Even though less than 10% of the population reported being diagnosed as positive for COVID-19, the seroprevalence studies found that more than 56% were IgG positive for SARS-CoV-2 (IgG 56.5%, IgM 28.7% and IgA 11.3%). These results, although not surprising, did convey an urgency to prioritize diagnosis in children since most of the children in this population reported different risk factors and 15% of them were diagnosed with Multisystem Inflammatory Syndrome in Children (MIS-C) or Kawasaki syndrome [14]. Finally, we decided to compare antibody levels between the non-vaccinated IgG-positive adult vs. child populations. We observed statistically significant differences showing higher levels of IgG in response to the infection in the adult population in comparison to the child population (

Table 1. Comparison of antibody levels between IgG-positive adults and children (non-vaccinated individuals).

Antibody Type	Population Compared	Statistical Test	Result Summary
IgG	Adults vs. Children	ANOVA: F(1, 72) = 21.45, p < 0.001	Adults showed significantly higher IgG levels (r(72) = 0.42, p < 0.001)
IgM	Adults vs. Children	Same ANOVA test	Adults also had significantly higher IgM levels (r(72) = 0.63, p < 0.001)
		Effect size: η2 = 0.09, ε = 0.84	Moderate effect size; Greenhouse-Geisser correction applied

). Therefore, we consider it important to follow up investigation of the antibody responses after vaccination in our child population.

Selene Zárate (UACM) highlighted the occurrence in Mexico of two different lineage dynamics, the first one during the first year of the pandemic, with the circulation of several lineages derived from B.1 without the dominance of a single one. Later, this dynamic changed with the rise of the variants of concern of SARS-CoV-2, characterized by the presence of a larger number of mutations than expected and their ability to replace other circulating lineages quickly. The first lineage in Mexico to become dominant was variant B.1.1.519 [3], which probably originated in central Mexico and spread rapidly during the second pandemic wave at the beginning of 2021 in the country’s center and south, reaching a maximum prevalence between March and April 2021. In the following months, the Alpha and Gamma variants started spreading mainly in the north and south of the country, respectively. In the case of the Alpha variant, the spread was very slow, reaching a mean prevalence of about 35 to 40% only in northern states, which were, interestingly, states where variant B.1.1.519 circulated at low levels [15]. By the summer of 2021, the Delta variant became dominant and displaced all other circulating variants, with a distinct geographical distribution of each Delta sublineage. Also, we have identified the northern border, the Yucatan peninsula, and Mexico City and the point of entry or origin of SARS-CoV-2 variants in our country. During the fourth wave, the fast spread of the BA.1 variant did not result in geographical clustering, with a dominance of BA.1.1. Dr. Zárate emphasized that genomic surveillance made it possible to determine that variants B.1.1.519, Delta, and Omicron became dominant and were associated with the second, third, fourth, and fifth waves, respectively. Some regional circulation patterns of variants are also determined. Especially the northern border of the country, Mexico City, Quintana Roo, and Baja California Sur appeared to be frequent points of entry and discovery of new variants; therefore, it is essential to strengthen the surveillance efforts in these regions.

Nelly Selem-Mojica (CCM-UNAM) reported the detection of a deletion of 411 nucleotides between ORF7 and ORF8 in the SARS-CoV-2 genome. The deletion of 411 nucleotides had been detected in variant B.1.1.243, which was present in 11 genomes sequenced in the United States. This deletion was searched within Mexican genomes with indelseek [16]; however, this failed due to the small read size of the Illumina platforms. Therefore, their team had developed program INDELMEX to detect deletions in the genome of SARS-CoV-2. InDEL-MEX [17] looked for consecutive alignments in a region, that is, reads that align twice in a region where a deletion was suspected. It then took all the aligned reads in each area to check if it is a deletion. The REDOG method was originally used for this, but it had failed because there had been reads that exceeded the size of the deletion, so another filter called NUNUDEL had been used. NUNUDEL calculated the intercession size of the reads. If the REDOG and NUNUDEL methods gave a value of zero, it was concluded that there was a deletion at that position. The results showed that variant B.1.243 had circulated and carried the deletion from March to May 2021; however, by June, variant B.1.243 no longer had the deletion. This had been verified using the Oxford Nanopore [18] and Sanger sequencing platforms, which demonstrated the presence of the deletion. The InDEL-MEX [17] program was applied to additional lines, and it was found that multiple deletions were present in 99 samples circulating in 2021. The deletions in ORF7 and ORF8, occurred repeatedly in Mexican genomes, and were distributed throughout the country. Deletions in ORF7 and ORF8 had occurred independently in the genome, and ORF8 was involved in immune evasion.

Hugo G. Castelán-Sánchez (CONACYT) showed the results from the first genomic surveillance effort in Mexico, a phylogenetic study of the first 17 genomes obtained in Mexico which were collected in early 2020. These were studied alongside foreign sequences to determine their origin through phylogenomic reconstructions, producing a European-origin clade (A2/G) and one from the United States (B/S). The results suggested that local transmission had existed since March 2020 in Mexico City. Two of these cases turned out to be cases of local transmission (from patients not having traveled abroad) that occurred in Mexico in mid-March 2020 and represent the first known events of local transmission in Mexico [3]. By the time of the meeting, it was known that more than 200 different lineages of SARS-CoV-2 had been detected in Mexico, including all VOCs. The patterns of introduction, spread, and replacement of the dominant lineages circulating in Mexico through November 2021 had been studied using a phylodynamic approach. This recurring turnover of lineages showed a dominant replacement pattern over other co-circulating viral lineages, with spikes in sampling frequency that often coincided with waves of infection in the country. Variant B.1.1.519 had shown comparable dynamics with unique clades originating in Mexico and had persisted for more than a year. During this time, there had been a bidirectional movement between Mexico and the United States. Variant B.1.1.222 had reached a maximum frequency of 3.5% in the United States and 35% in Mexico. The introduction and spread of the Alpha (B.1.1.7) and Gamma lineages in Mexico was characterized by several introduction events that had resulted in some extended local transmission clusters that were restricted to specific regions and lasted for shorter periods [19]. The Delta variant had reached a relative frequency of over 95% by late August 2021, coinciding with the peak of the third wave of infection in the country. The introduction and spread of the Delta variant in Mexico were also characterized by several introduction events (>140) that resulted in extensive local transmission clusters. In Mexico, two large clades of the Delta variant had been observed, one from the south (states of Chiapas and Campeche) towards the center and northern regions of the country (Mexico City and Chihuahua). The second spread had occurred from the country’s central region (Mexico City) to other central, northern, and southern states [19]. In the case of the Omicron lineage of SARS-CoV-2 virus in Mexico, 160 Omicron lineage introduction events were detected since the first detection in South Africa, which was followed by an increase in the prevalence of SARS-CoV-2 virus in January. During the peak of cases in January and February 2022 in Mexico, a predominance of the Omicron BA.1.1 sublineage was observed, followed by the BA.1 and BA.15 sublineages, which showed a correlation with the increase in human mobility. In addition, mutations were detected in the receptor-binding region of the spike protein, which may be related to evasion of the immune response. The remaining proteins in the genome remained highly conserved, although homoplastic mutations were detected in non-structural proteins, suggesting parallel evolution [20].

Table 2. Predominant SARS-CoV-2 variants circulating in Mexico during major epidemic waves.

Variant (PANGO Lineage)	Year First Detected in Mexico	Source	Circulation Period	Wave in Mexico	Behavior in Vaccinated (No Booster)	Behavior in Vaccinated (with Booster)	Origin/Introduction	Key Spike Mutations
B.1.1.222	April 2020	Castelán-Sánchez et al. 2023 [19]; Taboada et al. 2021 [3]. Rodríguez-Maldonado et al. 2021 [21].	Apr 2020–Jul 2021	First wave	Pre-vaccine circulation	Not applicable	Introduced from the USA; community transmission. Endemic lineage Mexico-USA	D614G
B.1.1.519	August 2020	Castelán-Sánchez et al. 2023 [19]	Aug 2020–Nov 2021	Second wave	Pre-vaccine circulation	Not applicable	Derived from B.1.1.222; Mexico-specific lineage	T478K, P681H
B.1.1.7 (Alpha)	December 2020	Zárate et al. 2022 [15]; Castelán-Sánchez et al. 2023 [19].	Dec 2020–Oct 2021	Second wave	Reinfections reported	Protection against severe	Multiple introductions from Europe, by the north of Mexico	N501Y, P681H, D614G
P.1 (Gamma)	January 2021	Castelán-Sánchez et al. 2023 [19].	Jan 2021–Nov 2021	Second wave	Moderate immune evasion	Protection against severe	Likely from South America, Higher prevalence in south Mexico	E484K, N501Y, K417T
B.1.617.2 (Delta)	January 2021	Castelán-Sánchez et al. 2023 [19]; Taboada et al. 2022 [5]	Jan 2021–Nov 2021	Third wave	High immune evasion	Protection against severe disease	Introduced from India or USA; rapid spread	L452R, T478K, P681R, D614G
XB (Recombinant)	July 8, 2020 August 18, 2021	Gutierrez et al. 2022 [22]	2021	Third wave	Unknown	Unknown	Second recombinant (B.1.631 + B.1.634)	Combination of B.1.631 + B.1.634 mutations
B.1.1.529 (Omicron BA.1)	November 2021	Castelán-Sánchez et al. 2023 [19]; Zarate et al., 2023 [23]	Dec 2021–Feb 2022	Fourth wave	High immune escape	Protection against severe	Imported from South Africa	S477N, T478K, E484A, N501Y, D614G
BA.2	2022	Taboada et al. 2023 [24]	Spring 2022	Fifth wave	Moderate immune escape	Protection against severe	Likely local replacement of BA.1, Preceded BA.4/5	T376A, D405N, R408S
BA.4	2022	Taboada et al. 2023 [24]	Summer 2022	Fifth wave	High immune escape	Protection against severe	Imported; spread through northern Mexico	L452R, F486V, R493Q
BA.5	2022	Taboada et al. 2023 [24]	Summer 2022	Fifth wave	High immune escape	Protection against severe	Imported; widespread in wave 5	L452R, F486V
BW.1	2022	García-López et al. 2023 [25]	Late 2022–Early 2023	Sixth wave	High immune escape; evades neutralizing antibodies	Partial protection; reduced neutralization	Derived locally from BA.5.6.2; identified in southeast Mexico, rapid spread in Yucatán region	Convergent mutations (R346T, K444T, F486S)

summarizes the main SARS-CoV-2 variants that circulated in Mexico from 2020 to 2023, including their period of predominance, behavior in vaccinated populations, and key mutational profiles.

The same pattern of variant dominance has been reported globally. For instance, Alpha emerged as the dominant variant in the United States and the United Kingdom prior to being outcompeted by Delta, which, in turn, facilitated extensive transmission and reinfection across Europe and North America. The Omicron sublineages (BA.1, BA.2, BA.4, BA.5) further elevated immune evasion, even among populations with high vaccination coverage rates [26,27].

Tao et al. (2023) noted that the occurrence of highly divergent lineages, like Alpha, Gamma, and Omicron, is most likely a product of extended viral replication in long-duration infections, enabling the accrual of an exceptionally high number of non-synonymous mutations, particularly in the spike gene [28]. This contrasts with the gradual progression of incremental evolutionary process of circulating lineages under ordinary transmission dynamics. This shift from sudden increases in diversity to more incremental mutation accumulation, as observed for the BA.5 sublineages in 2022, presents intriguing questions regarding SARS-CoV-2′s possible evolutionary future. These evolutionary patterns highlight the paramount necessity for genomic surveillance to discover and characterize novel mutations with the potential to influence transmissibility or immune evasion potential [26,27].

Concerning vaccines in the Mexican population, a study conducted by Garay et al. (2024) [29] assessed in a systematic way the humoral immune response generated by various COVID-19 vaccines given in Mexico using different SARS-CoV-2 variants. Their results showed that mRNA vaccines (e.g., BNT162b2) produced the highest neutralizing anti-body levels, followed by adenoviral vector vaccines (ChAdOx1 and Sputnik V), whereas inactivated virus vaccines (CoronaVac) yielded much lower responses. Neutralization activity was reduced sharply against the Omicron variant in all platforms, confirming its potential for immune escape. Heterologous boosting regimens increased cross-neutralization and antibody titers [29].

There have been similar patterns in other populations as well. For example, a comparison study in Chile found that individuals who received the CoronaVac vaccine had lower neutralizing capacity against the Omicron variant unless boosted by mRNA vaccines [30]. Similarly, studies in the United Kingdom and Germany also attested to greater neutralizing response from mRNA-based platforms, along with findings of high reduction in antibody activity against Omicron [31,32]. These results between nations validate the overall conclusion that while all platforms contribute protection, heterologous boosting especially with mRNA vaccines is key to overcoming immune escape by emerging variants.

Edgar E. Sevilla-Reyes (INER) talked about long-term persistence of SARS-CoV-2 in different groups of patients. He pointed out that there had been high-risk groups throughout the pandemic that may have been compromised by old age, comorbidities, and immunodeficiency; infection with SARS-CoV-2 in this group could result in an increased severity of COVID-19 and even death. Respiratory viruses have a long persistence, and early in the pandemic, SARS-CoV-2 was shown to remain detectable in pregnant women even after delivery in some cases [33]. In immunocompetent patients, persistence was 6.3 days [34]; in immunocompromised patients, persistence was 29.5 days [34]. In HIV patients infected with SARS-CoV-2, the virus was shown to replicate for up to 8 months [35]. In this population, the virus was highly persistent. A study of patients susceptible to long-term infections (pregnant women, immunocompromised, or having had a bone marrow transplant) in the healthcare sector was started by Sevilla-Reyes’s group in Mexico, studying 94 patients which were followed up for an extended period. Only four patients tested positive for the M gene during the first follow-up check and only one (who was morbidly obese) tested positive during the second, whereas other patients could not be followed up. In general, the SARS-CoV-2 virus was reported to have niches in the population where the virus persists over time. Dr. Sevilla-Reyes emphasized that conducting this type of longitudinal studies is a complex and detailed process that requires extensive follow-up.

3.3. Molecular Evolution of SARS-CoV-2 in Mexico and Colombia

Paola Rojas-Estevez (INS-Colombia) emphasized that the Genomic surveillance network from Colombia, is undoubtedly one of the best strategies for decentralizing and monitoring the detection of new variants. In this meeting, we invited Paola Rojas-Estevez, a member of the main (INS) entity that performs genomic surveillance in Colombia, to expose their experiences and strategies for genomic surveillance to establish future collaboration between Mexico and Colombia. Rojas-Estevez mentioned that in Colombia, genomic surveillance for the SARS-CoV-2 virus is being conducted throughout the country. The genomic surveillance network comprises 22 laboratories distributed in 9 strategic cities based on geographic location and population density. This network includes public and private universities, public health laboratories, and a national biotechnology-based company. The Nanopore platform was used at the national level to sequence the virus, resulting in approximately 23,987 genomes sequenced at the national level in Colombia, representing 7.3% of the genomes reported in Latin America. At the national level, 500 sequences were sequenced weekly and deposited at GISAID. Phylogenomic analyzes of the sequences obtained in the country showed that they originated in Europe and North America. At the beginning of the pandemic in Colombia, A and B lineages were circulating. Lineage A circulated without major success in the country, only in the Antioquia region. Cases were increasing with the internationally declared variants. In the first epidemiological peak, the Gamma variant was more prevalent. However, the number of cases was significantly low due to the use of physical measures and early detection of this variant, and thus, it was possible to control the dispersion of the Gamma variant in the whole country. One of the main objectives of Colombia’s Genomic Surveillance Network was to monitor the mutations registered for each lineage using bioinformatic approaches and manual curations in order to detect important changes in their sequences. This strategy allowed the network to promptly report the B.1.625 and Mu lineages. The Mu lineage was responsible for the largest epidemiological peak in the country. On April 21th, the network proposed to Pangolin the existence of a new lineage called B.1.621, and later on, in 30 August 2021, this lineage was declared as a variant of interest by the WHO. In July, the introduction of the Delta variant was detected. However, no epidemic peak was attributed to this variant. Constant monitoring of this variant revealed the appearance of more than 50 Delta sublineages circulating throughout the country. Subsequently, as in the rest of the world, the introduction of the omicron variant to Colombia produced the displacement of Delta and its sublineages. Currently, BA.5 is the predominant variant in Colombia. This is an overview of the SARS-CoV-2 viruses circulating in Colombia. However, the National Genomic Surveillance Network continues to work on developing sequencing protocols for emerging microorganisms and on training scientific personnel with skills and knowledge in omics sciences. It is important to note that Colombia’s network highlight the country as a regional reference for the Pan American Health Organization in obtaining and analyzing genomic data on emerging microorganisms.

Luis Delaye (Cinvestav-Irapuato) pointed out that with more than 12 million genome sequences deposited in GISAID database (July 2022), SARS-CoV-2 is the most sequenced pathogen in history. In Mexico alone, more than 72,000 viral genomes have been sequenced, from which various scientists are trying to extract relevant information. This large quantity of data is at the same time a treasure and a burden. There are two major problems with all this data: first, the metadata is sometimes flawed and needs to be corrected to be used precisely; second, it is not easy to get a representative sample of the genomes to analyze. To provide a solution to the above problems, Dr. Delaye’s groups developed CurSa (Curate and Sample) [36], a series of Perl scripts to cure metadata and perform representative sampling. Metadata is sometimes flawed because filling the information is manual; for instance, in the case of Mexico, 10% of the sequences have a typo in the name of the city or the state. In addition, about a quarter of all Mexican cities are not represented in Nextstrain metadata files [37], a popular software to study viral evolution. Therefore, CurSa identifies these errors and facilitates curation. On the other hand, CurSa performs a random sample from two sources: (i) the set of global representative sequences of Nextrain [37] and (ii) sequences downloaded from GISAID from a specified country (i.e., Mexico). Through this, it is possible to get a random sample of sequences from a country contextualized with sequences from all over the world. These sequences can be used next as input to Nextrtain for further sampling and analysis. CurSa is an optional facility for curating metadata and taking a representative sample for later analysis [36].

Maribel Hernández Rosales (Cinvestav-Irapuato) presented her work on human mobility networks during the pandemic COVID-19, which was used to analyze social behavior during the pandemic, identify crowds, and determine the relationship between social distancing measures to have empirical support for the effectiveness of the measures implemented for the National Healthy Distance Day. For this analysis, they used mobility networks to inform the public, government agencies, and decision makers to adopt appropriate distance measures. One way to build mobility networks is through geolocation data. For example, in Mexico, the basic geostatistical areas (AGEB) were used, divided into urban and rural areas, and based on these divisions, a node represented an AGEB within the mobility network, and an edge is placed connecting two nodes if there was mobility observed between the two nodes. Each arc or edge has a weight corresponding to the number of devices, used as proxies for people, moving from one node to another. Weights are normalized by dividing between the number of devices observed per day. This monitoring was performed per day. One of the first analyses was to see to where people move the most; the analysis showed that the center of Mexico City (CDMX) was the most visited region. Moreover, mobility was observed over long distances, and it was observed that in CDMX, many people travel between north to south. This analysis also showed that low mobility was maintained when healthy distance measures were considered, but these were not considered during holidays. The other question that was asked is how the pandemic affects the population socially, because segregation studies in the USA have shown that people did not visit neighborhoods where the majority is a black population. However, when carrying out this study in Mexico City, divided in different municipalities and crossing mobility with CONEVAL poverty index, we observed that the poverty rate is lower in the south of Mexico, in the municipality of Milpa Alta, which people did not visit; therefore, it was proposed that Milpa Alta is a somewhat segregated municipality, unlike other municipalities in CDMX, like Miguel Hidalgo. They also observed regions with high mobility, concentrated in the center of the metropolitan area. These mobility studies help to carry out social and economic studies necessary for the development of society.

Closing remarks by María Elena Alvarez Buylla-Roces highlighted that Mexico’s scientific progress and technological sovereignty are fundamental. She also acknowledged the capabilities and multi-institutional participation of young people in science to develop research and collective initiatives like those promoted by CONACYT National Research and Incidence Projects (Pronaii) (Pronaces-Salud).

4. Conclusions

This meeting comprised the efforts and results of 16 institutions, from governmental, academic, and private sectors from Mexico and Colombia in developing new and enhanced genomic surveillance strategies to combat and monitor the SARS-CoV-2 virus. This was a significant opportunity for senior scientists, young researchers, members of independent laboratories, and students from Mexico and Colombia to share their experience in SARS-CoV-2 genomic surveillance strategies to establish new collaborations and strengthen the existing ones. This record aims at sharing the information presented at the meeting and the contacts of the participants to the international scientific community and to establish future collaborations.