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

Up to November 2021, over 200 different SARS-CoV-2 lineages circulated in Mexico. To investigate lineage replacement dynamics, we applied a phylodynamic approach to explore the evolutionary trajectories of five dominant lineages that circulated during the first year of the local epidemic. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in the country. Lineages B.1.1.222 and B.1.1.519 showed comparable dynamics, represented by clades likely originating in Mexico and persisting for over a year. 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. We further explored viral movements across the country, applied within the largest clades identified (belonging to lineage B.1.617.2). 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.

Phylogenomics and population genomics of SARS-CoV-2 in Mexico reveals variants of interest (VOI) and a mutation in the Nucleocapsid protein associated with symptomatic versus asymptomatic carriers

Understanding the evolution of SARS-CoV-2 virus in various regions of the world during the Covid19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A RT-qPCR screening and phylogenomics reconstructions directed a sequence/structure analysis of the Spike glycoprotein, revealing mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show Spike protein mutations in the N-terminal domain (i.e., R190M), in the receptor-binding motif (i.e., T478K, E484K), within the S1-S2 subdomains (i.e., P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest (VOI) we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of Single Nucleotide Variants (SNVs) from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the Nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades, so we propose an additional VOI, 20A/N:194L.V2 (B.1.243). Our results highlight the dual and complementary role of Spike and Nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage. IMPACT STATEMENTFollowing self-sampling, screening of mutations of concern, and a combined phylogenomic and population genetics pipeline, we reveal the appearance of three VOI with mutations in the Spike protein, P.4 (B.1.1.28.4) and 20B/478K.V1 (B.1.1.222, leading to B.1.1.519), and in the Nucleocapsid protein, 20A/N:194L.V2 (B.1.243), in Mexico during the pre-vaccination stage. The mutation S194L in the Nucleocapsid was found to associate with symptomatic patients versus asymptomatic carriers in the population investigated. Our research can aid epidemiological genomics efforts during the vaccination stage in Mexico by contributing with a combined analytical platform and information about variants within different genetic lineages with the potential to evolve into variants of concern (VOC).

Co-circulation of SARS-CoV-2 and Influenza under vaccination scenarios

The interaction and possibly interference between viruses infecting a host population is addressed in this work. We model two viral diseases with a similar transmission mechanism and for which a vaccine exists. The vaccine is characterized by its coverage, induced temporary immunity, and efficacy. The population dynamics of both diseases consider infected individuals of each illness and hosts susceptible to one but recovered from the other. We do not incorporate co-infection. Two main transmission factors affecting the effective contact rates are postulated: i) the virus with a higher reproduction number can superinfect the one with a lower reproduction number, and ii) there exists some induced (indirect) protection induced by vaccination against the weaker virus that reduces the probability of infection by the stronger virus. Our results indicate that coexistence of the viruses is possible in the long term, even considering the absence of superinfection. Influenza and SARS-CoV-2 are employed to exemplify this last point, observing that the time-dependent effective contact rate may induce either alternating outbreaks of each disease or synchronous outbreaks. Finally, for a particular parameter range, a backward bifurcation has been observed for dynamics without vaccination.

The SARS-CoV-2 epidemic outbreak: a review of plausible scenarios of containment and mitigation for Mexico

We present here several variants of a mathematical model to explore three main issues related to SARS-CoV-2 spread in scenarios similar to those present in Mexico and elsewhere in Latin America. We explore the consequences for travel inside a given region, in this case Mexico, particularly focusing on airplane transportation but attempting to give a gross approximation to terrestrial movement since this is the main form of population movement across geographical areas in the country; then we proceed to study the effect of behavioral changes required to lower transmission by lowering the contact rate and infection probability and lastly, we explore the consequences of disease spread in a population subject to social isolation.These models are not suitable for predictive purposes although some rough predictions can be extracted from them. They are presented as a tool that can serve to explore plausible scenarios of spread and impact, effectiveness and consequences of contention and mitigation policies. Given the early stage at which the epidemic is at the date of writing in Mexico, we hope these ideas can be helpful for the understanding of the importance of isolation, social distancing and screening of the general population. Key findingsO_LIWe have estimated the parameters of the epidemic curve (growth rate, carrying capacity and dispersion) as well as a first estimate of the basic reproduction number for Mexico. C_LIO_LIWe provide expected trends of epidemic outbreaks depending upon of the number of imported cases per day arriving to a large airport. We illustrate this trends with data from Mexico City airport. C_LIO_LIWe provide expected trends of disease dispersal depending upon of the number of exported cases per day either by airplane or bus. We illustrate this trends with data from Mexico City. C_LIO_LIWe evaluate the effect of behavioral change to reduce the contact rate and compare diverse scenarios that evaluate the timing of initial enforcement of behavior, time horizon in which to diminish the contact rate and the proportion of people under isolation. C_LIO_LIWe evaluate the effect of social isolation by itself with respect to two main parameters: the starting time for the enforcement of control measures, and the learning time to achieve the desired contact rate reduction. We stress the importance of quick and direct actions to isolate and reduce contact rate simultaneously. C_LI