Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
Hugo G. Castelán‐SánchezLuis DelayeRhys P. D. InwardSimon DellicourBernardo GutiérrezNatalia Martínez de la ViñaCélia BoukadidaOliver G. PybusGuillermo de Anda‐JáureguiPlinio GuzmánMarisol Flores-GarridoÓscar FontanelliMaribel Hernández-RosalesAmilcar Meneses‐ViverosGabriela Olmedo‐ÁlvarezAlfredo Heriberto Herrera-EstrellaAlejandro Sánchez‐FloresJosé Esteban Muñoz‐MedinaAndreu Comas‐GarcíaBruno Gómez‐GilSelene ZárateBlanca TaboadaSusana LópezCarlos F. AriasMoritz U. G. KraemerAntonio LazcanoMarina Escalera‐Zamudio
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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.Keywords:
Lineage (genetic)
Evolutionary Dynamics
Abstract Recently, in 2022, new cases of human monkeypox virus (hMPXV) occurred in Europe and North America. The first case was reported in Europe in May 2022, and subsequently, more than 50 000 new cases were confirmed in 100 countries. Currently, the classification of hMPXV according to the nextstrain occurs in five big clades (1A, A.1, A.2, A.1.1, and B.1). According to the resurgence of smallpox‐like disease caused by hMPXV and the spread of the virus to the European and American continents, in the present study, we review and summarize the molecular evolution of the hMPXV, determining the molecular evolution of the main clades. A total of 442 hMPXV whole‐genome sequences with available information from the country and sampling date (between October 2017 and 2022), were obtained and evaluated using the Bayesian method. The clade B.1 which is currently circulating was the most frequent ( n = 415; 93.9%). The other clades presented the following frequencies: 1A ( n = 13; 2.9%), A.1 ( n = 10; 2.3%), A.2 ( n = 3; 0.7%) and A.1.1 ( n = 1; 0.2%) The overall nucleotide divergence of hMPXV was 5.590e‐5. The 1A clade was detected between 2017 and 2020. A.1 was observed, and between 2019 and 2022 some A.2 sequences were detected. In 2022, the great predominance of B.1 was observed. The common ancestor of the hMPXV belongs to the clade 1A and the time to the Most Recent Common Ancestor (tMRCA) was 2017‐04‐04 (Highest Posterior Density 95% (HPD95%): 2017‐03‐09; 2017‐08‐04) on the West African continent. The tMRCA of A.1 was 2018‐05‐21 (HPD95%: 2018‐05‐20; 2018‐07‐04) with divergence of 6.885e‐5 substitutions per site per year. This clade was of West African origin but was eventually detected in European countries. Also, A.2 was detected with sequences of North America and showed tMRCA of 2019‐07‐15 (HPD95%: 2018‐11‐18; 2020‐02‐24). A.1.1 showed tMRCA from 2021 to 06‐05 (HPD95%: 2021‐06‐05; 2021‐11‐26) and this clade was detected in North America and was the precursor for the globally spreading B.1 which tMRCA was 2022‐04‐26 (HPD95%: 2022‐02‐27; 2022‐04‐26). hMPXV has been spread from West Africa to the United Kingdom, Israel, Singapore, the USA, Canada, Portugal, Spain, Ireland, France, Belgium, the Netherlands, Switzerland, Germany, Italy, Slovenia, Austria, the Republic Czech, Sweden, and Finland. hMPXV also reached countries such as Brazil, Mexico, Australia, and Taiwan. The common ancestor of the hMPXV belongs to the clade 1A with origin in the West African continent. Clade B.1 was responsible for the recent widespread worldwide. Immunization to prevent the spread of hMPXV is not yet available to the public, future studies should focus on the development of effective vaccines to contain the spread of this virus.
Monkeypox
Molecular clock
Molecular Epidemiology
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Evolutionary Dynamics
Dynamics
Experimental Evolution
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Abstract 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.
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Dynamics
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Nonsynonymous substitution
Divergence (linguistics)
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Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread widely from China to the world. Although the viral genome has been well characterized, the evolutionary origin and global transmission dynamics of SARS-CoV-2 remain poorly investigated. To address this, we retrieved 313 SARS-CoV-2 genomes from the GISAID database (https://www.gisaid.org), from which 99 genomes generated from original clinical specimens with exact collection dates from 16 countries were selected and enrolled for Bayesian phylodynamic analysis. Here we show that the time to the Most Recent Common Ancestor (tMRCA) of SARS-CoV-2 is Dec 11, 2019 (95%HPD, Nov 21 - Dec 24). Two clades of global circulating strains of SARS-CoV-2 were suggested by Bayesian Maximum Clade Credibility (MCC) tree. The USA circulating strains of SARS-CoV-2 seemed to be from both of the two clades, the UK and Australia circulating strains were from Clade 1, the circulating strains in Singapore, Japan, Germany, France, and Italy were from Clade 2. Although we have not found any obvious bottle-neck-effect from the Bayesian Skyline Plot of the viral population dynamics reconstruction, a sharp reduction of the lower 95% HPD of the relative genetic diversity was observed from Feb 5, 2020, suggesting a possible initiation of a bottle-neck-effect. Thirteen (6 synonymous and 7 non-synonymous) mutations in the viral genome were observed, including two clade-specific mutations (C8782T and T1844C in Clade 1 rather than Clade 2) and eleven sub-clade specific mutations. All of the observed mutations occurred in the USA circulating strains, except one mutation T18488C only occurred in the UK circulating strains. A non-synonymous mutation in the 3’-UTR was also observed, suggesting an altered RNA replication capacity of SARS-CoV-2. We thus came to the conclusion that continuous evolution occurred in almost all regions of the SARS-CoV-2 genome and potentially in a country-specific manner. Further efforts on monitoring the genomic mutations of SARS-CoV-2 from different countries are recommended.
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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.
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Evolutionary Dynamics
Dynamics
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Abstract Objectives SARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe. Methods Maximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2. Results Phylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai. Conclusions Multiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.
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Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages have so far prevented a detailed elucidation of evolutionary dynamics in large bacterial populations. Here, we overcome this hurdle by developing a chromosomal barcoding technique that allows simultaneous tracking of ∼450,000 distinct lineages in E. coli. We used this technique to gather insights into the evolutionary dynamics of large (>10 7 cells) E. coli populations propagated for ∼420 generations in the presence of sub-inhibitory concentrations of common antibiotics. By deep sequencing the barcodes, we reconstructed trajectories of individual lineages at high frequency resolution (< 10 −5 ). Using quantitative tools from ecology, we found that populations lost lineage diversity at distinct rates corresponding to their antibiotic regimen. Additionally, by quantifying the reproducibility of these dynamics across replicate populations, we found that some lineages had similar fates over independent experiments. Combined with an analysis of individual lineage trajectories, these results suggest how standing genetic variation and new mutations may contribute to adaptation to sub-inhibitory antibiotic levels. Altogether, our results demonstrate the power of high-resolution barcoding in studying the dynamics of bacterial evolution.
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Experimental Evolution
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