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Lira-Morales JD, López-Cuevas O, Medrano-Félix JA, González-Gómez JP, González-López I, Castro-Del Campo N, Gomez-Gil B, Chaidez C. Genomic Surveillance of SARS-CoV-2 in México: Three Years since Wuhan, China's First Reported Case. Viruses 2023; 15:2223. [PMID: 38005903 PMCID: PMC10674944 DOI: 10.3390/v15112223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
OBJECTIVE The aim of this work was to analyze the metadata of the SARS-CoV-2 sequences obtained from samples collected in Mexico from 2020 to 2022. MATERIALS AND METHODS Metadata of SARS-CoV-2 sequences from samples collected in Mexico up to 31 December 2022 was retrieved from GISAID and manually cured for interpretation. RESULTS As of December 2022, Mexican health authorities and the scientific community have sequenced up to 81,983 SARS-CoV-2 viral genomes deposited in GISAID, representing 1.1% of confirmed cases. The number of sequences obtained per state corresponded to the gross domestic product (GDP) of each state for the first (Mexico City) and the last (Tlaxcala). Approximately 25% of the sequences were obtained from CoViGen-Mex, an interdisciplinary initiative of health and scientific institutions to collect and sequence samples nationwide. The metadata showed a clear dominance of sequences retrieved by women. A similar variant distribution over time was found in Mexico and overseas, with the Omicron variant predominating. Finally, the age group with the highest representation in the sequences was adults aged 21 to 50 years, accounting for more than 50% of the total. CONCLUSIONS Mexico presents diverse sociodemographic and economic characteristics. The COVID-19 pandemic has been and continues to be a challenge for collaboration across the country and around the world.
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Affiliation(s)
- Juan Daniel Lira-Morales
- Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Culiacán, Culiacan 80110, Mexico; (J.D.L.-M.); (O.L.-C.); (J.P.G.-G.); (I.G.-L.); (N.C.-D.C.)
| | - Osvaldo López-Cuevas
- Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Culiacán, Culiacan 80110, Mexico; (J.D.L.-M.); (O.L.-C.); (J.P.G.-G.); (I.G.-L.); (N.C.-D.C.)
| | - José Andrés Medrano-Félix
- Investigadoras e Investigadores por México-Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Culiacán, Culiacan 80110, Mexico;
| | - Jean Pierre González-Gómez
- Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Culiacán, Culiacan 80110, Mexico; (J.D.L.-M.); (O.L.-C.); (J.P.G.-G.); (I.G.-L.); (N.C.-D.C.)
| | - Irvin González-López
- Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Culiacán, Culiacan 80110, Mexico; (J.D.L.-M.); (O.L.-C.); (J.P.G.-G.); (I.G.-L.); (N.C.-D.C.)
| | - Nohelia Castro-Del Campo
- Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Culiacán, Culiacan 80110, Mexico; (J.D.L.-M.); (O.L.-C.); (J.P.G.-G.); (I.G.-L.); (N.C.-D.C.)
| | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Mazatlán, Mazatlan 82112, Mexico;
| | - Cristóbal Chaidez
- Centro de Investigación en Alimentación y Desarrollo A.C., Coordinación Regional Culiacán, Culiacan 80110, Mexico; (J.D.L.-M.); (O.L.-C.); (J.P.G.-G.); (I.G.-L.); (N.C.-D.C.)
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D'Bastiani E, Princepe D, Marquitti FMD, Boeger WA, Campião KM, Araujo SBL. Effect of Host-Switching on the Ecological and Evolutionary Patterns of Parasites. Syst Biol 2023; 72:912-924. [PMID: 37097763 DOI: 10.1093/sysbio/syad022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Speciation via host-switching is a macroevolutionary process that emerges from a microevolutionary dynamic where individual parasites switch hosts, establish a new association, and reduce reproductive contact with the original parasite lineage. Phylogenetic distance and geographic distribution of the hosts have been shown to be determinants of the capacity and opportunity of the parasite to change hosts. Although speciation via host-switching has been reported in many host-parasite systems, its dynamic on the individual, population and community levels is poorly understood. Here we propose a theoretical model to simulate parasite evolution considering host-switching events on the microevolutionary scale, taking into account the macroevolutionary history of the hosts, to evaluate how host-switching can affect ecological and evolutionary patterns of parasites in empirical communities at regional and local scales. In the model, parasite individuals can switch hosts under variable intensity and have their evolution driven by mutation and genetic drift. Mating is sexual and only individuals that are sufficiently similar can produce offspring. We assumed that parasite evolution occurs at the same evolutionary time scale as their hosts, and that the intensity of host-switching decreases as the host species differentiate. Ecological and evolutionary patterns were characterized by the turnover of parasite species among host species, and parasite evolutionary tree imbalance respectively. We found a range of host-switching intensity that reproduces ecological and evolutionary patterns observed in empirical communities. Our results showed that turnover decreased as host-switching intensity increased, with low variation among the model replications. On the other hand, tree imbalance showed wide variation and non-monotonic tendency. We concluded that tree imbalance was sensitive to stochastic events, whereas turnover may be a good indicator of host-switching. We found that local communities corresponded to higher host-switching intensity when compared to regional communities, highlighting that spatial scale is a limitation for host-switching. [Dispersal of parasites, opportunity and capacity of interaction, phylogenetic conservatism, and community structure.].
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Affiliation(s)
- Elvira D'Bastiani
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
| | - Débora Princepe
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, UNICAMP-Campinas, São Paulo, Brasil
| | - Flavia M D Marquitti
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, UNICAMP-Campinas, São Paulo, Brasil
- Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP-Campinas, São Paulo, Brasil
| | - Walter A Boeger
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
- Departamento de Zoologia, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
| | - Karla M Campião
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
- Departamento de Zoologia, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
| | - Sabrina B L Araujo
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
- Departamento de Física, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
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Apari P, Földvári G. Domestication and microbiome succession may drive pathogen spillover. Front Microbiol 2023; 14:1102337. [PMID: 37007505 PMCID: PMC10065160 DOI: 10.3389/fmicb.2023.1102337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.
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Affiliation(s)
- Péter Apari
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Gábor Földvári
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
- Centre for Eco-Epidemiology, National Laboratory for Health Security, Budapest, Hungary
- *Correspondence: Gábor Földvári,
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Begou P, Kassomenos P. The ecosyndemic framework of the global environmental change and the COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159327. [PMID: 36220476 PMCID: PMC9547397 DOI: 10.1016/j.scitotenv.2022.159327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The ecosyndemic theory combines the concept of 'synergy' with 'epidemic' and the term "eco" implies the role of the environmental changes. Each of the conditions enhances the negative impacts of the other in an additive way making our society more vulnerable and heightening individual risk factors. In this study, we analyze the mutually reinforcing links between the environment and health from the complexity angle of the ecosyndemic theory and propose the characterization of the COVID-19 pandemic as ecosyndemic. We use the term 'ecosyndemic' because the global environmental change contributes to local-scale, regional-scale and global-scale alterations of the Earth's systems. These changes have their root causes in the way that people interact with the physical, chemical, and biotic factors of the environment. These interactions disturb nature and the consequences have feedbacks in every living organism.
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Affiliation(s)
- Paraskevi Begou
- Laboratory of Meteorology and Climatology, Department of Physics, University of Ioannina, GR-45110 Ioannina, Greece.
| | - Pavlos Kassomenos
- Laboratory of Meteorology and Climatology, Department of Physics, University of Ioannina, GR-45110 Ioannina, Greece
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Boguslavsky DV, Sharova NP, Sharov KS. Evolutionary Challenges to Humanity Caused by Uncontrolled Carbon Emissions: The Stockholm Paradigm. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16920. [PMID: 36554799 PMCID: PMC9778811 DOI: 10.3390/ijerph192416920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
This review paper discusses the Stockholm Paradigm (SP) as a theoretical framework and practical computational instrument for studying and assessing the risk of emerging infectious diseases (EIDs) as a result of climate change. The SP resolves the long-standing parasite paradox and explains how carbon emissions in the atmosphere increase parasites' generalization and intensify host switches from animals to humans. The SP argues that the growing rate of novel EID occurrence caused by mutated zoonotic pathogens is related to the following factors brought together as a unified issue of humanity: (a) carbon emissions and consequent climate change; (b) resettlement/migration of people with hyper-urbanization; (c) overpopulation; and (d) human-induced distortion of the biosphere. The SP demonstrates that, in an evolutionary way, humans now play a role migratory birds once played in spreading parasite pathogens between the three Earth megabiotopes (northern coniferous forest belt; tropical/equatorial rainforest areas; and hot/cold deserts), i.e., the role of "super-spreaders" of parasitic viruses, bacteria, fungi and protozoa. This makes humans extremely vulnerable to the EID threat. The SP sees the +1.0-+1.2 °C limit as the optimal target for the slow, yet feasible curbing of the EID hazard to public health (150-200 years). Reaching merely the +2.0 °C level will obviously be an EID catastrophe, as it may cause two or three pandemics each year. We think it useful and advisable to include the SP-based research in the scientific repository of the Intergovernmental Panel on Climate Change, since EID appearance and spread are indirect but extremely dangerous consequences of climate change.
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Affiliation(s)
| | - Natalia P. Sharova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia
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